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ORCIDUlf Leser
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- affiliation: Humboldt University of Berlin, Germany
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2020 – today
- 2025
[i40]Fabian Lehmann, Jonathan Bader, Friedrich Tschirpke, Ninon De Mecquenem, Ansgar Lößer, Sören Becker, Katarzyna Ewa Lewinska, Lauritz Thamsen, Ulf Leser:
WOW: Workflow-Aware Data Movement and Task Scheduling for Dynamic Scientific Workflows. CoRR abs/2503.13072 (2025)- [i39]Kathleen West, Fabian Lehmann, Vasilis Bountris, Ulf Leser, Yehia Elkhatib, Lauritz Thamsen:
Exploring the Potential of Carbon-Aware Execution for Scientific Workflows. CoRR abs/2503.13705 (2025) - [i38]Arik Ermshaus, Patrick Schäfer, Ulf Leser:
CLaP - State Detection from Time Series. CoRR abs/2504.01783 (2025) - 2024
- [j91]Arik Ermshaus, Michael Piechotta, Gina Rüter, Ulrich Keilholz
, Ulf Leser, Manuela Benary:
preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology. Bioinform. 40(3) (2024) - [j90]Birgitta König-Ries, Ulf Leser, Bernhard Seeger, Sirko Schindler:
Beyond Silos: Next Steps in Research Data Management Report from the 2024 Spring Symposium of FG Datenbanken. Datenbank-Spektrum 24(2): 171-173 (2024) - [j89]Jonathan Bader, Fabian Lehmann, Lauritz Thamsen, Ulf Leser, Odej Kao:
Lotaru: Locally predicting workflow task runtimes for resource management on heterogeneous infrastructures. Future Gener. Comput. Syst. 150: 171-185 (2024) - [j88]Florian Schintke, Khalid Belhajjame, Ninon De Mecquenem, David Frantz, Vanessa Emanuela Guarino, Marcus Hilbrich, Fabian Lehmann, Paolo Missier, Rebecca Sattler, Jan Arne Sparka, Daniel T. Speckhard, Hermann Stolte, Anh Duc Vu, Ulf Leser:
Validity constraints for data analysis workflows. Future Gener. Comput. Syst. 157: 82-97 (2024) - [j87]Arik Ermshaus, Patrick Schäfer, Ulf Leser:
Raising the ClaSS of Streaming Time Series Segmentation. Proc. VLDB Endow. 17(8): 1953-1966 (2024) - [j86]Patrick Schäfer, Ulf Leser:
Discovering Leitmotifs in Multidimensional Time Series. Proc. VLDB Endow. 18(2): 377-389 (2024) - [c122]Arik Ermshaus, Patrick Schäfer, Ulf Leser:
Multivariate Human Activity Segmentation: Systematic Benchmark with ClaSP. AALTD@ECML/PKDD 2024: 18-34 - [c121]Oguz Serbetçi, Xing David Wang, Ulf Leser:
HU-WBI at BioASQ12B Phase A: Exploring Rank Fusion of Dense Retrievers and Re-rankers. CLEF (Working Notes) 2024: 269-275 - [c120]Fabian Lehmann, Jonathan Bader, Ninon De Mecquenem, Xing Wang, Vasilis Bountris, Florian Friederici, Ulf Leser, Lauritz Thamsen:
Ponder: Online Prediction of Task Memory Requirements for Scientific Workflows. e-Science 2024: 1-10 - [c119]Ninon De Mecquenem, Simon Bosse, Vasilis Bountris, Somayeh Mohammadi, Knut Reinert, Ulf Leser:
CuttleFlow: Infrastructure-Specific Workflow Adaption for Improved Reusability. e-Science 2024: 1-10 - [c118]Somayeh Mohammadi, Latif Pourkarimi, Manuel Zschäbitz, Tristan Aretz, Ninon De Mecquenem, Ulf Leser, Knut Reinert:
Optimizing Job/Task Granularity for Metagenomic Workflows in Heterogeneous Cluster Infrastructures. EDBT/ICDT Workshops 2024 - [c117]Marc-Andre Schulz, Jan Philipp Albrecht, Alpay Yilmaz, Alexander Koch, Dagmar Kainmüller, Ulf Leser, Kerstin Ritter:
TLIMB - A Transfer Learning Framework for IMage Analysis of the Brain. EDBT/ICDT Workshops 2024 - [i37]Samuele Garda, Ulf Leser:
BELHD: Improving Biomedical Entity Linking with Homonoym Disambiguation. CoRR abs/2401.05125 (2024) - [i36]Mario Sänger, Samuele Garda, Xing David Wang, Leon Weber-Genzel, Pia Droop, Benedikt Fuchs, Alan Akbik, Ulf Leser:
HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools. CoRR abs/2402.12372 (2024) - [i35]Fabian Lehmann, Jonathan Bader, Ninon De Mecquenem, Xing Wang, Vasilis Bountris, Florian Friederici, Ulf Leser, Lauritz Thamsen:
Ponder: Online Prediction of Task Memory Requirements for Scientific Workflows. CoRR abs/2408.00047 (2024) - [i34]Patrick Schäfer, Ulf Leser:
Discovering Leitmotifs in Multidimensional Time Series. CoRR abs/2410.12293 (2024) - [i33]Rafael Ferreira da Silva, Deborah Bard, Kyle Chard, Shaun De Witt, Ian T. Foster, Tom Gibbs, Carole A. Goble, William F. Godoy, Johan Gustafsson, Utz-Uwe Haus, Stephen Hudson, Shantenu Jha, Laila Los, Drew Paine, Frédéric Suter, Logan T. Ward, Sean R. Wilkinson, Marcos Amaris, Yadu N. Babuji, Jonathan Bader, Riccardo Balin, Daniel Balouek, Sarah J. Beecroft, Khalid Belhajjame, Rajat Bhattarai, Wes Brewer, Paul Brunk, Silvina Caíno-Lores, Henri Casanova, Daniela Cassol, Jared Coleman, Tainã Coleman, Iacopo Colonnelli, Anderson Andrei Da Silva, Daniel de Oliveira, Pascal Elahi, Nour Elfaramawy, Wael R. Elwasif, Brian Etz, Thomas Fahringer, Wesley Ferreira, Rosa Filgueira, Jacob Fosso Tande, Luiz Gadelha, Andy Gallo, Daniel Garijo, Yiannis Georgiou, Philipp Gritsch, Patricia Grubel, Amal Gueroudji, Quentin Guilloteau, Carlo Hamalainen, Rolando P. Hong Enriquez, Lauren Huet, Kevin Hunter Kesling, Paula Iborra, Shiva Jahangiri, Jan Janssen, Joe Jordan, Sehrish Kanwal, Liliane N. O. Kunstmann, Fabian Lehmann, Ulf Leser, Chen Li, Peini Liu, Jakob Lüttgau, Richard Lupat, José M. Fernández, Ketan Maheshwari, Tanu Malik, Jack Marquez, Motohiko Matsuda, Doriana Medic, Somayeh Mohammadi, Alberto Mulone, John-Luke Navarro, Kin Wai Ng, Klaus Nölp, Bruno de Paula Kinoshita, Ryan Prout, Michael R. Crusoe, Sashko Ristov, Stefan A Robila, Daniel Rosendo, Billy Rowell, Jedrzej Rybicki, Hector Sanchez, Nishant Saurabh, Sumit Kumar Saurav, Tom Scogland, Dinindu Senanayake, Woong Shin, Raül Sirvent, Tyler J. Skluzacek, Barry Sly-Delgado, Stian Soiland-Reyes, Abel Souza, Renan Souza, Domenico Talia, Nathan R. Tallent:
Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows. CoRR abs/2410.14943 (2024) - [i32]Patrick Schäfer, Jakob Brand, Ulf Leser, Botao Peng, Themis Palpanas:
Fast and Exact Similarity Search in less than a Blink of an Eye. CoRR abs/2411.17483 (2024) - 2023
- [j85]Samuele Garda, Leon Weber-Genzel, Robert Martin, Ulf Leser:
BELB: a biomedical entity linking benchmark. Bioinform. 39(10) (2023) - [j84]Leon Weber, Fabio Barth, Leonie Lorenz, Fabian Konrath, Kirsten Huska, Jana Wolf, Ulf Leser:
PEDL+: protein-centered relation extraction from PubMed at your fingertip. Bioinform. 39(11) (2023) - [j83]Arik Ermshaus, Patrick Schäfer, Ulf Leser:
