Publications – Institute of Computer Science

Book chapters

Köbschall, K., Hartung, L., and Kramer, S. (2025). Soft Hoeffding Tree: A Transparent and Differentiable Model on Data Streams. In Lecture Notes in Computer Science (pp. 167-182). Springer Nature Switzerland. DOI

Conference Papers

Salkhordeh, R., Schuhknecht, F. M., Asadi, H., et al. (2025). No Time to Halt: In-Situ Analysis for Large-Scale Data Processing via Virtual Snapshotting. In A. Simitsis, B. Kemme, A. Queralt, et al. (eds.), EDBT (pp. 438-450). OpenProceedings.org. Author/Publisher URL

Journal Articles

Al-Maaitah, N. O., Garcia-Blas, J., Sanchez-Gallegos, G., et al. (2025). A Comparative Study of Ad-hoc File Systems for Extreme Scale Computing. Future Generation Computer Systems, 170, 1-18. DOI Author/Publisher URL

Brinkmann, A., Salkhordeh, R., Wiegert, F., et al. (2025). HLN-Tree: A memory-efficient B+-Tree with huge leaf nodes and locality predictors. ACM Transactions on Storage, 21(2), 1-27. DOI

Zhang, T., Yin, Z., Xu, X., et al. (2025). RabbitSketch: a high-performance sketching library for genome analysis. Bioinformatics, 41(5). DOI

Cheng, W., Cheng, Q., Liu, Y., et al. (2025). 9Ring: A 3D-Stacked Memory-Based Accelerator for Flexible and Efficient Deep CNN Applications. ACM Transactions on Architecture and Code Optimization. Published online. DOI

Michalopoulos, A., Tsitsigkos, D., Bouros, P., et al. (2025). Efficient Distance Queries on Non-point Data. ACM Transactions on Spatial Algorithms and Systems, 11(1), 1-37. DOI

Cheng, W., Tu, S., Liu, Y., et al. (2025). FlashFox: a secret-sharing approach to securing data deletion for Flash-based SSD. The Computer Journal. Published online. DOI

Pensel, L., Kramer, S. (2025). Neural RELAGGS. MACHINE LEARNING, 114(5). DOI Author/Publisher URL

Spangenberg, J., Muendnich, S., Busch, A., et al. (2025). The RMaP challenge of predicting RNA modifications by nanopore sequencing. COMMUNICATIONS CHEMISTRY, 8(1). DOI Author/Publisher URL

Teschner, D., Gomez-Zepeda, D., Lacki, M. K., et al. (2025). Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data. JOURNAL OF PROTEOME RESEARCH, 24(5), 2358-2368. DOI Author/Publisher URL

Other

Pensel, L., and Kramer, S. (2025). Human Guided Learning of Transparent Regression Models. Author/Publisher URL

Book chapters

Heilmann, X., Henkys, V., Apeldoorn, D., et al. (2024). Studying Privacy Aspects of Learned Knowledge Bases in the Context of Synthetic and Medical Data. In Studies in Health Technology and Informatics. IOS Press. DOI

Althaus, E., Schnurbusch, D. (2024). Reducing Treewidth for SAT-Related Problems Using Simple Liftings (Vols. 14594, pp. 175-191). DOI Author/Publisher URL

Gallenbacher, J. (2024). Informatikunterricht bedeutet, unsere Lebenswelt gemeinsam zu gestalten. In D. Komm (ed.), Wirksamer Informatikunterricht (pp. 60-70). Schneider Verlag Hohengehren GmbH, Baltmannsweiler, Germany.

Conference Papers

Klopp, D., Pacak, A., Erdweg, S. (2024). Separate Compilation and Partial Linking: Modules for Datalog IR. Proceedings of the 23rd ACM SIGPLAN International Conference on Generative Programming: Concepts and Experiences, 94-106. DOI

Pacak, A., Kumar, P., Xu, R., Erdweg, S. (2024). AUTOINC: Incrementality for Free. Companion Proceedings of the 2024 ACM SIGPLAN International Conference on Systems, Programming, Languages, and Applications: Software for Humanity, 57-59. DOI

Marx, S., Erdweg, S. (2024). Abstract Interpretation of Java Bytecode in Sturdy. Proceedings of the 26th ACM International Workshop on Formal Techniques for Java-like Programs, 17-22. DOI

Niebler, S., Schmidt, B., Spichtinger, P., Tost, H. (2024). Scalable GPU-Enabled Creation of Three Dimensional Weather Fronts. Proceedings of the Platform for Advanced Scientific Computing Conference, 1-12. DOI

Borba, E., Salkhordeh, R., Mimouni, S., et al. (2024). A Hierarchical Modeling Approach for Assessing the Reliability and Performability of Burst Buffers. Proceedings of the 37th GI/IT International Conference on Architecture of Computing Systems (ARCS), Potsdam, Germany, May 14th – 16th.

Huang, H., Wang, P., Su, Q., et al. (2024). Palantir: Hierarchical Similarity Detection for Post-Deduplication Delta Compression. Proceedings of the ACM International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), Volume 2, La Jolla, CA, USA, 27 April 2024- 1 May, 830-845. DOI

Medeiros, D., Gregory, E. B., Couvee, P., et al. (2024). IO-SEA: Storage I/O and Data Management for Exascale Architectures Invited Paper. PROCEEDINGS OF THE 21ST ACM INTERNATIONAL CONFERENCE ON COMPUTING FRONTIERS 2024-WORKSHOPS AND SPECIAL SESSIONS, CF 2024 COMPANION, 94-100. DOI Author/Publisher URL

Qian, Y., Vef, M.-A., Farrell, P., et al. (2024). Combining Buffered I/O and Direct I/O in Distributed File Systems. Proceedings of the 22nd USENIX Conference on File and Storage Technologies (FAST), Santa Clara, CA, USA, February 27-29, 17-33. Author/Publisher URL

Wang, M., Yin, Z., Yan, L., et al. (2024). RabbitTrim: Highly Optimized Trimming of Illumina Sequencing Data on Multi-core Platforms. BIOINFORMATICS RESEARCH AND APPLICATIONS, PT II, ISBRA 2024, 14955, 26-37. DOI Author/Publisher URL

Weissenberger, A., Schmidt, B. (2024). Massively Parallel Inverse Block-sorting Transforms for bzip2 Decompression on GPUs. 53RD INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING, ICPP 2024, 856-865. DOI Author/Publisher URL

Yan, L., Yin, Z., Li, J., et al. (2024). RabbitSAlign: Accelerating Short-Read Alignment for CPU-GPU Heterogeneous Platforms. BIOINFORMATICS RESEARCH AND APPLICATIONS, PT II, ISBRA 2024, 14955, 83-94. DOI Author/Publisher URL

Zhang, S., Qi, J., Yao, X., Brinkmann, A. (2024). Hyper: Achieving High-Performance and Memory-Efficient Learned Index Via Hybrid Construction. To appear in International Conference on Management of Data (SIGMOD), Santiago, Chile, June 09 – 15. International Conference on Management of Data (SIGMOD), Santiago, Chile.

Journal Articles

Schreiber, Q., Wolpert, N., Schömer, E. (2024). METNet: A mesh exploring approach for segmenting 3D textured urban scenes. ISPRS Journal of Photogrammetry and Remote Sensing, 218, 498-509. DOI

Schmidt, B., Kallenborn, F., Chacon, A., Hundt, C. (2024). CUDASW++4.0: ultra-fast GPU-based Smith–Waterman protein sequence database search. BMC Bioinformatics, 25(1). DOI

Klopp, D., Erdweg, S., Pacak, A. (2024). A Typed Multi-level Datalog IR and Its Compiler Framework. Proceedings of the ACM on Programming Languages, 8(OOPSLA2), 1586-1614. DOI

Klopp, D., Erdweg, S., Pacak, A. (2024). Object-Oriented Fixpoint Programming with Datalog. Proceedings of the ACM on Programming Languages, 8(OOPSLA2), 60-86. DOI

Fischer, C., Fink, A. H., Schömer, E., et al. (2024). An objective identification technique for potential vorticity structures associated with African easterly waves. Geoscientific Model Development, 17(10), 4213-4228. DOI

Christodoulou, G., Bouros, P., Mamoulis, N. (2024). LIT: Lightning-fast In-memory Temporal Indexing. Proceedings of the ACM on Management of Data, 2(1), 1-27. DOI

King, R. D., Scassa, T., Kramer, S., Kitano, H. (2024). Stockholm declaration on AI ethics: why others should sign. Nature, 626(8000), 716-716. DOI

Christodoulou, G., Bouros, P., Mamoulis, N. (2024). HINT: a hierarchical interval index for Allen relationships. VLDB JOURNAL, 33(1), 73-100. DOI Author/Publisher URL

Derstroff, C., Brugger, J., Blüml, J., et al. (2024). Amplifying Exploration in Monte-Carlo Tree Search by Focusing on the Unknown. CoRR, abs/2402.08511. DOI Author/Publisher URL

Kallenborn, F., Schmidt, B. (2024). CAREx: context-aware read extension of paired-end sequencing data. BMC BIOINFORMATICS, 25(1). DOI Author/Publisher URL

Karimi, M., Salkhordeh, R., Brinkmann, A., Asadi, H. (2024). HybRAID: A High-Performance Hybrid RAID Storage Architecture for Write-Intensive Applications in All-Flash Storage Systems. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 35(12), 2608-2623. DOI Author/Publisher URL

Lopez, D. A., Hillen, B., Naegele, M., et al. (2024). StereoThermoLegs: label propagation with multimodal stereo cameras for automated annotation of posterior legs during running at different velocities. JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY. Published. DOI Author/Publisher URL

Lopez, D. A., Hillen, B., Naegele, M., et al. (2024). ThermoNet: advanced deep neural network-based thermogram processing pipeline for automatic time series analysis of specific skin areas in moving legs. JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY, 149(19), 11337-11348. DOI Author/Publisher URL

Raaf, P., Brinkmann, A., Borba, E., et al. (2024). From SSDs Back to HDDs: Optimizing VDO to Support Inline Deduplication and Compression for HDDs as Primary Storage Media. ACM TRANSACTIONS ON STORAGE, 20(4). DOI Author/Publisher URL

Schimmelpfennig, F., Brinkmann, A., Asadi, H., Salkhordeh, R. (2024). Skip TLB flushes for reused pages within mmap’s. CoRR, abs/2409.10946.

Schmidt, B., Hildebrandt, A. (2024). From GPUs to AI and quantum: three waves of acceleration in bioinformatics. DRUG DISCOVERY TODAY, 29(6). DOI Author/Publisher URL

Tarraf, A., Schreiber, M., Cascajo, A., et al. (2024). Malleability in Modern HPC Systems: Current Experiences, Challenges, and Future Opportunities. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 35(9), 1551-1564. DOI Author/Publisher URL

Tsitsigkos, D., Bouros, P., Lampropoulos, K., et al. (2024). Two-Layer Space-Oriented Partitioning for Non-Point Data. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING, 36(3), 1341-1355. DOI Author/Publisher URL

Other

Schmidt, B., Kallenborn, F., Wichmann, A., et al. (2024). gpuPairHMM: High-speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs. Author/Publisher URL

Kallenborn, F., Chacon, A., Hundt, C., et al. (2024). GPU-accelerated homology search with MMseqs2. In Cold Spring Harbor Laboratory. DOI

Boer, D., Koch, F., Kramer, S. (2024). Harnessing the Power of Semi-Structured Knowledge and LLMs with Triplet-Based Prefiltering for Question Answering. Author/Publisher URL

Andrés López, D., Hillen, B., Naegele, M., et al. (2024). StereoThermoLegs Dataset. DOI

Hartung, L., Althaus, E., Steiner, R. (2024). A Random Walk Approach to Broadcasting on Random Recursive Trees. DOI

Theses/Disssertations

Andrés López, D. (2024). ThermoNet: deep neural network thermogram analysis of human calves during physical exercise [PhD Thesis]. DOI Author/Publisher URL

Book chapters

Vexler, J., and Kramer, S. (2023). Classifying Aircraft Categories from Magnetometry Data Using a Hypotheses-Based Multi-Task Framework. In Frontiers in Artificial Intelligence and Applications. IOS Press. DOI

Althaus, E., Funke, S., and Schrauth, M. (2023). Privacy Preserving Queries of Shortest Path Distances. In Lecture Notes in Computer Science (pp. 94-101). Springer International Publishing. DOI

Dai, H., Wu, J., Brinkmann, A., and Wang, Y. (2023). Neighborhood-Oriented Decentralized Learning Communication in Multi-Agent System (Vols. 14256, pp. 490-502). DOI Author/Publisher URL

Kobus, R., Nelgen, J., Henkys, V., and Schmidt, B. (2023). Faster Segmented Sort on GPUs (Vols. 14100, pp. 664-678). DOI Author/Publisher URL

Niebler, S., Schmidt, B., Tost, H., and Spichtinger, P. (2023). Automated Identification and Location of Three Dimensional Atmospheric Frontal Systems. In Lecture Notes in Computer Science (pp. 3-17). Springer Nature Switzerland. DOI

Conference Papers

Moti, N., Brinkmann, A., Vef, M.-A., et al. (2023, November 12). The I/O Trace Initiative: Building a Collaborative I/O Archive to Advance HPC. Proceedings of the SC ’23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis. Published. SC-W 2023: Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis. DOI Author/Publisher URL

Vexler, J., Kramer, S. (2023). Identifying Aircraft Motions and Patterns from Magnetometry Data Using a Knowledge-Based Multi-Fusion Approach. 2023 26th International Conference on Information Fusion (FUSION), 1-8. DOI

Andrés López, D., Hillen, B., Simon, P., Schömer, E. (2023). Presentation | Improved deep neural network-driven automatic segmentation of skin’s thermal radiation in moving posterior legs during cardiopulmonary exercise testing for time series data analysis (A. Kiadó, ed.).

Bammert, L.-M., Kramer, S., Cerrato, M., Althaus, E. (2023). Privacy-Preserving Learning of Random Forests Without Revealing the Trees. In A. Bifet, A. C. Lorena, R. P. Ribeiro, et al. (eds.), DS (Vols. 14276, pp. 372-386). Springer. Author/Publisher URL

Birklein, L., Schömer, E., Brylka, R., et al. (2023). Neural Deformable Cone Beam CT. In C. Hansen, J. Procter, R. G. Raidou, et al. (eds.), Eurographics Workshop on Visual Computing for Biology and Medicine. The Eurographics Association. DOI

Bytyqi, Q., Wolpert, N., Schömer, E., Schwanecke, U. (2023). Prototype Softmax Cross Entropy: A New Perspective on Softmax Cross Entropy. In R. Gade, M. Felsberg, J.-K. Kämäräinen (eds.), Image Analysis (pp. 16-31). Cham:Springer Nature Switzerland. DOI

Carretero, J., Garcia-Blas, J., Aldinucci, M., et al. (2023). Adaptive multi-tier intelligent data manager for Exascale. Proceedings of the 20th ACM International Conference on Computing Frontiers {CF}, Bologna, Italy, May 9-11, 285-290. DOI

Cerrato, M., Köppel, M., Esposito, R., Kramer, S. (2023). Invariant Representations with Stochastically Quantized Neural Networks. In B. Williams, Y. Chen, J. Neville (eds.), Thirty-Seventh AAAI Conference on Artificial Intelligence, AAAI 2023, Thirty-Fifth Conference on Innovative Applications of Artificial Intelligence, IAAI 2023, Thirteenth Symposium on Educational Advances in Artificial Intelligence, EAAI 2023, Washington, DC, USA, February 7-14, 2023 (pp. 6962-6970). AAAI Press. DOI Author/Publisher URL

Gallenbacher, J. (2023). Quadrologik: Rechnertechnik “Hands on”. In L. Hellmig, M. Hennecke (eds.), Informatikunterricht zwischen Aktualität und Zeitlosigkeit: 20. GI-Fachtagung Informatik und Schule, INFOS 2023, Würzburg, Germany, September 20-22, 2023: Vol. P-336 (pp. 457-461). Gesellschaft für Informatik, Bonn. DOI Author/Publisher URL

Michalopoulos, A., Tsitsigkos, D., Bouros, P., et al. (2023). Efficient Nearest Neighbor Queries on Non-point Data. 31ST ACM SIGSPATIAL INTERNATIONAL CONFERENCE ON ADVANCES IN GEOGRAPHIC INFORMATION SYSTEMS, ACM SIGSPATIAL GIS 2023, 147-150. DOI Author/Publisher URL

Qian, Y., Cheng, W., Zeng, L., et al. (2023). Xfast: Extreme File Attribute Stat Acceleration for Lustre. Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC), Denver, CO, USA, November 12-17, 96:1-96:12. DOI Author/Publisher URL

Sarsour, A. A. R., Bouros, P., Chondrogiannis, T. (2023). Towards Generating Realistic Geosocial Networks. PROCEEDINGS OF THE 7TH ACM SIGSPATIAL INTERNATIONAL WORKSHOP ON LOCATION-BASED RECOMMENDATIONS, GEOSOCIAL NETWORKS AND GEOADVERTISING, LOCALREC 2023, 25-28. DOI Author/Publisher URL

Vef, M.-A., Miranda, A., Nou, R., Brinkmann, A. (2023). From Static to Malleable: Improving Flexibility and Compatibility in Burst Buffer File Systems. 2nd International Workshop on Malleability Techniques Applications in High-Performance Computing (HPCMall). Author/Publisher URL

Journal Articles

Lang, F., Sorn, P., Schrörs, B., et al. (2023). Multiple instance learning to predict immune checkpoint blockade efficacy using neoantigen candidates. iScience, 26(11), 108014. DOI Author/Publisher URL

Kreppel, F., Melzer, C., Olvera Millán, D. A., et al. (2023). Quantum Circuit Compiler for a Shuttling-Based Trapped-Ion Quantum Computer. Quantum, 7, 1176-1176. DOI

Althaus, E., Bumpus, B. M., Fairbanks, J. P., Rosiak, D. (2023). Compositional Algorithms on Compositional Data: Deciding Sheaves on Presheaves. CoRR, abs/2302.05575.

Birklein, L., Niebler, S., Schoemer, E., et al. (2023). Motion correction for separate mandibular and cranial movements in cone beam CT reconstructions. MEDICAL PHYSICS, 50(6), 3511-3525. DOI Author/Publisher URL

Cheng, W., Sang, D., Zeng, L., et al. (2023). Tianji: Securing A Practical Asynchronous Multi-User ORAM. IEEE Transactions on Dependable and Secure Computing, 1-13. DOI

Derstroff, C., Cerrato, M., Brugger, J., et al. (2023). Peer Learning: Learning Complex Policies in Groups from Scratch via Action Recommendations. CoRR, abs/2312.09950. DOI Author/Publisher URL

Duan, X., Shao, Q., Weng, J., et al. (2023). Bio-ESMD: A Data Centric Implementation for Large-Scale Biological System Simulation on Sunway TaihuLight Supercomputer. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 34(3), 881-893. DOI Author/Publisher URL

Gao, P., Duan, X., Schmidt, B., et al. (2023). Redesign and Accelerate the AIREBO Bond-Order Potential on the New Sunway Supercomputer. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 34(12), 3117-3132. DOI Author/Publisher URL

Hauptmann, T., Kramer, S. (2023). A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction. BMC BIOINFORMATICS, 24(1). DOI Author/Publisher URL

Hauptmann, T., Fellenz, S., Nathan, L., et al. (2023). Discriminative machine learning for maximal representative subsampling. SCIENTIFIC REPORTS, 13(1). DOI Author/Publisher URL

Hillen, B., Lopez, D. A., Marzano-Felisatti, J. M., et al. (2023). Acute physiological responses to a pyramidal exercise protocol and the associations with skin temperature variation in different body areas. JOURNAL OF THERMAL BIOLOGY, 115. DOI Author/Publisher URL

Hillen, B., Lopez, D. A., Pfirrmann, D., et al. (2023). An exploratory, intra- and interindividual comparison of the deep neural network automatically measured calf surface radiation temperature during cardiopulmonary running and cycling exercise testing: A preliminary study. JOURNAL OF THERMAL BIOLOGY, 113. DOI Author/Publisher URL

Keidel, S., Erdweg, S., Hombuecher, T. (2023). Combinator-Based Fixpoint Algorithms for Big-Step Abstract Interpreters. PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL, 7(ICFP). DOI Author/Publisher URL

Kemmer, T., Hack, S., Schmidt, B., Hildebrandt, A. (2023). CUDA-accelerated protein electrostatics in linear space. JOURNAL OF COMPUTATIONAL SCIENCE, 70. DOI Author/Publisher URL

Kramer, S., Cerrato, M., Dzeroski, S., King, R. D. (2023). Automated Scientific Discovery: From Equation Discovery to Autonomous Discovery Systems. CoRR, abs/2305.02251. DOI Author/Publisher URL

Lerner, R., Baker, D., Schwitter, C., et al. (2023). Four-dimensional trapped ion mobility spectrometry lipidomics for high throughput clinical profiling of human blood samples. NATURE COMMUNICATIONS, 14(1). DOI Author/Publisher URL

Neuhauser, C., Hieronymus, M., Kern, M., et al. (2023). Visual analysis of model parameter sensitivities along warm conveyor belt trajectories using Met.3D (1.6.0-multivar1). GEOSCIENTIFIC MODEL DEVELOPMENT, 16(16), 4617-4638. DOI Author/Publisher URL

Pacak, A., Erdweg, S. (2023). Interactive Debugging of Datalog Programs. PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL, 7(OOPSLA). DOI Author/Publisher URL

Teschner, D., Gomez-Zepeda, D., Declercq, A., et al. (2023). Ionmob: a Python package for prediction of peptide collisional cross-section values. BIOINFORMATICS, 39(9). DOI Author/Publisher URL

Wichmann, A., Buschong, E., Mueller, A., et al. (2023). MetaTransformer: deep metagenomic sequencing read classification using self-attention models. NAR GENOMICS AND BIOINFORMATICS, 5(3). DOI Author/Publisher URL

Xu, X., Yin, Z., Yan, L., et al. (2023). RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures. BIOINFORMATICS, 39(11). DOI Author/Publisher URL

Yan, L., Yin, Z., Zhang, H., et al. (2023). RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data. METHODS, 216, 39-50. DOI Author/Publisher URL

Zhang, H., Song, H., Xu, X., et al. (2023). RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 20(3), 2341-2348. DOI Author/Publisher URL

Zhang, H., Yin, Z., Wei, Y., et al. (2023). DeepFilter: A Deep Learning Based Variant Filter for VarDict. TSINGHUA SCIENCE AND TECHNOLOGY, 28(4), 665-672. DOI Author/Publisher URL

Other

Schmidt, B., Kallenborn, F., Chacon, A., and Hundt, C. (2023). CUDASW++4.0: Ultra-fast GPU-based Smith-Waterman Protein Sequence Database Search. In Cold Spring Harbor Laboratory. DOI

Tsitsigkos, D., Bouros, P., Lampropoulos, K., et al. (2023). Two-layer Space-oriented Partitioning for Non-point Data. Author/Publisher URL

Hieronymus, M., Neuhauser, C., Kern, M., et al. (2023). Multi-parameter sensitivities along warm conveyor belt trajectories: A visual analysis using Met.3D. In Copernicus GmbH. DOI

Neuhauser, C., Hieronymus, M., Kern, M., et al. (2023). Visual analysis of model parameter sensitivities along warm conveyor belt trajectories using Met.3D (1.6.0-multivar0). In Copernicus GmbH. DOI

Althaus, E., Bumpus, B. M., Fairbanks, J., Rosiak, D. (2023). Compositional Algorithms on Compositional Data: Deciding Sheaves on Presheaves. Author/Publisher URL

Distler, U., Łącki, M. K., Startek, M. P., et al. (2023). midiaPASEF maximizes information content in data-independent acquisition proteomics. In Cold Spring Harbor Laboratory. DOI

Zhang, H., Song, H., Yin, Z., et al. (2023). RabbitVar: ultra-fast and accurate somatic small-variant calling on multi-core architectures. In Cold Spring Harbor Laboratory. DOI

Theses/Disssertations

Rodrigues Borba, E. (2023). Stochastic Modeling of Data Storage Systems for Evaluating Performance, Dependability, and Energy Consumption (E. Tavares, P. Maciel, and A. Brinkmann, eds.) [PhD Thesis]. Author/Publisher URL

Vef, M.-A. (2023). New techniques for tracing and designing HPC storage systems (A. Brinkmann, ed.) [PhD Thesis]. Author/Publisher URL

Conference Papers

Yan, L., Yin, Z., Zhang, H., et al. (2022). RabbitQCPlus: More Efficient Quality Control for Sequencing Data. 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 619-626. DOI

Moti, N., Salkhordeh, R., Brinkmann, A. (2022). Protected Functions: User Space Privileged Function Calls. Proceedings of the 35th International Conference on the Architecture of Computing Systems (ARCS), Heilbronn, Germany, September 13-15, 117-131. Author/Publisher URL

Althaus, E., Berenbrink, P., Brinkmann, A., Steiner, R. (2022). On the Optimality of the Greedy Garbage Collection Strategy for SSDs. Proceedings of the 42nd IEEE International Conference on Distributed Computing Systems (ICDCS), 78-88. DOI Author/Publisher URL

Adesso, M. F., Hegewald, R., Wolpert, N., et al. (2022). Automatic Classification and Disassembly of Fasteners in Industrial 3D CAD-Scenarios. 2022 IEEE INTERNATIONAL CONFERENCE ON ROBOTICS AND AUTOMATION, ICRA 2022, 9874-9880. DOI Author/Publisher URL

Cheng, W., Zheng, T., Zeng, L., et al. (2022). DPLFS: A Dual-Mode PCM-based Log-Structured File System. 2022 IEEE 40TH INTERNATIONAL CONFERENCE ON COMPUTER DESIGN (ICCD 2022), 324-331. DOI Author/Publisher URL

Dorn, S., Wolpert, N., Schoemer, E. (2022). An Assembly Sequence Planning Framework for Complex Data using General Voronoi Diagram. 2022 IEEE INTERNATIONAL CONFERENCE ON ROBOTICS AND AUTOMATION, ICRA 2022, 9896-9902. DOI Author/Publisher URL

Hegewald, R., Wolpert, N., Schoemer, E. (2022). Iterative Mesh Modification Planning: A new Method for Automatic Disassembly Planning of Complex Industrial Components. 2022 IEEE INTERNATIONAL CONFERENCE ON ROBOTICS AND AUTOMATION (ICRA 2022). Published. DOI Author/Publisher URL

Hegewald, R., Wolpert, N., Schoemer, E. (2022). Simulation and Optimization of Industrial Disassembly Paths using Position Based Dynamics. 2022 26TH INTERNATIONAL CONFERENCE ON METHODS AND MODELS IN AUTOMATION AND ROBOTICS, MMAR 2022, 282-287. DOI Author/Publisher URL

Henkys, V., Schmidt, B., Berger, N. (2022). Online Event Selection for Mu3e using GPUs. ISPDC, 17-24. Author/Publisher URL

Müller, A., Schmidt, B., Membarth, R., et al. (2022). AnySeq/GPU: a novel approach for faster sequence alignment on GPUs. In L. Rauchwerger, K. W. Cameron, D. S. Nikolopoulos, and D. N. Pnevmatikatos (eds.), ICS (pp. 20:1-20:1). ACM. Author/Publisher URL

Qian, Y., Cheng, W., Zeng, L., et al. (2022). MetaWBC: POSIX-Compliant Metadata Write-Back Caching for Distributed File Systems. SC, 56:1-56:1.

Qian, Y., Cheng, W., Zeng, L., et al. (2022). MetaWBC: POSIX-compliant metadata write-back caching for distributed file systems. Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC), 795-814.

Siekiera, J., Köppel, M., Simpson, E., et al. (2022). Ranking Creative Language Characteristics in Small Data Scenarios. In M. M. Hedblom, A. A. Kantosalo, R. Confalonieri, et al. (eds.), Proceedings of the 13th International Conference on Computational Creativity, Bozen-Bolzano, Italy, June 27 – July 1, 2022 (pp. 136-140). Association for Computational Creativity (ACC). Author/Publisher URL

Journal Articles

Ajdari, M., Raaf, P., Kishani, M., et al. (2022). An Enterprise-Grade Open-Source Data Reduction Architecture for All-Flash Storage Systems. Proc. ACM Meas. Anal. Comput. Syst., 6. DOI

Cheng, W., Luo, M., Zeng, L., et al. (2022). Lifespan-based garbage collection to improve SSD’s reliability and performance. Journal of Parallel and Distributed Computing, 164, 28-39. DOI

Bob, K., Teschner, D., Kemmer, T., et al. (2022). Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data. BMC BIOINFORMATICS, 23(1). DOI Author/Publisher URL

Brodehl, S., Mueller, R., Schoemer, E., et al. (2022). End-to-End Prediction of Lightning Events from Geostationary Satellite Images. REMOTE SENSING, 14(15). DOI Author/Publisher URL

Cascitti, J., Niebler, S., Mueller, A., Schmidt, B. (2022). RNACache: A scalable approach to rapid transcriptomic read mapping using locality sensitive hashing. JOURNAL OF COMPUTATIONAL SCIENCE, 60. DOI Author/Publisher URL

Cerrato, M., Coronel, A. V., Köppel, M., et al. (2022). Fair Interpretable Representation Learning with Correction Vectors. CoRR, abs/2202.03078. Author/Publisher URL

Cerrato, M., Köppel, M., Esposito, R., Kramer, S. (2022). Invariant Representations with Stochastically Quantized Neural Networks. CoRR, abs/2208.02656. DOI Author/Publisher URL

Cerrato, M., Köppel, M., Segner, A., Kramer, S. (2022). Fair Group-Shared Representations with Normalizing Flows. CoRR, abs/2201.06336. Author/Publisher URL

Cerrato, M., Köppel, M., Segner, A., Kramer, S. (2022). Fair Interpretable Learning via Correction Vectors. CoRR, abs/2201.06343. Author/Publisher URL

Fischer, C., Fink, A. H., Schoemer, E., et al. (2022). A novel method for objective identification of 3-D potential vorticity anomalies. GEOSCIENTIFIC MODEL DEVELOPMENT, 15(11). DOI Author/Publisher URL

Gao, P., Duan, X., Schmidt, B., et al. (2022). Optimization of Reactive Force Field Simulation: Refactor, Parallelization, and Vectorization for Interactions. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 33(2), 359-373. DOI Author/Publisher URL

Garcon, A., Vexler, J., Budker, D., Kramer, S. (2022). Deep neural networks to recover unknown physical parameters from oscillating time series. PLOS ONE, 17(5). DOI Author/Publisher URL

Hillen, B., Lopez, D. A., Schömer, E., et al. (2022). Towards Exercise Radiomics: Deep Neural Network-Based Automatic Analysis of Thermal Images Captured During Exercise. IEEE Journal of Biomedical and Health Informatics, 1-11. DOI

Juenger, D., Kobus, R., Mueller, A., et al. (2022). General-purpose GPU hashing data structures and their application in accelerated genomics. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 163, 256-268. DOI Author/Publisher URL

Kallenborn, F., Cascitti, J., Schmidt, B. (2022). CARE 2.0: reducing false-positive sequencing error corrections using machine learning. BMC BIOINFORMATICS, 23(1). DOI Author/Publisher URL

Krueger, M., Wilson, J., Wietzoreck, M., et al. (2022). Convolutional neural network prediction of molecular properties for aerosol chemistry and health effects. NATURAL SCIENCES, 2(4). DOI Author/Publisher URL

Meng, J., Zhuang, C., Chen, P., et al. (2022). Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 33(11), 2885-2899. DOI Author/Publisher URL

Müller, A., Schmidt, B., Membarth, R., et al. (2022). AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs. CoRR, abs/2205.07610.

Niebler, S., Miltenberger, A., Schmidt, B., Spichtinger, P. (2022). Automated detection and classification of synoptic-scale fronts from atmospheric data grids. WEATHER AND CLIMATE DYNAMICS, 3(1), 113-137. DOI Author/Publisher URL

Pohler, A., Abdelfatah, S., Riedl, M., et al. (2022). Potential Coronaviral Inhibitors of the Nucleocapsid Protein Identified In Silico and In Vitro from a Large Natural Product Library. PHARMACEUTICALS, 15(9). DOI Author/Publisher URL

Xu, K., Duan, X., Muller, A., et al. (2022). FMapper: Scalable read mapper based on succinct hash index on SunWay TaihuLight. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 161, 72-82. DOI Author/Publisher URL

Xu, K., Zhang, J., Duan, X., et al. (2022). Redesigning and Optimizing UCSF DOCK3.7 on Sunway TaihuLight. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 33(12), 4458-4471. DOI Author/Publisher URL

Zhang, H., Chang, Q., Yin, Z., et al. (2022). RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures. Bioinform., 38, 2932-2933.

Other

Pensel, L., and Kramer, S. (2022). Neural RELAGGS. Author/Publisher URL

Xu, X., Yin, Z., Yan, L., et al. (2022). RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches. In Cold Spring Harbor Laboratory. DOI

Hauptmann, T., Kramer, S. (2022). A Fair Experimental Comparison of Neural Network Architectures for Latent Representations of Multi-Omics for Drug Response Prediction. Author/Publisher URL

Brodehl, S., Müller, R., Schömer, E., et al. (2022). End-to-End Prediction of Lightning Events from Geostationary Satellite Images. In MDPI AG. DOI

Theses/Disssertations

Schnur, R. (2022). Interactive Motion Planning in Mixed Reality (E. Schömer and M. Wand, eds.) [Master’s Thesis]. Author/Publisher URL

Book chapters

Althaus, E., and Ziegler, S. (2021). Optimal Tree Decompositions Revisited: A Simpler Linear-Time FPT Algorithm. In C. Gentile, G. Stecca, and P. Ventura (eds.), Graphs and Combinatorial Optimization: from Theory to Applications: CTW2020 Proceedings (pp. 67-78). Cham:Springer International Publishing. DOI

Althaus, E., Hildebrandt, A., and Mosca, D. (2021). Learning Molecular Classes from Small Numbers of Positive Examples Using Graph Grammars. In Lecture Notes in Computer Science (pp. 3-15). Springer International Publishing. DOI

Gallenbacher, J. (2021). Besser rechnen mit Strom. In Abenteuer Informatik (pp. 365-388). Berlin, Heidelberg:Springer Berlin Heidelberg. DOI Author/Publisher URL

Conference Papers

Tsitsigkos, D., Lampropoulos, K., Bouros, P., et al. (2021). A Two-layer Partitioning for Non-point Spatial Data. 2021 IEEE 37th International Conference on Data Engineering (ICDE), 1787-1798. DOI

Adesso, M. F., Wolpert, N., Schoemer, E. (2021). ConfusionTree-Pattern: A Hierarchical Design for an Efficient and Performant Multi-Class Pattern. 20TH IEEE INTERNATIONAL CONFERENCE ON MACHINE LEARNING AND APPLICATIONS (ICMLA 2021), 754-759. DOI Author/Publisher URL

Althaus, E., Schnurbusch, D., Wüschner, J., Ziegler, S. (2021). On Tamaki’s Algorithm to Compute Treewidths. In D. Coudert and E. Natale (eds.), SEA (Vols. 190, pp. 9:1-9:1). Schloss Dagstuhl – Leibniz-Zentrum für Informatik. Author/Publisher URL

Cascitti, J., Niebler, S., Müller, A., Schmidt, B. (2021). RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing. 367-381. DOI

Dorn, S., Wolpert, N., Schoemer, E. (2021). Expansive Voronoi Tree: A Motion Planner for Assembly Sequence Planning. 2021 IEEE INTERNATIONAL CONFERENCE ON ROBOTICS AND AUTOMATION (ICRA 2021), 7880-7886. DOI Author/Publisher URL

Erdweg, S., Szabo, T., Pacak, A. (2021). Concise, Type-Safe, and Efficient Structural Diffing. PROCEEDINGS OF THE 42ND ACM SIGPLAN INTERNATIONAL CONFERENCE ON PROGRAMMING LANGUAGE DESIGN AND IMPLEMENTATION (PLDI ’21), 406-419. DOI Author/Publisher URL

Hegewald, R., Wolpert, N., Schoemer, E. (2021). Saliency Features for 3D CAD-Data in the Context of Sampling-Based Motion Planning. 2021 IEEE INTERNATIONAL CONFERENCE ON ROBOTICS AND AUTOMATION (ICRA 2021), 7858-7864. DOI Author/Publisher URL

Hildebrandt, A. K., Althaus, E., Hildebrandt, A. (2021). Privately Querying Privacy: Privacy Estimation with Guaranteed Privacy of User and Database Party. 56-72. Author/Publisher URL

Häcker, C., Bouros, P., Chondrogiannis, T., Althaus, E. (2021). Most Diverse Near-Shortest Paths. 229-239. Author/Publisher URL

Kobus, R., Mueller, A., Juenger, D., et al. (2021). MetaCache-GPU: Ultra-Fast Metagenomic Classification. 50TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING. Published. DOI Author/Publisher URL

Kramer, S. (2021). Myths and Misconceptions about Machine Learning and How They Are Related to Software Engineering. In R. Ali, H. Kaindl, and L. A. Maciaszek (eds.), Proceedings of the 16th International Conference on Evaluation of Novel Approaches to Software Engineering, ENASE 2021, Online Streaming, April 26-27, 2021 (pp. 5-5). SCITEPRESS.

Kramer, S. (2021). Myths and Misconceptions about Machine Learning and How They Are Related to Software Engineering. In J. Filipe, M. Smialek, A. Brodsky, and S. Hammoudi (eds.), Proceedings of the 23rd International Conference on Enterprise Information Systems, ICEIS 2021, Online Streaming, April 26-28, 2021, Volume 1 (pp. 7-7). SCITEPRESS.

Li, W., Abels, P., Ahmadi, Z., et al. (2021). Topic-Guided Knowledge Graph Construction for Argument Mining. In L. Chen and B. Fernández-Manjón (eds.), 2021 IEEE International Conference on Big Knowledge, ICBK 2021, Auckland, New Zealand, December 7-8, 2021 (pp. 315-322). IEEE. DOI

Mehmeti-Göpel, C. H. X. A., Hartmann, D., Wand, M. (2021). Ringing ReLUs: Harmonic Distortion Analysis of Nonlinear Feedforward Networks. ICLR. Author/Publisher URL

Oliver, N., Pérez-Cruz, F., Kramer, S., … Lozano, J. A. (eds.). (2021). Machine Learning and Knowledge Discovery in Databases. Research Track – European Conference, ECML PKDD 2021, Bilbao, Spain, September 13-17, 2021, Proceedings, Part I. 12975. DOI

Szabo, T., Erdweg, S., Bergmann, G. (2021). Incremental Whole-Program Analysis in Datalog with Lattices. PROCEEDINGS OF THE 42ND ACM SIGPLAN INTERNATIONAL CONFERENCE ON PROGRAMMING LANGUAGE DESIGN AND IMPLEMENTATION (PLDI ’21), 1-15. DOI Author/Publisher URL

Weissenberger, A., Schmidt, B. (2021). Accelerating JPEG Decompression on GPUs. 2021 IEEE 28TH INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING, DATA, AND ANALYTICS (HIPC 2021), 121-130. DOI Author/Publisher URL

Journal Articles

Burkhardt, S., Brugger, J., Wagner, N., et al. (2021). Rule Extraction From Binary Neural Networks With Convolutional Rules for Model Validation. Frontiers in Artificial Intelligence, 4. DOI

Yin, Z., Xu, X., Zhang, J., et al. (2021). RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures. Bioinformatics, 37(6), 873-875. DOI

Bouros, P., Dasu, T., Kanza, Y., et al. (2021). The Fourth ACM SIGSPATIAL Workshop on Location-Based Recommendations, Geosocial Networks and Geoadvertising. SIGSPATIAL Special, 12(3), 7-10. DOI

Garcon, A., Vexler, J., Budker, D., Kramer, S. (2021). Deep Neural Networks to Recover Unknown Physical Parameters from Oscillating Time Series. Author/Publisher URL

Abels, P., Ahmadi, Z., Burkhardt, S., et al. (2021). Focusing Knowledge-based Graph Argument Mining via Topic Modeling. CoRR, abs/2102.02086. Author/Publisher URL

Althaus, E., Dousti, M. S., Kramer, S. (2021). Fast Private Parameter Learning and Evaluation for Sum-Product Networks. CoRR, abs/2104.07353.

Bouros, P., Mamoulis, N., Tsitsigkos, D., Terrovitis, M. (2021). In-Memory Interval Joins. VLDB JOURNAL, 30(4), 667-691. DOI Author/Publisher URL

Cheng, W., Deng, S., Zeng, L., et al. (2021). AIOC2: A deep Q-learning approach to autonomic I/O congestion control in Lustre. Parallel Comput., 108, 102855-102855. DOI

Dratsch, T., Korenkov, M., Zopfs, D., et al. (2021). Practical applications of deep learning: classifying the most common categories of plain radiographs in a PACS using a neural network. EUROPEAN RADIOLOGY, 31(4), 1812-1818. DOI Author/Publisher URL

Hartmann, D., Franzen, D., Brodehl, S. (2021). Studying the Evolution of Neural Activation Patterns During Training of Feed-Forward ReLU Networks. FRONTIERS IN ARTIFICIAL INTELLIGENCE, 4. DOI Author/Publisher URL

Raza, A., Kramer, S. (2021). Pattern Sampling for Shapelet-based Time Series Classification. CoRR, abs/2102.08498. Author/Publisher URL

Ringe, K. I., Vo Chieu, V. D., Wacker, F., et al. (2021). Fully automated detection of primary sclerosing cholangitis (PSC)-compatible bile duct changes based on 3D magnetic resonance cholangiopancreatography using machine learning. EUROPEAN RADIOLOGY, 31(4), 2482-2489. DOI Author/Publisher URL

Siekiera, J., Kramer, S. (2021). Deep Unsupervised Identification of Selected SNPs between Adapted Populations on Pool-seq Data. CoRR, abs/2101.00004. Author/Publisher URL

Weißenberger, A., Schmidt, B. (2021). Accelerating JPEG Decompression on GPUs. CoRR, abs/2111.09219.

Werner, S., Galliot, A., Pichot, F., et al. (2021). NOseq: amplicon sequencing evaluation method for RNA m6A sites after chemical deamination. NUCLEIC ACIDS RESEARCH, 49(4). DOI Author/Publisher URL

Winther, H., Hundt, C., Ringe, K. I., et al. (2021). A 3D Deep Neural Network for Liver Volumetry in 3T Contrast-Enhanced MRI. ROFO-FORTSCHRITTE AUF DEM GEBIET DER RONTGENSTRAHLEN UND DER BILDGEBENDEN VERFAHREN, 193(03), 305-314. DOI Author/Publisher URL

Yin, Z., Zhang, H., Liu, M., et al. (2021). RabbitQC: high-speed scalable quality control for sequencing data. BIOINFORMATICS, 37(4), 573-574. DOI Author/Publisher URL

Other

Bob, K., Teschner, D., Kemmer, T., et al. (2021). Locality-sensitive hashing enables signal classification in high-throughput mass spectrometry raw data at scale. In Cold Spring Harbor Laboratory. DOI

Hildebrandt, A.-K., Bob, K., Teschner, D., et al. (2021). CorCast: A Distributed Architecture for Bayesian Epidemic Nowcasting and its Application to District-Level SARS-CoV-2 Infection Numbers in Germany. In Cold Spring Harbor Laboratory. DOI

Christodoulou, G., Bouros, P., Mamoulis, N. (2021). HINT: A Hierarchical Index for Intervals in Main Memory. Author/Publisher URL

Althaus, E., Dousti, M. S., Kramer, S., Rassau, N. J. P. (2021). Fast Private Parameter Learning and Inference for Sum-Product Networks. Author/Publisher URL

Kobus, R., Müller, A., Jünger, D., et al. (2021). MetaCache-GPU: Ultra-Fast Metagenomic Classification.

Theses/Disssertations

Kemmer, T. (2021). Space-efficient and exact system representations for the nonlocal protein electrostatics problem (A. Hildebrandt, ed.) [PhD Thesis]. DOI Author/Publisher URL

Conference Papers

Qi, S., Bouros, P., Mamoulis, N. (2020). Top-k String Similarity Joins. 32nd International Conference on Scientific and Statistical Database Management, 1-12. DOI

Andrés López, D., Hillen, B., Simon, P., Schömer, E. (2020). Presentation | Deep learning based segmentation of uncovered body parts in thermal images during dynamic exercise. Book of Abstracts, 24-25. Author/Publisher URL

Andrés López, D., Hillen, B., Simon, P., Schömer, E. (2020). Presentation | Thermonet: Automatic Segmentation of Blood Vessel Patterns detected by Infrared Thermography during dynamic Exercise (F. Dela, E. Müller, and E. Tsolakidis, eds.; Issue Book of Abstracts, pp. 127-127). Author/Publisher URL

Bouros, P., Lampropoulos, K., Tsitsigkos, D., et al. (2020). Band Joins for Interval Data. In A. Bonifati, Y. Zhou, M. A. V. Salles, et al. (eds.), Proceedings of the 23rd International Conference on Extending Database Technology, EDBT 2020, Copenhagen, Denmark, March 30 – April 02, 2020 (pp. 443-446). OpenProceedings.org. DOI

Burkhardt, S., Siekiera, J., Glodde, J., et al. (2020). Towards Identifying Drug Side Effects from Social Media Using Active Learning andCrowd Sourcing. Pacific Symposium on Biocomputing 2020, Fairmont Orchid, Hawaii, USA, January 3-7, 2020, 319-330. Author/Publisher URL

Cerrato, M., Köppel, M., Segner, A., et al. (2020). Fair pairwise learning to rank. In G. I. Webb, Z. Zhang, V. S. Tseng, et al. (eds.), 7th IEEE International Conference on Data Science and Advanced Analytics, DSAA 2020, Sydney, Australia, October 6-9, 2020 (pp. 729-738). IEEE. DOI

Chopite, J. G., Hullin, M. B., Wand, M., Iseringhausen, J. (2020). Deep Non-Line-of-Sight Reconstruction. CVPR, 957-966. Author/Publisher URL

Costa, C. F., Chondrogiannis, T., Nascimento, M. A., Bouros, P. (2020). RRAMEN: An Interactive Tool for Evaluating Choices and Changes in Transportation Networks. In A. Bonifati, Y. Zhou, M. A. V. Salles, et al. (eds.), Proceedings of the 23rd International Conference on Extending Database Technology, EDBT 2020, Copenhagen, Denmark, March 30 – April 02, 2020 (pp. 599-602). OpenProceedings.org. DOI

Dorn, S., Wolpert, N., Schoemer, E. (2020). Voxel-based General Voronoi Diagram for Complex Data with Application on Motion Planning. 2020 IEEE INTERNATIONAL CONFERENCE ON ROBOTICS AND AUTOMATION (ICRA), 137-143. DOI Author/Publisher URL

Duan, X., Gao, P., Zhang, M., et al. (2020). Cell-List based Molecular Dynamics on Many-Core Processors: A Case Study on Sunway TaihuLight Supercomputer. PROCEEDINGS OF SC20: THE INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS (SC20). Published. DOI Author/Publisher URL

Duan, X., Gao, P., Zhang, M., et al. (2020). Neighbor-list-free Molecular Dynamics on Sunway TaihuLight Supercomputer. PROCEEDINGS OF THE 25TH ACM SIGPLAN SYMPOSIUM ON PRINCIPLES AND PRACTICE OF PARALLEL PROGRAMMING (PPOPP ’20), 413-414. DOI Author/Publisher URL

Juenger, D., Kobus, R., Mueller, A., et al. (2020). WarpCore: A Library for fast Hash Tables on GPUs. 2020 IEEE 27TH INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING, DATA, AND ANALYTICS (HIPC 2020), 11-20. DOI Author/Publisher URL

Keidel, S., Erdweg, S. (2020). A Systematic Approach to Abstract Interpretation of Program Transformations. In D. Beyer, D. Zufferey (eds.), VMCAI (Vols. 11990, pp. 136-157). Springer. Author/Publisher URL

Kramer, S. (2020). A Brief History of Learning Symbolic Higher-Level Representations from Data (And a Curious Look Forward). In C. Bessiere (ed.), Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, IJCAI 2020 (pp. 4868-4876). ijcai.org. DOI Author/Publisher URL

Müller, A., Schmidt, B., Hildebrandt, A., et al. (2020). AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. IPDPS, 1030-1040. Author/Publisher URL

Schmidt, B., Hundt, C. (2020). cuDTW plus plus : Ultra-Fast Dynamic Time Warping on CUDA-Enabled GPUs. EURO-PAR 2020: PARALLEL PROCESSING, 12247, 597-612. DOI Author/Publisher URL

Xu, K., Duan, X., Meng, X., et al. (2020). SWMapper: Scalable Read Mapper on SunWay TaihuLight. PROCEEDINGS OF THE 49TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING, ICPP 2020. Published. DOI Author/Publisher URL

Journal Articles

Pacak, A., Erdweg, S., Szabó, T. (2020). A systematic approach to deriving incremental type checkers. Proceedings of the ACM on Programming Languages, 4(OOPSLA), 1-28. DOI

Zannoni, N., Wikelski, M., Gagliardo, A., et al. (2020). Identifying volatile organic compounds used for olfactory navigation by homing pigeons. Sci. Rep., 10(1), 15879. DOI Author/Publisher URL

Tacke, M., Kochs, E. F., Mueller, M., et al. (2020). Machine learning for a combined electroencephalographic anesthesia index to detect awareness under anesthesia. PLoS One, 15(8), e0238249. DOI Author/Publisher URL

Hieronymus, M., Schmidt, B., Böser, S. (2020). Reconstruction of Low Energy Neutrino Events with GPUs at IceCube. Computational Science – ICCS 2020, 12137, 118-131. DOI

Abuin, J. M., Lopes, N., Ferreira, L., et al. (2020). Big Data in metagenomics: Apache Spark vs MPI. PLOS ONE, 15(10). DOI Author/Publisher URL

Althaus, E., Rauterberg, F., Ziegler, S. (2020). Computing Euclidean Steiner trees over segments. EURO JOURNAL ON COMPUTATIONAL OPTIMIZATION, 8(3-4), 309-325. DOI Author/Publisher URL

Boer, D., Kramer, S. (2020). Secure Sum Outperforms Homomorphic Encryption in (Current) Collaborative Deep Learning. CoRR, abs/2006.02894. Author/Publisher URL

Burkhardt, S., Brugger, J., Wagner, N., et al. (2020). Rule Extraction from Binary Neural Networks with Convolutional Rules for Model Validation. CoRR, abs/2012.08459. Author/Publisher URL

Chondrogiannis, T., Bouros, P., Gamper, J., et al. (2020). Finding k-shortest paths with limited overlap. VLDB JOURNAL, 29(5), 1023-1047. DOI Author/Publisher URL

Gao, P., Duan, X., Zhang, T., et al. (2020). Millimeter-Scale and Billion-Atom Reactive Force Field Simulation on Sunway Taihulight. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 31(12), 2954-2967. DOI Author/Publisher URL

Hellmann, S. L., Ripp, F., Bikar, S.-E., et al. (2020). Identification and quantification of meat product ingredients by whole-genome metagenomics (All-Food-Seq). EUROPEAN FOOD RESEARCH AND TECHNOLOGY, 246(1), 193-200. DOI Author/Publisher URL

Jungmann, F., Brodehl, S., Buhl, R., et al. (2020). Workflow-centred open-source fully automated lung volumetry in chest CT. CLINICAL RADIOLOGY, 75(1). DOI Author/Publisher URL

Jünger, D., Kobus, R., Müller, A., et al. (2020). WarpCore: A Library for fast Hash Tables on GPUs. CoRR, abs/2009.07914.

Kaindl, H., Kramer, S. (2020). Towards Probability-based Safety Verification of Systems with Components from Machine Learning. CoRR, abs/2003.01155. Author/Publisher URL

Kallenborn, F., Hildebrandt, A., Schmidt, B. (2020). CARE: Context-Aware Sequencing Read Error Correction. Bioinformatics.

Kobus, R., Abuin, J. M., Mueller, A., et al. (2020). A big data approach to metagenomics for all-food-sequencing. BMC BIOINFORMATICS, 21(1). DOI Author/Publisher URL

Kobus, R., Abuín, J. M., Müller, A., et al. (2020). A big data approach to metagenomics for all-food-sequencing. BMC Bioinformatics, 21, 1-15.

Lan, H., Meng, J., Hundt, C., et al. (2020). FeatherCNN: Fast Inference Computation with TensorGEMM on ARM Architectures. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 31(3), 580-594. DOI Author/Publisher URL

Maehringer-Kunz, A., Wagner, F., Hahn, F., et al. (2020). Predicting survival after transarterial chemoembolization for hepatocellular carcinoma using a neural network: A Pilot Study. LIVER INTERNATIONAL, 40(3), 694-703. DOI Author/Publisher URL

Müller, A., Schmidt, B., Hildebrandt, A., et al. (2020). AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. arXiv preprint arXiv:2002.04561.

Niebler, S., Mueller, A., Hankeln, T., Schmidt, B. (2020). RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads. BMC BIOINFORMATICS, 21(1). DOI Author/Publisher URL

Pedergnana, A., Calandra, I., Bob, K., et al. (2020). Evaluating the microscopic effect of brushing stone tools as a cleaning procedure. Quaternary International.

Pedergnana, A., Calandra, I., Evans, A. A., et al. (2020). Polish is quantitatively different on quartzite flakes used on different worked materials. PLOS ONE, 15(12). DOI Author/Publisher URL

Qi, S., Bouros, P., Mamoulis, N. (2020). Top-k spatial distance joins. GEOINFORMATICA, 24(3), 591-631. DOI Author/Publisher URL

Raza, A., Kramer, S. (2020). Accelerating pattern-based time series classification : a linear time and space string mining approach. Knowledge and information systems, 62, Seiten: 1113-1141. Author/Publisher URL

Schmidt, B., Hildebrandt, A. (2020). Deep learning in next-generation sequencing. Drug Discovery Today.

Siekiera, J., Köppel, M., Simpson, E., et al. (2020). Ranking Creative Language Characteristics in Small Data Scenarios. CoRR, abs/2010.12613. Author/Publisher URL

Werner, S., Schmidt, L., Marchand, V., et al. (2020). Machine learning of reverse transcription signatures of variegated polymerases allows mapping and discrimination of methylated purines in limited transcriptomes. Nucleic acids research, 48, 3734-3746.

Winther, H. B., Gutberlet, M., Hundt, C., et al. (2020). Deep semantic lung segmentation for tracking potential pulmonary perfusion biomarkers in chronic obstructive pulmonary disease (COPD): The multi-ethnic study of atherosclerosis COPD study. JOURNAL OF MAGNETIC RESONANCE IMAGING, 51(2), 571-579. DOI Author/Publisher URL

Other

Boer, D., and Kramer, S. (2020). Secure Sum Outperforms Homomorphic Encryption in (Current) Collaborative Deep Learning. Author/Publisher URL

Tsitsigkos, D., Lampropoulos, K., Bouros, P., et al. (2020). A Two-level Spatial In-Memory Index. Author/Publisher URL

Theses/Disssertations

Schnur, R. (2020). Optimierung des adiabatischen Lichtleiters für das Wavelength-shifting Optical Module (E. Schömer and S. Böser, eds.) [Undergraduate Dissertation]. Author/Publisher URL

Book chapters

Boer, D., Ahmadi, Z., Kramer, S. (2019). Privacy preserving client/vertical-servers classification. In C. Alzate (ed.), ECML PKDD 2018 Workshops : MIDAS 2018 and PAP 2018, Dublin, Ireland, September 10-14, 2018, Proceedings (pp. Seiten: 125-140). Cham:Springer International Publishing. Author/Publisher URL

Schmidt, B., Hildebrandt, A. (2019). Dedicated Bioinformatics Analysis Hardware. In Encyclopedia of Bioinformatics and Computational Biology (pp. 1142-1150). Academic Press.

Vexler, J., Kramer, S. (2019). Integrating LSTMs with Online Density Estimation for the Probabilistic Forecast of Energy Consumption (Vols. 11828, pp. 533-543). DOI Author/Publisher URL

Williams, J., Stönner, C., Edtbauer, A., et al. (2019). What can we learn from the air chemistry of crowds?. In A. Hansel (ed.), 8th International Conference on Proton Transfer Reaction Mass Spectrometry and its Applications (PTRMS 2019) (pp. Seiten: 121-123). Innsbruck:innsbruck university press.

Conference Papers

Kobus, R., Jünger, D., Hundt, C., Schmidt, B. (2019, August 5). Gossip: Efficient Communication Primitives for Multi-GPU Systems. Proceedings of the 48th International Conference on Parallel Processing. Published. ICPP 2019: 48th International Conference on Parallel Processing. DOI

Yin, Z., Zhang, T., Muller, A., et al. (2019). Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core Architectures. 2019 IEEE 21st International Conference on High Performance Computing and Communications; IEEE 17th International Conference on Smart City; IEEE 5th International Conference on Data Science and Systems (HPCC/SmartCity/DSS), 168-176. DOI

Büren, F., Jünger, D., Kobus, R., et al. (2019, June 17). Suffix Array Construction on Multi-GPU Systems. Proceedings of the 28th International Symposium on High-Performance Parallel and Distributed Computing. HPDC ’19: The 28th International Symposium on High-Performance Parallel and Distributed Computing. DOI

Ahmadi, Z., Kramer, S. (2019). Modeling Multi-label Recurrence in Data Streams. In Y. Gao, R. Möller, X. Wu, and R. Kotagiri (eds.), 2019 IEEE International Conference on Big Knowledge, ICBK 2019, Beijing, China, November 10-11, 2019 (pp. 9-16). IEEE. DOI

Alzate, C., Monreale, A., Assem, H., … Sinn, M. (eds.). (2019). ECML PKDD 2018 Workshops – Nemesis 2018, UrbReas 2018, SoGood 2018, IWAISe 2018, and Green Data Mining 2018, Dublin, Ireland, September 10-14, 2018, Proceedings. 11329. DOI

Bierwirth, B., Schwanecke, U., Gietzen, T., et al. (2019). SmartAirCargoTrailer : autonomous short distance transports in air cargo. Hamburg International Conference of Logistics (HICL) 2019, 151-185. DOI Author/Publisher URL

Bouros, P., Assent, I., Jeppesen, J., Toftegaard, T. S. (2019). Processing Satellite Imagery for Decision-Making in Precision Agriculture. In P. Papotti (ed.), Proceedings of the Workshops of the EDBT/ICDT 2019 Joint Conference, EDBT/ICDT 2019, Lisbon, Portugal, March 26, 2019 (Vols. 2322). CEUR-WS.org. Author/Publisher URL

Chondrogiannis, T., Nascimento, M. A., Bouros, P. (2019). Relative Reachability Analysis as a Tool for Urban Mobility Planning (Position Paper). PROCEEDINGS OF THE 12TH INTERNATIONAL WORKSHOP ON COMPUTATIONAL TRANSPORTATION SCIENCE, IWCTS 2019. Published. DOI Author/Publisher URL

Hartmann, D., Wand, M. (2019). Progressive Stochastic Binarization of Deep Networks. EMC2@NeurIPS, 31-35. Author/Publisher URL

Hochthurn, T., Gallenbacher, J. (2019). Innovative Gestaltung und Einsatz von Erklärvideos im Informatikunterricht. In A. Pasternak (ed.), Informatik für alle, 18. GI-Fachtagung Informatik und Schule, INFOS 2019, 16.-18. September 2019, Dortmund: Vol. P-288 (pp. 221-230). Gesellschaft für Informatik. DOI Author/Publisher URL

Jördens, T., Gallenbacher, J. (2019). Quadrologik – Modularisierung von Schaltnetzen und Schaltwerken. In A. Pasternak (ed.), Informatik für alle, 18. GI-Fachtagung Informatik und Schule, INFOS 2019, 16.-18. September 2019, Dortmund: Vol. P-288 (pp. 379-379). Gesellschaft für Informatik. DOI Author/Publisher URL

Köppel, M., Segner, A., Wagener, M., et al. (2019). Pairwise Learning to Rank by Neural Networks Revisited: Reconstruction, Theoretical Analysis and Practical Performance. In U. Brefeld, Élisa Fromont, A. Hotho, et al. (eds.), ECML/PKDD (3) (Vols. 11908, pp. 237-252). Springer. Author/Publisher URL

Pacak, A., Erdweg, S. (2019). Generating incremental type services. In O. Nierstrasz, J. Gray, B. C. D. S. Oliveira (eds.), SLE (pp. 197-201). ACM. Author/Publisher URL

Pensel, L., Kramer, S. (2019). Forecast of Study Success in the STEM Disciplines Based Solely on Academic Records. In P. Cellier, K. Driessens (eds.), PKDD/ECML Workshops (1) (Vols. 1167, pp. 647-657). Springer. Author/Publisher URL

Portaneri, C., Alliez, P., Hemmer, M., et al. (2019). Cost-Driven Framework for Progressive Compression of Textured Meshes. PROCEEDINGS OF THE 10TH ACM MULTIMEDIA SYSTEMS CONFERENCE (ACM MMSYS’19), 175-188. DOI Author/Publisher URL

Saha, S., Sarkar, D., Kramer, S. (2019). Exploring Multi-Objective Optimization for Multi-Label Classifier Ensembles. IEEE Congress on Evolutionary Computation, CEC 2019, Wellington, New Zealand, June 10-13, 2019, 2753-2760. DOI

Tsitsigkos, D., Bouros, P., Mamoulis, N., Terrovitis, M. (2019). Parallel In-Memory Evaluation of Spatial Joins. 27TH ACM SIGSPATIAL INTERNATIONAL CONFERENCE ON ADVANCES IN GEOGRAPHIC INFORMATION SYSTEMS (ACM SIGSPATIAL GIS 2019), 516-519. DOI Author/Publisher URL

Weissenberger, A., Schmidt, B. (2019). Massively Parallel ANS Decoding on GPUs. PROCEEDINGS OF THE 48TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING (ICPP 2019). Published. DOI Author/Publisher URL

Yin, Z., Zhang, H., Xu, K., et al. (2019). XLCS: A New Bit-Parallel Longest Common Subsequence Algorithm on Xeon Phi Clusters. In Z. Xiao, L. T. Yang, P. Balaji, et al. (eds.), HPCC/SmartCity/DSS (pp. 1477-1483). IEEE. Author/Publisher URL

Journal Articles

Keidel, S., Erdweg, S. (2019). Sound and reusable components for abstract interpretation. Proceedings of the ACM on Programming Languages, 3(OOPSLA), 1-28. DOI

Salvaneschi, G., Köhler, M., Sokolowski, D., et al. (2019). Language-integrated privacy-aware distributed queries. Proceedings of the ACM on Programming Languages, 3(OOPSLA), 1-30. DOI

Bouros, P., Mamoulis, N. (2019). Spatial joins. SIGSPATIAL Special, 11(1), 13-21. DOI

Bouros, P., Renz, M., Sacharidis, D. (2019). LocalRec 2018 workshop report the second ACM SIGSPATIAL workshop on recommendations for location-based services and social networks * Seattle, Washington, USA – November 6, 2018. SIGSPATIAL Special, 10(3), 23-25. DOI

Althaus, E., Ziegler, S. (2019). Optimal Tree Decompositions Revisited: A Simpler Linear-Time FPT Algorithm. CoRR, abs/1912.09144.