ClaSP: parameter-free time series segmentation. Data Min. Knowl. Discov. 37(3): 1262-1300 (2023) - [j82]Patrick Schäfer, Ulf Leser:
WEASEL 2.0: a random dilated dictionary transform for fast, accurate and memory constrained time series classification. Mach. Learn. 112(12): 4763-4788 (2023) - [j81]Somayeh Mohammadi, Latif Pourkarimi, Felix Droop, Ninon De Mecquenem, Ulf Leser, Knut Reinert:
A mathematical programming approach for resource allocation of data analysis workflows on heterogeneous clusters. J. Supercomput. 79(17): 19019-19048 (2023) - [c116]Arik Ermshaus, Patrick Schäfer, Anthony J. Bagnall, Thomas Guyet, Georgiana Ifrim, Vincent Lemaire, Ulf Leser, Colin Leverger, Simon Malinowski:
Human Activity Segmentation Challenge @ ECML/PKDD'23. AALTD@ECML/PKDD 2023: 3-13 - [c115]Fabian Lehmann, Jonathan Bader, Friedrich Tschirpke, Lauritz Thamsen, Ulf Leser:
How Workflow Engines Should Talk to Resource Managers: A Proposal for a Common Workflow Scheduling Interface. CCGrid 2023: 166-179 - [c114]Anh Duc Vu, Jan Arne Sparka, Ninon De Mecquenem, Timo Kehrer, Ulf Leser, Lars Grunske:
Design by Contract Revisited in the Context of Scientific Data Analysis Workflows. e-Science 2023: 1-2 - [c113]Anh Duc Vu, Jan Arne Sparka, Ninon De Mecquenem, Timo Kehrer, Ulf Leser, Lars Grunske:
Contract-Driven Design of Scientific Data Analysis Workflows. e-Science 2023: 1-10 - [c112]Arik Ermshaus, Sunita Singh, Ulf Leser:
Time Series Segmentation Applied to a New Data Set for Mobile Sensing of Human Activities. EDBT/ICDT Workshops 2023 - [c111]Fabio Barth, Leon Weber-Genzel, Ulf Leser:
Comparing Humans and Algorithms in Feature Ranking: A Case-Study in the Medical Domain. LWDA 2023: 442-453 - [c110]Oguz Serbetçi, Ulf Leser:
Applicability of Models Trained on Generated Clinical German Datasets on Out-domain Data. LWDA 2023: 521-525 - [c109]Jonathan Bader, Jim Belak, Matthew T. Bement, Matthew Berry, Robert Carson, Daniela Cassol, Stephen Chan, John Coleman, Kastan Day, Alejandro Duque, Kjiersten Fagnan, Jeff Froula, Shantenu Jha, Daniel S. Katz, Piotr Kica, Volodymyr V. Kindratenko, Edward Kirton, Ramani Kothadia, Daniel E. Laney, Fabian Lehmann, Ulf Leser, Sabina Licholai, Maciej Malawski, Mario Melara, Elais Player Jackson, Matthew Rolchigo, Setareh Sarrafan, Seung-Jin Sul, Abdullah Syed, Lauritz Thamsen, Mikhail Titov, Matteo Turilli, Silvina Caíno-Lores, Anirban Mandal:
Novel Approaches Toward Scalable Composable Workflows in Hyper-Heterogeneous Computing Environments. SC Workshops 2023: 2097-2108 - [d3]Fabian Lehmann, Jonathan Bader, Friedrich Tschirpke, Lauritz Thamsen, Ulf Leser:
Nextflow with the Common Workflow Scheduler Interface for Kubernetes. Zenodo, 2023
- [d2]Fabian Lehmann, Jonathan Bader, Friedrich Tschirpke, Lauritz Thamsen, Ulf Leser:
Common Workflow Scheduler for Kubernetes. Zenodo, 2023 - [d1]Fabian Lehmann, Jonathan Bader, Friedrich Tschirpke, Lauritz Thamsen, Ulf Leser:
Common Workflow Scheduler Evaluation with Nextflow and Kubernetes. Zenodo, 2023 - [i31]Patrick Schäfer, Ulf Leser:
WEASEL 2.0 - A Random Dilated Dictionary Transform for Fast, Accurate and Memory Constrained Time Series Classification. CoRR abs/2301.10194 (2023) - [i30]Fabian Lehmann, Jonathan Bader, Friedrich Tschirpke, Lauritz Thamsen, Ulf Leser:
How Workflow Engines Should Talk to Resource Managers: A Proposal for a Common Workflow Scheduling Interface. CoRR abs/2302.07652 (2023) - [i29]Florian Schintke, Ninon De Mecquenem, David Frantz, Vanessa Emanuela Guarino, Marcus Hilbrich, Fabian Lehmann, Rebecca Sattler, Jan Arne Sparka, Daniel T. Speckhard, Hermann Stolte, Anh Duc Vu, Ulf Leser:
Validity Constraints for Data Analysis Workflows. CoRR abs/2305.08409 (2023) - [i28]Samuele Garda, Leon Weber-Genzel, Robert Martin, Ulf Leser:
BELB: a Biomedical Entity Linking Benchmark. CoRR abs/2308.11537 (2023) - [i27]Jonathan Bader, Fabian Lehmann, Lauritz Thamsen, Ulf Leser, Odej Kao:
Lotaru: Locally Predicting Workflow Task Runtimes for Resource Management on Heterogeneous Infrastructures. CoRR abs/2309.06918 (2023) - [i26]Arik Ermshaus, Patrick Schäfer, Ulf Leser:
Raising the ClaSS of Streaming Time Series Segmentation. CoRR abs/2310.20431 (2023) - [i25]Mario Sänger, Ninon De Mecquenem, Katarzyna Ewa Lewinska, Vasilis Bountris, Fabian Lehmann, Ulf Leser, Thomas Kosch:
Large Language Models to the Rescue: Reducing the Complexity in Scientific Workflow Development Using ChatGPT. CoRR abs/2311.01825 (2023) - [i24]Fabian Lehmann, Jonathan Bader, Lauritz Thamsen, Ulf Leser:
The Common Workflow Scheduler Interface: Status Quo and Future Plans. CoRR abs/2311.15929 (2023) - [i23]Rosa M. Badia, Laure Berti-Équille, Rafael Ferreira da Silva, Ulf Leser:
Integrating HPC, AI, and Workflows for Scientific Data Analysis (Dagstuhl Seminar 23352). Dagstuhl Reports 13(8): 129-164 (2023) - 2022
- [j80]Samuele Garda, Freyda Lenihan-Geels, Sebastian Proft, Stefanie Hochmuth, Markus Schuelke, Dominik Seelow, Ulf Leser:
RegEl corpus: identifying DNA regulatory elements in the scientific literature. Database J. Biol. Databases Curation 2022(2022) (2022) - [j79]Leon Weber, Mario Sänger, Samuele Garda, Fabio Barth, Christoph Alt, Ulf Leser:
Chemical-protein relation extraction with ensembles of carefully tuned pretrained language models. Database J. Biol. Databases Curation 2022(2022) (2022) - [j78]Patrick Schäfer, Ulf Leser:
Motiflets - Simple and Accurate Detection of Motifs in Time Series. Proc. VLDB Endow. 16(4): 725-737 (2022) - [c108]Arik Ermshaus, Patrick Schäfer, Ulf Leser:
Window Size Selection in Unsupervised Time Series Analytics: A Review and Benchmark. AALTD@ECML/PKDD 2022: 83-101 - [c107]Xing David Wang, Ulf Leser, Leon Weber:
BEEDS: Large-Scale Biomedical Event Extraction using Distant Supervision and Question Answering. BioNLP@ACL 2022: 298-309 - [c106]Jonathan Bader, Fabian Lehmann, Alexander Groth, Lauritz Thamsen, Dominik Scheinert, Jonathan Will, Ulf Leser, Odej Kao:
Reshi: Recommending Resources for Scientific Workflow Tasks on Heterogeneous Infrastructures. IPCCC 2022: 269-274 - [c105]Jonathan Bader, Fabian Lehmann, Lauritz Thamsen, Jonathan Will, Ulf Leser, Odej Kao:
Lotaru: Locally Estimating Runtimes of Scientific Workflow Tasks in Heterogeneous Clusters. SSDBM 2022: 1:1-1:12 - [i22]Jonathan Bader, Fabian Lehmann, Lauritz Thamsen, Jonathan Will, Ulf Leser, Odej Kao:
Lotaru: Locally Estimating Runtimes of Scientific Workflow Tasks in Heterogeneous Clusters. CoRR abs/2205.11181 (2022) - [i21]Patrick Schäfer, Ulf Leser:
Motiflets - Fast and Accurate Detection of Motifs in Time Series. CoRR abs/2206.03735 (2022) - [i20]Arik Ermshaus, Patrick Schäfer, Ulf Leser:
ClaSP - Parameter-free Time Series Segmentation. CoRR abs/2207.13987 (2022) - [i19]Jonathan Bader, Fabian Lehmann, Alexander Groth, Lauritz Thamsen, Dominik Scheinert, Jonathan Will, Ulf Leser, Odej Kao:
Reshi: Recommending Resources for Scientific Workflow Tasks on Heterogeneous Infrastructures. CoRR abs/2208.07905 (2022) - 2021
- [j77]Mario Sänger, Ulf Leser:
Large-scale entity representation learning for biomedical relationship extraction. Bioinform. 37(2): 236-242 (2021) - [j76]Leon Weber, Mario Sänger, Jannes Münchmeyer, Maryam Habibi, Ulf Leser, Alan Akbik:
HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition. Bioinform. 37(17): 2792-2794 (2021) - [j75]Ulf Leser, Marcus Hilbrich, Claudia Draxl, Peter Eisert, Lars Grunske, Patrick Hostert, Dagmar Kainmüller, Odej Kao, Birte Kehr, Timo Kehrer, Christoph Koch, Volker Markl, Henning Meyerhenke, Tilmann Rabl, Alexander Reinefeld, Knut Reinert, Kerstin Ritter, Björn Scheuermann, Florian Schintke, Nicole Schweikardt, Matthias Weidlich:
The Collaborative Research Center FONDA. Datenbank-Spektrum 21(3): 255-260 (2021) - [c104]Matthias Vogt, Ulf Leser, Alan Akbik:
Early Detection of Sexual Predators in Chats. ACL/IJCNLP (1) 2021: 4985-4999 - [c103]Mario Sänger, Leon Weber, Ulf Leser:
WBI at MEDIQA 2021: Summarizing Consumer Health Questions with Generative Transformers. BioNLP@NAACL-HLT 2021: 86-95 - [c102]Patrick Schäfer, Arik Ermshaus, Ulf Leser:
ClaSP - Time Series Segmentation. CIKM 2021: 1578-1587 - [c101]Fabian Lehmann, David Frantz, Sören Becker, Ulf Leser, Patrick Hostert:
FORCE on Nextflow: Scalable Analysis of Earth Observation Data on Commodity Clusters. CIKM Workshops 2021 - [c100]Leon Weber, Jannes Münchmeyer, Samuele Garda, Ulf Leser:
Extend, don't rebuild: Phrasing conditional graph modification as autoregressive sequence labelling. EMNLP (1) 2021: 1213-1224 - [c99]Rafael Ferreira da Silva, Henri Casanova, Kyle Chard, Ilkay Altintas, Rosa M. Badia, Bartosz Balis, Tainã Coleman, Frederik Coppens, Frank Di Natale, Bjoern Enders, Thomas Fahringer, Rosa Filgueira, Grigori Fursin, Daniel Garijo, Carole A. Goble, Dorran Howell, Shantenu Jha, Daniel S. Katz, Daniel E. Laney, Ulf Leser, Maciej Malawski, Kshitij Mehta, Loïc Pottier, Jonathan Ozik, J. Luc Peterson, Lavanya Ramakrishnan, Stian Soiland-Reyes, Douglas Thain, Matthew Wolf:
A Community Roadmap for Scientific Workflows Research and Development. WORKS 2021: 81-90 - [i18]Rafael Ferreira da Silva, Henri Casanova, Kyle Chard, Tainã Coleman, Dan Laney, Dong H. Ahn, Shantenu Jha, Dorran Howell, Stian Soiland-Reyes, Ilkay Altintas, Douglas Thain, Rosa Filgueira, Yadu N. Babuji, Rosa M. Badia, Bartosz Balis, Silvina Caíno-Lores, Scott Callaghan, Frederik Coppens, Michael R. Crusoe, Kaushik De, Frank Di Natale, Tu Mai Anh Do, Bjoern Enders, Thomas Fahringer, Anne Fouilloux, Grigori Fursin, Alban Gaignard, Alex Ganose, Daniel Garijo, Sandra Gesing, Carole A. Goble, Adil Hasan, Sebastiaan Huber, Daniel S. Katz, Ulf Leser, Douglas Lowe, Bertram Ludäscher, Ketan Maheshwari, Maciej Malawski, Rajiv Mayani, Kshitij Mehta, André Merzky, Todd S. Munson, Jonathan Ozik, Loïc Pottier, Sashko Ristov, Mehdi Roozmeh, Renan Souza, Frédéric Suter, Benjamín Tovar, Matteo Turilli, Karan Vahi, Alvaro Vidal-Torreira, Wendy R. Whitcup, Michael Wilde, Alan R. Williams, Matthew Wolf, Justin M. Wozniak:
Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development. CoRR abs/2106.05177 (2021) - [i17]Rafael Ferreira da Silva, Henri Casanova, Kyle Chard, Ilkay Altintas, Rosa M. Badia, Bartosz Balis, Tainã Coleman, Frederik Coppens, Frank Di Natale, Bjoern Enders, Thomas Fahringer, Rosa Filgueira, Grigori Fursin, Daniel Garijo, Carole A. Goble, Dorran Howell, Shantenu Jha, Daniel S. Katz, Daniel E. Laney, Ulf Leser, Maciej Malawski, Kshitij Mehta, Loïc Pottier, Jonathan Ozik, J. Luc Peterson, Lavanya Ramakrishnan, Stian Soiland-Reyes, Douglas Thain, Matthew Wolf:
A Community Roadmap for Scientific Workflows Research and Development. CoRR abs/2110.02168 (2021) - 2020
- [j74]Maryam Habibi, Astrid Rheinländer, Wolfgang Thielemann, Robert Adams, Peter Fischer, Sylvia Krolkiewicz, David Luis Wiegandt, Ulf Leser:
PatSeg: A Sequential Patent Segmentation Approach. Big Data Res. 19-20: 100133 (2020) - [j73]Leon Weber, Jannes Münchmeyer, Tim Rocktäschel, Maryam Habibi, Ulf Leser:
HUNER: improving biomedical NER with pretraining. Bioinform. 36(1): 295-302 (2020) - [j72]Leon Weber, Kirsten Thobe, Oscar Arturo Migueles Lozano, Jana Wolf, Ulf Leser:
PEDL: extracting protein-protein associations using deep language models and distant supervision. Bioinform. 36(Supplement-1): i490-i498 (2020) - [j71]Patrick Schäfer, Ulf Leser:
TEASER: early and accurate time series classification. Data Min. Knowl. Discov. 34(5): 1336-1362 (2020) - [j70]Maryam Habibi, Johannes Starlinger, Ulf Leser:
DeepTable: a permutation invariant neural network for table orientation classification. Data Min. Knowl. Discov. 34(6): 1963-1983 (2020) - [j69]Theodoros Chondrogiannis, Panagiotis Bouros, Johann Gamper, Ulf Leser, David B. Blumenthal:
Finding k-shortest paths with limited overlap. VLDB J. 29(5): 1023-1047 (2020) - [c98]Xing David Wang, Leon Weber, Ulf Leser:
Biomedical Event Extraction as Multi-turn Question Answering. LOUHI@EMNLP 2020: 88-96 - [c97]Maryam Habibi, Johannes Starlinger, Ulf Leser:
TabSim: A Siamese Neural Network for Accurate Estimation of Table Similarity. IEEE BigData 2020: 930-937 - [i16]Christopher Schiefer, Marc Bux, Jörgen Brandt, Clemens Messerschmidt, Knut Reinert, Dieter Beule, Ulf Leser:
Portability of Scientific Workflows in NGS Data Analysis: A Case Study. CoRR abs/2006.03104 (2020) - [i15]Leon Weber, Mario Sänger, Jannes Münchmeyer, Maryam Habibi, Ulf Leser, Alan Akbik:
HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition. CoRR abs/2008.07347 (2020) - [i14]Maryam Habibi, Johannes Starlinger, Ulf Leser:
TabSim: A Siamese Neural Network for Accurate Estimation of Table Similarity. CoRR abs/2008.10856 (2020)
2010 – 2019
- 2019
- [j68]Jurica Seva, David Luis Wiegandt, Julian Goetze, Mario Lamping, Damian Rieke, Reinhold Schaefer, Patrick Jähnichen, Madeleine Kittner, Steffen Pallarz, Johannes Starlinger, Ulrich Keilholz, Ulf Leser:
VIST - a Variant-Information Search Tool for precision oncology. BMC Bioinform. 20(1): 429:1-429:11 (2019) - [j67]Carl Witt, Marc Bux, Wladislaw Gusew, Ulf Leser:
Predictive performance modeling for distributed batch processing using black box monitoring and machine learning. Inf. Syst. 82: 33-52 (2019) - [c96]Leon Weber, Pasquale Minervini, Jannes Münchmeyer, Ulf Leser, Tim Rocktäschel:
NLProlog: Reasoning with Weak Unification for Question Answering in Natural Language. ACL (1) 2019: 6151-6161 - [c95]Jurica Seva, Julian Goetze, Mario Lamping, Damian Tobias Rieke, Reinhold Schaefer, Ulf Leser:
Information Retrieval for Precision Oncology. BTW 2019: 533-536 - [c94]Mario Sänger, Leon Weber, Madeleine Kittner, Ulf Leser:
Classifying German Animal Experiment Summaries with Multi-lingual BERT at CLEF eHealth 2019 Task 1. CLEF (Working Notes) 2019 - [c93]Stefan Sprenger, Patrick Schäfer, Ulf Leser:
BB-Tree: A practical and efficient main-memory index structure for multidimensional workloads. EDBT 2019: 169-180 - [c92]Stefan Sprenger, Patrick Schäfer, Ulf Leser:
BB-Tree: A Main-Memory Index Structure for Multidimensional Range Queries. ICDE 2019: 1566-1569 - [c91]Carl Witt, Jakob van Santen, Ulf Leser:
Learning Low-Wastage Memory Allocations for Scientific Workflows at IceCube. HPCS 2019: 233-240 - [c90]Carl Witt, Dennis Wagner, Ulf Leser:
Feedback-Based Resource Allocation for Batch Scheduling of Scientific Workflows. HPCS 2019: 761-768 - [i13]Leon Weber, Pasquale Minervini, Jannes Münchmeyer, Ulf Leser, Tim Rocktäschel:
NLProlog: Reasoning with Weak Unification for Question Answering in Natural Language. CoRR abs/1906.06187 (2019) - [i12]Patrick Schäfer, Ulf Leser:
TEASER: Early and Accurate Time Series Classification. CoRR abs/1908.03405 (2019) - 2018
- [j66]Sebastian Wandelt, Xiaoqian Sun, Ulf Leser:
Column-wise compression of open relational data. Inf. Sci. 457-458: 48-61 (2018) - [j65]Johannes Starlinger, Steffen Pallarz, Jurica Seva, Damian Rieke, Christine Sers, Ulrich Keilholz, Ulf Leser:
Variant information systems for precision oncology. BMC Medical Informatics Decis. Mak. 18(1): 107:1-107:19 (2018) - [j64]Fabian Fier, Nikolaus Augsten, Panagiotis Bouros, Ulf Leser, Johann-Christoph Freytag:
Set Similarity Joins on MapReduce: An Experimental Survey. Proc. VLDB Endow. 11(10): 1110-1122 (2018) - [c89]Jurica Seva, Martin Wackerbauer, Ulf Leser:
Identifying Key Sentences for Precision Oncology Using Semi-Supervised Learning. BioNLP 2018: 35-46 - [c88]Jurica Seva, Mario Sänger, Ulf Leser:
WBI at CLEF eHealth 2018 Task 1: Language-independent ICD-10 Coding using Multi-lingual Embeddings and Recurrent Neural Networks. CLEF (Working Notes) 2018 - [c87]Carl Witt, Dennis Wagner, Ulf Leser:
POS: Online Learning for Memory-Aware Scheduling of Scientific Workflows. eScience 2018: 399-400 - [c86]Patrick Schäfer, Dirk Pflugmacher, Patrick Hostert, Ulf Leser:
Classifying Land Cover from Satellite Images Using Time Series Analytics. EDBT/ICDT Workshops 2018: 10-15 - [c85]Theodoros Chondrogiannis, Panagiotis Bouros, Johann Gamper, Ulf Leser, David B. Blumenthal:
Finding k-dissimilar paths with minimum collective length. SIGSPATIAL/GIS 2018: 404-407 - [c84]Stefan Sprenger, Steffen Zeuch, Ulf Leser:
Exploiting Automatic Vectorization to Employ SPMD on SIMD Registers. ICDE Workshops 2018: 90-95 - [c83]Michael Loster, Manuel Hegner, Felix Naumann, Ulf Leser:
Dissecting Company Names using Sequence Labeling. LWDA 2018: 227-238 - [c82]Stefan Sprenger, Patrick Schäfer, Ulf Leser:
Multidimensional range queries on modern hardware. SSDBM 2018: 4:1-4:12 - [r4]Ulf Leser:
Semantic Data Integration for Life Science Entities. Encyclopedia of Database Systems (2nd ed.) 2018 - [r3]Ulf Leser, Silke Trißl:
Graph Management in the Life Sciences. Encyclopedia of Database Systems (2nd ed.) 2018 - [i11]Stefan Sprenger, Patrick Schäfer, Ulf Leser:
Multidimensional Range Queries on Modern Hardware. CoRR abs/1801.03644 (2018) - [i10]Roland Roller, Madeleine Kittner, Dirk Weissenborn, Ulf Leser:
Cross-lingual Candidate Search for Biomedical Concept Normalization. CoRR abs/1805.01646 (2018) - [i9]Carl Witt, Marc Bux, Wladislaw Gusew, Ulf Leser:
Predictive Performance Modeling for Distributed Computing using Black-Box Monitoring and Machine Learning. CoRR abs/1805.11877 (2018) - [i8]Theodoros Chondrogiannis, Panagiotis Bouros, Johann Gamper, Ulf Leser, David B. Blumenthal:
Finding k-Dissimilar Paths with Minimum Collective Length. CoRR abs/1809.06831 (2018) - 2017
- [j63]Yvonne Lichtblau, Karin Zimmermann, Berit Haldemann, Dido Lenze, Michael Hummel, Ulf Leser:
Comparative assessment of differential network analysis methods. Briefings Bioinform. 18(5): 837-850 (2017) - [j62]Maryam Habibi, Leon Weber, Mariana L. Neves, David Luis Wiegandt, Ulf Leser:
Deep learning with word embeddings improves biomedical named entity recognition. Bioinform. 33(14): i37-i48 (2017) - [j61]Saskia Trescher, Jannes Münchmeyer, Ulf Leser:
Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization. BMC Syst. Biol. 11(1): 41:1-41:18 (2017) - [j60]Astrid Rheinländer, Ulf Leser, Goetz Graefe:
Optimization of Complex Dataflows with User-Defined Functions. ACM Comput. Surv. 50(3): 38:1-38:39 (2017) - [j59]Johannes Starlinger, Madeleine Kittner, Oliver Blankenstein, Ulf Leser:
How to improve information extraction from German medical records. it Inf. Technol. 59(4): 171 (2017) - [j58]Jörgen Brandt, Wolfgang Reisig, Ulf Leser:
Computation semantics of the functional scientific workflow language Cuneiform. J. Funct. Program. 27: e22 (2017) - [c81]Patrick Schäfer, Ulf Leser:
Benchmarking Univariate Time Series Classifiers. BTW 2017: 289-298 - [c80]Patrick Schäfer, Ulf Leser:
Fast and Accurate Time Series Classification with WEASEL. CIKM 2017: 637-646 - [c79]Jurica Seva, Madeleine Kittner, Roland Roller, Ulf Leser:
Multi-lingual ICD-10 Coding using a Hybrid rule-based and Supervised Classification Approach at CLEF eHealth 2017. CLEF (Working Notes) 2017 - [c78]Georgia Kougka, Anastasios Gounaris, Ulf Leser:
Modeling Data Flow Execution in a Parallel Environment. DaWaK 2017: 183-196 - [c77]Theodoros Chondrogiannis, Panagiotis Bouros, Johann Gamper, Ulf Leser:
Exact and Approximate Algorithms for Finding k-Shortest Paths with Limited Overlap. EDBT 2017: 414-425 - [c76]Marc Bux, Jörgen Brandt, Carl Witt, Jim Dowling, Ulf Leser:
Hi-WAY: Execution of Scientific Workflows on Hadoop YARN. EDBT 2017: 668-679 - [c75]Mario Sänger, Ulf Leser, Roman Klinger:
Fine-Grained Opinion Mining from Mobile App Reviews with Word Embedding Features. NLDB 2017: 3-14 - [i7]Patrick Schäfer, Ulf Leser:
Fast and Accurate Time Series Classification with WEASEL. CoRR abs/1701.07681 (2017) - [i6]Patrick Schäfer, Ulf Leser:
Multivariate Time Series Classification with WEASEL+MUSE. CoRR abs/1711.11343 (2017) - 2016
- [j57]Liam Harold Childs, Soulafa Mamlouk, Jörgen Brandt, Christine Sers, Ulf Leser:
SoFIA: a data integration framework for annotating high-throughput datasets. Bioinform. 32(17): 2590-2597 (2016) - [j56]Philippe Thomas, Tim Rocktäschel, Jörg Hakenberg, Yvonne Lichtblau, Ulf Leser:
SETH detects and normalizes genetic variants in text. Bioinform. 32(18): 2883-2885 (2016) - [j55]Johannes Starlinger, Sarah Cohen Boulakia, Sanjeev Khanna, Susan B. Davidson, Ulf Leser:
Effective and efficient similarity search in scientific workflow repositories. Future Gener. Comput. Syst. 56: 584-594 (2016) - [j54]Maryam Habibi, David Luis Wiegandt, Florian Schmedding, Ulf Leser:
Recognizing chemicals in patents: a comparative analysis. J. Cheminformatics 8(1): 59:1-59:15 (2016) - [j53]Thomas Krause, Ulf Leser, Anke Lüdeling:
graphANNIS: A Fast Query Engine for Deeply Annotated Linguistic Corpora. J. Lang. Technol. Comput. Linguistics 31(1): 1-25 (2016) - [j52]Daniel Taliun, Johann Gamper, Ulf Leser, Cristian Pattaro:
Fast Sampling-Based Whole-Genome Haplotype Block Recognition. IEEE ACM Trans. Comput. Biol. Bioinform. 13(2): 315-325 (2016) - [c74]Mario Sänger, Ulf Leser, Steffen Kemmerer, Peter Adolphs, Roman Klinger:
SCARE ― The Sentiment Corpus of App Reviews with Fine-grained Annotations in German. LREC 2016 - [c73]David Luis Wiegandt, Johannes Starlinger, Ulf Leser:
Graph n-grams for Scientific Workflow Similarity Search. LWDA 2016: 213-224 - [c72]Astrid Rheinländer, Mario Lehmann, Anja Kunkel, Jörg Meier, Ulf Leser:
Potential and Pitfalls of Domain-Specific Information Extraction at Web Scale. SIGMOD Conference 2016: 759-771 - [c71]Maryam Habibi, David Luis Wiegandt, Florian Schmedding, Ulf Leser:
Performance of Gene Name Recognition Tools on Patents. SMBM 2016: 3-10 - [c70]Anja Kunkel, Astrid Rheinländer, Christopher Schiefer, Sven Helmer, Panagiotis Bouros, Ulf Leser:
PIEJoin: Towards Parallel Set Containment Joins. SSDBM 2016: 11:1-11:12 - [c69]Stefan Sprenger, Steffen Zeuch, Ulf Leser:
Cache-Sensitive Skip List: Efficient Range Queries on Modern CPUs. ADMS/IMDM@VLDB 2016: 1-17 - 2015
- [j51]Philippe Thomas, Pawel Durek, Illés Solt, Bertram Klinger, Franziska Witzel, Pascal Schulthess, Yvonne Mayer, Domonkos Tikk, Nils Blüthgen, Ulf Leser:
Computer-assisted curation of a human regulatory core network from the biological literature. Bioinform. 31(8): 1258-1266 (2015) - [j50]Marc Bux, Ulf Leser:
DynamicCloudSim: Simulating heterogeneity in computational clouds. Future Gener. Comput. Syst. 46: 85-99 (2015) - [j49]Astrid Rheinländer, Arvid Heise, Fabian Hueske, Ulf Leser, Felix Naumann:
SOFA: An extensible logical optimizer for UDF-heavy data flows. Inf. Syst. 52: 96-125 (2015) - [j48]Sebastian Wandelt, Ulf Leser:
MRCSI: Compressing and Searching String Collections with Multiple References. Proc. VLDB Endow. 8(5): 461-472 (2015) - [j47]Marc Bux, Jörgen Brandt, Carsten Lipka, Kamal Hakimzadeh, Jim Dowling, Ulf Leser:
SAASFEE: Scalable Scientific Workflow Execution Engine. Proc. VLDB Endow. 8(12): 1892-1895 (2015) - [c68]Jörgen Brandt, Marc Bux, Ulf Leser:
Cuneiform: a Functional Language for Large Scale Scientific Data Analysis. EDBT/ICDT Workshops 2015: 7-16 - [c67]Tobias Rawald, Mike Sips, Norbert Marwan, Ulf Leser:
Massively Parallel Analysis of Similarity Matrices on Heterogeneous Hardware. EDBT/ICDT Workshops 2015: 56-62 - [c66]Theodoros Chondrogiannis, Panagiotis Bouros, Johann Gamper, Ulf Leser:
Alternative routing: k-shortest paths with limited overlap. SIGSPATIAL/GIS 2015: 68:1-68:4 - [c65]Alysson Bessani, Jörgen Brandt, Marc Bux, Vinicius Vielmo Cogo, Lora Dimitrova, Jim Dowling, Ali Gholami, Kamal Hakimzadeh, Michael Hummel, Mahmoud Ismail, Erwin Laure, Ulf Leser, Jan-Eric Litton, Roxanna Martinez, Salman Niazi, Jane Reichel, Karin Zimmermann:
BiobankCloud: A Platform for the Secure Storage, Sharing, and Processing of Large Biomedical Data Sets. Big-O(Q)/DMAH@VLDB 2015: 89-105 - 2014
- [j46]Mariana L. Neves, Ulf Leser:
A survey on annotation tools for the biomedical literature. Briefings Bioinform. 15(2): 327-340 (2014) - [j45]Harald Stachelscheid, Stefanie Seltmann, Fritz Lekschas, Jean-Fred Fontaine, Nancy Mah, Mariana L. Neves, Miguel A. Andrade-Navarro, Ulf Leser, Andreas Kurtz:
CellFinder: a cell data repository. Nucleic Acids Res. 42(Database-Issue): 950-958 (2014) - [j44]Johannes Starlinger, Bryan Brancotte, Sarah Cohen Boulakia, Ulf Leser:
Similarity Search for Scientific Workflows. Proc. VLDB Endow. 7(12): 1143-1154 (2014) - [j43]Sebastian Wandelt, Dong Deng, Stefan Gerdjikov, Shashwat Mishra, Petar Mitankin, Manish Patil, Enrico Siragusa, Alexander Tiskin, Wei Wang, Jiaying Wang, Ulf Leser:
State-of-the-art in string similarity search and join. SIGMOD Rec. 43(1): 64-76 (2014) - [j42]Alexander Alexandrov, Rico Bergmann, Stephan Ewen, Johann-Christoph Freytag, Fabian Hueske, Arvid Heise, Odej Kao, Marcus Leich, Ulf Leser, Volker Markl, Felix Naumann, Mathias Peters, Astrid Rheinländer, Matthias J. Sax, Sebastian Schelter, Mareike Höger, Kostas Tzoumas, Daniel Warneke:
The Stratosphere platform for big data analytics. VLDB J. 23(6): 939-964 (2014) - [c64]Sebastian Wandelt, Ulf Leser:
RRCA: Ultra-Fast Multiple In-species Genome Alignments. AlCoB 2014: 247-261 - [c63]Johannes Starlinger, Sarah Cohen Boulakia, Sanjeev Khanna, Susan B. Davidson, Ulf Leser:
Layer Decomposition: An Effective Structure-Based Approach for Scientific Workflow Similarity. eScience 2014: 169-176 - [c62]Ulf Leser:
Next Generation Data Integration (for the Life Sciences). Grundlagen von Datenbanken 2014: 9 - [c61]Astrid Rheinländer, Martin Beckmann, Anja Kunkel, Arvid Heise, Thomas Stoltmann, Ulf Leser:
Versatile optimization of UDF-heavy data flows with sofa. SIGMOD Conference 2014: 685-688 - [c60]Lars Döhling, Ulf Leser:
Extracting and aggregating temporal events from text. WWW (Companion Volume) 2014: 839-844 - 2013
- [j41]Mariana L. Neves, Alexander Damaschun, Nancy Mah, Fritz Lekschas, Stefanie Seltmann, Harald Stachelscheid, Jean-Fred Fontaine, Andreas Kurtz, Ulf Leser:
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. Database J. Biol. Databases Curation 2013 (2013) - [j40]Georg Fuellen, Ludger Jansen, Ulf Leser, Andreas Kurtz:
Using ontologies to study cell transitions. J. Biomed. Semant. 4: 25 (2013) - [j39]Domonkos Tikk, Illés Solt, Philippe Thomas, Ulf Leser:
A detailed error analysis of 13 kernel methods for protein-protein interaction extraction. BMC Bioinform. 14: 12 (2013) - [j38]Stefanie Seltmann, Harald Stachelscheid, Alexander Damaschun, Ludger Jansen, Fritz Lekschas, Jean-Fred Fontaine, Throng-Nghia Nguyen-Dobinsky, Ulf Leser, Andreas Kurtz:
CELDA - an ontology for the comprehensive representation of cells in complex systems. BMC Bioinform. 14: 228 (2013) - [j37]Sebastian Wandelt, Johannes Starlinger, Marc Bux, Ulf Leser:
RCSI: Scalable similarity search in thousand(s) of genomes. Proc. VLDB Endow. 6(13): 1534-1545 (2013) - [j36]Sebastian Wandelt, Ulf Leser:
FRESCO: Referential Compression of Highly Similar Sequences. IEEE ACM Trans. Comput. Biol. Bioinform. 10(5): 1275-1288 (2013) - [c59]Sebastian Wandelt, Ulf Leser:
QGramProjector: Q-Gram Projection for Indexing Highly-Similar Strings. ADBIS 2013: 260-273 - [c58]Philippe Thomas, Johannes Starlinger, Ulf Leser:
Experiences from Developing the Domain-Specific Entity Search Engine GeneView. BTW 2013: 225-239 - [c57]Thomas Stoltmann, Karin Zimmermann, André Koschmieder, Ulf Leser:
OmixAnalyzer - A Web-Based System for Management and Analysis of High-Throughput Omics Data Sets. DILS 2013: 46-53 - [c56]Holger Pirk, Florian Funke, Martin Grund, Thomas Neumann, Ulf Leser, Stefan Manegold, Alfons Kemper, Martin L. Kersten:
CPU and cache efficient management of memory-resident databases. ICDE 2013: 14-25 - [c55]Tim Rocktäschel, Torsten Huber, Michael Weidlich, Ulf Leser:
WBI-NER: The impact of domain-specific features on the performance of identifying and classifying mentions of drugs. SemEval@NAACL-HLT 2013: 356-363 - [c54]Philippe Thomas, Mariana L. Neves, Tim Rocktäschel, Ulf Leser:
WBI-DDI: Drug-Drug Interaction Extraction using Majority Voting. SemEval@NAACL-HLT 2013: 628-635 - [c53]Marc Bux, Ulf Leser:
DynamicCloudSim: simulating heterogeneity in computational clouds. SWEET@SIGMOD 2013: 1:1-1:12 - [i5]Marc Bux, Ulf Leser:
Parallelization in Scientific Workflow Management Systems. CoRR abs/1303.7195 (2013) - [i4]Astrid Rheinländer, Arvid Heise, Fabian Hueske, Ulf Leser, Felix Naumann:
SOFA: An Extensible Logical Optimizer for UDF-heavy Dataflows. CoRR abs/1311.6335 (2013) - 2012
- [j35]Sebastian Wandelt, Ulf Leser:
Adaptive efficient compression of genomes. Algorithms Mol. Biol. 7: 30 (2012) - [j34]André Koschmieder, Karin Zimmermann, Silke Trißl, Thomas Stoltmann, Ulf Leser:
Tools for managing and analyzing microarray data. Briefings Bioinform. 13(1): 46-60 (2012) - [j33]Tim Rocktäschel, Michael Weidlich, Ulf Leser:
ChemSpot: a hybrid system for chemical named entity recognition. Bioinform. 28(12): 1633-1640 (2012) - [j32]Sebastian Wandelt, Astrid Rheinländer, Marc Bux, Lisa Thalheim, Berit Haldemann, Ulf Leser:
Data Management Challenges in Next Generation Sequencing. Datenbank-Spektrum 12(3): 161-171 (2012) - [j31]Heiko Müller, Johann Christoph Freytag, Ulf Leser:
Improving data quality by source analysis. ACM J. Data Inf. Qual. 2(4): 15:1-15:38 (2012) - [j30]Philippe Thomas, Johannes Starlinger, Alexander Vowinkel, Sebastian Arzt, Ulf Leser:
GeneView: a comprehensive semantic search engine for PubMed. Nucleic Acids Res. 40(Web-Server-Issue): 585-591 (2012) - [c52]Jana Bauckmann, Ziawasch Abedjan, Ulf Leser, Heiko Müller, Felix Naumann:
Discovering conditional inclusion dependencies. CIKM 2012: 2094-2098 - [c51]Silke Trißl, Philipp Hussels, Ulf Leser:
InterOnto - Ranking Inter-Ontology Links. DILS 2012: 5-20 - [c50]Sebastian Wandelt, Ulf Leser:
String Searching in Referentially Compressed Genomes. KDIR 2012: 95-102 - [c49]André Koschmieder, Ulf Leser:
Regular Path Queries on Large Graphs. SSDBM 2012: 177-194 - [c48]Dandy Fenz, Dustin Lange, Astrid Rheinländer, Felix Naumann, Ulf Leser:
Efficient Similarity Search in Very Large String Sets. SSDBM 2012: 262-279 - [c47]Johannes Starlinger, Sarah Cohen Boulakia, Ulf Leser:
(Re)Use in Public Scientific Workflow Repositories. SSDBM 2012: 361-378 - 2011
- [j29]Cecilia N. Arighi, Phoebe M. Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle G. Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu, Lois J. Maltais, Naoaki Okazaki, Livia Perfetto, Fabio Rinaldi, Rune Sætre, David Salgado, Padmini Srinivasan, Philippe E. Thomas, Luca Toldo, Lynette Hirschman, Cathy H. Wu:
BioCreative III interactive task: an overview. BMC Bioinform. 12(S-8): S4 (2011) - [j28]Jörg Hakenberg, Illés Solt, Domonkos Tikk, Nguyen Ha Vo, Luis Tari, Quang Long Nguyen, Chitta Baral, Ulf Leser:
Molecular Event Extraction from Link Grammar Parse Trees in the BioNLP'09 Shared Task. Comput. Intell. 27(4): 665-680 (2011) - [j27]Sarah Cohen Boulakia, Ulf Leser:
Search, adapt, and reuse: the future of scientific workflows. SIGMOD Rec. 40(2): 6-16 (2011) - [c46]Philippe Thomas, Stefan Pietschmann, Illés Solt, Domonkos Tikk, Ulf Leser:
Not all links are equal: Exploiting Dependency Types for the Extraction of Protein-Protein Interactions from Text. BioNLP@ACL 2011: 1-9 - [c45]Astrid Rheinländer, Ulf Leser:
Scalable Sequence Similarity Search and Join in Main Memory on Multi-cores. Euro-Par Workshops (2) 2011: 13-22 - [c44]Sebastian Arzt, Johannes Starlinger, Oliver Arnold, Stefan Kroeger, Samira Jaeger, Ulf Leser:
Pipa: custom integration of protein interactions and pathways. GI-Jahrestagung 2011: 158 - [c43]Sarah Cohen Boulakia, Ulf Leser:
Next generation data integration for Life Sciences. ICDE 2011: 1366-1369 - 2010
- [j26]Philip Groth, Ivan Kalev, Ivaylo Kirov, Borislav Traikov, Ulf Leser, Bertram Weiss:
Phenoclustering: online mining of cross-species phenotypes. Bioinform. 26(15): 1924-1925 (2010) - [j25]Quang Long Nguyen, Domonkos Tikk, Ulf Leser:
Simple tricks for improving pattern-based information extraction from the biomedical literature. J. Biomed. Semant. 1: 9 (2010) - [j24]Illés Solt, Domonkos Tikk, Ulf Leser:
Species identification for gene name normalization. BMC Bioinform. 11(S-5): P5 (2010) - [j23]Domonkos Tikk, Peter Palaga, Ulf Leser:
A fast and effective dependency graph kernel for PPI relation extraction. BMC Bioinform. 11(S-5): P8 (2010) - [j22]Domonkos Tikk, Philippe Thomas, Peter Palaga, Jörg Hakenberg, Ulf Leser:
A Comprehensive Benchmark of Kernel Methods to Extract Protein-Protein Interactions from Literature. PLoS Comput. Biol. 6(7) (2010) - [j21]Thomas Kabisch, Eduard Constantin Dragut, Clement T. Yu, Ulf Leser:
Deep Web Integration with VisQI. Proc. VLDB Endow. 3(2): 1613-1616 (2010) - [c42]Silke Trißl, Ulf Leser:
Estimating Result Size and Execution Times for Graph Queries. ADBIS (Local Proceedings) 2010: 11-20 - [c41]Tobia Lakes, Ulf Leser, Cornelius Senf:
An urban health risk analysis for Berlin: exploration and integration of spatio-temporal information on the urban environment. EnviroInfo 2010: 593-603 - [c40]Roger Castillo, Ulf Leser:
Selecting Materialized Views for RDF Data. ICWE Workshops 2010: 126-137 - [c39]Astrid Rheinländer, Martin Knobloch, Nicky Hochmuth, Ulf Leser:
Prefix Tree Indexing for Similarity Search and Similarity Joins on Genomic Data. SSDBM 2010: 519-536 - [c38]Falk Brauer, Michael Huber, Gregor Hackenbroich, Ulf Leser, Felix Naumann, Wojciech M. Barczynski:
Graph-based concept identification and disambiguation for enterprise search. WWW 2010: 171-180
2000 – 2009
- 2009
- [j20]Thomas Kabisch, Eduard Constantin Dragut, Clement T. Yu, Ulf Leser:
A Hierarchical Approach to Model Web Query Interfaces for Web Source Integration. Proc. VLDB Endow. 2(1): 325-336 (2009) - [c37]Jörg Hakenberg, Illés Solt, Domonkos Tikk, Luis Tari, Astrid Rheinländer, Quang Long Nguyen, Graciela Gonzalez, Ulf Leser:
Molecular event extraction from Link Grammar parse trees. BioNLP@HLT-NAACL (Shared Task) 2009: 86-94 - [c36]Peter Palaga, Long Nguyen, Ulf Leser, Jörg Hakenberg:
High-performance information extraction with AliBaba. EDBT 2009: 1140-1143 - [c35]Alessandro De Stasio, Marcus Ertelt, Wolfgang Kemmner, Ulf Leser, Michele Ceccarelli:
Exploiting scientific workflows for large-scale gene expression data analysis. ISCIS 2009: 448-453 - [c34]Christoph Böhm, Philip Groth, Ulf Leser:
Graph-Based Ontology Construction from Heterogenous Evidences. ISWC 2009: 81-96 - [c33]Johannes Starlinger, Florian Leitner, Alfonso Valencia, Ulf Leser:
SOA-Based Integration of Text Mining Services. SERVICES I 2009: 99-106 - [c32]Alexandra Rostin, Oliver Albrecht, Jana Bauckmann, Felix Naumann, Ulf Leser:
A Machine Learning Approach to Foreign Key Discovery. WebDB 2009 - [p1]Torsten Schiemann, Ulf Leser, Jörg Hakenberg:
Word Sense Disambiguation in Biomedical Applications. Information Retrieval in Biomedicine 2009: 142-161 - [r2]Ulf Leser, Silke Trißl:
Graph Management in the Life Sciences. Encyclopedia of Database Systems 2009: 1266-1271 - [r1]Ulf Leser:
Semantic Data Integration for Life Science Entities. Encyclopedia of Database Systems 2009: 2555-2559 - 2008
- [j19]Philip Groth, Bertram Weiss, Hans-Dieter Pohlenz, Ulf Leser:
Mining phenotypes for gene function prediction. BMC Bioinform. 9 (2008) - [j18]Samira Jaeger, Sylvain Gaudan, Ulf Leser, Dietrich Rebholz-Schuhmann:
Integrating protein-protein interactions and text mining for protein function prediction. BMC Bioinform. 9(S-8) (2008) - [j17]Christian Chiarcos, Stefanie Dipper, Michael Götze, Ulf Leser, Anke Lüdeling, Julia Ritz, Manfred Stede:
A Flexible Framework for Integrating Annotations from Different Tools and Tag Sets. Trait. Autom. des Langues 49(2): 217-246 (2008) - [c31]Bastian Quilitz, Ulf Leser:
Querying Distributed RDF Data Sources with SPARQL. ESWC 2008: 524-538 - [e3]Michael Ashburner, Ulf Leser, Dietrich Rebholz-Schuhmann:
Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, 24.03. - 28.03.2008. Dagstuhl Seminar Proceedings 08131, Internationales Begegnungs- und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Germany 2008 [contents] - [i3]Michael Ashburner, Ulf Leser, Dietrich Rebholz-Schuhmann:
08131 Executive Summary -- Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives. Ontologies and Text Mining for Life Sciences 2008 - [i2]Ulf Leser, Philip Groth, Bertram Weiss, Hans-Dieter Pohlenz:
Mining Phenotypes for Protein Function Prediction. Ontologies and Text Mining for Life Sciences 2008 - 2007
- [b3]Ulf Leser, Felix Naumann:
Informationsintegration - Architekturen und Methoden zur Integration verteilter und heterogener Datenquellen. dpunkt.verlag 2007, pp. I-XIII, 1-464 - [c30]Philipp Hussels, Silke Trißl, Ulf Leser:
What's New? What's Certain? - Scoring Search Results in the Presence of Overlapping Data Sources. DILS 2007: 231-246 - [c29]Samira Jaeger, Ulf Leser:
High-Precision Function Prediction using Conserved Interactions. German Conference on Bioinformatics 2007: 146-162 - [c28]Jana Bauckmann, Ulf Leser, Felix Naumann, Veronique Tietz:
Efficiently Detecting Inclusion Dependencies. ICDE 2007: 1448-1450 - [c27]Silke Trißl, Ulf Leser:
Fast and practical indexing and querying of very large graphs. SIGMOD Conference 2007: 845-856 - 2006
- [b2]Ulf Leser, Felix Naumann:
Informationsintegration: Architekturen und Methoden zur Integration verteilter und heterogener Datenquellen. dpunkt 2006, ISBN 3-89864-400-6 - [j16]Uwe Radetzki, Ulf Leser, S. C. Schulze-Rauschenbach, Jörg Zimmermann, Jens Lüssem, Thomas Bode, Armin B. Cremers:
Adapters, shims, and glue - service interoperability for in silico experiments. Bioinform. 22(9): 1137-1143 (2006) - [j15]Conrad Plake, Torsten Schiemann, Marcus Pankalla, Jörg Hakenberg, Ulf Leser:
ALIBABA: PubMed as a graph. Bioinform. 22(19): 2444-2445 (2006) - [j14]Kristian Rother, Mathias Dunkel, Elke Michalsky, Silke Trißl, Andrean Goede, Ulf Leser, Robert Preissner:
A structural keystone for drug design. J. Integr. Bioinform. 3(1) (2006) - [c26]Heiko Müller, Johann Christoph Freytag, Ulf Leser:
Describing differences between databases. CIKM 2006: 612-621 - [c25]Lukas Faulstich, Ulf Leser, Thorsten Vitt:
Implementing a Linguistic Query Language for Historic Texts. EDBT Workshops 2006: 601-612 - [c24]Heiko Müller, Ulf Leser, Johann Christoph Freytag:
Classification of Contradiction Patterns. GfKl 2006: 171-178 - [c23]Jana Bauckmann, Ulf Leser, Felix Naumann:
Efficiently Computing Inclusion Dependencies for Schema Discovery. ICDE Workshops 2006: 2 - [c22]Jörg Hakenberg, Ulf Leser, Harald Kirsch, Dietrich Rebholz-Schuhmann:
Collecting a Large Corpus from all of Medline. SMBM 2006 - [e2]Ulf Leser, Felix Naumann, Barbara A. Eckman:
Data Integration in the Life Sciences, Third International Workshop, DILS 2006, Hinxton, UK, July 20-22, 2006, Proceedings. Lecture Notes in Computer Science 4075, Springer 2006, ISBN 3-540-36593-1 [contents] - 2005
- [j13]Ulf Leser, Jörg Hakenberg:
What makes a gene name? Named entity recognition in the biomedical literature. Briefings Bioinform. 6(4): 357-369 (2005) - [j12]Daniel Schober, Ulf Leser, Martin Zenke, Jens G. Reich:
GandrKB--ontological microarray annotation and visualization. Bioinform. 21(11): 2785-2786 (2005) - [j11]Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser, Tobias Scheffer:
Systematic feature evaluation for gene name recognition. BMC Bioinform. 6(S-1) (2005) - [j10]Silke Trißl, Kristian Rother, Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel, Ulf Leser:
Columba: an integrated database of proteins, structures, and annotations. BMC Bioinform. 6: 81 (2005) - [j9]Heiko Müller, Melanie Weis, Jens Bleiholder, Ulf Leser:
Erkennen und Bereinigen von Datenfehlern in naturwissenschaftlichen Daten. Datenbank-Spektrum 15(14): 36- (2005) - [c21]Ulf Leser, Felix Naumann:
(Almost) Hands-Off Information Integration for the Life Sciences. CIDR 2005: 131-143 - [c20]Silke Trißl, Ulf Leser:
Querying Ontologies in Relational Database Systems. DILS 2005: 63-79 - [c19]Emilie Guérin, Gwenaëlle Marquet, Anita Burgun, Olivier Loréal, Laure Berti-Équille, Ulf Leser, Fouzia Moussouni:
Integrating and Warehousing Liver Gene Expression Data and Related Biomedical Resources in GEDAW. DILS 2005: 158-174 - [c18]Ulf Leser:
A query language for biological networks. ECCB/JBI 2005: 39 - [c17]Conrad Plake, Jörg Hakenberg, Ulf Leser:
Optimizing syntax patterns for discovering protein-protein interactions. SAC 2005: 195-201 - 2004
- [j8]Felix Naumann, Johann Christoph Freytag, Ulf Leser:
Completeness of integrated information sources. Inf. Syst. 29(7): 583-615 (2004) - [c16]Steffen Jurk, Ulf Leser, José-Luis Marzo:
Cooperative Transaction Processing between Clients and Servers. ADBIS (Local Proceedings) 2004 - [c15]Kristian Rother, Heiko Müller, Silke Trißl, Ina Koch, Thomas Steinke, Robert Preissner, Cornelius Frömmel, Ulf Leser:
Columba: Multidimensional Data Integration of Protein Annotations. DILS 2004: 156-171 - [c14]Heiko Müller, Ulf Leser, Johann Christoph Freytag:
Mining for Patterns in Contradictory Data. IQIS 2004: 51-58 - [i1]Raghu Ramakrishnan, Rakesh Agrawal, Johann-Christoph Freytag, Toni Bollinger, Christopher W. Clifton, Saso Dzeroski, Jochen Hipp, Daniel A. Keim, Stefan Kramer, Hans-Peter Kriegel, Ulf Leser, Bing Liu, Heikki Mannila, Rosa Meo, Shinichi Morishita, Raymond T. Ng, Jian Pei, Prabhakar Raghavan, Myra Spiliopoulou, Jaideep Srivastava, Vicenç Torra:
Data Mining: The Next Generation. Perspectives Workshop: Data Mining: The Next Generation 2004 - 2003
- [j7]Ulf Leser, Peter Rieger:
Integration molekularbiologischer Daten. Datenbank-Spektrum 6: 56-66 (2003) - 2000
- [b1]Ulf Leser:
Query planning in mediator based information systems. Technical University of Berlin, Germany, 2000 - [c13]Susanne Busse, Ralf-Detlef Kutsche, Ulf Leser:
Strategies for the Conceptual Design of Federated Information Systems. EFIS 2000: 23-32 - [c12]Ulf Leser, Felix Naumann:
Query Planning with Information Quality Bounds. FQAS 2000: 85-94
1990 – 1999
- 1999
- [j6]Emmanuel Barillot, Ulf Leser, Philip Lijnzaad, Christophe Cussat-Blanc, Kim Jungfer, Frédéric Guyon, Guy Vaysseix, Carsten Helgesen, Patricia Rodriguez-Tomé:
A proposal for a standard CORBA interface for genome maps. Bioinform. 15(2): 157-169 (1999) - [j5]Steffen Möller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler:
EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation. Bioinform. 15(3): 219-227 (1999) - [j4]Ulf Leser, Hugues Roest Crollius, Hans Lehrach, Ralf Sudbrak:
IXDB, an X chromosome integrated database (update). Nucleic Acids Res. 27(1): 123-127 (1999) - [c11]Ulf Leser:
Designing a Global Information Resource for Molecular Biology. BTW 1999: 362-368 - [c10]Kim Jungfer, Ulf Leser, Patricia Rodriguez-Tomé:
Constructing IDL Views on Relational Databases. CAiSE 1999: 255-268 - [c9]Heiko Müller, Ulf Leser:
Integration durch Standards: Erfahrungen mit CORBA in Life Science Research. Föderierte Datenbanken 1999: 89-102 - [c8]Felix Naumann, Ulf Leser:
Density Scores for Cooperative Query Answering. Föderierte Datenbanken 1999: 103-116 - [c7]Ulf Leser:
Globale Anfragebearbeitung mit verteilten und heterogenen Datenquellen. GI Jahrestagung 1999: 265-272 - [c6]Felix Naumann, Ulf Leser, Johann Christoph Freytag:
Quality-driven Integration of Heterogenous Information Systems. VLDB 1999: 447-458 - [e1]Ralf-Detlef Kutsche, Ulf Leser, Johann Christoph Freytag:
4. Workshop Föderierte Datenbanken, Berlin, Germany, November 25-26, 1999. CEUR Workshop Proceedings 25, CEUR-WS.org 1999 [contents] - 1998
- [j3]Ulf Leser, Hans Lehrach, Hugues Roest Crollius:
Issues in developing integrated genomic databases and application to the human X chromosome. Bioinform. 14(7): 583-590 (1998) - [j2]Ulf Leser, Robert Wagner, Andrei Grigoriev, Hans Lehrach, Hugues Roest Crollius:
IXDB, an X chromosome integrated database. Nucleic Acids Res. 26(1): 108-111 (1998) - [c5]Ulf Leser:
Query Mediation for Heterogeneous Data Sources. Föderierte Datenbanken 1998: 33-44 - [c4]Steffen Möller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler:
EDITtoTrEMBL: A distributed approach to high-quality automated protein sequence annotation. German Conference on Bioinformatics 1998 - [c3]Ulf Leser, Stefan Tai, Susanne Busse:
Design Issues of Database Access in a CORBA Environment. Workshop Integration heterogener Softwaresysteme 1998: 74-87 - [c2]Ulf Leser:
Combining Heterogeneous Data Sources through Query Correspondence Assertions. Workshop on Web Information and Data Management 1998: 29-32 - 1997
- [j1]Ulf Leser:
Ansätze zur Föderation moleklargenetischer Datenbanken. Datenbank Rundbr. 20: 57-61 (1997) - [c1]Ulf Leser, Robert Wagner, Hans Lehrach, Hugues Roest Crollius:
IXDB, an integrated database for genomic data of the Human X Chromosome. German Conference on Bioinformatics 1997: 161-162
Coauthor Index
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