Bracevac, O., Salvaneschi, G., Erdweg, S., Mezini, M. (2019). Type-safe, Polyvariadic Event Correlation. CoRR, abs/1907.02990.

Burkhardt, S., Kramer, S. (2019). A Survey of Multi-Label Topic Models. SIGKDD Explor., 21, 61-79. DOI

Burkhardt, S., Kramer, S. (2019). Decoupling sparsity and smoothness in the Dirichlet variational autoencoder topic model. Journal of machine learning research, 20, Art. 131. Author/Publisher URL

Burkhardt, S., Kramer, S. (2019). Multi-label classification using stacked hierarchical Dirichlet processes with reduced sampling complexity. Knowledge and information systems, 59(1), Seiten: 93-115. Author/Publisher URL

Calandra, I., Schunk, L., Bob, K., et al. (2019). The effect of numerical aperture on quantitative use-wear studies and its implication on reproducibility. Scientific reports, 9, 1-10.

Calandra, I., Schunk, L., Bob, K., et al. (2019). The effect of numerical aperture on quantitative use-wear studies and its implication on reproducibility. SCIENTIFIC REPORTS, 9. DOI Author/Publisher URL

Chamani, J. G., Dousti, M. S., Jalili, R., Papadopoulos, D. (2019). SESOS: A Verifiable Searchable Outsourcing Scheme for Ordered Structured Data in Cloud Computing. ISECURE-ISC INTERNATIONAL JOURNAL OF INFORMATION SECURITY, 11(1), 15-34. Author/Publisher URL

dos Santos, D. P., Brodehl, S., Baessler, B., et al. (2019). Structured report data can be used to develop deep learning algorithms: a proof of concept in ankle radiographs. INSIGHTS INTO IMAGING, 10(1). DOI Author/Publisher URL

dos Santos, D. P., Giese, D., Brodehl, S., et al. (2019). Medical students’ attitude towards artificial intelligence: a multicentre survey. EUROPEAN RADIOLOGY, 29(4), 1640-1646. DOI Author/Publisher URL

Gallenbacher, J. (2019). Ohne Informatik keine Allgemeinbildung. Inform. Spektrum, 42, 88-96. DOI Author/Publisher URL

Gietzen, T., Brylka, R., Achenbach, J., et al. (2019). A method for automatic forensic facial reconstruction based on dense statistics of soft tissue thickness. PLOS ONE, 14(1). DOI Author/Publisher URL

Jiang, P., Luo, J., Wang, Y., et al. (2019). kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers. BIOINFORMATICS, 35(23), 4871-4878. DOI Author/Publisher URL

Kallenborn, F., Hundt, C., Boeser, S., Schmidt, B. (2019). Massively parallel computation of atmospheric neutrino oscillations on CUDA-enabled accelerators. COMPUTER PHYSICS COMMUNICATIONS, 234, 235-244. DOI Author/Publisher URL

Köppel, M., Segner, A., Wagener, M., et al. (2019). Pairwise Learning to Rank by Neural Networks Revisited: Reconstruction, Theoretical Analysis and Practical Performance. CoRR, abs/1909.02768.

Niebler, S., Schoemer, E., Tjaden, H., et al. (2019). Projection-based improvement of 3D reconstructions from motion-impaired dental cone beam CT data. MEDICAL PHYSICS, 46(10), 4470-4480. DOI Author/Publisher URL

Schmidt, L., Werner, S., Kemmer, T., et al. (2019). Graphical workflow system for modification calling by machine learning of reverse transcription signatures. Frontiers in genetics, 10, 876-876.

Theocharidis, K., Liagouris, J., Mamoulis, N., et al. (2019). SRX: efficient management of spatial RDF data. VLDB JOURNAL, 28(5), 703-733. DOI Author/Publisher URL

Tjaden, H., Schwanecke, U., Schoemer, E., Cremers, D. (2019). A Region-Based Gauss-Newton Approach to Real-Time Monocular Multiple Object Tracking. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 41(8), 1797-1812. DOI Author/Publisher URL

Zhang, J., Lan, H., Chan, Y., et al. (2019). BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures. BIOINFORMATICS, 35(13), 2306-2308. DOI Author/Publisher URL

Other

Köppel, M., Segner, A., Wagener, M., et al. (2019). Pairwise Learning to Rank by Neural Networks Revisited: Reconstruction, Theoretical Analysis and Practical Performance. Author/Publisher URL

Tsitsigkos, D., Bouros, P., Mamoulis, N., Terrovitis, M. (2019). Parallel In-Memory Evaluation of Spatial Joins. Author/Publisher URL

Bračevac, O., Salvaneschi, G., Erdweg, S., Mezini, M. (2019). Type-safe, Polyvariadic Event Correlation. Author/Publisher URL

Althaus, E., Ziegler, S. (2019). Optimal Tree Decompositions Revisited: A Simpler Linear-Time FPT Algorithm. In CoRR: Vol. abs/1912.09144. Author/Publisher URL

Gallenbacher, J. (2019). Abenteuer Informatik: Dauerausstellung im Foyer der TU Wien. Wien, Österreich:TU Wien. Author/Publisher URL

Gallenbacher, J. (2019). Abenteuer Informatik: Dauerausstellung im Foyer der Universität Rostock. Rostock:Universität Rostock. Author/Publisher URL

Patents

Helm, M., Hauenschild, R., Tserovski, L., et al. (2019). Method for detecting known nucleotide modifications in an rna (Patent).

Theses/Disssertations

Mosca, D. (2019). Graph-Grammatiken zur Suche und Klassifikation von molekularen Strukturen [PhD Thesis]. DOI Author/Publisher URL

Book chapters

Endler, S. (2018). Marathon. In A. Baca (ed.), Modelling and simulation in sport and exercise (pp. Seiten: 169-186). London:Routledge.

Endler, S., Flechsenhar, F., Schmidt-Arndt, F. (2018). Veränderungen des taktischen Verhaltens durch die Materialveränderung im Tischtennis. In D. Link (ed.), Sportinformatik XII : 12. Symposium der dvs-Sektion (pp. Seiten: 69-70). Hamburg:Feldhaus, Edition Czwalina.

Kaindl, H., Kramer, S., Hoch, R. (2018). An inductive learning perspective on automated generation of feature models from given product specifications. In T. Berger (ed.), Proceedings of the 22nd International Systems and Software Product Line Conference. Volume 1 : Gothenburg, Sweden, September 10 – 14, 2018 (pp. Seiten: 25-30). New York, NY:ACM. Author/Publisher URL

Rehn, P., Ahmadi, Z., Kramer, S. (2018). Forest of normalized trees : fast and accurate density estimation of streaming data. In F. Bonchi (ed.), 2018 IEEE 5th International Conference on Data Science and Advanced Analytics (DSAA). Piscataway, NJ:IEEE. Author/Publisher URL

Shao, J., Yang, Q., Zhang, Z., et al. (2018). Graph clustering with local density-cut. In J. Pei (ed.), Database Systems for Advanced Applications : 23rd International Conference, DASFAA 2018, Gold Coast, QLD, Australia, May 21-24, 2018, Proceedings, Part I (pp. Seiten: 187-202). Cham:Springer International Publishing. Author/Publisher URL

Books

Parallel Programming. (2018). Elsevier. DOI

Conference Papers

Xu, K., Kobus, R., Chan, Y., et al. (2018). SPECTR. Proceedings of the 47th International Conference on Parallel Processing, 1-10. DOI

Amorim, L. E. de S., Steindorfer, M. J., Erdweg, S., Visser, E. (2018). Declarative specification of indentation rules: a tooling perspective on parsing and pretty-printing layout-sensitive languages. In D. J. Pearce, T. Mayerhofer, and F. Steimann (eds.), SLE (pp. 3-15). ACM. Author/Publisher URL

Bouros, P., Mamoulis, N. (2018). Interval Count Semi-Joins. In M. H. Böhlen, R. Pichler, N. May, et al. (eds.), Proceedings of the 21st International Conference on Extending Database Technology, EDBT 2018, Vienna, Austria, March 26-29, 2018 (pp. 425-428). OpenProceedings.org. DOI

Chondrogiannis, T., Bouros, P., Gamper, J., et al. (2018). Finding k-Dissimilar Paths with Minimum Collective Length. 26TH ACM SIGSPATIAL INTERNATIONAL CONFERENCE ON ADVANCES IN GEOGRAPHIC INFORMATION SYSTEMS (ACM SIGSPATIAL GIS 2018), 404-407. DOI Author/Publisher URL

Erdweg, S., … Oliveira, B. C. D. S. (eds.). (2018). Proceedings of the 9th ACM SIGPLAN International Symposium on Scala, SCALA@ICFP 2018, St. Louis, MO, USA, September 28, 2018. SCALA@ICFP.

Gallenbacher, J. (2018). The Adventure of Computer Science – Understanding the Impact of Informatics on General Education and Designing the Living Environment. In H.-J. Böckenhauer, D. Komm, W. Unger (eds.), Adventures Between Lower Bounds and Higher Altitudes – Essays Dedicated to Juraj Hromkovič on the Occasion of His 60th Birthday (Vols. 11011, pp. 538-548). Springer. DOI Author/Publisher URL

Grewe, S., Erdweg, S., Pacak, A., Mezini, M. (2018). System Description: An Infrastructure for Combining Domain Knowledge with Automated Theorem Provers. In D. Sabel, P. Thiemann (eds.), PPDP (pp. 24:1-24:1). ACM. Author/Publisher URL

Juenger, D., Hundt, C., Schmidt, B. (2018). WarpDrive: Massively Parallel Hashing on Multi-GPU Nodes. 2018 32ND IEEE INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS), 441-450. DOI Author/Publisher URL

Kobus, R., Lamoth, A., Müller, A., et al. (2018). cuBool: bit-parallel Boolean Matrix Factorization on CUDA-enabled accelerators. Seiten: 465-472. Author/Publisher URL

Konat, G., Erdweg, S., Visser, E. (2018). Scalable incremental building with dynamic task dependencies. In M. Huchard, C. Kästner, G. Fraser (eds.), ASE (pp. 76-86). ACM. Author/Publisher URL

Szabó, T., Kuci, E., Bijman, M., et al. (2018). Incremental overload resolution in object-oriented programming languages. In J. Dolby, W. G. J. Halfond, A. Mishra (eds.), ISSTA/ECOOP Workshops (pp. 27-33). ACM. Author/Publisher URL

Weissenberger, A., Schmidt, B. (2018). Massively Parallel Huffman Decoding on GPUs. PROCEEDINGS OF THE 47TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING. Published. DOI Author/Publisher URL

Xu, K., Kobus, R., Chan, Y., et al. (2018). SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures. PROCEEDINGS OF THE 47TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING. Published. DOI Author/Publisher URL

Journal Articles

Leißa, R., Boesche, K., Hack, S., et al. (2018). AnyDSL: a partial evaluation framework for programming high-performance libraries. Proceedings of the ACM on Programming Languages, 2(OOPSLA), 1-30. DOI

Szabó, T., Bergmann, G., Erdweg, S., Voelter, M. (2018). Incrementalizing lattice-based program analyses in Datalog. Proceedings of the ACM on Programming Languages, 2(OOPSLA), 1-29. DOI

Bračevac, O., Amin, N., Salvaneschi, G., et al. (2018). Versatile event correlation with algebraic effects. Proceedings of the ACM on Programming Languages, 2(ICFP), 1-31. DOI

Keidel, S., Poulsen, C. B., Erdweg, S. (2018). Compositional soundness proofs of abstract interpreters. Proceedings of the ACM on Programming Languages, 2(ICFP), 1-26. DOI

Winther, H. B., Hundt, C., Schmidt, B., et al. (2018). ν-net. JACC: Cardiovascular Imaging, 11(7), 1036-1038. DOI

Grewe, S., Erdweg, S., Pacak, A., et al. (2018). Exploration of language specifications by compilation to first-order logic. Science of Computer Programming, 155, 146-172. DOI

Konat, G., Steindorfer, M. J., Erdweg, S., Visser, E. (2018). PIE: A Domain-Specific Language for Interactive Software Development Pipelines. The Art, Science, and Engineering of Programming, 2(3). DOI

Althaus, E., Brinkmann, A., Kling, P., et al. (2018). Scheduling shared continuous resources on many-cores. Journal of Scheduling, 21, 77-92. DOI

Bouros, P., Renz, M., Sacharidis, D. (2018). Localrec 2017 workshop report: the First ACM SIGSPATIAL Workshop on Recommendations for Location-Based Services and Social Networks. SIGSPATIAL Special, 9(3), 26-27. DOI

Ahmadi, Z., Kramer, S. (2018). A label compression method for online multi-label classification. Pattern recognition letters, 111, Seiten: 64-71. Author/Publisher URL

Ahmadi, Z., Kramer, S. (2018). Modeling recurring concepts in data streams : a graph-based framework. Knowledge and information systems, 55(1), Seiten: 15-44. Author/Publisher URL

Ahmadi, Z., Kramer, S. (2018). Online Multi-Label Classification: A Label Compression Method. CoRR, abs/1804.01491. Author/Publisher URL

Burkhardt, S., Kramer, S. (2018). Online multi-label dependency topic models for text classification. Machine learning, 107(5), Seiten: 859-886. Author/Publisher URL

Chan, Y., Xu, K., Lan, H., et al. (2018). MyPhi: Efficient Levenshtein Distance Computation on Xeon Phi Based Architectures. CURRENT BIOINFORMATICS, 13(5), 479-486. DOI Author/Publisher URL

Fier, F., Augsten, N., Bouros, P., et al. (2018). Set Similarity Joins on MapReduce: An Experimental Survey. PROCEEDINGS OF THE VLDB ENDOWMENT, 11(10), 1110-1122. DOI Author/Publisher URL

Geilke, M., Karwath, A., Frank, E., Kramer, S. (2018). Online estimation of discrete, continuous, and conditional joint densities using classifier chains. Data mining and knowledge discovery, 32(3), Seiten: 561-603. Author/Publisher URL

Gonzalez-Dominguez, J., Hundt, C., Schmidt, B. (2018). parSRA: A framework for the parallel execution of short read aligners on compute clusters. JOURNAL OF COMPUTATIONAL SCIENCE, 25, 134-139. DOI Author/Publisher URL

Kemmer, T., Rjasanow, S., Hildebrandt, A. (2018). NESSie. jl–Efficient and intuitive finite element and boundary element methods for nonlocal protein electrostatics in the Julia language. Journal of computational science, 28, 193-203.

Konat, G., Steindorfer, M. J., Erdweg, S., Visser, E. (2018). PIE: A Domain-Specific Language for Interactive Software Development Pipelines. CoRR, abs/1803.10197.

Lang-Yona, N., Pickersgill, D. A., Maurus, I., et al. (2018). Species Richness, rRNA Gene Abundance, and Seasonal Dynamics of Airborne Plant-Pathogenic Oomycetes. FRONTIERS IN MICROBIOLOGY, 9. DOI Author/Publisher URL

Leissa, R., Boesche, K., Hack, S., et al. (2018). AnyDSL: A Partial Evaluation Framework for Programming High-Performance Libraries. PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL, 2. DOI Author/Publisher URL

Liu, Y., Schmidt, B. (2018). LightSpMV: Faster CUDA-Compatible Sparse Matrix-Vector Multiplication Using Compressed Sparse Rows. JOURNAL OF SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY, 90(1), 69-86. DOI Author/Publisher URL

Ludwig, M., Hoffmann, K., Endler, S., et al. (2018). Measurement, prediction, and control of individual heart rate responses to exercise-basics and options for wearable devices. Frontiers in physiology, 9, Art. 778. Author/Publisher URL

Pelzer, T., Ullrich, B., Endler, S., et al. (2018). A biomechanical comparison of countermovement performance after short-term traditional and daily-undulated loaded vertical jump training. Journal of sports sciences, 36(16), Seiten: 1816-1826. DOI

Saha, S., Mitra, S., Kramer, S. (2018). Exploring multiobjective optimization for multiview clustering. ACM transactions on knowledge discovery from data, 12(4), Art. 44. Author/Publisher URL

Wehking, J., Pickersgill, D. A., Bowers, R. M., et al. (2018). Community composition and seasonal changes of archaea in coarse and fine air particulate matter. BIOGEOSCIENCES, 15(13), 4205-4214. DOI Author/Publisher URL

Zhang, H., Chan, Y., Fan, K., et al. (2018). Fast and efficient short read mapping based on a succinct hash index. BMC BIOINFORMATICS, 19. DOI Author/Publisher URL

Other

Konat, G., Steindorfer, M. J., Erdweg, S., and Visser, E. (2018). PIE: A Domain-Specific Language for Interactive Software Development Pipelines. Author/Publisher URL

Chondrogiannis, T., Bouros, P., Gamper, J., et al. (2018). Finding k-Dissimilar Paths with Minimum Collective Length. Author/Publisher URL

Book chapters

Ahmadi, Z., Skowron, M., Stier, A., and Kramer, S. (2017). An in-depth experimental comparison of RNTNs and CNNs for sentence modeling. In A. Yamamoto (ed.), Discovery Science : 20th International Conference, DS 2017, Kyoto, Japan, October 1517, 2017, Proceedings (pp. Seiten: 144-152). Cham:Springer International Publishing. Author/Publisher URL

Burkhardt, S., and Kramer, S. (2017). Multi-label classification using stacked hierarchical dirichlet processes with reduced sampling complexity. In X. Wu (ed.), 2017 IEEE International Conference on Big Knowledge : 9-10 August 2017, Hefei, China : proceedings (pp. Seiten: 1-8). Piscataway, NJ:IEEE. Author/Publisher URL

Burkhardt, S., and Kramer, S. (2017). Online sparse collapsed hybrid variational-gibbs algorithm for hierarchical Dirichlet process topic models. In M. Ceci (ed.), Machine Learning and Knowledge Discovery in Databases : European Conference, ECML PKDD 2017, Skopje, Macedonia, September 18–22, 2017, Proceedings, Part II (pp. Seiten: 189-204). Cham:Springer International Publishing. Author/Publisher URL

Endler, S., and Ostheimer, P. (2017). Bestimmung der aktuellen Laufgeschwindigkeit mit Hilfe von Sensordaten einer Smartwatch. In A. Schwirtz (ed.), Innovation & Technologie im Sport : 23. dvs-Hochschultag, München, 13.-15. September 2017 : Abstracts (p. Seite: 126). Hamburg:Feldhaus, Edition Czwilina.

Geilke, M., and Kramer, S. (2017). Privacy-preserving pattern mining on online density estimates. In X. Wu (ed.), 2017 IEEE International Conference on Big Knowledge : 9-10 August 2017, Hefei, China : proceedings (pp. Seiten: 25-32). Piscataway, NJ:IEEE. Author/Publisher URL

Hildebrandt, A. K., Kemmer, T., and Hildebrandt, A. (2017). The Electromagnetic Nature of Protein-Protein Interactions. In Conductive Polymers – Electrical Interactions in Cell Biology and Medicine. CRC Press.

Karwath, A., Hubrich, M., and Kramer, S. (2017). Convolutional neural networks for the identification of regions of interest in PET scans : a study of representation learning for diagnosing Alzheimer’s disease. In A. ten Teije (ed.), Artificial Intelligence in Medicine : 16th Conference on Artificial Intelligence in Medicine, AIME 2017, Vienna, Austria, June 21-24, 2017, Proceedings (pp. Seiten: 316-321). Cham:Springer International Publishing. Author/Publisher URL

Kramer, S. (2017). Inductive Database Approach to Graphmining. In C. Sammut and G. I. Webb (eds.), Encyclopedia of Machine Learning and Data Mining (pp. 641-642). Springer. DOI

Liu, Y., and Schmidt, B. (2017). CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment. In Algorithms for Next-Generation Sequencing Data (pp. 203-233). Springer International Publishing. DOI

Books

Schmidt, B., Gonzalez-Dominguez, J., Hundt, C., and Schlarb, M. (2017). Parallel Programming Concepts and Practice. Morgan Kaufmann.

Gallenbacher, J. (2017). Abenteuer Informatik. Berlin, Heidelberg:Springer Berlin Heidelberg. DOI

Conference Papers

Ahmadi, Z., Stier, A., Skowron, M., Kramer, S. (2017). To Parse or Not to Parse: An Experimental Comparison of RNTNs and CNNs for Sentiment Analysis. In M. Dragoni and D. R. Recupero (eds.), Proceedings of the 3rd International Workshop at ESWC on Emotions, Modality, Sentiment Analysis and the Semantic Web co-located with 14th ESWC 2017, Portroz, Slovenia, May 28, 2017 (Vols. 1874). CEUR-WS.org. Author/Publisher URL

Althaus, E., Hildebrandt, A., Mosca, D. (2017). Graph Rewriting Based Search for Molecular Structures: Definitions, Algorithms, Hardness. Federation of International Conferences on Software Technologies: Applications and Foundations, 43-59.

Andrés López, D., Diensberg, B., Schömer, E., Schwanecke, U. (2017). VCIT – Visually corrected inertial tracking. Lecture Notes in Informatics (LNI), Proceedings – Series of the Gesellschaft fur Informatik (GI). DOI

Chan, Y., Xu, K., Lan, H., et al. (2017). PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment. 2017 31ST IEEE INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS), 52-61. DOI Author/Publisher URL

Chondrogiannis, T., Bouros, P., Gamper, J., Leser, U. (2017). Exact and Approximate Algorithms for Finding k-Shortest Paths with Limited Overlap. In V. Markl, S. Orlando, B. Mitschang, et al. (eds.), Proceedings of the 20th International Conference on Extending Database Technology, EDBT 2017, Venice, Italy, March 21-24, 2017 (pp. 414-425). OpenProceedings.org. DOI

Duan, X., Xu, K., Chan, Y., et al. (2017). S-Aligner: Ultrascalable read mapping on Sunway Taihu Light. 2017 IEEE INTERNATIONAL CONFERENCE ON CLUSTER COMPUTING (CLUSTER), 36-46. DOI Author/Publisher URL

Flatt, M., … Erdweg, S. (eds.). (2017). Proceedings of the 16th ACM SIGPLAN International Conference on Generative Programming: Concepts and Experiences, GPCE 2017, Vancouver, BC, Canada, October 23-24, 2017. GPCE.

Gallenbacher, J. (2017). Allgemeinbildung in der digitalen, gestalteten Lebenswelt. In I. Diethelm (ed.), Informatische Bildung zum Verstehen und Gestalten der digitalen Welt, Proceedings der 17. GI-Fachtagung Informatik und Schule, INFOS 2017, 13.-15. September 2017, Oldenburg: Vol. P-274 (pp. 19-28). Author/Publisher URL

Gietzen, T., Brylka, R., Schwanecke, U., Schömer, E. (2017). A Dense Statistical Model of Facial Soft Tissue Thickness. In M. Eibl, M. Gaedke (eds.), INFORMATIK 2017 (pp. 891-898). Gesellschaft für Informatik, Bonn. DOI

Junger, D., Hundt, C., Gonzalez-Dominguez, J., Schmidt, B. (2017). Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs. EURO-PAR 2016: PARALLEL PROCESSING WORKSHOPS, 10104, 421-432. DOI Author/Publisher URL

Jördens, T., Gallenbacher, J. (2017). Quadrologik – Modellbildung und Modularisierung auf Basis von Rechnertechnik. In I. Diethelm (ed.), Informatische Bildung zum Verstehen und Gestalten der digitalen Welt, Proceedings der 17. GI-Fachtagung Informatik und Schule, INFOS 2017, 13.-15. September 2017, Oldenburg: Vol. P-274 (pp. 267-276). Author/Publisher URL

Keidel, S., Erdweg, S. (2017). Toward abstract interpretation of program transformations. In S. Chiba, E. G. Boix, S. Marr (eds.), META@SPLASH (pp. 1-5). ACM. Author/Publisher URL

Kuci, E., Erdweg, S., Bracevac, O., et al. (2017). A Co-contextual Type Checker for Featherweight Java . In P. Müller (ed.), ECOOP (Vols. 74, pp. 18:1-18:1). Schloss Dagstuhl – Leibniz-Zentrum für Informatik. Author/Publisher URL

Lan, H., Liu, W., Liu, Y., Schmidt, B. (2017). SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search. 2017 31ST IEEE INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS), 42-51. DOI Author/Publisher URL

Peng, S., Zhang, X., Yang, S., et al. (2017). mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework. 2017 17TH IEEE/ACM INTERNATIONAL SYMPOSIUM ON CLUSTER, CLOUD AND GRID COMPUTING (CCGRID), 671-676. DOI Author/Publisher URL

Sacharidis, D., Bouros, P., Chondrogiannis, T. (2017). Finding The Most Preferred Path. 25TH ACM SIGSPATIAL INTERNATIONAL CONFERENCE ON ADVANCES IN GEOGRAPHIC INFORMATION SYSTEMS (ACM SIGSPATIAL GIS 2017). Published. DOI Author/Publisher URL

Tjaden, H., Schwanecke, U., Schömer, E. (2017). Real-Time Monocular Pose Estimation of 3D Objects Using Temporally Consistent Local Color Histograms. 2017 IEEE International Conference on Computer Vision (ICCV), 124-132. DOI

Journal Articles

Althaus, E., Beber, B., Damm, W., et al. (2017). Verification of linear hybrid systems with large discrete state spaces using counterexample-guided abstraction refinement. Science of Computer Programming, 148, 123-160. DOI

Erdweg, S., Ostermann, K. (2017). A Module-System Discipline for Model-Driven Software Development. The Art, Science, and Engineering of Programming, 1(2). DOI

Latino, D. A. R. S., Wicker, J., Gütlein, M., et al. (2017). Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data. Environ. Sci. Process. Impacts, 19(3), 449-464. DOI Author/Publisher URL

Bouros, P., Mamoulis, N. (2017). A Forward Scan based Plane Sweep Algorithm for Parallel Interval Joins. PROCEEDINGS OF THE VLDB ENDOWMENT, 10(11), 1346-1357. DOI Author/Publisher URL

Dang, H.-V., Schmidt, B., Hildebrandt, A., et al. (2017). CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm (Reprinted from vol 30, pg 200-211, 2016). INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 31, 181-+.

Endler, S., Hoffmann, S., Sterzing, B., et al. (2017). The PerPot simulated anaerobic threshold : a comparison to typical lactate-based thresholds. International journal of human movement and sports sciences, 5(1), Seiten: 9-15. Author/Publisher URL

Erdweg, S., Ostermann, K. (2017). A Module-System Discipline for Model-Driven Software Development. CoRR, abs/1703.10895.

Gallenbacher, J. (2017). Allmächtiger Computer!?. Abenteuer Informatik: IT zum Anfassen für alle von 9 bis 99–vom Navi bis Social Media, 389-410. Author/Publisher URL

Gribko, A., Hahlbrock, A., Strieth, S., et al. (2017). Disease-relevant signalling-pathways in head and neck cancer : Taspase1’s proteolytic activity fine-tunes TFIIA function. Scientific reports, 7, Art. 14937. Author/Publisher URL

Gribko, A., Hahlbrock, A., Strieth, S., et al. (2017). Disease-relevant signalling-pathways in head and neck cancer: Taspase1’s proteolytic activity fine-tunes TFIIA function. Scientific reports, 7, 1-10.

Hundt, C., Schlarb, M., Schmidt, B. (2017). SAUCE: A web application for interactive teaching and learning of parallel programming. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 105, 163-173. DOI Author/Publisher URL

Juenger, D., Hundt, C., Gonzalez Dominguez, J., Schmidt, B. (2017). Speed and accuracy improvement of higher-order epistasis detection on CUDA-enabled GPUs. CLUSTER COMPUTING-THE JOURNAL OF NETWORKS SOFTWARE TOOLS AND APPLICATIONS, 20(3), 1899-1908. DOI Author/Publisher URL

Kobus, R., Hundt, C., Müller, A., Schmidt, B. (2017). Accelerating metagenomic read classification on CUDA-enabled GPUs. BMC Bioinformatics, 18(11), 10 S. Author/Publisher URL

Kolossa, D., Bin Azhar, M. A., Rasche, C., et al. (2017). Performance estimation using the fitness-fatigue model with Kalman filter feedback. International journal of computer science in sport, 16(2), Seiten: 117-129. Author/Publisher URL

Kuci, E., Erdweg, S., Bracevac, O., et al. (2017). A Co-contextual Type Checker for Featherweight Java (incl. Proofs). CoRR, abs/1705.05828.

Liu, Y., Ripp, F., Koeppel, R., et al. (2017). AFS: identification and quantification of species composition by metagenomic sequencing. BIOINFORMATICS, 33(9), 1396-1398. DOI Author/Publisher URL

Müller, A., Hundt, C., Hildebrandt, A., et al. (2017). MetaCache: context-aware classification of metagenomic reads using minhashing. Bioinformatics, 33, 3740-3748.

Qi, S., Sacharidis, D., Bouros, P., Mamoulis, N. (2017). Snapshot and continuous points-based trajectory search. GEOINFORMATICA, 21(4), 669-701. DOI Author/Publisher URL

Raza, A., Kramer, S. (2017). Ensembles of randomized time series shapelets provide improved accuracy while reducing computational costs. De.arXiv.org, abs/1702.0. Author/Publisher URL

Schmidt, B., Hildebrandt, A. (2017). Next-generation sequencing: big data meets high performance computing. Drug discovery today, 22, 712-717.

Schroder, J., Wirawan, A., Schmidt, B., Papenfuss, A. T. (2017). CLOVE: classification of genomic fusions into structural variation events. BMC BIOINFORMATICS, 18. DOI Author/Publisher URL

Wicker, J., Kramer, S. (2017). The best privacy defense is a good privacy offense : obfuscating a search engine user’s profile. Data mining and knowledge discovery, 31(5), Seiten: 1419-1443. Author/Publisher URL

Winther, H. B., Hundt, C., Schmidt, B., et al. (2017). $ν$-net: Deep Learning for Generalized Biventricular Cardiac Mass and Function Parameters. CoRR, abs/1706.04397.

Zhang, S., Wang, Z., Peng, Y., et al. (2017). Mapping of option pricing algorithms onto heterogeneous many-core architectures. JOURNAL OF SUPERCOMPUTING, 73(9), 3715-3737. DOI Author/Publisher URL

Other

Kuci, E., Erdweg, S., Bračevac, O., et al. (2017). A Co-contextual Type Checker for Featherweight Java (incl. Proofs). Author/Publisher URL

Erdweg, S., Ostermann, K. (2017). A Module-System Discipline for Model-Driven Software Development. Author/Publisher URL

Book chapters

Endler, S., and Ebert, J. (2016). Automatisierte Einteilung von Laufdaten in Trainingsmethoden mittels Machine Learning Algorithmen. In K. Witte (ed.), Sportinformatik XI : Jahrestagung der dvs-Sektion Sportinformatik 2016 in Magdeburg (pp. Seiten: 23-28). Aachen:Shaker.

Endler, S., and Friedrich, O. K. (2016). Determining reference speeds and heart rates for endurance running prescription in altitude profile. In L. Lamas (ed.), Proceedings of the 2016 International Association of Computer Science in Sport (IACSS) Conference (pp. Seiten: 96-101). Brasilia, Brazil:.

Geilke, M., Karwath, A., and Kramer, S. (2016). Online density estimation of heterogeneous data streams in higher dimensions. In P. Frasconi (ed.), Machine learning and knowledge discovery in databases : European Conference, ECML PKDD 2016, Riva del Garda, Italy, September 19-23, 2016 : proceedings. Part 1 (pp. Seiten: 65-80). Cham:Springer International Publishing. Author/Publisher URL

Raza, A., Wicker, J., and Kramer, S. (2016). Trading off accuracy for efficiency by randomized greedy warping. In Proceedings of the 31st Annual ACM Symposium on Applied Computing : Pisa, Italy, April 4-8, 2016 (pp. Seiten: 883-890). New York, NY:ACM. Author/Publisher URL

Tjaden, H., Schwanecke, U., and Schömer, E. (2016). Real-Time Monocular Segmentation and Pose Tracking of Multiple Objects. In B. Leibe, J. Matas, N. Sebe, and M. Welling (eds.), Computer Vision – ECCV 2016: 14th European Conference, Amsterdam, The Netherlands, October 11–14, 2016, Proceedings, Part IV (pp. 423-438). Cham:Springer International Publishing. DOI

Wicker, J., Fenner, K., and Kramer, S. (2016). A hybrid machine learning and knowledge based approach to limit combinatorial explosion in biodegradation prediction. In J. Lässig (ed.), Computational sustainability (pp. Seiten: 75-97). Cham:Springer. Author/Publisher URL

Wicker, J., Tyukin, A., and Kramer, S. (2016). A nonlinear label compression and transformation method for multi-label classification using autoencoders. In J. Bailey (ed.), Advances in knowledge discovery and data mining : 20th Pacific-Asia Conference, PAKDD 2016, Auckland, New Zealand, April 19-22, 2016, Proceedings. Pt. I (pp. Seiten: 328-340). Cham:Springer. Author/Publisher URL

Conference Papers

Kunkel, A., Rheinländer, A., Schiefer, C., et al. (2016, July 18). PIEJoin: Towards Parallel Set Containment Joins. Proceedings of the 28th International Conference on Scientific and Statistical Database Management. Published. SSDBM ’16: Conference on Scientific and Statistical Database Management. DOI

Aliaga, D. G., Demir, I., Benes, B., Wand, M. (2016). Inverse procedural modeling of 3D models for virtual worlds. SIGGRAPH Courses, 16:1-16:1. Author/Publisher URL

Amorim, L. E. de S., Erdweg, S., Wachsmuth, G., Visser, E. (2016). Principled syntactic code completion using placeholders. In T. van der Storm, E. Balland, and D. Varró (eds.), SLE (pp. 163-175). ACM. Author/Publisher URL

Bracevac, O., Erdweg, S., Salvaneschi, G., Mezini, M. (2016). CPL: a core language for cloud computing. In L. Fuentes, D. S. Batory, and K. Czarnecki (eds.), MODULARITY (pp. 94-105). ACM. Author/Publisher URL

Grewe, S., Erdweg, S., Mezini, M. (2016). Automating Proof Steps of Progress Proofs: Comparing Vampire and Dafny. In L. Kovács and A. Voronkov (eds.), Vampire@IJCAR (Vols. 44, pp. 33-45). EasyChair. Author/Publisher URL

Grewe, S., Erdweg, S., Raulf, M., Mezini, M. (2016). Exploration of language specifications by compilation to first-order logic. In J. Cheney and G. Vidal (eds.), PPDP (pp. 104-117). ACM. Author/Publisher URL

Kaessens, J. C., Wienbrandt, L., Schimmler, M., et al. (2016). Combining GPU and FPGA Technology for Efficient Exhaustive Interaction Analysis in GWAS. 2016 IEEE 27TH INTERNATIONAL CONFERENCE ON APPLICATION-SPECIFIC SYSTEMS, ARCHITECTURES AND PROCESSORS (ASAP), 170-175. Author/Publisher URL

Keidel, S., Pfeiffer, W., Erdweg, S. (2016). The IDE portability problem and its solution in Monto. In T. van der Storm, E. Balland, and D. Varró (eds.), SLE (pp. 152-162). ACM. Author/Publisher URL

Konat, G., Erdweg, S., Visser, E. (2016). Bootstrapping domain-specific meta-languages in language workbenches. In B. Fischer and I. Schaefer (eds.), GPCE (pp. 47-58). ACM. Author/Publisher URL

Kugelstadt, T., Schömer, E. (2016). Position and Orientation Based Cosserat Rods. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, 169-178. Author/Publisher URL

Li, C., Wand, M. (2016). Precomputed Real-Time Texture Synthesis with Markovian Generative Adversarial Networks. In B. Leibe, J. Matas, N. Sebe, and M. Welling (eds.), ECCV (3) (Vols. 9907, pp. 702-716). Springer. Author/Publisher URL

Li, C., Wand, M. (2016). Combining Markov Random Fields and Convolutional Neural Networks for Image Synthesis. 2016 IEEE CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR), 2479-2486. DOI Author/Publisher URL

Lorenzen, F., Erdweg, S. (2016). Sound type-dependent syntactic language extension. In R. Bodík and R. Majumdar (eds.), POPL (pp. 204-216). ACM. Author/Publisher URL

Szabó, T., Alperovich, S., Voelter, M., Erdweg, S. (2016). An extensible framework for variable-precision data-flow analyses in MPS. In D. Lo, S. Apel, and S. Khurshid (eds.), ASE (pp. 870-875). ACM. Author/Publisher URL

Szabó, T., Erdweg, S., Voelter, M. (2016). IncA: a DSL for the definition of incremental program analyses. In D. Lo, S. Apel, and S. Khurshid (eds.), ASE (pp. 320-331). ACM. Author/Publisher URL

Voelter, M., Szabó, T., Lisson, S., et al. (2016). Efficient development of consistent projectional editors using grammar cells. In T. van der Storm, E. Balland, and D. Varró (eds.), SLE (pp. 28-40). ACM. Author/Publisher URL

Journal Articles

Mann, W., Augsten, N., Bouros, P. (2016). An Empirical Evaluation of Set Similarity Join Techniques. PROCEEDINGS OF THE VLDB ENDOWMENT, 9(9), 636-647. Author/Publisher URL

Wicker, J., Lorsbach, T., Gütlein, M., et al. (2016). enviPath–The environmental contaminant biotransformation pathway resource. Nucleic Acids Res., 44(D1), D502-D508. DOI Author/Publisher URL

Batke, M., Gütlein, M., Partosch, F., et al. (2016). Innovative strategies to develop chemical categories using a combination of structural and toxicological properties. Frontiers in pharmacology, 7, Art. 321. Author/Publisher URL

Bouros, P., Mamoulis, N., Ge, S., Terrovitis, M. (2016). Set containment join revisited. KNOWLEDGE AND INFORMATION SYSTEMS, 49(1), 375-402. DOI Author/Publisher URL

Bracevac, O., Erdweg, S., Salvaneschi, G., Mezini, M. (2016). CPL: A Core Language for Cloud Computing – Technical Report. CoRR, abs/1602.00981.

Dang, H.-V., Schmidt, B., Hildebrandt, A., et al. (2016). CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm. The International Journal of High Performance Computing Applications, 30, 200-211.

Demetrescu, C., Erdweg, S., Hammer, M. A., Krishnamurthi, S. (2016). Programming Language Techniques for Incremental and Reactive Computing (Dagstuhl Seminar 16402). Dagstuhl Reports, 6, 1-12. DOI

Dousti, M. S., Jalili, R. (2016). An efficient statistical zero-knowledge authentication protocol for smart cards. INTERNATIONAL JOURNAL OF COMPUTER MATHEMATICS, 93(3), 453-481. DOI Author/Publisher URL

Droby, A., Panagoulias, M., Albrecht, P., et al. (2016). A novel automated segmentation method for retinal layers in OCT images proves retinal degeneration after optic neuritis. British Journal of Ophthalmology, 100, 484-490.

Endler, S. (2016). Modelling Speed-HR Relation using PerPot. Dagstuhl Reports, 5(9), Seite: 51. Author/Publisher URL

Gallenbacher, J. (2016). IT-Grundlagen für Kinder – Buchstaben kodieren: Hintergrund. c’t – Magazin, 158-158.

Gallenbacher, J. (2016). Multiplikation im Binärsystem mit Kindern ausprobieren: Hintergrund. c’t – Magazin, 158-158.

Gallenbacher, J. (2016). Zahlendarstellung im Binärsystem einfach erklärt: Hintergrund. c’t – Magazin, 144-144.

Gonzalez-Dominguez, J., Liu, Y., Tourino, J., Schmidt, B. (2016). MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems. BIOINFORMATICS, 32(24), 3826-3828. DOI Author/Publisher URL

Gonzalez-Dominguez, J., Ramos, S., Tourino, J., Schmidt, B. (2016). Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 27(8), 2329-2340. DOI Author/Publisher URL

Gonzalez-Dominguez, J., Schmidt, B. (2016). ParDRe: faster parallel duplicated reads removal tool for sequencing studies. BIOINFORMATICS, 32(10), 1562-1564. DOI Author/Publisher URL

González-Domínguez, J., Liu, Y., Schmidt, B. (2016). Parallel and scalable short-read alignment on multi-core clusters using UPC++. PLoS one, 11(1), e0145490. Author/Publisher URL

Gütlein, M., Kramer, S. (2016). Filtered circular fingerprints improve either prediction or runtime performance while retaining interpretability. Journal of cheminformatics, 8, Art. 60. Author/Publisher URL

Hauenschild, R., Werner, S., Tserovski, L., et al. (2016). CoverageAnalyzer (CAn): A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles. Biomolecules, 6, 42-42.

Hundt, C., Hildebrandt, A., Schmidt, B. (2016). rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs. BMC bioinformatics, 17, 394-394.

Kölling, S., Steinacker, J. M., Endler, S., et al. (2016). The longer the better : sleep–wake patterns during preparation of the World Rowing Junior Championships. Chronobiology international, 33(1), Seiten: 73-84. Author/Publisher URL

Kölling, S., Wiewelhove, T., Raeder, C., et al. (2016). Sleep monitoring of a six-day microcycle in strength and high-intensity training. European journal of sport science, 16(5), Seiten: 507-515. Author/Publisher URL

Lan, H., Chan, Y., Xu, K., et al. (2016). Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters. BMC BIOINFORMATICS, 17. DOI Author/Publisher URL

Liu, Y., Hankeln, T., Schmidt, B. (2016). Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 13(3), 592-598. DOI Author/Publisher URL

Liu, Y., Loewer, M., Aluru, S., Schmidt, B. (2016). SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations. BMC SYSTEMS BIOLOGY, 10. DOI Author/Publisher URL

Schneider, L., Stöckel, D., Kehl, T., et al. (2016). DrugTargetInspector: An assistance tool for patient treatment stratification. International Journal of Cancer, 138, 1765-1776.

Shao, J., Yang, Q., Dang, H.-V., et al. (2016). Scalable clustering by iterative partitioning and point attractor representation. ACM transactions on knowledge discovery from data, 11(1), Art. 5. Author/Publisher URL

Shao, J., Yang, Q., Liu, J., Kramer, S. (2016). Graph clustering with Density-Cut. arXiv.org., arXiv:1606.00950. Author/Publisher URL

Tenzer, S., Leidinger, P., Backes, C., et al. (2016). Integrated quantitative proteomic and transcriptomic analysis of lung tumor and control tissue: a lung cancer showcase. Oncotarget, 7, 14857-14857.

Tuan, T. T., Liu, Y., Schmidt, B. (2016). Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi. PARALLEL COMPUTING, 54, 128-138. DOI Author/Publisher URL

Williams, J., Stönner, C., Wicker, J., et al. (2016). Cinema audiences reproducibly vary the chemical composition of air during films, by broadcasting scene specific emissions on breath. Scientific reports, 6, Art. 25464. Author/Publisher URL

Zheng, Z., Wei, X., Hildebrandt, A., Schmidt, B. (2016). A computational method for studying the relation between alternative splicing and DNA methylation. Nucleic acids research, 44, e19-e19.

Other

Bouros, P., Mamoulis, N., Ge, S., and Terrovitis, M. (2016). Set Containment Join Revisited. Author/Publisher URL

Bračevac, O., Erdweg, S., Salvaneschi, G., and Mezini, M. (2016). CPL: A Core Language for Cloud Computing — Technical Report. Author/Publisher URL

Theses/Disssertations

Andrés López, D. (2016). Kombination von Outside-In und Inside-Out Tracking zur Regelung autonomer Luftfahrzeuge [Master’s Thesis]. Hochschule RheinMain.

Book chapters

Burkhardt, S., Kramer, S. (2015). On the spectrum between binary relevance and classifier chains in multi-label classification. In R. L. Wainwright (ed.), Proceedings of the 30th Annual ACM Symposium on Applied Computing 2015 : Salamanca, Spain, April 13 – 17, 2015 (pp. Seiten: 885-892). New York, NY:ACM. Author/Publisher URL

Endler, S., Hoffmann, S., Pfeiffer, M. (2015). Comparison between PerPot simulated and lactate based anaerobic threshold in handball players. In A. Radmann (ed.), 20th annual congress of the European college of sport science, 24th-27th June 2015, Malmö, Schweden : book of abstracts (p. Seite: 239). Malmö, Schweden:European College of Sport Science.

Endler, S., Secker, C., Bügner, J. (2015). What is the best fitting function? : Evaluation oflactate curves with common methods from the literature. In P. Chung (ed.), Proceedings of the 10th International Symposium on Computer Science in Sports (ISCSS) (pp. Seiten: 185-192). Cham:Springer. Author/Publisher URL

Frank, E., Mayo, M., Kramer, S. (2015). Alternating model trees. In R. L. Wainwright (ed.), Proceedings of the 30th Annual ACM Symposium on Applied Computing 2015 : Salamanca, Spain, April 13 – 17, 2015 (pp. Seiten: 871-878). New York, NY:ACM. Author/Publisher URL

Geilke, M., Karwath, A., Kramer, S. (2015). Modeling recurrent distributions in streams using possible worlds. In E. Gaussier (ed.), Proceedings of the 2015 IEEE International Conference on Data Science and Advanced Analytics : IEEE/ACM DSAA’2015 : 19-21 Oct 2015, Paris, France (pp. Seiten: 1-9). Piscataway, NJ:IEEE. Author/Publisher URL

Li, C., Wand, M., Wu, X., Seidel, H.-P. (2015). Approximate 3D partial symmetry detection using co-occurrence analysis. In M. Brown (ed.), 2015 International Conference on 3D Vision, 3DV 2015 : 19-22 October 2015, ENS, Lyon, France : proceedings (pp. Seiten: 425-433). Piscataway, NJ:IEEE. Author/Publisher URL

Tyukin, A., Kramer, S., Wicker, J. (2015). Scavenger : a framework for efficient evaluation of dynamic and modular algorithms. In A. Bifet (ed.), Machine learning and knowledge discovery in databases : European conference, ECML PKDD 2015, Porto, Portugal, September 7-11, 2015; proceedings. Pt. 3 (pp. Seiten: 325-328). Cham:Springer. Author/Publisher URL

Wicker, J., Krauter, N., Derstorff, B., et al. (2015). Cinema data mining : the smell of fear. In Proceedings of the 21st ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, August 10 – 13, 2015, Sydney, Australia (pp. Seiten: 1295-1304). New York, NY:ACM. Author/Publisher URL

Conference Papers

Chondrogiannis, T., Bouros, P., Gamper, J., Leser, U. (2015, November 3). Alternative routing: k-shortest paths with limited overlap. Proceedings of the 23rd SIGSPATIAL International Conference on Advances in Geographic Information Systems. Published. SIGSPATIAL’15: 23rd SIGSPATIAL International Conference on Advances in Geographic Information Systems. DOI

Liu, Y., Loewer, M., Aluru, S., Schmidt, B. (2015). SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 83-90. DOI

Bouros, P., Lathia, N., Renz, M., et al. (2015, September 16). LocalRec’15: Workshop on Location-Aware Recommendations. Proceedings of the 9th ACM Conference on Recommender Systems. Published. RecSys ’15: Ninth ACM Conference on Recommender Systems. DOI

Schneider, D., Schomer, E., Wolpert, N. (2015). A motion planning algorithm for the invalid initial state disassembly problem. 2015 20th International Conference on Methods and Models in Automation and Robotics (MMAR), 35-40. DOI Author/Publisher URL

Schneider, D., Schomer, E., Wolpert, N. (2015). Completely randomized RRT-connect: A case study on 3D rigid body motion planning. 2015 IEEE International Conference on Robotics and Automation (ICRA), 2944-2950. DOI Author/Publisher URL

Althaus, E., Muttary, U. (2015). University Course Timetabling with Conflict Minimization and Elective Courses. 12th Workshop on Models and Algorithms for Planning and Scheduling Problems, 224-229.

Althaus, E., Beber, B., Kupilas, J., Scholl, C. (2015). Improving Interpolants for Linear Arithmetic. In B. Finkbeiner, G. Pu, and L. Zhang (eds.), ATVA (Vols. 9364, pp. 48-63). Springer. Author/Publisher URL

Arzt, S., Nadi, S., Ali, K., et al. (2015). Towards secure integration of cryptographic software. In G. C. Murphy and G. L. S. Jr (eds.), Onward! (pp. 1-13). ACM. Author/Publisher URL

Bahr, P., … Erdweg, S. (eds.). (2015). Proceedings of the 11th ACM SIGPLAN Workshop on Generic Programming, WGP@ICFP 2015, Vancouver, BC, Canada, August 30, 2015. WGP@ICFP.

Erdweg, S., Bracevac, O., Kuci, E., et al. (2015). A co-contextual formulation of type rules and its application to incremental type checking. In J. Aldrich and P. Eugster (eds.), OOPSLA (pp. 880-897). ACM. Author/Publisher URL

Erdweg, S., Lichter, M., Weiel, M. (2015). A sound and optimal incremental build system with dynamic dependencies. In J. Aldrich and P. Eugster (eds.), OOPSLA (pp. 89-106). ACM. Author/Publisher URL

Erdweg, S., Storm, T. van der, Dai, Y. (2015). Capture-Avoiding Program Transformations with name-fix. In U. Aßmann, B. Demuth, T. Spitta, et al. (eds.), Software Engineering & Management: Vol. P-239 (pp. 93-94). GI. Author/Publisher URL

Gallenbacher, J. (ed.). (2015). Informatik allgemeinbildend begreifen, INFOS 2015, 16. GI-Fachtagung Informatik und Schule, 20.-23. September 2015, Darmstadt, Germany. P-249. Author/Publisher URL

Gallenbacher, J., Gose, K., Heun, D. (2015). Gestrandet auf der Schatzinsel – Schätze heben mit Informatik in der Grundschule. In J. Gallenbacher (ed.), Informatik allgemeinbildend begreifen, INFOS 2015, 16. GI-Fachtagung Informatik und Schule, 20.-23. September 2015, Darmstadt, Germany: Vol. P-249 (pp. 101-109). GI. Author/Publisher URL

Gallenbacher, J., Heun, D., Kothe, W. (2015). Jubel, Trubel, Informatik – Ein Schülerworkshop für den Klassenraum. In J. Gallenbacher (ed.), Informatik allgemeinbildend begreifen, INFOS 2015, 16. GI-Fachtagung Informatik und Schule, 20.-23. September 2015, Darmstadt, Germany: Vol. P-249 (pp. 111-118). GI. Author/Publisher URL

Grewe, S., Erdweg, S., Mezini, M. (2015). Using Vampire in Soundness Proofs of Type Systems. In L. Kovács, A. Voronkov (eds.), Vampire Workshop (Vols. 38, pp. 33-51). EasyChair. Author/Publisher URL

Grewe, S., Erdweg, S., Wittmann, P., Mezini, M. (2015). Type systems for the masses: deriving soundness proofs and efficient checkers. In G. C. Murphy, G. L. S. Jr (eds.), Onward! (pp. 137-150). ACM. Author/Publisher URL

Kuci, E., Erdweg, S., Mezini, M. (2015). Toward incremental type checking for Java. In J. Aldrich, P. Eugster (eds.), SPLASH (Companion Volume) (pp. 46-47). ACM. Author/Publisher URL

Lan, H., Liu, W., Schmidt, B., Wang, B. (2015). Accelerating Large-Scale Biological Database Search on Xeon Phi-based Neo-Heterogeneous Architectures. PROCEEDINGS 2015 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE, 503-510. Author/Publisher URL

Liu, Y., Schmidt, B. (2015). LightSpMV: Faster CSR-based Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs. PROCEEDINGS OF THE ASAP2015 2015 IEEE 26TH INTERNATIONAL CONFERENCE ON APPLICATION-SPECIFIC SYSTEMS, ARCHITECTURES AND PROCESSORS, 82-89. Author/Publisher URL

Qi, S., Bouros, P., Sacharidis, D., Mamoulis, N. (2015). Efficient Point-Based Trajectory Search. In C. Claramunt, M. Schneider, R. C.-W. Wong, et al. (eds.), Advances in Spatial and Temporal Databases – 14th International Symposium, SSTD 2015, Hong Kong, China, August 26-28, 2015. Proceedings (Vols. 9239, pp. 179-196). Springer. DOI

Ritschel, N., Erdweg, S. (2015). Modular capture avoidance for program transformations. In R. F. Paige, D. D. Ruscio, M. Völter (eds.), SLE (pp. 59-70). ACM. Author/Publisher URL

Schlarb, M., Hundt, C., Schmidt, B. (2015). SAUCE: A Web-Based Automated Assessment Tool for Teaching Parallel Programming. EURO-PAR 2015: PARALLEL PROCESSING WORKSHOPS, 9523, 54-65. DOI Author/Publisher URL

Shehu, A., Brunton, A., Wuhrer, S., Wand, M. (2015). Characterization of Partial Intrinsic Symmetries. COMPUTER VISION – ECCV 2014 WORKSHOPS, PT IV, 8928, 267-282. DOI Author/Publisher URL

Tjaden, H., Schwanecke, U., Stein, F. A., Schömer, E. (2015). High-Speed and Robust Monocular Tracking. In J. Braz, S. Battiato, F. H. Imai (eds.), VISAPP 2015 – Proceedings of the 10th International Conference on Computer Vision Theory and Applications, Volume 3, Berlin, Germany, 11-14 March, 2015. (Vols. 3, pp. 462-471). SciTePress. DOI

Journal Articles

Erdweg, S., van der Storm, T., Völter, M., et al. (2015). Evaluating and comparing language workbenches. Computer Languages, Systems & Structures, 44, 24-47. DOI

Gomez-Pulido, J. A., Schmidt, B., Feng, W.- chun. (2015). Accelerating bioinformatics applications via emerging parallel computing systems [Guest editorial]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(5), 971-972. DOI

von Dziegielewski, A., Hemmer, M., Schomer, E. (2015). High Precision Conservative Surface Mesh Generation for Swept Volumes. IEEE Transactions on Automation Science and Engineering, 12, 183-191. DOI Author/Publisher URL

Brochhausen, C., Winther, H., Hundt, C., et al. (2015). A virtual microscope for academic medical education : the Pate project. Interactive journal of medical research, 4(2), e11. Author/Publisher URL

Dietzen, M., Kalinina, O. V., Taškova, K., et al. (2015). Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces. Proteins: Structure, Function, and Bioinformatics, 83, 1887-1899.

Dousti, M. S., Jalili, R. (2015). FORSAKES: A FORWARD-SECURE AUTHENTICATED KEY EXCHANGE PROTOCOL BASED ON SYMMETRIC KEY-EVOLVING SCHEMES. ADVANCES IN MATHEMATICS OF COMMUNICATIONS, 9(4), 471-514. DOI Author/Publisher URL

Droby, A., Fleischer, V., Carnini, M., et al. (2015). The impact of isolated lesions on white-matter fiber tracts in multiple sclerosis patients. NeuroImage: Clinical, 8, 110-116.

Erdweg, S., Erwig, M., Paige, R. F., Visser, E. (2015). Domain-Specific Languages (Dagstuhl Seminar 15062). Dagstuhl Reports, 5, 26-43. DOI

Gonzalez-Dominguez, J., Kaessens, J. C., Wienbrandt, L., Schmidt, B. (2015). Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model. INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 29(4), 506-510. DOI Author/Publisher URL

Gonzalez-Dominguez, J., Schmidt, B. (2015). GPU-accelerated exhaustive search for third-order epistatic interactions in case-control studies. JOURNAL OF COMPUTATIONAL SCIENCE, 8, 93-100. DOI Author/Publisher URL

Gonzalez-Dominguez, J., Wienbrandt, L., Kaessens, J. C., et al. (2015). Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 12(5), 982-994. DOI Author/Publisher URL

Hauenschild, R., Tserovski, L., Schmid, K., et al. (2015). The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent. Nucleic Acids Research, 43, 9950-9964.

Hauenschild, R., Tserovski, L., Schmid, K., et al. (2015). The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent. NUCLEIC ACIDS RESEARCH, 43(20), 9950-9964. DOI Author/Publisher URL

Hildebrandt, A. K., Stöckel, D., Fischer, N. M., et al. (2015). Ballaxy: web services for structural bioinformatics. Bioinformatics, 31, 121-122.

Kaessens, J. C., Wienbrandt, L., Gonzalez-Dominguez, J., et al. (2015). High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs. JOURNAL OF COMPUTATIONAL SCIENCE, 9, 131-136. DOI Author/Publisher URL

Kölling, S., Endler, S., Ferrauti, A., et al. (2015). Comparing subjective with objective sleep parameters via multisensory actigraphy in German physical education students. Behavioral sleep medicine, 13(1), Seiten: 1-17. Author/Publisher URL

Li, C., Wand, M. (2015). Approximate translational building blocks for image decomposition and synthesis. ACM transactions on graphics, 34(5), Art. 158. Author/Publisher URL

Li, R., Perneczky, R., Drzezga, A., Kramer, S. (2015). Efficient redundancy reduced subgroup discovery via quadratic programming. Journal of intelligent information systems, 44(2), Seiten: 271-288. Author/Publisher URL

Li, R., Perneczky, R., Drzezga, A., Kramer, S. (2015). Gaussian mixture models and model selection for [18F] fluorodeoxyglucose positron emission tomography classification in Alzheimer’s disease. PLoS one, 10(4), e0122731. Author/Publisher URL

Li, R., Perneczky, R., Drzezga, A., Kramer, S. (2015). Survival analysis, the infinite Gaussian mixture model, FDG-PET and non-imaging data in the prediction of progression from mild cognitive impairment. arXiv.org, arXiv:1512.03955. Author/Publisher URL

Liu, Y., Schmidt, B. (2015). GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 27(4), 958-972. DOI Author/Publisher URL

Storm, T. van der, Erdweg, S. (2015). Proceedings of the 3rd Workshop on Domain-Specific Language Design and Implementation (DSLDI 2015). CoRR, abs/1508.03536.

Thuy-Diem, N., Schmidt, B., Zheng, Z., Kwoh, C.-K. (2015). Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 12(5), 1060-1073. DOI Author/Publisher URL

Tjaden, H., Schwanecke, U., Stein, F. A., Schömer, E. (2015). High-speed and robust monocular tracking. VISAPP 2015 – 10th International Conference on Computer Vision Theory and Applications; VISIGRAPP, Proceedings, 3, 462-471. DOI

Wicker, J., Lorsbach, T., Gütlein, M., et al. (2015). enviPath : the environmental contaminant biotransformation pathway resource. Nucleic acids research, 44(Database issue), Seiten: D502-D508. Author/Publisher URL

Other

Storm, T. van der, and Erdweg, S. (2015). Proceedings of the 3rd Workshop on Domain-Specific Language Design and Implementation (DSLDI 2015). Author/Publisher URL

Book chapters

Geilke, M., Karwath, A., Kramer, S. (2014). A probabilistic condensed representation of data for stream mining. In L. Cao (ed.), 2014 International Conference on Data Science and Advanced Analytics (DSAA 2014) : Shanghai, China, 30 October – 1 November 2014 (pp. Seiten: 297-303). Piscataway, NJ:IEEE. Author/Publisher URL

Li, R., Ahmadi, Z., Kramer, S. (2014). Constrained latent dirichlet allocation for subgroup discovery with topic rules. In T. Schaub (ed.), ECAI 2014 : 21st European Conference on Artificial Intelligence, 18-22 August 2014, Prague, Czech Republic ; including Prestigious applications of intelligent systems (PAIS 2014) ; proceedings (pp. Seiten: 519-524). Amsterdam:IOS Press. Author/Publisher URL

Liu, Y., Schmidt, B. (2014). Multiple Protein Sequence Alignment with MSAProbs. In MULTIPLE SEQUENCE ALIGNMENT METHODS (Vols. 1079, pp. 211-218). DOI Author/Publisher URL

Seeland, M., Karwath, A., Kramer, S. (2014). Structural clustering of millions of molecular graphs. In Proceedings of the 29th Annual ACM Symposium on Applied Computing 2014 : Gyeongju, Korea, March 24 – 28, 2014 (pp. Seiten: 121-128). New York, NY:ACM. Author/Publisher URL

Seeland, M., Maunz, A., Karwath, A., Kramer, S. (2014). Extracting information from support vector machines for pattern-based classification. In Proceedings of the 29th Annual ACM Symposium on Applied Computing 2014 : Gyeongju, Korea, March 24 – 28, 2014 (pp. Seiten: 129-136). New York, NY:ACM. Author/Publisher URL

Shao, J., Ahmadi, Z., Kramer, S. (2014). Prototype-based learning on concept-drifting data streams. In S. Macskassy (ed.), Proceedings of the 20th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, August 24 – 27, 2014, New York, NY, USA (pp. Seiten: 412-421). New York, NY:ACM. Author/Publisher URL

Tyukin, A., Kramer, S., Wicker, J. (2014). BMaD : a boolean matrix decomposition framework. In Machine Learning and Knowledge Discovery in Databases : European Conference, ECML PKDD 2014, Nancy, France, September 15-19, 2014. Proceedings, Part III (pp. Seiten: 481-484). Berlin:Springer. Author/Publisher URL

Wu, X., Li, C., Wand, M., et al. (2014). 3D model retargeting using offset statistics. In 2014 2nd International Conference on 3D Vision (3DV 2014) : Tokyo, Japan, 8 – 11 December 2014; [proceedings]. Vol. 1 (pp. Seiten: 353-360). Piscataway, NJ:IEEE. Author/Publisher URL

Conference Papers

Bouros, P., Sacharidis, D., Bikakis, N. (2014, November 4). Regionally influential users in location-aware social networks. Proceedings of the 22nd ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems. Published. SIGSPATIAL ’14: 22nd SIGSPATIAL International Conference on Advances in Geographic Information Systems. DOI

Tran, T. T., Schindel, S., Liu, Y., Schmidt, B. (2014). Bit-Parallel Approximate Pattern Matching on the Xeon Phi Coprocessor. 2014 IEEE 26th International Symposium on Computer Architecture and High Performance Computing, 81-88. DOI

Nguyen, T.-D., Schmidt, B., Kwoh, C.-K. (2014). Fast dendrogram-based OTU clustering using sequence embedding. Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 63-72. DOI

Kassens, J. C., Gonzalez-Dominguez, J., Wienbrandt, L., Schmidt, B. (2014). UPC++ for bioinformatics: A case study using genome-wide association studies. 2014 IEEE International Conference on Cluster Computing (CLUSTER), 248-256. DOI

Liu, Y., Schmidt, B. (2014). SWAPHI: Smith-waterman protein database search on Xeon Phi coprocessors. 2014 IEEE 25th International Conference on Application-Specific Systems, Architectures and Processors, 184-185. DOI

Althaus, E., Hildebrandt, A., Hildebrandt, A. K. (2014). A Greedy Algorithm for Hierarchical Complete Linkage Clustering. International Conference on Algorithms for Computational Biology, 25-34.

Dang, H.-V., Schmidt, B., Hildebrandt, A., Hildebrandt, A. K. (2014). Parallelized clustering of protein structures on cuda-enabled gpus. 2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, 1-8.

Erdweg, S., Storm, T. van der, Dai, Y. (2014). Capture-Avoiding and Hygienic Program Transformations. In R. E. Jones (ed.), ECOOP (Vols. 8586, pp. 489-514). Springer. Author/Publisher URL

Erdweg, S., Vergu, V. A., Mezini, M., Visser, E. (2014). Finding bugs in program generators by dynamic analysis of syntactic language constraints. In W. Binder, E. Ernst, A. Peternier, and R. Hirschfeld (eds.), MODULARITY (Companion) (pp. 17-20). ACM. Author/Publisher URL

Erdweg, S., Vergu, V. A., Mezini, M., Visser, E. (2014). Modular specification and dynamic enforcement of syntactic language constraints when generating code. In W. Binder, E. Ernst, A. Peternier, and R. Hirschfeld (eds.), MODULARITY (pp. 241-252). ACM. Author/Publisher URL

Erdweg, S., Welc, A. (2014). DSLDI 2014: second workshop on domain specific languages design and implementation. In A. P. Black (ed.), SPLASH (Companion Volume) (pp. 71-72). ACM. Author/Publisher URL

González-Domínguez, J., Schmidt, B., Kässens, J. C., Wienbrandt, L. (2014). Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS. 680-691. DOI

Hildebrandt, A., Krupp, M. (2014). Algorithms for the maximum weight connected k-induced subgraph problem. Combinatorial Optimization and Applications, 268-268.

Hundt, C., Schmidt, B., Schoemer, E. (2014). CUDA-Accelerated Alignment of Subsequences in Streamed Time Series Data. 2014 43RD INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING (ICPP), 10-19. DOI Author/Publisher URL

Hundt, C., Schmidt, B., Schömer, E., et al. (2014). GEM: an elastic and translation-invariant similarity measure with automatic trend adjustment. In Y. Cho, S. Y. Shin, S.-W. Kim, et al. (eds.), SAC (pp. 105-112). ACM. Author/Publisher URL

Inostroza, P., Storm, T. van der, Erdweg, S. (2014). Tracing Program Transformations with String Origins. In D. D. Ruscio, D. Varró (eds.), ICMT (Vols. 8568, pp. 154-169). Springer. Author/Publisher URL

Liu, Y., Schmidt, B. (2014). Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences. PARALLEL PROCESSING AND APPLIED MATHEMATICS (PPAM 2013), PT II, 8385, 247-257. DOI Author/Publisher URL

Liu, Y., Tran, T.-T., Lauenroth, F., Schmidt, B. (2014). SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi Coprocessors for Long DNA Sequences. 2014 IEEE INTERNATIONAL CONFERENCE ON CLUSTER COMPUTING (CLUSTER), 257-265. Author/Publisher URL

Mitra, N. J., Wand, M., Zhang, H., et al. (2014). Structure-aware shape processing. SIGGRAPH Courses, 13:1-13:1. Author/Publisher URL

Mitschke, R., Erdweg, S., Köhler, M., et al. (2014). i3QL: language-integrated live data views. In A. P. Black, T. D. Millstein (eds.), OOPSLA (pp. 417-432). ACM. Author/Publisher URL

Scholl, C., Pigorsch, F., Disch, S., Althaus, E. (2014). Simple interpolants for linear arithmetic. In G. P. Fettweis, W. Nebel (eds.), DATE (pp. 1-6). European Design and Automation Association. Author/Publisher URL

Thuy-Diem, N., Schmidt, B., Kwoh, C.-K. (2014). SparseHC: a memory-efficient online hierarchical clustering algorithm. 2014 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, 29, 8-19. DOI Author/Publisher URL

Weiel, M., Maier, I., Erdweg, S., et al. (2014). Towards virtual traits in Scala. In P. Haller, H. Miller (eds.), SCALA@ECOOP (pp. 67-75). ACM. Author/Publisher URL

Wienbrandt, L., Kaessens, J. C., Gonzalez-Dominguez, J., et al. (2014). FPGA-based acceleration of detecting statistical epistasis in GWAS. 2014 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, 29, 220-230. DOI Author/Publisher URL

Journal Articles

Erdweg, S., Fehrenbach, S., Ostermann, K. (2014). Evolution of Software Systems with Extensible Languages and DSLs. IEEE Software, 31(5), 68-75. DOI

Liagouris, J., Mamoulis, N., Bouros, P., Terrovitis, M. (2014). An effective encoding scheme for spatial RDF data. Proceedings of the VLDB Endowment, 7(12), 1271-1282. DOI

Böck, M., Hinley, J., Schmitt, C., et al. (2014). Identification of ELF3 as an early transcriptional regulator of human urothelium. Developmental biology, 386(2), Seiten: 321-330. Author/Publisher URL

Dietzen, M., Zotenko, E., Hildebrandt, A., Lengauer, T. (2014). Correction to On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking. Journal of chemical information and modeling, 54, 3453-3453.

Erdweg, S., Storm, T. van der, Dai, Y. (2014). Capture-Avoiding and Hygienic Program Transformations (incl. Proofs). CoRR, abs/1404.5770.

Gallenbacher, J. (2014). Aufgaben zum Überzeugen. LOG IN, 34, 145-150. DOI Author/Publisher URL

Gütlein, M., Karwath, A., Kramer, S. (2014). CheS-Mapper 2.0 for visual validation of (Q)SAR models. Journal of cheminformatics, 6(1), Art. 41. Author/Publisher URL

Hapfelmeier, A., Pfahringer, B., Kramer, S. (2014). Pruning incremental linear model trees with approximate lookahead. IEEE transactions on knowledge and data engineering, 26(8), Seiten: 2072-2076. Author/Publisher URL

Hildebrandt, A. K., Dietzen, M., Lengauer, T., et al. (2014). Efficient computation of root mean square deviations under rigid transformations. Journal of computational chemistry, 35, 765-771.

Hoevelmeyer, N., Woerns, M. A., Reissig, S., et al. (2014). Overexpression of Bcl-3 inhibits the development of marginal zone B cells. EUROPEAN JOURNAL OF IMMUNOLOGY, 44(2), 545-552. DOI Author/Publisher URL

Jordan, E., Roosen-Runge, F., Leibfarth, S., et al. (2014). Competing Salt Effects on Phase Behavior of Protein Solutions: Tailoring of Protein Interaction by the Binding of Multivalent Ions and Charge Screening. The Journal of Physical Chemistry B, 118, 11365-11374.

Liu, Y., Popp, B., Schmidt, B. (2014). CUSHAW3 : sensitive and accurate base-space and color-space short-read alignment with hybrid seeding. PLoS one, 9(1), e86869. Author/Publisher URL

Liu, Y., Schmidt, B. (2014). CUSHAW2-GPU: Empowering Faster Gapped Short-Read Alignment Using GPU Computing. IEEE DESIGN & TEST, 31(1), 31-39. DOI Author/Publisher URL

Liu, Y., Schmidt, B. (2014). SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors. PROCEEDINGS OF THE 2014 IEEE 25TH INTERNATIONAL CONFERENCE ON APPLICATION-SPECIFIC SYSTEMS, ARCHITECTURES AND PROCESSORS (ASAP 2014), 184-185. Author/Publisher URL

Ripp, F., Krombholz, C. F., Liu, Y., et al. (2014). All-Food-Seq (AFS) : a quantifiable screen for species in biological samples by deep DNA sequencing. BMC genomics, 15, Art. 639. Author/Publisher URL

Schmidt, J., Kramer, S. (2014). Online induction of probabilistic real-time automata. Journal of computer science and technology, 29(3), Seiten: 345-360. Author/Publisher URL

Seifert, T., Lund, A., Kneissl, B., et al. (2014). SKINK: a web server for string kernel based kink prediction in α-helices. Bioinformatics, 30, 1769-1770.

Staib, F., Krupp, M., Maass, T., et al. (2014). CellMinerHCC: a microarray-based expression database for hepatocellular carcinoma cell lines. LIVER INTERNATIONAL, 34(4), 621-631. DOI Author/Publisher URL

Wirawan, A., Harris, R. S., Liu, Y., et al. (2014). HECTOR : a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC bioinformatics, 15, Art. 131. Author/Publisher URL

Other

Erdweg, S., Storm, T. van der, and Dai, Y. (2014). Capture-Avoiding and Hygienic Program Transformations (incl. Proofs). Author/Publisher URL

Book chapters

Erbes, R., Mantel, A., Schömer, E., and Wolpert, N. (2013). Parallel Collision Queries on the GPU (pp. 84-95). DOI

Geilke, M., Frank, E., Karwath, A., and Kramer, S. (2013). Online estimation of discrete densities. In IEEE 13th International Conference on Data Mining (ICDM), 2013 : 7 – 10 Dec. 2013, Dallas, Texas (pp. Seiten: 191-200). Piscataway, NJ:IEEE. Author/Publisher URL

Hapfelmeier, A., Schmidt, J., and Kramer, S. (2013). Incremental linear model trees on massive datasets : keep it simple, keep it fast. In Proceedings of the 28th Annual ACM Symposium on Applied Computing (pp. Seiten: 129-135). New York, NY:ACM. Author/Publisher URL

Hoffmann, S., Endler, S., Sterzing, B., and Pfeiffer, M. (2013). Der Vergleich der anaeroben Schwelle anhand des sportinformatischen Modells PerPot mit der klassischen Laktatleistungsdiagnostik. In F. Mess (ed.), Sportwissenschaft grenzenlos?! : 25.-27. September 2013 ; abstracts (p. Seite: 86). Hamburg:Feldhaus Ed. Czwalina. Author/Publisher URL

Seeland, M., Kramer, S., and Pfahringer, B. (2013). Model selection based product kernel learning for regression on graphs. In Proceedings of the 28th Annual ACM Symposium on Applied Computing (pp. Seiten: 136-143). New York, NY:ACM. Author/Publisher URL

Conference Papers

Sacharidis, D., Bouros, P. (2013, November 5). Routing directions: keeping it fast and simple. Proceedings of the 21st ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems. Published. SIGSPATIAL’13: 21st SIGSPATIAL International Conference on Advances in Geographic Information Systems. DOI

Aly, M., Charfi, A., Erdweg, S., Mezini, M. (2013). XPoints: Extension Interfaces for Multilayered Applications. 2013 17th IEEE International Enterprise Distributed Object Computing Conference, 237-246. DOI

Haghighat, A. T., Kargar, M. A., Dousti, M. S., Jalili, R. (2013). Minimal assumptions to achieve privacy in e-voting protocols. 2013 10th International ISC Conference on Information Security and Cryptology (ISCISC), 1-5. DOI

Haghighat, A. T., Dousti, M. S., Jalili, R. (2013). An efficient and provably-secure coercion-resistant e-voting protocol. 2013 Eleventh Annual Conference on Privacy, Security and Trust, 161-168. DOI

Erdweg, S., Rieger, F. (2013). A framework for extensible languages. In J. Järvi and C. Kästner (eds.), GPCE (pp. 3-12). ACM. Author/Publisher URL

Erdweg, S., Storm, T. van der, Völter, M., et al. (2013). The State of the Art in Language Workbenches – Conclusions from the Language Workbench Challenge. In M. Erwig, R. F. Paige, and E. V. Wyk (eds.), SLE (Vols. 8225, pp. 197-217). Springer. Author/Publisher URL

Fehrenbach, S., Erdweg, S., Ostermann, K. (2013). Software Evolution to Domain-Specific Languages. In M. Erwig, R. F. Paige, and E. V. Wyk (eds.), SLE (Vols. 8225, pp. 96-116). Springer. Author/Publisher URL

Gallenbacher, J., Heun, D. (2013). Ein moderner Ansatz für Anchored Instruction im Informatikunterricht. In N. Breier, P. Stechert, and T. Wilke (eds.), Informatik erweitert Horizonte, INFOS 2013, 15. GI-Fachtagung Informatik und Schule, 26.-28. September 2013, Kiel, Germany: Vol. P-219 (pp. 87-96). GI. Author/Publisher URL

Hildebrandt, A. K., Althaus, E., Lenhof, H.-P., et al. (2013). Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics. German Conference on Bioinformatics 2013, 34, 56-67.

Lorenzen, F., Erdweg, S. (2013). Modular and automated type-soundness verification for language extensions. In G. Morrisett and T. Uustalu (eds.), ICFP (pp. 331-342). ACM. Author/Publisher URL

Martin, M., Mezini, M., Erdweg, S. (2013). Template constructors for reusable object initialization. In J. Järvi and C. Kästner (eds.), GPCE (pp. 43-52). ACM. Author/Publisher URL

Mitra, N. J., Ovsjanikov, M., Pauly, M., et al. (2013). Symmetry in Shapes – Theory and Practice. In D. Gutierrez and K. Myszkowski (eds.), Eurographics (Tutorials). Eurographics Association. Author/Publisher URL

Mitra, N. J., Wand, M., Zhang, H. R., et al. (2013). Structure-aware shape processing. In Y. Yu (ed.), SIGGRAPH ASIA Courses (pp. 1:1-1:1). ACM. Author/Publisher URL

Mitra, N. J., Wand, M., Zhang, H., et al. (2013). Structure-Aware Shape Processing. In M. Sbert and L. Szirmay-Kalos (eds.), Eurographics (State of the Art Reports) (pp. 175-197). Eurographics Association. Author/Publisher URL

Nickels, S., Stöckel, D., Mueller, S. C., et al. (2013). PresentaBALL—A powerful package for presentations and lessons in structural biology. Biological Data Visualization (BioVis), 2013 IEEE Symposium on, 33-40.

Qi, S., Bouros, P., Mamoulis, N. (2013). Efficient Top-k Spatial Distance Joins. In M. A. Nascimento, T. K. Sellis, R. Cheng, et al. (eds.), Advances in Spatial and Temporal Databases – 13th International Symposium, SSTD 2013, Munich, Germany, August 21-23, 2013. Proceedings (Vols. 8098, pp. 1-18). Springer. DOI

Journal Articles

Liu, Y., Schröder, J., Schmidt, B. (2013). Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. [Print-Electronic]. Bioinformatics (Oxford, England), 29(3), 308-315. DOI

Althaus, E., Kupilas, J., Naujoks, R. (2013). On the low-dimensional Steiner minimum tree problem in Hamming metric. Theoretical computer science, 505, Seiten: 2-10. Author/Publisher URL

Cabezas-Wallscheid, N., Eichwald, V., de Graaf, J., et al. (2013). Instruction of haematopoietic lineage choices, evolution of transcriptional landscapes and cancer stem cell hierarchies derived from an AML1-ETO mouse model. EMBO molecular medicine, 5, 1804-1820.

Chen, Y., Schmidt, B., Maskell, D. L. (2013). A hybrid short read mapping accelerator. BMC BIOINFORMATICS, 14. DOI Author/Publisher URL

Chen, Y., Schmidt, B., Maskell, D. L. (2013). Reconfigurable Accelerator for the Word-Matching Stage of BLASTN. IEEE TRANSACTIONS ON VERY LARGE SCALE INTEGRATION (VLSI) SYSTEMS, 21(4), 659-669. DOI Author/Publisher URL

Dang, H.-V., Schmidt, B. (2013). CUDA-enabled Sparse Matrix-Vector Multiplication on GPUs using atomic operations. PARALLEL COMPUTING, 39(11), 737-750. DOI Author/Publisher URL

Dehof, A. K., Loew, S., Lenhof, H.-P., Hildebrandt, A. (2013). NightShift: NMR shift inference by general hybrid model training-a framework for NMR chemical shift prediction. BMC bioinformatics, 14, 98-98.

Girschick, T., Almeida, P. R., Kramer, S., Stalring, J. (2013). Similarity boosted quantitative structure-activity relationship : a systematic study of enhancing structural descriptors by molecular similarity. Journal of chemical information and modeling, 53(5), Seiten: 1017-1025. Author/Publisher URL

Girschick, T., Puchbauer, L., Kramer, S. (2013). Improving structural similarity based virtual screening using background knowledge. Journal of cheminformatics, 5, Art. 50. Author/Publisher URL

Girschick, T., Rückert, U., Kramer, S. (2013). Adapted transfer of distance measures for quantitative structure-activity relationships and data-driven selection of source datasets. The computer journal, 56(3), Seiten: 274-288. Author/Publisher URL

Gütlein, M., Helma, C., Karwath, A., Kramer, S. (2013). A large-scale empirical evaluation of cross-validation and external test set validation in (Q)SAR. Molecular informatics, 32(5-6), Seiten: 516-528. Author/Publisher URL

Liu, Y., Schroeder, J., Schmidt, B. (2013). Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. BIOINFORMATICS, 29(3), 308-315. DOI Author/Publisher URL

Liu, Y., Wirawan, A., Schmidt, B. (2013). CUDASW++ 3.0 : accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions. BMC bioinformatics, 14, Art. 117. Author/Publisher URL

Schmidt, B., Aribowo, H., Hoang-Vu, D. (2013). Iterative sparse matrix-vector multiplication for accelerating the block Wiedemann algorithm over GF(2) on multi-graphics processing unit systems. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 25(4), 586-603. DOI Author/Publisher URL

Schmidt, J., Ghorbani, A., Hapfelmeier, A., Kramer, S. (2013). Learning probabilistic real-time automata from multi-attribute event logs. Intelligent data analysis, 17(1), Seiten: 93-123. Author/Publisher URL

Other

Sacharidis, D., and Bouros, P. (2013). Routing Directions: Keeping it Fast and Simple. Author/Publisher URL

Theses/Disssertations

Andrés López, D. (2013). Integration des Internets der Dinge in Unternehmensnetzwerke [Undergraduate Dissertation]. Duale Hochschule Baden-Württemberg Mannheim.

Endler, S. (2013). Anpassung des Metamodells PerPot an den ausdauerorientierten Laufsport zur Trainings- und Wettkampfoptimierung [PhD Thesis]. DOI Author/Publisher URL

Book chapters

Duchrow, T., Schröer, M., Griesbach, B., et al. (2012). Towards electric mobility data mining. In 2012 IEEE International Electric Vehicle Conference (IEVC 2012) : Greenville, South Carolina, USA, 4 – 8 March 2012 (pp. Seiten: 268-273). Piscataway, NJ:IEEE. Author/Publisher URL

Endler, S., Perl, J. (2012). Optimizing practice and competition in marathon running by means of the meta-model PerPot. In Y. Jiang (ed.), Proceedings of 2012 pre-Olympic congress on sports science and computer science in sport : Liverpool, United Kingdom, July 24-25, 2012 (pp. Seiten: 127-131). Edgbaston:World Academic Union.

Li, R., Kramer, S. (2012). Efficient redundancy reduced subgroup discovery via quadratic programming. In J.-G. Ganascia (ed.), Discovery science : 15th international conference, DS 2012, Lyon, France, October 29-31, 2012 (pp. Seiten: 125-138). Berlin u.a.:Springer. Author/Publisher URL

Perl, J., Memmert, D., Baca, A., et al. (2012). Sensors, monitoring and model-based data analysis in sports, exercise and rehabilitation. In D. T. H. Lai (ed.), Healthcare sensor networks : challenges toward practical implementation (pp. Seiten: 375-405). Boca Raton, Fla:CRC, Taylor & Francis.

Schmidt, J., Ansorge, S., Kramer, S. (2012). Scalable induction of probabilistic real-time automata using maximum frequent pattern based clustering. In 12th SIAM International Conference on Data Mining 2012 : Anaheim, California, USA, 26 – 28 April 2012 (pp. Seiten: 272-283). Philadelphia, PA:Society for Industrial and Applied Mathematics. Author/Publisher URL

Schmidt, J., Kramer, S. (2012). Online induction of probabilistic real time automata. In M. J. Zaki (ed.), IEEE 12th International Conference on Data Mining (ICDM), 2012 : 10 – 13 Dec. 2012, Brussels, Belgium (pp. Seiten: 625-634). Piscataway, NJ:IEEE. Author/Publisher URL

Seeland, M., Buchwald, F., Kramer, S., Pfahringer, B. (2012). Maximum common subgraph based locally weighted regression. In The 27th annual ACM Symposium on Applied Computing : Riva del Garda, Trento, Italy, March 26 – 30, 2012 (pp. Seiten: 165-172). New York, NY:ACM. Author/Publisher URL

Seeland, M., Karwath, A., Kramer, S. (2012). A structural cluster kernel for learning on graphs. In Proceedings of the 18th ACM SIGKDD international conference on knowledge discovery and data mining (KDD-2012), August 12 – 16, 2012, Beijing, China (pp. Seiten: 516-524). New York, NY:ACM. Author/Publisher URL

Wicker, J., Pfahringer, B., Kramer, S. (2012). Multi-label classification using Boolean matrix decomposition. In The 27th annual ACM Symposium on Applied Computing : Riva del Garda, Trento, Italy, March 26 – 30, 2012 (pp. Seiten: 179-186). New York, NY:ACM. Author/Publisher URL

Books

Tampier, M., Endler, S., Baca, A., and Perl, J. (2012). Entwicklung eines intelligenten Echtzeit Feedback Systems (pp. Seiten: 64-67). Konstanz:Bibliothek der Universität Konstanz. Author/Publisher URL

Conference Papers

Althaus, E., Hoffmann, S., Kupilas, J., Thaden, E. (2012). A Column Generation Approach to Scheduling of Real-Time Networks – Best Paper Award of International Conference on Computer Science and Applications 2012 (S. I. Ao, C. Douglas, W. S. Grundfest, and J. Burgstone, eds.; pp. 224-229). Newswood Limited.

Chen, Y., Schmidt, B., Maksell, D. L. (2012). An FPGA aligner for short read mapping. 22nd International Conference on Field Programmable Logic and Applications (FPL), 511-514. DOI

Ihrke, I., Reshetouski, I., Manakov, A., et al. (2012). A kaleidoscopic approach to surround geometry and reflectance acquisition. 2012 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 29-36. DOI

Liu, Y., Schmidt, B. (2012). Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform. 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 684-690. DOI

von Dziegielewski, A., Hemmer, M., Schömer, E. (2012). High quality conservative surface mesh generation for swept volumes. 2012 IEEE International Conference on Robotics and Automation, 764-769. DOI Author/Publisher URL

Chen, Y., Schmidt, B., Maskell, D. L. (2012). Accelerating short read mapping on an FPGA (abstract only). Proceedings of the ACM/SIGDA international symposium on Field Programmable Gate Arrays, 265-265. DOI

Benz, F., Hildebrandt, A., Hack, S. (2012). A dynamic program analysis to find floating-point accuracy problems. ACM SIGPLAN Notices, 47, 453-462.

Chang, W., Li, H., Mitra, N. J., et al. (2012). Dynamic Geometry Processing. In R. Pajarola and M. Spagnuolo (eds.), Eurographics (Tutorials). Eurographics Association. Author/Publisher URL

Dang, H.-V., Schmidt, B. (2012). The Sliced COO Format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs. Procedia Computer Science, 9, 57-66. DOI

Droby, A., Fleischer, V., Zimmermann, H., et al. (2012). Impact of infratentorial lesions on affected fibers in multiple sclerosis. MULTIPLE SCLEROSIS JOURNAL, 18, 517-517.

Erdweg, S., Giarrusso, P. G., Rendel, T. (2012). Language composition untangled. In A. Sloane and S. Andova (eds.), LDTA (pp. 7-7). ACM. Author/Publisher URL

Erdweg, S., Rendel, T., Kästner, C., Ostermann, K. (2012). Layout-Sensitive Generalized Parsing. In K. Czarnecki and G. Hedin (eds.), SLE (Vols. 7745, pp. 244-263). Springer. Author/Publisher URL

Erdweg, S., Rieger, F., Rendel, T., Ostermann, K. (2012). Layout-sensitive language extensibility with SugarHaskell. In J. Voigtländer (ed.), Haskell (pp. 149-160). ACM. Author/Publisher URL

Gallenbacher, J. (2012). Abenteuer informatik: hands-on exhibits for learning about computational thinking. In M. Knobelsdorf and R. Romeike (eds.), Workshop in Primary and Secondary Computing Education, WIPSCE ’12, Hamburg, Germany, November 8-9, 2012 (pp. 149-150). ACM. DOI

Kästner, C., Ostermann, K., Erdweg, S. (2012). A variability-aware module system. In G. T. Leavens and M. B. Dwyer (eds.), OOPSLA (pp. 773-792). ACM. Author/Publisher URL

Kästner, C., Rhein, A. von, Erdweg, S., et al. (2012). Toward variability-aware testing. In I. Schaefer and T. Thüm (eds.), FOSD (pp. 1-8). ACM. Author/Publisher URL

Mitra, N. J., Pauly, M., Wand, M., Ceylan, D. (2012). Symmetry in 3D Geometry: Extraction and Applications. In M.-P. Cani and F. Ganovelli (eds.), Eurographics (State of the Art Reports) (pp. 29-51). Eurographics Association. Author/Publisher URL

Nickels, S., Sminia, H., Mueller, S. C., et al. (2012). ProteinScanAR-An augmented reality web application for high school education in biomolecular life sciences. 2012 16th International Conference on Information Visualisation, 578-583.

Schmidt, B., Maskell, D. (2012). Fourth Workshop on using Emerging Parallel Architectures. Procedia Computer Science, 9, 1867-1869. DOI

Journal Articles

Bouros, P., Ge, S., Mamoulis, N. (2012). Spatio-textual similarity joins. Proceedings of the VLDB Endowment, 6(1), 1-12. DOI

Gross, D., Heil, U., Schulze, R., et al. (2012). Auto calibration of a cone-beam-CT. Medical Physics, 39, 5959-5970. DOI

Schlitt, S., Gorelik, T. E., Stewart, A. A., et al. (2012). Application of clustering techniques to electron-diffraction data: determination of unit-cell parameters. Acta Crystallographica Section A Foundations of Crystallography, 68, 536-546. DOI Author/Publisher URL

Althaus, E., Dumitriu, D. (2012). Certifying feasibility and objective value of linear programs. Operations Research Letters, 40(4), 292-297. DOI

Limbach, S., Schömer, E., Wernli, H. (2012). Detection, tracking and event localization of jet stream features in 4-D atmospheric data. Geoscientific Model Development, 5, 457-470. DOI Author/Publisher URL

Benz, F., Hildebrandt, A., Hack, S. (2012). A Dynamic Program Analysis to find Floating-Point Accuracy Problems. ACM SIGPLAN NOTICES, 47(6), 453-462. DOI Author/Publisher URL

Bouros, P., Sacharidis, D., Dalamagas, T., et al. (2012). Evaluating Path Queries over Frequently Updated Route Collections. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING, 24(7), 1276-1290. DOI Author/Publisher URL

Böck, M., Ogishima, S., Tanaka, H., et al. (2012). Hub-centered gene network reconstruction using automatic relevance determination. PLoS one, 7(5), e35077. Author/Publisher URL

Dietzen, M., Zotenko, E., Hildebrandt, A., Lengauer, T. (2012). On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking. Journal of chemical information and modeling, 52, 844-856.

Ganzert, S., Kramer, S., Guttmann, J. (2012). Predicting the lung compliance of mechanically ventilated patients via statistical modeling. Physiological measurement, 33(3), Seiten: 345-359. Author/Publisher URL

Gütlein, M., Karwath, A., Kramer, S. (2012). CheS-Mapper : Chemical Space Mapping and visualization in 3D. Journal of cheminformatics, 4, Art. 7. Author/Publisher URL

Krupp, M., Itzel, T., Maass, T., et al. (2012). CellLineNavigator: a workbench for cancer cell line analysis. Nucleic acids research, 41, D942-D948.

Liu, Y., Schmidt, B. (2012). Long read alignment based on maximal exact match seeds. BIOINFORMATICS, 28(18), I318-I324. DOI Author/Publisher URL

Liu, Y., Schmidt, B., Maskell, D. L. (2012). CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. BIOINFORMATICS, 28(14), 1830-1837. DOI Author/Publisher URL

Perl, J., Endler, S. (2012). PerPot individual anaerobe threshold marathon scheduling. International journal of computer science in sport, 11(2), Seiten: 52-60.

Slawski, M., Hussong, R., Tholey, A., et al. (2012). Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching. BMC bioinformatics, 13, 291-291.

Zheng, Z., Kramer, S., Schmidt, B. (2012). DySC : software for greedy clustering of 16S rRNA reads. Bioinformatics, 28(16), Seiten: 2182-2183. Author/Publisher URL

Book chapters

Varré, J.-S., Schmidt, B., Janot, S., Giraud, M. (2011). Manycore High-Performance Computing in Bioinformatics. In Science, Engineering, and Biology Informatics (pp. 179-207). WORLD SCIENTIFIC. DOI

Alphonse, E., Girschick, T., Buchwald, F., Kramer, S. (2011). A numerical refinement operator based on multi-instance learning. In P. Frasconi (ed.), Inductive Logic Programming : 20th International Conference, ILP 2010, Florence, Italy, June 27-30, 2010 (pp. Seiten: 14-21). Berlin u.a.:Springer. Author/Publisher URL

Endler, S., Perl, J. (2011). Leistungsoptimierung beim Marathon mit sportinformatischen Modellen. In D. Link (ed.), Sportinformatik trifft Sporttechnologie : 8. Symposium der dvs-Sektion Sportinformatik in Kooperation mit der Deutschen Interdisziplinären Vereinigung für Sporttechnologie vom 15. – 17. September 2010 in Darmstadt (pp. Seiten: 221-225). Hamburg:Feldhaus, Ed. Czwalina.

Endler, S., Pietzonka, M., Pfeiffer, M., et al. (2011). Ein Methodenvergleich zwischen laktatbasierten und informatischem Schwellenkonzepten. In K. Hottenrott (ed.), Kreativität – Innovation – Leistung : Wissenschaft bewegt SPORT bewegt Wissenschaft : 21.-23. September 2011 ; abstracts (p. Seite: 127). Hamburg:Feldhaus Ed. Czwalina.

Grunz, A., Endler, S., Memmert, D., Perl, J. (2011). Netz-gestützte Konstellations-Analyse im Fußball. In D. Link (ed.), Sportinformatik trifft Sporttechnologie : 8. Symposium der dvs-Sektion Sportinformatik in Kooperation mit der Deutschen Interdisziplinären Vereinigung für Sporttechnologie vom 15. – 17. September 2010 in Darmstadt (pp. Seiten: 111-115). Hamburg:Feldhaus, Ed. Czwalina.

Kramer, S., Schmidt, J., Brändle, E. M. (2011). Clustering with attribute-level constraints. In D. Cook (ed.), 11th IEEE International Conference on Data Mining : Vancouver, Canada, 11-14 December 2011 (pp. Seiten: 1206-1211). Piscataway, NJ:IEEE. Author/Publisher URL

Li, R., Hapfelmeier, A., Schmidt, J., et al. (2011). A case study of stacked multi-view learning in dementia research. In M. Peleg (ed.), Artificial intelligence in medicine : 13th Conference on Artificial Intelligence in Medicine, AIME 2011, Bled, Slovenia, July 2-6, 2011 (pp. Seiten: 60-69). Berlin u.a.:Springer. Author/Publisher URL

Ligowski, Łukasz, Rudnicki, W. R., Liu, Y., Schmidt, B. (2011). Accurate Scanning of Sequence Databases with the Smith-Waterman Algorithm. In GPU Computing Gems Emerald Edition (pp. 155-171). Elsevier. DOI

Schmidt, J., Kramer, S. (2011). The augmented itemset tree : a data structure for online maximum frequent pattern mining. In T. Elomaa (ed.), Discovery science : 14th international conference, DS 2011, Espoo, Finland, October 5-7, 2011 (pp. Seiten: 277-291). Berlin u.a.:Springer. Author/Publisher URL

Seeland, M., Berger, S. A., Stamatakis, A., Kramer, S. (2011). Parallel structural graph clustering. In Machine learning and knowledge discovery in databases : European conference, ECML PKDD 2011, Athens, Greece, September 5-9, 2011 ; proceedings, Part III (pp. Seiten: 256-272). Berlin u.a.:Springer. Author/Publisher URL

Books

Schmidt, B. (2011). Bioinformatics High Performance Parallel Computer Architectures. CRC Press.

Conference Papers

Liu, W., Schmidt, B., Liu, Y., et al. (2011). Mapping of BLASTP Algorithm onto GPU Clusters. 2011 IEEE 17th International Conference on Parallel and Distributed Systems, 236-243. DOI

Heil, U., Gross, D., Schulze, R., et al. (2011). Metal artifact reduction in x-ray computed tomography: Inpainting versus missing value. 2011 IEEE Nuclear Science Symposium Conference Record, 2675-2677. DOI Author/Publisher URL

Thum, T., Kastner, C., Erdweg, S., Siegmund, N. (2011). Abstract Features in Feature Modeling. 2011 15th International Software Product Line Conference, 191-200. DOI

Lasowski, R., Tevs, A., Wand, M., Seidel, H.-P. (2011). Wavelet belief propagation for large scale inference problems. CVPR 2011, 1921-1928. DOI

Liu, Y., Schmidt, B., Maskell, D. L. (2011). An Ultrafast Scalable Many-Core Motif Discovery Algorithm for Multiple GPUs. 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum, 428-434. DOI

Terrovitis, M., Bouros, P., Vassiliadis, P., et al. (2011). Efficient answering of set containment queries for skewed item distributions. Proceedings of the 14th International Conference on Extending Database Technology, 225-236. DOI

Althaus, E., Altmeyer, S., Naujoks, R. (2011). Precise and efficient parametric path analysis. In J. Vitek and B. D. Sutter (eds.), LCTES (pp. 141-150). ACM. Author/Publisher URL

Althaus, E., Altmeyer, S., Naujoks, R. (2011). Symbolic Worst Case Execution Times. In A. Cerone and P. Pihlajasaari (eds.), ICTAC (Vols. 6916, pp. 25-44). Springer. Author/Publisher URL

Althaus, E., Becker, B., Dumitriu, D., Kupferschmid, S. (2011). Integration of an LP Solver into Interval Constraint Propagation. In W. Wang, X. Zhu, and D.-Z. Du (eds.), COCOA (Vols. 6831, pp. 343-356). Springer. Author/Publisher URL

Althaus, E., Kupilas, J., Naujoks, R. (2011). On the Low-Dimensional Steiner Minimum Tree Problem in Hamming Metric. In M. Ogihara and J. Tarui (eds.), TAMC (Vols. 6648, pp. 308-319). Springer. Author/Publisher URL

Althaus, E., Naujoks, R., Thaden, E. (2011). A Column Generation Approach to Scheduling of Periodic Tasks. In P. M. Pardalos and S. Rebennack (eds.), SEA (Vols. 6630, pp. 340-351). Springer. Author/Publisher URL

Aluru, S., Bandyopadhyay, S., Çatalyürek, Ümit V., … Schmidt, B. (eds.). (2011). Contemporary Computing – 4th International Conference, IC3 2011, Noida, India, August 8-10, 2011. Proceedings. IC3, 168.

Bardhan, J. P., Hildebrandt, A. (2011). A fast solver for nonlocal electrostatic theory in biomolecular science and engineering. Proceedings of the 48th Design Automation Conference, 801-805.

Bouros, P., Sacharidis, D., Dalamagas, T., Sellis, T. K. (2011). Dynamic Pickup and Delivery with Transfers. In D. Pfoser, Y. Tao, K. Mouratidis, et al. (eds.), Advances in Spatial and Temporal Databases – 12th International Symposium, SSTD 2011, Minneapolis, MN, USA, August 24-26, 2011, Proceedings (Vols. 6849, pp. 112-129). Springer. DOI

Chang, W., Li, H., Mitra, N. J., et al. (2011). Computing Correspondences in Geometric Data Sets. In R. Martin, J. C. Torres (eds.), Eurographics (Tutorials). Eurographics Association. Author/Publisher URL

Dehof, A. (2011). Predicting Protein NMR Chemical Shifts in the Presence of Ligands and Ions using Force Field-based Features. German Conference on Bioinformatics (GCB 2011).

Erdweg, S., Kats, L. C. L., Rendel, T., et al. (2011). Growing a language environment with editor libraries. In E. Denney, U. P. Schultz (eds.), GPCE (pp. 167-176). ACM. Author/Publisher URL

Erdweg, S., Kats, L. C. L., Rendel, T., et al. (2011). Library-based model-driven software development with SugarJ. In C. V. Lopes, K. Fisher (eds.), OOPSLA Companion (pp. 17-18). ACM. Author/Publisher URL

Erdweg, S., Kats, L. C. L., Rendel, T., et al. (2011). SugarJ: library-based language extensibility. In C. V. Lopes, K. Fisher (eds.), OOPSLA Companion (pp. 187-188). ACM. Author/Publisher URL

Erdweg, S., Rendel, T., Kästner, C., Ostermann, K. (2011). SugarJ: library-based syntactic language extensibility. In C. V. Lopes, K. Fisher (eds.), OOPSLA (pp. 391-406). ACM. Author/Publisher URL

Kerber, J., Wand, M., Krüger, J. H., Seidel, H.-P. (2011). Partial Symmetry Detection in Volume Data. In P. Eisert, J. Hornegger, K. Polthier (eds.), VMV (pp. 41-48). Eurographics Association. Author/Publisher URL

Kästner, C., Giarrusso, P. G., Rendel, T., et al. (2011). Variability-aware parsing in the presence of lexical macros and conditional compilation. In C. V. Lopes, K. Fisher (eds.), OOPSLA (pp. 805-824). ACM. Author/Publisher URL

Schmidt, B., Aribowo, H., Dang, H.-V. (2011). Iterative Sparse Matrix-Vector Multiplication for Integer Factorization on GPUs. 413-424. DOI

Schmidt, B., Maskell, D. (2011). Third Workshop on using Emerging Parallel Architectures. Procedia Computer Science, 4, 1964-1966. DOI

Zheng, Z., Nguyen, T.-D., Schmidt, B. (2011). CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA. 37-49. DOI

Journal Articles

Shi, H., Schmidt, B., Liu, W., Müller-Wittig, W. (2011). Parallel mutual information estimation for inferring gene regulatory networks on GPUs. BMC Research Notes, 4(1). DOI

Althaus, E., Canzar, S., Elbassioni, K., et al. (2011). Approximation Algorithms for the Interval Constrained Coloring Problem. Algorithmica, 61(2), 342-361. DOI

Schulze, R., Heil, U., Groβ D., et al. (2011). Artefacts in CBCT: a review. Dentomaxillofacial Radiology, 40, 265-273. DOI Author/Publisher URL

Hemmer, M., Dupont, L., Petitjean, S., Schömer, E. (2011). A complete, exact and efficient implementation for computing the edge-adjacency graph of an arrangement of quadrics. Journal of Symbolic Computation, 46, 467-494. DOI Author/Publisher URL

Buchwald, F., Girschick, T., Seeland, M., Kramer, S. (2011). Using local models to improve (Q)SAR predictivity. Molecular informatics, 30(2-3), Seiten: 205-218. Author/Publisher URL

Buchwald, F., Richter, L., Kramer, S. (2011). Predicting a small molecule-kinase interaction map : a machine learning approach. Journal of cheminformatics, 3, Art. 22. Author/Publisher URL

Dehof, A. K., Rurainski, A., Bui, Q. B. A., et al. (2011). Automated bond order assignment as an optimization problem. Bioinformatics, 27, 619-625.

Hamp, T., Birzele, F., Buchwald, F., Kramer, S. (2011). Improving structure alignment-based prediction of SCOP families using Vorolign kernels. Bioinformatics, 27(2), Seiten: 204-210. Author/Publisher URL

Kneissl, B., Mueller, S. C., Tautermann, C. S., Hildebrandt, A. (2011). String Kernels and High-Quality Data Set for Improved Prediction of Kinked Helices in α-Helical Membrane Proteins. Journal of chemical information and modeling, 51, 3017-3025.

Kuttippurathu, L., Hsing, M., Liu, Y., et al. (2011). CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. BIOINFORMATICS, 27(5), 715-717. DOI Author/Publisher URL

Liu, W., Schmidt, B., Mueller-Wittig, W. (2011). CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 8(6), 1678-1684. DOI Author/Publisher URL

Liu, Y., Schmidt, B., Maskell, D. L. (2011). Parallelized short read assembly of large genomes using de Bruijn graphs. BMC bioinformatics, 12, Art. 354. Author/Publisher URL

Liu, Y., Schmidt, B., Maskell, D. L. (2011). DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI. BMC BIOINFORMATICS, 12. DOI Author/Publisher URL

Maunz, A., Helma, C., Kramer, S. (2011). Efficient mining for structurally diverse subgraph patterns in large molecular databases. Machine learning, 83(2), Seiten: 193-218. Author/Publisher URL

Book chapters

Buchwald, F., Girschick, T., Frank, E., and Kramer, S. (2010). Fast conditional density estimation for quantitative structure-activity relationships. In Proceedings of the Twenty-Fourth AAAI Conference on Artificial Intelligence and the Twenty-Second Innovative Applications of Artificial Intelligence Conference : 11 – 15 July 2010, Atlanta, Georgia, USA. Vol. 3. Special track on AI and the web (pp. Seiten: 1268-1273). Menlo Park, Calif.:AAAI Press.

Endler, S., and Perl, J. (2010). Leistungsoptimierung beim Marathon mit sportinformatischen Modellen. In J. Wiemeyer (ed.), Sportinformatik trifft Sporttechnologie : Abstractband ; Tagung der dvs-Sektion Sportinformatik und der deutschen interdisziplinären Vereinigung für Sporttechnologie vom 15. – 17. September 2010 in Darmstadt (pp. Seiten: 152-154). Darmstadt:Inst. für Sportwiss. d. Techn. Univ.

Endler, S., and Perl, J. (2010). Leistungsoptimierung beim Marathon mit sportinformatischen Modellen. In K. Mattes (ed.), Bewegung und Leistung – Sport, Gesundheit & Alter : 8. Gemeinsames Symposium der dvs-Sektionen Biomechanik, Sportmotorik und Trainingswissenschaft vom 02. – 04. September 2010 in Hamburg ; Abstracts (pp. Seiten: 98-98). Hamburg:Feldhaus, Ed. Czwalina.

Gajananan, K., Nakasone, A., Hildebrandt, A., and Prendinger, H. (2010). A novel three-dimensional collaborative online platform for bio-molecular modeling (pp. 44-55).

Ganzert, S., Guttmann, J., Steinmann, D., and Kramer, S. (2010). Equation discovery for model identification in respiratory mechanics of the mechanically ventilated human lung. In B. Pfahringer (ed.), Discovery science : 13th international conference ; proceedings / DS 2010, Canberra, Australia, October 6 – 8, 2010 (pp. Seiten: 296-310). Berlin:Springer. Author/Publisher URL

Grunz, A., Perl, J., Memmert, D., and Endler, S. (2010). Klassifizierung taktischer Muster im Fussball mit hierarchischen Neuronalen Netzen. In J. Wiemeyer (ed.), Sportinformatik trifft Sporttechnologie : Abstractband ; Tagung der dvs-Sektion Sportinformatik und der deutschen interdisziplinären Vereinigung für Sporttechnologie vom 15. – 17. September 2010 in Darmstadt (pp. Seiten: 74-75). Darmstadt:Inst. für Sportwiss. d. Techn. Univ.

Hopf, T., and Kramer, S. (2010). Mining class-correlated patterns for sequence labeling. In Discovery Science : 13th International Conference, DS 2010, Canberra, Australia, October 6-8, 2010 (pp. Seiten: 311-325). Berlin u.a.:Springer Berlin Heidelberg. Author/Publisher URL

Hussong, R., and Hildebrandt, A. (2010). Signal processing in proteomics. In Proteome Bioinformatics (pp. 145-161). Humana Press.

Kramer, S. (2010). Inductive Database Approach to Graphmining. In C. Sammut and G. I. Webb (eds.), Encyclopedia of Machine Learning (pp. 522-523). Springer. DOI

Maunz, A., Helma, C., Cramer, T., and Kramer, S. (2010). Latent structure pattern mining. In J. Balcazar (ed.), Machine learning and knowledge discovery in databases : European conference ; proceedings / ECML PKDD 2010, Barcelona, Spain, September 20 – 24, 2010. Vol. 2. Lecture notes in artificial intelligence (pp. Seiten: 353-368). Berlin:Springer. Author/Publisher URL

Müller, M., and Kramer, S. (2010). Integer linear programming models for constrained clustering. In B. Pfahringer (ed.), Discovery science : 13th international conference ; proceedings / DS 2010, Canberra, Australia, October 6 – 8, 2010 (pp. Seiten: 159-173). Berlin:Springer. Author/Publisher URL

Richter, L., Augustin, R., and Kramer, S. (2010). Finding relational associations in HIV resistance mutation data. In L. De Raedt (ed.), Inductive Logic Programming : 19th International Conference, ILP 2009, Leuven, Belgium, July 02-04, 2009 (pp. Seiten: 202-208). Berlin u.a.:Springer Berlin Heidelberg. Author/Publisher URL

Richter, L., Wicker, J., and Kramer, S. (2010). SINDBAD and SiQL : overview, applications and future developments. In S. Džeroski (ed.), Inductive databases and constraint-based data mining (pp. Seiten: 289-310). New York:Springer New York.

Rückert, U., Girschick, T., Buchwald, F., and Kramer, S. (2010). Adapted transfer of distance measures for quantitative structure-activity relationships. In B. Pfahringer (ed.), Discovery science : 13th international conference ; proceedings / DS 2010, Canberra, Australia, October 6 – 8, 2010 (pp. Seiten: 341-355). Berlin:Springer. Author/Publisher URL

Seeland, M., Girschick, T., Buchwald, F., and Kramer, S. (2010). Online structural graph clustering using frequent subgraph mining. In J. Balcazar (ed.), Machine learning and knowledge discovery in databases : European conference ; proceedings / ECML PKDD 2010, Barcelona, Spain, September 20 – 24, 2010. Vol. 3. Lecture notes in artificial intelligence (pp. Seiten: 213-228). Berlin:Springer. Author/Publisher URL

Conference Papers

Zheng, Z., Schmidt, B., Bourque, G. (2010). Prediction of low coverage prone regions for Illumina sequencing projects using a support vector machine. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 13-16. DOI

Granados, M., Ajdin, B., Wand, M., et al. (2010). Optimal HDR reconstruction with linear digital cameras. 2010 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 215-222. DOI

Schmidt, B., Maskell, D. (2010). Second Workshop on using Emerging Parallel Architectures. Procedia Computer Science, 1(1), 1015-1017. DOI

Shi, H., Schmidt, B., Liu, W., Müller-Wittig, W. (2010). Quality-score guided error correction for short-read sequencing data using CUDA. Procedia Computer Science, 1(1), 1129-1138. DOI

Bouros, P., Vassiliou, Y. (2010). Evaluating path queries over route collections. 2010 IEEE 26th International Conference on Data Engineering Workshops (ICDEW 2010), 325-328. DOI

Chang, W., Huang, Q.-X., Li, H., et al. (2010). Geometric Registration for Deformable Shapes. In U. Assarsson and D. Weiskopf (eds.), Eurographics (Tutorials). Eurographics Association. Author/Publisher URL

Kerber, J., Bokeloh, M., Wand, M., et al. (2010). Feature Preserving Sketching of Volume Data. In R. Koch, A. Kolb, and C. Rezk-Salama (eds.), VMV (pp. 195-202). Eurographics Association. Author/Publisher URL

Kramer, S. (2010). Learning Real-Time Automata from Multi-Attribute Event Logs. In R. G. Pensa, F. Cordero, C. Rouveirol, et al. (eds.), Proceedings of the 1st Workshop on Dynamic Networks and Knowledge Discovery, Barcelona, Spain, September 24, 2010 (Vols. 655). CEUR-WS.org. Author/Publisher URL

Marsalek, L., Dehof, A. K., Georgiev, I., et al. (2010). Real-time ray tracing of complex molecular scenes. 2010 14th International Conference Information Visualisation, 239-245.

Phillips, M., Georgiev, I., Dehof, A. K., et al. (2010). Measuring properties of molecular surfaces using ray casting. 2010 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW), 1-7.

von Dziegielewski, A., Erbes, R., Schömer, E. (2010). Conservative swept volume boundary approximation. In G. Elber, A. Fischer, J. Keyser, M.-S. Kim (eds.), ACM Symposium on Solid and Physical Modeling, Proceedings of the 15th ACM Symposium on Solid and Physical Modeling, SPM 2010, Haifa, Israel, September 1-3, 2010 (pp. 171-176). ACM. DOI Author/Publisher URL

Journal Articles

Althaus, E., Canzar, S., Ehrler, C., et al. (2010). Computing H/D-Exchange rates of single residues from data of proteolytic fragments. BMC Bioinformatics, 11(1). DOI

Liu, Y., Schmidt, B., Maskell, D. L. (2010). CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions. BMC Research Notes, 3(1). DOI

Ahmad, S., Chetty, M., Schmidt, B. (2010). Pattern Recognition in Bioinformatics. Pattern Recognition Letters, 31(14), 2071-2072. DOI

Brüllmann, D., Seelge, M., Schömer, E., et al. (2010). Alignment of cone beam computed tomography data using intra-oral fiducial markers. Computerized Medical Imaging and Graphics, 34, 543-552. DOI Author/Publisher URL

Schmidt, B. (ed.). (2010). Bioinformatics. Published online. DOI

Gross, D., Heil, U., Schulze, R., et al. (2010). GPU-Based Volume Reconstruction from Very Few Arbitrarily Aligned X-Ray Images. SIAM Journal on Scientific Computing, 31, 4204-4221. DOI Author/Publisher URL

Althaus, E., Hachenberger, P. (2010). Fully Automatic Trunk Packing with Free Placements. CoRR, abs/1008.3773.

Edelstein, M., Buchwald, F., Richter, L., Kramer, S. (2010). Integrating background knowledge from internet databases into predictive toxicology models. SAR and QSAR in environmental research, 21(1-2), Seiten: 21-35. Author/Publisher URL

Gregorius, B., Schaumlöffel, D., Hildebrandt, A., Tholey, A. (2010). Characterization of metal-labelled peptides by matrix-assisted laser desorption/ionization mass spectrometry and tandem mass spectrometry. Rapid Communications in Mass Spectrometry, 24, 3279-3289.

Hardy, B., Douglas, N., Helma, C., et al. (2010). Collaborative development of predictive toxicology applications. Journal of cheminformatics, 2, Art. 7. Author/Publisher URL

Hildebrandt, A., Dehof, A. K., Rurainski, A., et al. (2010). BALL-biochemical algorithms library 1.3. BMC bioinformatics, 11, 531-531.

Liu, Y., Schmidt, B., Liu, W., Maskell, D. L. (2010). CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units. PATTERN RECOGNITION LETTERS, 31(14), 2170-2177. DOI Author/Publisher URL

Liu, Y., Schmidt, B., Maskell, D. L. (2010). MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. BIOINFORMATICS, 26(16), 1958-1964. DOI Author/Publisher URL

Schmidt, J., Hapfelmeier, A., Müller, M., et al. (2010). Interpreting PET scans by structured patient data : a data mining case study in dementia research. Knowledge and information systems, 24(1), Seiten: 149-170. Author/Publisher URL

Shi, H., Schmidt, B., Liu, W., Mueller-Wittig, W. (2010). A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware. JOURNAL OF COMPUTATIONAL BIOLOGY, 17(4), 603-615. DOI Author/Publisher URL

Singh, K. K., Erkelenz, S., Rattay, S., et al. (2010). Human SAP18 mediates assembly of a splicing regulatory multiprotein complex via its ubiquitin-like fold. RNA, 16, 2442-2454.

Smialowski, P., Frishman, D., Kramer, S. (2010). Pitfalls of supervised feature selection. Bioinformatics, 26(3), Seiten: 440-443. Author/Publisher URL

Weggler, S., Rutka, V., Hildebrandt, A. (2010). A new numerical method for nonlocal electrostatics in biomolecular simulations. Journal of Computational Physics, 229, 4059-4074.

Wicker, J., Fenner, K., Ellis, L., et al. (2010). Predicting biodegradation products and pathways : a hybrid knowledge- and machine learning-based approach. Bioinformatics, 26(6), Seiten: 814-821. Author/Publisher URL

Wirawan, A., Kwoh, C. K., Schmidt, B. (2010). Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures. BIOINFORMATICS, 26(10), 1368-1369. DOI Author/Publisher URL

Zhang, F., Weggler, S., Ziller, M. J., et al. (2010). Universality of protein reentrant condensation in solution induced by multivalent metal ions. Proteins: Structure, Function, and Bioinformatics, 78, 3450-3457.

Zimek, A., Buchwald, F., Frank, E., Kramer, S. (2010). A study of hierarchical and flat classification of proteins. IEEE ACM transactions on computational biology and bioinformatics, 7(3), Seiten: 563-571. Author/Publisher URL

Other

Althaus, E., and Hachenberger, P. (2010). Fully Automatic Trunk Packing with Free Placements. In CoRR: Vol. abs/1008.3773. Author/Publisher URL

Book chapters

Ganzert, S., Kramer, S., Möller, K., et al. (2009). Prediction of mechanical lung parameters using gaussian process models. In C. Combi (ed.), Artificial intelligence in medicine : 12th Conference on Artificial Intelligence in Medicine, AIME 2009, Verona, Italy, July 18 – 22, 2009 (pp. Seiten: 380-384). Berlin u.a.:Springer. Author/Publisher URL

Lipowsky, C., Dranischnikow, E., Göttler, H., et al. (2009). Alignment of noisy and uniformly scaled time series. In S. S. Bhowmick (ed.), Database and expert systems applications : 20th international conference ; proceedings / DEXA 2009, Linz, Austria, August 31 – September 4, 2009 (pp. Seiten: 675-688). Berlin:Springer. DOI Author/Publisher URL

Maunz, A., Helma, C., Kramer, S. (2009). Large-scale graph mining using backbone refinement classes. In Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining (pp. Seiten: 617-626). New York, NY:ACM. Author/Publisher URL

Möller, K., Ganzert, S., Kramer, S., et al. (2009). Identifying mathematical models of the mechanically ventilated lung using equation discovery. In O. Dössel (ed.), World Congress on Medical Physics and Biomedical Engineering, September 7 – 12, 2009, Munich, Germany (pp. Seiten: 1524-1527). Berlin u.a.:Springer Berlin Heidelberg. Author/Publisher URL

Müller, M., Rosales, R., Steck, H., et al. (2009). Data-efficient information-theoretic test selection. In Artificial Intelligence in Medicine : 12th Conference on Artificial Intelligence in Medicine, AIME 2009, Verona, Italy, July 18-22, 2009 (pp. Seiten: 410-415). Berlin u.a.:Springer. Author/Publisher URL

Müller, M., Rosales, R., Steck, H., et al. (2009). Subgroup discovery for test selection : a novel approach and its application to breast cancer diagnosis. In N. M. Adams (ed.), Advances in intelligent data analysis VIII : 8th International Symposium on Intelligent Data Analysis, IDA 2009, Lyon, France, August 31 – September 2, 2009 (pp. Seiten: 119-130). Berlin u.a.:Springer.

Conference Papers

Lasowski, R., Tevs, A., Seidel, H.-P., Wand, M. (2009). A probabilistic framework for partial intrinsic symmetries in geometric data. 2009 IEEE 12th International Conference on Computer Vision, 963-970. DOI

Yongchao Liu, Schmidt, B., Maskell, D. L. (2009). MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA. 2009 20th IEEE International Conference on Application-specific Systems, Architectures and Processors, 121-128. DOI

Hasler, N., Rosenhahn, B., Thormahlen, T., et al. (2009). Markerless Motion Capture with unsynchronized moving cameras. 2009 IEEE Conference on Computer Vision and Pattern Recognition, 224-231. DOI

Meyer-Baese, A., Cappendijk, S., Althaus, E. (2009). Global uniform stability analysis of biological networks with different time-scales under perturbations. 2009 International Joint Conference on Neural Networks, 2098-2102. DOI

Tevs, A., Bokeloh, M., Wand, M., et al. (2009). Isometric registration of ambiguous and partial data. 2009 IEEE Conference on Computer Vision and Pattern Recognition, 1185-1192. DOI

Haixiang Shi, Schmidt, B., Weiguo Liu, Muller-Wittig, W. (2009). Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA. 2009 IEEE International Symposium on Parallel & Distributed Processing, 1-8. DOI

Yongchao Liu, Schmidt, B., Maskell, D. L. (2009). Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA. 2009 IEEE International Symposium on Parallel & Distributed Processing, 1-8. DOI

Althaus, E., Canzar, S., Ehrler, C., et al. (2009). Discrete Fitting of Hydrogen-Deuterium-Exchange-data of Overlapping Fragments. In H. R. Arabnia and M. Q. Yang (eds.), BIOCOMP (pp. 496-502). CSREA Press. Author/Publisher URL

Althaus, E., Dumitriu, D. (2009). Fast and Accurate Bounds on Linear Programs. In J. Vahrenhold (ed.), SEA (Vols. 5526, pp. 40-50). Springer. Author/Publisher URL

Althaus, E., Klau, G. W., Kohlbacher, O., et al. (2009). Integer Linear Programming in Computational Biology. In S. Albers, H. Alt, and S. Näher (eds.), Efficient Algorithms (Vols. 5760, pp. 199-218). Springer. Author/Publisher URL

Althaus, E., Kruglov, E., Weidenbach, C. (2009). Superposition Modulo Linear Arithmetic SUP(LA). In S. Ghilardi and R. Sebastiani (eds.), FroCoS (Vols. 5749, pp. 84-99). Springer. Author/Publisher URL

Bouros, P., Skiadopoulos, S., Dalamagas, T., et al. (2009). Evaluating Reachability Queries over Path Collections. In M. Winslett (ed.), Scientific and Statistical Database Management, 21st International Conference, SSDBM 2009, New Orleans, LA, USA, June 2-4, 2009, Proceedings (Vols. 5566, pp. 398-416). Springer. DOI

Chen, Y., Schmidt, B., Maskell, D. L. (2009). A Reconfigurable Bloom Filter Architecture for BLASTN. 40-49. DOI

Dranischnikow, E., Schömer, E., Schwanecke, U., et al. (2009). A parallel approach for alignment of multi-modal gridbased data. In H. Weghorn and P. T. Isaías (eds.), Proceedings of the IADIS International Conference Applied Computing 2009, 19-21 November, Rome, Italy, 2 Volumes (pp. 330-337). IADIS Press.

Gallenbacher, J. (2009). Abenteuer Informatik – “Informatik begreifen” wörtlich gemeint. In B. Koerber (ed.), Zukunft braucht Herkunft: 25 Jahre “INFOS – Informatik und Schule”. 13. GI-Fachtagung “Informatik und Schule”, 21. bis 24. September 2009 an der Freien Universität Berlin: Vol. P-156 (pp. 28-37). GI. Author/Publisher URL

Hemmer, M., Limbach, S., Schömer, E. (2009). Continued Work on the Computation of an Exact Arrangement of Quadrics.

Meyer-Bäse, A., Cappendijk, S., Althaus, E. (2009). Robust Stability Analysis of the Tryptophan Regulatory Network of E.Coli. In H. R. Arabnia and M. Q. Yang (eds.), BIOCOMP (pp. 510-513). CSREA Press. Author/Publisher URL

Schmidt, B., Maskell, D. L. (2009). Workshop on Using Emerging Parallel Architectures for Computational Science. In G. Allen, J. Nabrzyski, E. Seidel, et al. (eds.), ICCS (1) (Vols. 5544, pp. 861-863). Springer. Author/Publisher URL

Wach, C., Gallenbacher, J. (2009). Spielend Sortieren mit Las Vegas Cardsort. In B. Koerber (ed.), Zukunft braucht Herkunft: 25 Jahre “INFOS – Informatik und Schule”. 13. GI-Fachtagung “Informatik und Schule”, 21. bis 24. September 2009 an der Freien Universität Berlin: Vol. P-156 (pp. 256-267). GI. Author/Publisher URL

Wirawan, A., Schmidt, B., Kwoh, C. K. (2009). Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine. 954-963. DOI

Journal Articles

Duchrow, T., Shtatland, T., Guettler, D., et al. (2009). Enhancing navigation in biomedical databases by community voting and database-driven text classification. BMC bioinformatics, 10, Art. 317. Author/Publisher URL

Hussong, R., Gregorius, B., Tholey, A., Hildebrandt, A. (2009). Highly accelerated feature detection in proteomics data sets using modern graphics processing units. Bioinformatics, 25, 1937-1943.

Kneissl, B., Leonhardt, B., Hildebrandt, A., Tautermann, C. S. (2009). Revisiting automated G-protein coupled receptor modeling: the benefit of additional template structures for a neurokinin-1 receptor model. Journal of medicinal chemistry, 52, 3166-3173.

Liu, Y., Maskell, D. L., Schmidt, B. (2009). CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Research Notes, 2(1), 73-73. DOI

Mueller, A., Schneider, J. J., Schoemer, E. (2009). Packing a multidisperse system of hard disks in a circular environment. PHYSICAL REVIEW E, 79(2). DOI Author/Publisher URL

Oliver, T. F., Schmidt, B., Jakop, Y., Maskell, D. L. (2009). High Speed Biological Sequence Analysis With Hidden Markov Models on Reconfigurable Platforms. IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE, 13(5), 740-746. DOI Author/Publisher URL

Rurainski, A., Hildebrandt, A., Lenhof, H.-P. (2009). A consensus line search algorithm for molecular potential energy functions. Journal of computational chemistry, 30, 1499-1509.

Schmidt, B., Sinha, R., Beresford-Smith, B., Puglisi, S. J. (2009). A fast hybrid short read fragment assembly algorithm. BIOINFORMATICS, 25(17), 2279-2280. DOI Author/Publisher URL

Schneider, J. J., Mueller, A., Schoemer, E. (2009). Ultrametricity property of energy landscapes of multidisperse packing problems. PHYSICAL REVIEW E, 79(3). DOI Author/Publisher URL

Schroeder, J., Schroeder, H., Puglisi, S. J., et al. (2009). SHREC: a short-read error correction method. BIOINFORMATICS, 25(17), 2157-2163. DOI Author/Publisher URL

Wirawan, A., Schmidt, B., Zhang, H., Kwoh, C. K. (2009). High performance protein sequence database scanning on the Cell Broadband Engine. Sci. Program., 17, 97-111.

Book chapters

Artamonova, I., Kramer, S., Frishman, D. (2008). Data mining in genome annotation. In D. Frishman (ed.), Modern genome annotation (pp. Seiten: 191-212). Wien:Springer. Author/Publisher URL

Hapfelmeier, A., Schmidt, J., Müller, M., et al. (2008). Interpreting PET scans by structured patient data : a data mining case study in dementia research. In Eighth IEEE International Conference on Data Mining, 2008 : ICDM ’08 ; Pisa, Italy, 15 – 19 Dec. 2008 (pp. Seiten: 213-222). Piscataway, NJ:IEEE. Author/Publisher URL

Rückert, U., Kramer, S. (2008). Kernel-based inductive transfer. In W. Daelemans (ed.), Machine learning and knowledge discovery in databases. Pt. 2 (pp. Seiten: 220-233). Berlin u.a.:Springer. Author/Publisher URL

Wicker, J., Richter, L., Kessler, K., Kramer, S. (2008). SINDBAD and SiQL : an inductive database and query language in the relational model. In W. Daelemans (ed.), Machine learning and knowledge discovery in databases. Pt. 2 (pp. Seiten: 690-694). Berlin u.a.:Springer. Author/Publisher URL

Conference Papers

Adams, B., Ovsjanikov, M., Wand, M., et al. (2008). Meshless Modeling of Deformable Shapes and their Motion. [Print]. Computer animation. ACM SIGGRAPH Symposium on Computer Animation, 2008, 77-86. DOI

Althaus, E., Naujoks, R. (2008). Reconstructing Phylogenetic Networks with One Recombination. In C. C. McGeoch (ed.), WEA (Vols. 5038, pp. 275-288). Springer. Author/Publisher URL

Althaus, E., Canzar, S. (2008). LASA: A Tool for Non-heuristic Alignment of Multiple Sequences. In M. Elloumi, J. Küng, M. Linial, et al. (eds.), BIRD (Vols. 13, pp. 489-498). Springer. Author/Publisher URL

Althaus, E., Canzar, S., Elbassioni, K. M., et al. (2008). Approximating the Interval Constrained Coloring Problem. In J. Gudmundsson (ed.), SWAT (Vols. 5124, pp. 210-221). Springer. Author/Publisher URL

Althaus, E., Canzar, S., Emmett, M. R., et al. (2008). Computing H/D-exchange speeds of single residues from data of peptic fragments. In R. L. Wainwright, H. Haddad (eds.), SAC (pp. 1273-1277). ACM. Author/Publisher URL

Berner, A., Bokeloh, M., Wand, M., et al. (2008). A Graph-Based Approach to Symmetry Detection. In H.-C. Hege, D. H. Laidlaw, R. Pajarola, O. G. Staadt (eds.), VG/PBG@SIGGRAPH (pp. 1-8). Eurographics Association. Author/Publisher URL

Chen, C., Schmidt, B., Weiguo, L., Müller-Wittig, W. (2008). GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences. 448-459. DOI

Jenke, P., Wand, M., Straßer, W. (2008). Patch-Graph Reconstruction for Piecewise Smooth Surfaces. In O. Deussen, D. A. Keim, D. Saupe (eds.), VMV (pp. 3-12). Aka GmbH. Author/Publisher URL

Richter, L., Wicker, J., Kessler, K., Kramer, S. (2008). An inductive database and query language in the relational model. In A. Kemper, P. Valduriez, N. Mouaddib, et al. (eds.), EDBT 2008, 11th International Conference on Extending Database Technology, Nantes, France, March 25-29, 2008, Proceedings (Vols. 261, pp. 740-744). ACM. DOI

Sacharidis, D., Bouros, P., Sellis, T. K. (2008). Caching Dynamic Skyline Queries. In B. Ludäscher, N. Mamoulis (eds.), Scientific and Statistical Database Management, 20th International Conference, SSDBM 2008, Hong Kong, China, July 9-11, 2008, Proceedings (Vols. 5069, pp. 455-472). Springer. DOI

Zhang, H., Schmidt, B., Müller-Wittig, W. (2008). Accelerating BLASTP on the Cell Broadband Engine. 460-470. DOI

Journal Articles

Althaus, E., Canzar, S. (2008). A Lagrangian relaxation approach for the multiple sequence alignment problem. Journal of Combinatorial Optimization, 16(2), 127-154. DOI

Singh, D. T., Trehan, R., Schmidt, B., Bretschneider, T. (2008). Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment. BMC Bioinformatics, 9(S1). DOI

Schulze, R., Heil, U., Weinheimer, O., et al. (2008). Accurate registration of random radiographic projections based on three spherical references for the purpose of few-view 3D reconstruction. Medical Physics, 35, 546-555. DOI

Fenner, K., Gao, J., Kramer, S., et al. (2008). Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction. Bioinformatics, 24(18), Seiten: 2079-2085. Author/Publisher URL

Fröhler, S., Kramer, S. (2008). Inductive logic programming for gene regulation prediction. Machine Learning, 70(2-3), Seiten: 225-240. Author/Publisher URL

Gallenbacher, J. (2008). Abenteuer Informatik: Das Affenpuzzle. LOG IN, 28, 26-30.

Liu, W., Schmidt, B., Voss, G., Mueller-Wittig, W. (2008). Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA. COMPUTER PHYSICS COMMUNICATIONS, 179(9), 634-641. DOI Author/Publisher URL

Oliver, T., Yeow, L. Y., Schmidt, B. (2008). Integrating FPGA acceleration into HMMer. PARALLEL COMPUTING, 34(11), 681-691. DOI Author/Publisher URL

Rückert, U., Kramer, S. (2008). Margin-based first-order rule learning. Machine learning, 70(2-3), Seiten: 189-206. Author/Publisher URL

Schulz-Trieglaff, O., Hussong, R., Groepl, C., et al. (2008). Computational quantification of peptides from LC-MS data. Journal of Computational Biology, 15, 685-704.

Singh, A., Chen, C., Liu, W., et al. (2008). A hybrid computational grid architecture for comparative genomics. IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE, 12(2), 218-225. DOI Author/Publisher URL

Sturm, M., Bertsch, A., Groepl, C., et al. (2008). OpenMS-An open-source software framework for mass spectrometry. BMC BIOINFORMATICS, 9. DOI Author/Publisher URL

Sturm, M., Bertsch, A., Gröpl, C., et al. (2008). OpenMS – an open-source software framework for mass spectrometry. BMC bioinformatics, 9(163), Art. 163. Author/Publisher URL

Sturm, M., Bertsch, A., Gröpl, C., et al. (2008). OpenMS–an open-source software framework for mass spectrometry. BMC bioinformatics, 9, 1-11.

Wirawan, A., Kwoh, C. K., Hieu, N. T., Schmidt, B. (2008). CBESW: Sequence Alignment on the Playstation 3. BMC BIOINFORMATICS, 9. DOI Author/Publisher URL

Zhang, F., Skoda, M. W. A., Jacobs, R. M. J., et al. (2008). Reentrant condensation of proteins in solution induced by multivalent counterions. Physical review letters, 101, 148101-148101.

Book chapters

Schmidt, B., Chen, C., Liu, W. (2007). Hierarchical Grid Computing for High‐Performance Bioinformatics (pp. 87-121). Wiley. DOI

Dönigus, D., Endler, S., Fischlin, M., et al. (2007). Security of invertible media authentication schemes revisited. In Information hiding : 9th international workshop ; revised selected papers / IH 2007, Saint Malo, France, June 11 – 13, 2007 (pp. Seiten: 189-203). Berlin:Springer. Author/Publisher URL

Fröhler, S., Kramer, S. (2007). Inductive logic programming for gene regulation prediction. In S. Muggleton (ed.), Inductive logic programming : 16th international conference ; revised selected papers / ILP 2006, Santiago de Compostela, Spain, August 24 – 27, 2006 (pp. Seiten: 34-36). Berlin:Springer. Author/Publisher URL

Hildebrandt, A., Kohlbacher, O., Lenhof, H.-P. (2007). Modeling Protein-Protein and Protein-DNA Docking (pp. 601-650). Wiley-VCH Verlag GmbH.

Rückert, U., Kramer, S. (2007). Margin-based first-order rule learning. In S. Muggleton (ed.), Inductive Logic Programming : 16th International Conference, ILP 2006, Santiago de Compostela, Spain, August 24-27, 2006, Revised Selected Papers (pp. Seiten: 46-48). Berlin:Springer. Author/Publisher URL

Books

Gallenbacher, J. (2007). Abenteuer Informatik – IT zum Anfassen von Routenplaner bis Online-Banking. Spektrum.

Conference Papers

Dalamagas, T., Bouros, P., Galanis, T., et al. (2007). Mining user navigation patterns for personalizing topic directories. Proceedings of the 9th annual ACM international workshop on Web information and data management, 81-88. DOI

Liu, W., Muller-Wittig, W., Schmidt, B. (2007). Performance Predictions for General-Purpose Computation on GPUs. 2007 International Conference on Parallel Processing (ICPP 2007), 50-50. DOI

Feng, J., Chakraborty, S., Schmidt, B., et al. (2007). Fast Schedulability Analysis Using Commodity Graphics Hardware. 13th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (RTCSA 2007), 400-408. DOI

Althaus, E., Canzar, S. (2007). A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem. In A. W. M. Dress, Y. Xu, and B. Zhu (eds.), COCOA (Vols. 4616, pp. 267-278). Springer. Author/Publisher URL

Althaus, E., Baumann, T., Schömer, E., Werth, K. (2007). Trunk Packing Revisited. 420-432. DOI

Aung, Y. L., Maskell, D. L., Oliver, T. F., et al. (2007). C-Based Design Methodology for FPGA Implementation of ClustalW MSA. 11-18. DOI

Gallenbacher, J. (2007). Abenteuer Informatik oder “hands on” beim Problemlösemethoden. In S. E. Schubert (ed.), Didaktik der Informatik in Theorie und Praxis. INFOS 2007: 12. GI-Fachtagung Informatik und Schule, 19.-21. September 2007 in Siegen: Vol. P-112 (pp. 319-320). GI. Author/Publisher URL

Huang, Q.-X., Adams, B., Wand, M. (2007). Bayesian surface reconstruction via iterative scan alignment to an optimized prototype. In A. G. Belyaev and M. Garland (eds.), Symposium on Geometry Processing (Vols. 257, pp. 213-223). Eurographics Association. Author/Publisher URL

Hussong, R., Hildebrandt, A. (2007). The isotope wavelet: a signal theoretic framework for analyzing mass spectrometry data. Eleventh Annual International Conference on Research in Computational Molecular Biology, 67, 68-69.

Hussong, R., Tholey, A., Hildebrandt, A. (2007). Efficient analysis of mass spectrometry data using the isotope wavelet. COMPLIFE 2007: The Third International Symposium on Computational Life Science, 940, 139-149.

Oliver, T., Yeow, L. Y., Schmidt, B. (2007). High Performance Database Searching with HMMer on FPGAs. 2007 IEEE International Parallel and Distributed Processing Symposium, 1-7. DOI

Rajapakse, J. C., Schmidt, B., … Volkert, L. G. (eds.). (2007). Pattern Recognition in Bioinformatics, Second IAPR International Workshop, PRIB 2007, Singapore, October 1-2, 2007, Proceedings. PRIB, 4774.

Rajapakse, M., Lin, F. (2007). Predicting Binding Peptides with Simultaneous Optimization of Entropy and Evolutionary Distance. In J. C. Rajapakse, B. Schmidt, and L. G. Volkert (eds.), PRIB (Vols. 4774, pp. 349-355). Springer. Author/Publisher URL

Rückert, U., Kramer, S. (2007). Optimizing Feature Sets for Structured Data. In J. N. Kok, J. Koronacki, R. L. de Mántaras, et al. (eds.), Machine Learning: ECML 2007, 18th European Conference on Machine Learning, Warsaw, Poland, September 17-21, 2007, Proceedings (Vols. 4701, pp. 716-723). Springer. DOI

Schulz-Trieglaff, O., Hussong, R., Gröpl, C., et al. (2007). A fast and accurate algorithm for the quantification of peptides from mass spectrometry data. Annual International Conference on Research in Computational Molecular Biology, 473-487.

Wand, M., Berner, A., Bokeloh, M., et al. (2007). Interactive Editing of Large Point Clouds. In M. Botsch, R. Pajarola, B. Chen, M. Zwicker (eds.), PBG@Eurographics (pp. 37-45). Eurographics Association. Author/Publisher URL

Wand, M., Jenke, P., Huang, Q.-X., et al. (2007). Reconstruction of deforming geometry from time-varying point clouds. In A. G. Belyaev, M. Garland (eds.), Symposium on Geometry Processing (Vols. 257, pp. 49-58). Eurographics Association. Author/Publisher URL

Journal Articles

Eisenbrand, F., Funke, S., Karrenbauer, A., et al. (2007). Packing a Truck — Now with a twist!. International Journal of Computational Geometry & Applications, 17, 505-527. DOI Author/Publisher URL

Lin, F., Schröder, H., Schmidt, B. (2007). Solving the Bottleneck Problem in Bioinformatics Computing: An Architectural Perspective. The Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology, 48(3), 185-188. DOI

Schimmler, M., Schmidt, B., Lang, H.-W., Heithecker, S. (2007). An area-efficient bit-serial integer and GF(2n) multiplier. Microelectronic Engineering, 84(2), 253-259. DOI

Grégoire, M., Schömer, E. (2007). Interactive simulation of one-dimensional flexible parts. Computer-Aided Design, 39, 694-707. DOI Author/Publisher URL

Hildebrandt, A., Blossey, R., Rjasanow, S., et al. (2007). Electrostatic potentials of proteins in water: a structured continuum approach. Bioinformatics, 23, e99-e103.

Liu, W., Mueller-Wittig, W., Schmidt, B. (2007). Performance analysis of general-purpose computation on commodity graphics hardware:: A case study using bioinformatics. JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY, 48(3), 209-221. DOI Author/Publisher URL

Liu, W., Schmidt, B., Voss, G., Mueller-Wittig, W. (2007). Streaming algorithms for biological sequence alignment on GPUs. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 18(9), 1270-1281. DOI Author/Publisher URL

Rajapakse, M., Schmidt, B., Feng, L., Brusic, V. (2007). Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms. BMC BIOINFORMATICS, 8. DOI Author/Publisher URL

Rückert, U., Kramer, S. (2007). Margin-based first-order rule learning. Machine learning, 70(2/3), Seiten: 189-206. Author/Publisher URL

Schmidt, B. (2007). A survey of desktop grid applications for e-science. International Journal of Web and Grid Services, 3(3), 354-354. DOI

Sommer, S., Kramer, S. (2007). Three data mining techniques to improve lazy structure-activity relationships for non-congeneric compounds. Journal of chemical information and modeling, 47(6), Seiten: 2035-2043. Author/Publisher URL

Walters, J. P., Meng, X., Chaudhary, V., et al. (2007). MPI-HMMER-Boost: Distributed FPGA acceleration. JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY, 48(3), 223-238. DOI Author/Publisher URL

Book chapters

Fischer, J., Heun, V., and Kramer, S. (2006). Optimal string mining under frequency constraints. In J. Fürnkranz (ed.), Knowledge discovery in databases: PKDD 2006 ; 10th European Conference on Principles and Practice of Knowledge Discovery in Databases, Berlin, Germany, September 18 – 22, 2006 ; proceedings (pp. Seiten: 139-150). Berlin:Springer. Author/Publisher URL

Richter, L., Hechtl, S., and Kramer, S. (2006). Leveraging chemical background knowledge for the prediction of growth inhibition. In Sixth IEEE Symposium on Bioinformatics and Bioengineering, 2006 : BIBE 2006 ; [16 – 18 October 2006, Arlington, Virginia ; proceedings] (pp. Seiten: 319-324). Los Alamitos, Calif.:IEEE Computer Society. Author/Publisher URL

Richter, L., Rückert, U., and Kramer, S. (2006). Learning a predictive model for growth inhibition from the NCI DTP human tumor cell line screening data : does gene expression make a difference?. In R. B. Altman (ed.), Pacific Symposium on Biocomputing 2006 : Maui, Hawaii, 3 – 7 January 2006 (pp. Seiten: 596-607). Singapore:World Scientific Publ. Author/Publisher URL

Rückert, U., and Kramer, S. (2006). A statistical approach to rule learning. In W. W. Cohen (ed.), Proceedings / Twenty-Third International Conference on Machine Learning : [June 25 – 29, 2006, Pittsburgh, PA, USA] / [ACM] (pp. Seiten: 785-792). New York:ACM Press. Author/Publisher URL

Conference Papers

Althaus, E., Naujoks, R. (2006). Computing steiner minimum trees in Hamming metric. SODA, 172-181. Author/Publisher URL

Bokeloh, M., Wand, M. (2006). Hardware accelerated multi-resolution geometry synthesis. In M. Olano and C. H. Séquin (eds.), SI3D (pp. 191-198). ACM. Author/Publisher URL

Lange, E., Gropl, C., Reinert, K., et al. (2006). High-Accuracy Peak Picking of Proteomics Data Using Wavelet Techniques. Pacific Symposium on Biocomputing, 11, 243-254.

Lange, E., Gröpl, C., Kohlbacher, O., Hildebrandt, A. (2006). High-accuracy peak picking of proteomics data. Dagstuhl Seminar Proceedings.

Liu, W., Schmidt, B., Voss, G., Müller-Wittig, W. (2006). GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment. 363-374. DOI

Oliver, T. F., Schmidt, B., Jakop, Y., Maskell, D. L. (2006). Accelerating the Viterbi algorithm for Profile Hidden Markov Models using reconfigurable hardware. COMPUTATIONAL SCIENCE – ICCS 2006, PT 1, PROCEEDINGS, 3991, 522-529. Author/Publisher URL

Rajapakse, M., Schmidt, B., Brusic, V. (2006). Multi-objective evolutionary algorithm for discovering peptide binding motifs. APPLICATIONS OF EVOLUTIONARY COMPUTING, PROCEEDINGS, 3907, 149-158. Author/Publisher URL

Toll, H., Berger, P., Hofmann, A., et al. (2006). Glycosylation Patterns of Proteins Studied by Liquid Chromatography-Mass Spectrometry and Bioinformatic Tools. Dagstuhl Seminar Proceedings.

Weiguo Liu, Schmidt, B., Voss, G., et al. (2006). Bio-sequence database scanning on a GPU. Proceedings 20th IEEE International Parallel & Distributed Processing Symposium, 8 pp.-8 pp. DOI

Wirawan, A., Schmidt, B. (2006). Parallel Discovery of Transcription Factor Binding Sites. APCCAS, 700-703. Author/Publisher URL

Journal Articles

Eigenwillig, A., Kettner, L., Schömer, E., Wolpert, N. (2006). Exact, Efficient, and Complete Arrangement Computation for Cubic Curves. Comput. Geom. Theory Appl., 35, 36-73.

Althaus, E., Călinescu, G., Măndoiu, I. I., et al. (2006). Power Efficient Range Assignment for Symmetric Connectivity in Static Ad Hoc Wireless Networks. Wireless Networks, 12(3), 287-299. DOI

LIU, W. (2006). Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids. IEICE Transactions on Information and Systems, E89-D(2), 589-596. DOI

Althaus, E., Caprara, A., Lenhof, H.-P., Reinert, K. (2006). A branch-and-cut algorithm for multiple sequence alignment. Mathematical Programming, 105(2-3), 387-425. DOI

Schömer, E., Wolpert, N. (2006). An Exact and Efficient Approach for Computing a Cell in an Arrangement of Quadrics. Comput. Geom. Theory Appl., 33, 65-97.

Birzele, F., Kramer, S. (2006). A new representation for protein secondary structure prediction based on frequent patterns. Bioinformatics, 22(21), Seiten: 2628-2634. Author/Publisher URL

Blockeel, H., Jensen, D., Kramer, S. (2006). Introduction to the special issue on multi-relational data mining and statistical relational learning. Machine learning, 62(1), Seiten: 3-5. Author/Publisher URL

Chen, C., Schmidt, B. (2006). Constructing large suffix trees on a computational grid. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 66(12), 1512-1523. DOI Author/Publisher URL

Keller, A., Ludwig, N., Comtesse, N., et al. (2006). A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors. BMC bioinformatics, 7, 539-539.

Küntzer, J., Blum, T., Gerasch, A., et al. (2006). BN++–A biological information system. Journal of Integrative Bioinformatics, 3, 148-161.

Lenhof, H.-P., Kohlbacher, O., Kaufmann, M., et al. (2006). BN++-A Biological Information System. http://journal. imbio. de/index. php? paper_id= 34.

Liu, W., Schmidt, B. (2006). Parallel pattern-based systems for computational biology: A case study. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 17(8), 750-763. Author/Publisher URL

Moll, A., Hildebrandt, A., Lenhof, H.-P., Kohlbacher, O. (2006). BALLView: a tool for research and education in molecular modeling. Bioinformatics, 22, 365-366.

Oliver, T., Schmidt, B., Maskell, D., et al. (2006). High-speed Multiple Sequence Alignment on a reconfigurable platform. International Journal of Bioinformatics Research and Applications, 2(4), 394-394. DOI

Perl, J., Endler, S. (2006). Training- and contest-scheduling in endurance sports by means of course profiles and PerPot-based analysis. International journal of computer science in sport, 5(2), Seiten: 42-46.

Toll, H., Berger, P., Hofmann, A., et al. (2006). Glycosylation patterns of human chorionic gonadotropin revealed by liquid chromatography-mass spectrometry and bioinformatics. Electrophoresis, 27, 2734-2746.

Book chapters

Dong, L., Frank, E., and Kramer, S. (2005). Ensembles of balanced nested dichotomies for multi-class problems. In Knowledge discovery in databases: PKDD 2005 : 9th European Conference on Principles and Practice of Knowledge Discovery in Databases, Porto, Portugal, October 3 – 7, 2005 (pp. Seiten: 84-95). Berlin:Springer. Author/Publisher URL

Fischer, J., Heun, V., and Kramer, S. (2005). Fast frequent string mining using suffix arrays. In J. Han (ed.), Proceedings / Fifth IEEE International Conference on Data Mining, ICDM 2005 : 27 – 30 November 2005, Houston, Texas (pp. Seiten: 609-612). Los Alamitos, Calif.:IEEE Computer Society. Author/Publisher URL

Harput, V., Kaindl, H., and Kramer, S. (2005). Extending function point analysis to object-oriented requirements specifications. In 2005 11th International Symposium on Software Metrics (METRICS) : 19 – 22 September 2005, Como, Italy / [IEEE] (pp. Seiten: 10-39). Piscataway, NJ:IEEE Operations Center. Author/Publisher URL

Kramer, S., and Helma, C. (2005). Machine learning and data mining. In C. Helma (ed.), Predictive toxicology (pp. Seiten: 223-254). Boca Raton:Taylor & Francis.

Conference Papers

Oliver, T., Schmidt, B., Maskell, D. (2005). Hyper customized processors for bio-sequence database scanning on FPGAs. Proceedings of the 2005 ACM/SIGDA 13th international symposium on Field-programmable gate arrays, 229-237. DOI

Biber, P., Fleck, S., Busch, F., et al. (2005). 3D modeling of indoor environments by a mobile platform with a laser scanner and panoramic camera. EUSIPCO, 1-4. Author/Publisher URL

Chen, C., Schmidt, B. (2005). Parallel Construction of Large Suffix Trees on a PC Cluster. In J. C. Cunha and P. D. Medeiros (eds.), Euro-Par (Vols. 3648, pp. 1227-1236). Springer. Author/Publisher URL

Georgii, E., Richter, L., Rückert, U., Kramer, S. (2005). Analyzing microarray data using quantitative association rules. ECCB/JBI’05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28 – October 1, 2005, 129-129. DOI Author/Publisher URL

Harput, V., Kaindl, H., Kramer, S. (2005). Extending Function Point Analysis of Object-Oriented Requirements Specifications. 11th IEEE International Symposium on Software Metrics (METRICS 2005), 19-22 September 2005, Como Italy, 39-39. DOI

Kramer, S., Aufschild, V., Hapfelmeier, A., et al. (2005). Inductive Databases in the Relational Model: The Data as the Bridge. In F. Bonchi and J.-F. Boulicaut (eds.), Knowledge Discovery in Inductive Databases, 4th International Workshop, KDID 2005, Porto, Portugal, October 3, 2005, Revised Selected and Invited Papers (Vols. 3933, pp. 124-138). Springer. DOI

Kramer, S., … Pfahringer, B. (eds.). (2005). Inductive Logic Programming, 15th International Conference, ILP 2005, Bonn, Germany, August 10-13, 2005, Proceedings. 3625. DOI

Oliver, T. F., Schmidt, B., Maskell, D. L., Vinod, A. P. (2005). A reconfigurable architecture for scanning biosequence databases. ISCAS (5), 4799-4802. Author/Publisher URL

Rajapakse, M., Wyse, L., Schmidt, B., Brusic, V. (2005). Deriving matrix of peptide-MHC interactions in diabetic mouse by genetic algorithm. INTELLIGENT DATA ENGINEERING AND AUTOMATED LEARNING IDEAL 2005, PROCEEDINGS, 3578, 440-447. Author/Publisher URL

Wetekam, G., Staneker, D., Kanus, U., Wand, M. (2005). A hardware architecture for multi-resolution volume rendering. In M. Meißner and B.-O. Schneider (eds.), Graphics Hardware (pp. 45-51). Eurographics Association. Author/Publisher URL

Yanto, J., Oliver, T. F., Schmidt, B., Maskell, D. L. (2005). Biological Sequence Analysis with Hidden Markov Models on an FPGA. In T. Srikanthan, J. Xue, and C.-H. Chang (eds.), Asia-Pacific Computer Systems Architecture Conference (Vols. 3740, pp. 429-439). Springer. Author/Publisher URL

Journal Articles

Schulze, R. K. W., Weinheimer, O., Brüllmann, D. D., et al. (2005). Software for automated application of a reference-based method for a posteriori determination of the effective radiographic imaging geometry. Dentomaxillofacial Radiology, 34, 205-211. DOI Author/Publisher URL

Althaus, E., Funke, S., Har-Peled, S., et al. (2005). Approximating k-hop minimum-spanning trees. Operations Research Letters, 33(2), 115-120. DOI

Chen, C. X., Schmidt, B. (2005). An adaptive grid implementation of DNA sequence alignment. FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE, 21(7), 988-1003. DOI Author/Publisher URL

Comtesse, N., Zippel, A., Walle, S., et al. (2005). Complex humoral immune response against a benign tumor: frequent antibody response against specific antigens as diagnostic targets. Proceedings of the National Academy of Sciences, 102, 9601-9606.

Georgii, E., Richter, L., Rückert, U., Kramer, S. (2005). Analyzing microarray data using quantitative association rules. Bioinformatics, 21(Suppl. 2), Seiten: ii123-ii129. Author/Publisher URL

Liu, T., Schmidt, B. (2005). Parallel RNA secondary structure prediction using stochastic context-free grammars. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 17(14), 1669-1685. DOI Author/Publisher URL

Moll, A., Hildebrandt, A., Lenhof, H.-P., Kohlbacher, O. (2005). BALLView: An object-oriented molecular visualization and modeling framework. Journal of computer-aided molecular design, 19, 791-800.

Oliver, T. F., Schmidt, B., Maskell, D. L. (2005). Reconfigurable architectures for bio-sequence database scanning on FPGAs. IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS, 52(12), 851-855. DOI Author/Publisher URL

Oliver, T., Schmidt, B., Nathan, D., et al. (2005). Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. BIOINFORMATICS, 21(16), 3431-3432. DOI Author/Publisher URL

Book chapters

Frank, E., and Kramer, S. (2004). Ensembles of nested dichotomies for multi-class problems. In R. Greiner (ed.), Proceedings / Twenty-First International Conference on Machine Learning : [July 4 – 8, 2004, Banff, Alberta, Canada] (pp. Seiten: 305-312). Banff, Alberta, Canada:.

Rückert, U., and Kramer, S. (2004). Frequent free tree discovery in graph data. In H. M. Haddad (ed.), Applied computing 2004 : proceedings of the 2004 ACM Symposium on Applied Computing, Nicosia, Cyprus, March 14 – 17, 2004 (pp. Seiten: 564-570). New York, NY:Association for Computing Machinery. Author/Publisher URL

Rückert, U., and Kramer, S. (2004). Towards tight bounds for rule learning. In R. Greiner (ed.), Proceedings / Twenty-First International Conference on Machine Learning : [July 4 – 8, 2004, Banff, Alberta, Canada] (pp. Seiten: 711-718). Banff, Alberta, Canada:. Author/Publisher URL

Rückert, U., Richter, L., and Kramer, S. (2004). Quantitative association rules based on half-spaces : an optimization approach. In R. Rastogi (ed.), Proceedings / Fourth IEEE International Conference on Data Mining, 2004, ICDM 2004 : 1 – 4 Nov. 2004, [Brighton, United Kingdom] (pp. Seiten: 507-510). Los Alamitos, Calif.:IEEE Computer Society. Author/Publisher URL

Conference Papers

Althaus, E., Eisenbrand, F., Funke, S., Mehlhorn, K. (2004). Point containment in the integer hull of a polyhedron. In J. I. Munro (ed.), SODA (pp. 929-933). SIAM. Author/Publisher URL

Althaus, E., Karamanis, N., Koller, A. (2004). Computing Locally Coherent Discourses. In D. Scott, W. Daelemans, and M. A. Walker (eds.), ACL (pp. 399-406). ACL. Author/Publisher URL

Bouros, P., Dalamagas, T., Sellis, T. K., Terrovitis, M. (2004). PatManQL: A Language to Manipulate Patterns and Data in Hierarchical Catalogs. In Y. Theodoridis and P. Vassiliadis (eds.), Proceedings of the Intl. Workshop on Pattern Representation and Management, Heraklion, Greece, March 18, 2004, PaRMa 2004 was held in conjunction with the 9th Int. Conference on Extending Database Technology (EDBT 2004) (Vols. 96). CEUR-WS.org. Author/Publisher URL

Chen, C., Schmidt, B. (2004). Load Balancing for Hierarchical Grid Computing: A Case Study. In L. Bougé and V. K. Prasanna (eds.), HiPC (Vols. 3296, pp. 353-362). Springer. Author/Publisher URL

Liu, W. G., Schmidt, B. (2004). A generic parallel pattern-based system for bioinformatics. EURO-PAR 2004 PARALLEL PROCESSING, PROCEEDINGS, 3149, 989-996. Author/Publisher URL

Liu, W., Schmidt, B. (2004). A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications. In L. Bougé and V. K. Prasanna (eds.), HiPC (Vols. 3296, pp. 91-100). Springer. Author/Publisher URL

Ramakrishnan, R., Agrawal, R., Freytag, J.-C., et al. (2004). Data Mining: The Next Generation. In R. Agrawal, J.-C. Freytag, and R. Ramakrishnan (eds.), Perspectives Workshop: Data Mining: The Next Generation, 11.07. – 16.07.2004 (Vols. 04292). Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany. Author/Publisher URL

Wand, M. (2004). Punktbasierte Multiskalendarstellung.: Vol. D-5 (T. Dreier, O. Günther, S. Hölldobler, et al., eds.; pp. 183-192). GI. Author/Publisher URL

Wand, M., Straßer, W. (2004). Multi-Resolution Sound Rendering. In M. H. Gross, H. Pfister, M. Alexa, and S. Rusinkiewicz (eds.), PBG (pp. 3-11). Eurographics Association. Author/Publisher URL

Wands, B. (2004). Thoughts on Hesse, Digital Art and Visual Music: excerpts from the “variations” artist statements (1999-2003). In S. Gollifer (ed.), SIGGRAPH Art Gallery (pp. 128-130). ACM. Author/Publisher URL

Journal Articles

Schimmler *, M., Schmidt, B., Lang ‡, H.-W. (2004). A bit-serial floating-point unit for a massively parallel system on a chip. Parallel Algorithms and Applications, 19(2-3), 79-95. DOI

Blockeel, H., Dzeroski, S., Kompare, B., et al. (2004). Experiments in predicting biodegradability. Applied artificial intelligence, 18(2), Seiten: 157-181. Author/Publisher URL

Helma, C., Kramer, S., De Raedt, L. (2004). Data mining and machine learning techniques for the identification of mutagenicity inducing substructures and structure activity relationships of noncongeneric compounds. Journal of chemical information and modeling, 44(4), Seiten: 1402-1411. Author/Publisher URL

Hildebrandt, A., Blossey, R., Rjasanow, S., et al. (2004). Novel formulation of nonlocal electrostatics. Physical review letters, 93, 108104-108104.

Kaindl, H., Kramer, S., Hailing, M., Harput, V. (2004). Interactive metamodel-compliance checking of requirements in a semiformal representation. INCOSE International Symposium, 14(1), Seiten: 1154-1167. Author/Publisher URL

Kramer, S., Kaindl, H. (2004). Coupling and cohesion metrics for knowledge-based systems using frames and rules. ACM transactions on software engineering and methodology, 13(3), Seiten: 332-358. Author/Publisher URL

Schmidt, B., Feng, L., Laud, A., Santoso, Y. (2004). Development of distributed bioinformatics applications with GMP. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 16(9), 945-959. DOI Author/Publisher URL

Book chapters

De Raedt, L., and Kramer, S. (2003). Inductive databases for bio- and chemo-informatics. In P. Frasconi (ed.), Artificial intelligence and heuristic methods in bioinformatics : [proceedings of the NATO Advanced Study Institute on Artificial Intelligence and Heuristic Methods in Bioinformatics, 1 – 11 October 2001, San Miniato, Italy] (pp. Seiten: 193-207). Amsterdam:IOS Press.

Rückert, U., and Kramer, S. (2003). Stochastic local search in k-Term DNF learning. In T. Fawcett (ed.), Proceedings / Twentieth International Conference on Machine Learning : [August 21 – 24, 2003, Washington, DC, USA]. Vol. 2 (pp. Seiten: 648-655). Menlo Park, Calif.:AAAI Press.

Conference Papers

Ahmad, I., Jonker, P., Schmidt, B., Uhl, A. (2003). Topic Introduction. In H. Kosch, L. Böszörményi, and H. Hellwagner (eds.), Euro-Par (Vols. 2790, pp. 850-850). Springer. Author/Publisher URL

Althaus, E., Calinescu, G., Mandoiu, I. I., et al. (2003). Power efficient range assignment in ad-hoc wireless networks. WCNC, 1889-1894. Author/Publisher URL

Althaus, E., Polzin, T., Daneshmand, S. V. (2003). Improving Linear Programming Approaches for the Steiner Tree Problem. In K. Jansen, M. Margraf, M. Mastrolilli, and J. D. P. Rolim (eds.), WEA (Vols. 2647, pp. 1-14). Springer. Author/Publisher URL

Amor, M., Boo, M., del Rio, A., et al. (2003). A new algorithm for high-speed projection in point rendering applications. Euromicro Symposium on Digital System Design, 2003. Proceedings., 338-345. DOI

Cehn, Schmidt. (2003). Computing large-scale alignments on a multi-cluster. Proceedings IEEE International Conference on Cluster Computing CLUSTR-03, 38-45. DOI

Kaindl, H., Kramer, S., Hailing, M., Harput, V. (2003). Metamodel-Compliance Checking of Requirements in a Semiformal Representation. In J. Eder and T. Welzer (eds.), The 15th Conference on Advanced Information Systems Engineering (CAiSE ’03), Klagenfurt/Velden, Austria, 16-20 June, 2003, CAiSE Forum, Short Paper Proceedings, Information Systems for a Connected Society (Vols. 74). CEUR-WS.org. Author/Publisher URL

Rückert, U., Kramer, S. (2003). Generalized Version Space Trees. In J.-F. Boulicaut and S. Dzeroski (eds.), Proceedings of the Second International Workshop on Inductive Databases, 22 September, Cavtat-Dubrovnik, Croatia (pp. 119-129). Rudjer Boskovic Institute, Zagreb, Croatia.

Schimmler, M., Schmidt, B., Lang, H.-W. (2003). Design of a Bit-Serial Floating Point Unit for a Fine Grained Parallel Processor Array. In H. R. Arabnia and Y. Mun (eds.), PDPTA (pp. 255-261). CSREA Press. Author/Publisher URL

Schimmler, M., Schmidt, B., Lang, H.-W., Heithecker, S. (2003). An Area-Efficient Bit-Serial Integer Multiplier. In H. R. Arabnia and L. T. Yang (eds.), VLSI (pp. 131-137). CSREA Press. Author/Publisher URL

Wand, M., Straßer, W. (2003). Multi-Resolution Point-Sample Raytracing. Graphics Interface, 139-148. Author/Publisher URL

Weiguo Liu, Schmidt. (2003). Parallel design pattern for computational biology and scientific computing applications. Proceedings IEEE International Conference on Cluster Computing CLUSTR-03, 456-459. DOI

Journal Articles

Althaus, E., Duchier, D., Koller, A., et al. (2003). An efficient graph algorithm for dominance constraints. Journal of Algorithms, 48(1), 194-219. DOI

Helma, C., Kramer, S. (2003). A Survey of the predictive toxicology challenge 2000-2001. Bioinformatics, 19(10), Seiten: 1179-1182. Author/Publisher URL

Toivonen, H., Srinivasan, A., King, R., et al. (2003). Statistical evaluation of the predictive toxicology challenge 2000-2001. Bioinformatics, 19(10), Seiten: 1183-1193. Author/Publisher URL

Book chapters

Kersting, K., Raiko, T., Kramer, S., and De Raedt, L. (2002). Towards discovering structural signatures of Protein folds based on logical hidden Markov models. In R. B. Altman (ed.), Pacific Symposium on Biocomputing 2003 : Kauai, Hawaii, 3 – 7 January 2003 (pp. Seiten: 192-203). River Edge, NJ:World Scientific Publ.

Rückert, U., Kramer, S., and De Raedt, L. (2002). Phase transitions and stochastic local search in k-term DNF learning. In T. Elomaa (ed.), Machine learning : proceedings / ECML 2002, 13th European Conference on Machine Learning, Helsinki, Finland, August 19 – 23, 2002 (pp. Seiten: 405-417). Berlin:Springer. Author/Publisher URL

Conference Papers

Althaus, E., Bockmayr, A., Elf, M., et al. (2002). SCIL – Symbolic Constraints in Integer Linear Programming. In R. H. Möhring and R. Raman (eds.), ESA (Vols. 2461, pp. 75-87). Springer. Author/Publisher URL

Althaus, E., Caprara, A., Lenhof, H.-P., Reinert, K. (2002). Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics. ECCB, 4-16. Author/Publisher URL

Althaus, E., Fink, C. (2002). A Polyhedral Approach to Surface Reconstruction from Planar Contours. In W. J. Cook and A. S. Schulz (eds.), IPCO (Vols. 2337, pp. 258-272). Springer. Author/Publisher URL

Bringmann, B., Kramer, S., Neubarth, F., et al. (2002). Transformation-Based Regression. In C. Sammut and A. G. Hoffmann (eds.), Machine Learning, Proceedings of the Nineteenth International Conference (ICML 2002), University of New South Wales, Sydney, Australia, July 8-12, 2002 (pp. 59-66). Morgan Kaufmann.

Klein, J., Krokowski, J., Fischer, M., et al. (2002). The randomized sample tree: a data structure for interactive walkthroughs in externally stored virtual environments. In J. Shi, L. F. Hodges, H. Sun, and Q. Peng (eds.), VRST (pp. 137-146). ACM. Author/Publisher URL

Schmidt, B., Schroder, H., Schimmler, M. (2002). Massively parallel solutions for molecular sequence analysis. Proceedings 16th International Parallel and Distributed Processing Symposium, 8 pp-8 pp. DOI

Journal Articles

Ganzert, S., Guttmann, J., Kersting, K., et al. (2002). Analysis of respiratory pressure-volume curves in intensive care medicine using inductive machine learning. Artif. Intell. Med., 26(1-2), 69-86. DOI Author/Publisher URL

Althaus, E., Kohlbacher, O., Lenhof, H.-P., Müller, P. (2002). A Combinatorial Approach to Protein Docking with Flexible Side Chains. Journal of Computational Biology, 9(4), 597-612. DOI

Ganzert, S., Guttmann, J., Kersting, K., et al. (2002). Analysis of respiratory pressure-volume curves in intensive care medicine using symbolic machine learning. Artificial intelligence in medicine, 26(1/2), Seiten: 69-86. Author/Publisher URL

Hildebrandt, A., Kohlbacher, O., Blossey, R., Lenhof, H.-P. (2002). Using nonlocal electrostatics for solvation free energy computations: ions and small molecules. arXiv preprint physics/0212074.

Kramer, S., Frank, E., Helma, C. (2002). Fragment generation and support vector machines for inducing SARs. SAR and QSAR in environmental research, 13(5), Seiten: 509-523. Author/Publisher URL

Schmidt, B., Schröder, H., Schimmler, M. (2002). A hybrid architecture for bioinformatics. FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE, 18(6), 855-862. DOI Author/Publisher URL

Book chapters

De Raedt, L., and Kramer, S. (2001). The Levelwise Version Space Algorithm and Its Application to Molecular Fragment Finding. In B. Nebel (ed.), Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence : Seattle, Washington, August 4 – 10, 2001 / IJCAI-01. Vol. 2 (pp. Seiten: 853-859). San Francisco, Calif.:Kaufmann.

Kaindl, H., Kramer, S., and Hailing, M. (2001). An interactive guide through a defined modelling process. In A. Blandford (ed.), People and computers XV : interaction without frontiers ; joint proceedings of HCI 2001 and IHM 2001 (pp. Seiten: 107-123). London:Springer. Author/Publisher URL

Kramer, S. (2001). Demand-driven construction of structural features in ILP. In C. Rouveirol (ed.), Inductive logic programming : 11th international conference ; proceedings / ILP 2001, Strasbourg, France, September 9 – 11, 2001 (pp. Seiten: 132-141). Berlin:Springer. Author/Publisher URL

Kramer, S., and De Raedt, L. (2001). Feature construction with version spaces for biochemical applications. In B. Nebel (ed.), Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence : Seattle, Washington, August 4 – 10, 2001 / IJCAI-01. Vol. 1 (pp. Seiten: 258-265). San Francisco, Calif.:Kaufmann.

Kramer, S., and Widmer, G. (2001). Inducing classification and regression trees in first order logic. In S. Džeroski (ed.), Relational data mining : with 69 tables (pp. Seiten: 140-159). Berlin:Springer. Author/Publisher URL

Kramer, S., De Raedt, L., and Helma, C. (2001). Molecular feature mining in HIV data. In F. Provost (ed.), Proceedings of the Seventh ACM SIGKDD International Conference on Knowledge Discovery and Data Mining / KDD-2001 : August 26 – 29, 2001, San Francisco, CA, USA (pp. Seiten: 136-143). New York, NY:ACM. Author/Publisher URL

Kramer, S., Lavrač, N., and Flach, P. (2001). Propositionalization approaches to relational data mining. In S. Džeroski (ed.), Relational data mining : with 69 tables (pp. Seiten: 262-291). Berlin:Springer. Author/Publisher URL

Conference Papers

Althaus, E., Duchier, D., Koller, A., et al. (2001). An efficient algorithm for the configuration problem of dominance graphs. In S. R. Kosaraju (ed.), SODA (pp. 815-824). ACM/SIAM. Author/Publisher URL

Kohlbacher, O., Burchardt, A., Moll, A., et al. (2001). A NMR-spectra-based scoring function for protein docking. Proceedings of the fifth annual international conference on Computational biology, 184-192.

Schmidt, B., Schröder, H., Schimmler, M. (2001). Protein Sequence Comparison on the Instruction Systolic Array. In V. E. Malyshkin (ed.), PaCT (Vols. 2127, pp. 498-509). Springer. Author/Publisher URL

Schmidt, B., Schröder, H., Schimmler, M. (2001). Scanning Biosequence Databases on a Hybrid Parallel Architecture. In R. Sakellariou, J. A. Keane, J. R. Gurd, and L. Freeman (eds.), Euro-Par (Vols. 2150, pp. 360-370). Springer. Author/Publisher URL

Wand, M., Fischer, M., Peter, I., et al. (2001). The randomized z-buffer algorithm: interactive rendering of highly complex scenes. In L. Pocock (ed.), SIGGRAPH (pp. 361-370). ACM. Author/Publisher URL

Journal Articles

Althaus, E., Mehlhorn, K. (2001). Traveling Salesman-Based Curve Reconstruction in Polynomial Time. SIAM Journal on Computing, 31(1), 27-66. DOI

Gottmann, E., Kramer, S., Pfahringer, B., Helma, C. (2001). Data quality in predictive toxicology : reproducibility of rodent carcinogenicity experiments. Environmental health perspectives, 109(5), Seiten: 509-514. Author/Publisher URL

Helma, C., King, R. D., Kramer, S., Srinivasan, A. (2001). The Predictive Toxicology Challenge 2000-2001. Bioinform., 17, 107-108. DOI Author/Publisher URL

Kohlbacher, O., Burchardt, A., Moll, A., et al. (2001). Structure prediction of protein complexes by an NMR-based protein docking algorithm. Journal of biomolecular NMR, 20, 15-21.

Kramer, S., Widmer, G., Pfahringer, B., De Groeve, M. (2001). Prediction of ordinal classes using regression trees. Fundamenta informaticae, 47(1/2), Seiten: 1-13.

Schmidt, B., Schröder, H. (2001). A Hybrid Architecture for Multimedia Processors. Comput. Artif. Intell., 20, 225-244.

Schmidt, B., Schröder, H., Schimmler, M. (2001). Tomographic Image Reconstruction on the Instruction Systolic Array. Comput. Artif. Intell., 20, 27-42.

Conference Papers

Althaus, E., and Mehlhorn, K. (2000). TSP-based curve reconstruction in polynomial time. In D. B. Shmoys (ed.), SODA (pp. 686-695). ACM/SIAM. Author/Publisher URL

Althaus, E., Kohlbacher, O., Lenhof, H.-P., and Müller, P. (2000). A combinatorial approach to protein docking with flexible side-chains. In R. Shamir, S. Miyano, S. Istrail, et al. (eds.), RECOMB (pp. 15-24). ACM. Author/Publisher URL

Fürnkranz, J., Pfahringer, B., Kaindl, H., and Kramer, S. (2000). Learning to Use Operational Advice. In W. Horn (ed.), ECAI 2000, Proceedings of the 14th European Conference on Artificial Intelligence, Berlin, Germany, August 20-25, 2000 (pp. 291-295). IOS Press.

Kramer, S., and Frank, E. (2000). Bottom-Up Propositionalization. In J. Cussens, A. M. Frisch (eds.), Inductive Logic Programming, 10th International Conference, ILP 2000, Work-in-progress reports, London, UK, July 2000, Proceedings (Vols. 35). CEUR-WS.org. Author/Publisher URL

Kramer, S., Widmer, G., Pfahringer, B., and Groeve, M. de. (2000). Prediction of Ordinal Classes Using Regression Trees. In Z. W. Ras, S. Ohsuga (eds.), Foundations of Intelligent Systems, 12th International Symposium, ISMIS 2000, Charlotte, NC, USA, October 11-14, 2000, Proceedings (Vols. 1932, pp. 426-434). Springer. DOI

Schmidt, B. (2000). Design of a parallel accelerator for volume rendering. EURO-PAR 2000 PARALLEL PROCESSING, PROCEEDINGS, 1900, 1095-1104. Author/Publisher URL

Journal Articles

Schömer, E., Sellen, J., Teichmann, M., and Chee, Y. (2000). Smallest Enclosing Cylinders. Algorithmica, 27, 170-186. DOI

Kramer, S. (2000). Thesis: Relational learning vs. propositionalization. AI Commun., 13, 275-276. Author/Publisher URL

Schmidt, B., and Schimmler, M. (2000). KPROC – An Instruction Systolic Architecture for Parallel Prefix Applications. Scalable Comput. Pract. Exp., 3.

Theses/Disssertations

Althaus, E. (2000). Curve reconstruction and the traveling salesman problem. Author/Publisher URL

Conference Papers

Dzeroski, S., Blockeel, H., Kompare, B., et al. (1999). Experiments in Predicting Biodegradability. In S. Dzeroski and P. A. Flach (eds.), Inductive Logic Programming, 9th International Workshop, ILP-99, Bled, Slovenia, June 24-27, 1999, Proceedings (Vols. 1634, pp. 80-91). Springer. DOI

Kaindl, H., Kramer, S., Diallo, P. S. N. (1999). Semiautomatic Generation of Glossary Links: A Practical Solution. In J. Westbomke, U. K. Wiil, J. J. Leggett, et al. (eds.), HYPERTEXT ’99, Proceedings of the 10th ACM Conference on Hypertext and Hypermedia: Returning to Our Diverse Roots, February 21-25, 1999, Darmstadt, Germany (pp. 3-12). ACM. DOI

Schmidt, B., Schimmler, M. (1999). A parallel accelerator architecture for multimedia video compression. EURO-PAR’99: PARALLEL PROCESSING, 1685, 950-960. Author/Publisher URL

Kaindl, H., Kramer, S., Afonso, L. M. (1998). Combining Structure Search and Content Search for the World-Wide Web. In R. M. Akscyn (ed.), HYPERTEXT ’98. Proceedings of the Ninth ACM Conference on Hypertext and Hypermedia: Links, Objects, Time and Space – Structure in Hypermedia Systems, June 20-24, 1998, Pittsburgh, PA, USA (pp. 217-224). ACM. DOI

Kaindl, H., Kramer, S., Kacsich, R. (1998). A Case Study of Decomposing Functional Requirements Using Scenarios. 3rd International Conference on Requirements Engineering (ICRE ’98), Putting Requirements Engineering to Practice, April 6-10, 1998, Colorado Springs, CO, USA, Proceedings, 156-163. DOI

Kramer, S., Pfahringer, B., Helma, C. (1998). Stochastic Propositionalization of Non-determinate Background Knowledge. In D. Page (ed.), Inductive Logic Programming, 8th International Workshop, ILP-98, Madison, Wisconsin, USA, July 22-24, 1998, Proceedings (Vols. 1446, pp. 80-94). Springer. DOI Author/Publisher URL

Schmidt, B., Schimmler, M., Schröder, H. (1998). Long operand arithmetic on instruction systolic computer architectures and its application in RSA cryptography. EURO-PAR ’98 PARALLEL PROCESSING, 1470, 916-922. Author/Publisher URL

Kramer, S., Kaindl, H., Schlee, S. (1997). Can We Benefit from Metrics in KBS Development?. Proceedings of the Fifteenth International Joint Conference on Artificial Intelligence, IJCAI 97, Nagoya, Japan, August 23-29, 1997, 2 Volumes, 662-667.

Kramer, S., Pfahringer, B., Helma, C. (1997). Mining for Causes of Cancer: Machine Learning Experiments at Various Levels of Detail. In D. Heckerman, H. Mannila, D. Pregibon (eds.), Proceedings of the Third International Conference on Knowledge Discovery and Data Mining (KDD-97), Newport Beach, California, USA, August 14-17, 1997 (pp. 223-226). AAAI Press. Author/Publisher URL

Schmidt, B., Schimmler, M., Schröder, H. (1997). Morphological Hough Transform on the Instruction Systolic Array. In C. Lengauer, M. Griebl, S. Gorlatch (eds.), Euro-Par (Vols. 1300, pp. 798-806). Springer. Author/Publisher URL

Kramer, S. (1996). Structural Regression Trees. In W. J. Clancey, D. S. Weld (eds.), Proceedings of the Thirteenth National Conference on Artificial Intelligence and Eighth Innovative Applications of Artificial Intelligence Conference, AAAI 96, IAAI 96, Portland, Oregon, USA, August 4-8, 1996, Volume 1 (pp. 812-819). AAAI Press / The MIT Press. Author/Publisher URL

Kramer, S., Pfahringer, B. (1996). Efficient Search for Strong Partial Determinations. In E. Simoudis, J. Han, U. M. Fayyad (eds.), Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96), Portland, Oregon, USA (pp. 371-374). AAAI Press. Author/Publisher URL

Journal Articles

Buck, M., and Schömer, E. (1998). Interactive rigid body manipulation with obstacle contacts. The Journal of Visualization and Computer Animation, 9, 243-257. Author/Publisher URL

Althaus, E., and Mehlhorn, K. (1998). Maximum network flow with floating point arithmetic. Information Processing Letters, 66(3), 109-113. DOI

Follert, F., Schömer, E., Sellen, J., et al. (1997). Computing a Largest Empty Anchored Cylinder, and Related Problems. International Journal of Computational Geometry & Applications, 07, 563-580. DOI Author/Publisher URL

Schmidt, B., Schimmler, M., Schröder, H. (1997). Morphological hough transform on the instruction systolic array. 798-806. DOI