Selected publications

For a full list of publications, please see my Google Scholar profile.


L. Weber, F. Barth, L. Lorenz, F. Konrath, K. Huska, J. Wolf and U. Leser (2023). PEDL+: Protein-centered relation extraction from PubMed at your fingertip. Bioinformatics (accepted). [code]

R. Litschko*, M. Müller-Eberstein*, R. van der Goot, L. Weber, B. Plank (2023). Establishing Trustworthiness: Rethinking Tasks and Model Evaluation. EMNLP 2023 (accepted) *:Equal contribution

L. Weber-Genzel, R. Litschko, E. Artemova, and B. Plank (2023). Donkii: Can annotation error detection methods find errors in instruction-tuning datasets? arXiv. [paper]

L. Weber, B. Plank (2023). ActiveAED: A Human in the Loop Improves Annotation Error Detection. Findings of ACL 2023. [paper] [code]


L. Weber, M. Sänger, S. Garda, F. Barth, C. Alt, U. Leser. (2022). Chemical–protein relation extraction with ensembles of carefully tuned pretrained language models. Database. [paper] [code]

J.A. Fries*, L. Weber*, N. Seelam*, G. Altay*, D. Datta^, S. Garda^, M. Kang^, R. Su^, W. Kusa^, S. Cahyawijaya^, F. Barth^, S. Ott^, M. Samwald^, S. Bach^, S. Biderman^, M. Sänger^, B. Wang, A. Callahan, D.L. Periñán, T. Gigant, P. Haller, J. Chim, J.D. Posada, J.M. Giorgi, K.R. Sivaraman, M. Pàmies, M. Nezhurina, R. Martin, M. Cullan, M. Freidank, N. Dahlberg, S. Mishra, S. Bose, N.M. Broad, Y. Labrak, S.S. Deshmukh, S. Kiblawi, A. Singh, M.C. Vu, T. Neeraj, J. Golde, A.V. del Moral and B. Beilharz (2022). Bigbio: A framework for data-centric biomedical natural language processing. NeurIPS 2022 Datasets and Benchmarks Track *:Equal contribution, ^:Equal contribution [paper] [code] [datasets]

J.A. Fries*, N. Seelam*, G. Altay*, L. Weber*, M. Kang*, D. Datta*, R. Su*, S. Garda*, B. Wang, S. Ott, M. Samwald, W. Kusa (2022). Dataset Debt in Biomedical Language Modeling. Workshop on Challenges & Perspectives in Creating Large Language Models 2022. [paper] *:Equal contribution

X. Wang, U. Leser and L. Weber (2022). BEEDS: Large-Scale Biomedical Event Extraction using Distant Supervision and Question Answering. BioNLP 2022. [paper] [code]


L. Weber, M. Sänger, S. Garda, F. Barth, C. Alt and U. Leser (2021). Humboldt @ DrugProt: Chemical-Protein Relation Extraction with Pretrained Transformers and Entity Descriptions. 7th International BioCreative Challenge Evaluation. [paper] [code]. 1st rank out of 30 participating teams in the BC7 DrugProt competition on drug-protein relation extraction

L. Weber, S. Garda, J. Münchmeyer and U. Leser. “Extend, don’t rebuild: Phrasing conditional graph modification as autoregressive sequence labelling”. EMNLP 2021, Punta Cana, Dominican Republic. [paper] [code]

M. Sänger*, L. Weber*, U. Leser. “Wbi at mediqa 2021: Summarizing consumer health questions with generative transformers”. 20th Workshop on Biomedical Language Processing (BioNLP) 2021. [paper] [code]. 2nd rank out of 23 participating teams in the BioNLP MEDIQA 2021 competition on question summarization *:Equal contribution

L. Weber*, M. Sänger*, J. Münchmeyer, M. Habibi and U. Leser. “HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition.” Bioinformatics (btab042) 2021 [paper] [code] *:Equal contribution


W. D. Xing, L. Weber and U. Leser. “Biomedical Event Extraction as Multi-turn Question Answering.” Int. Workshop on Health Text Mining and Information Analysis 2020 [paper] [code]

L. Weber, K. Thobe, O. A. M. Lozano, J. Wolf and U. Leser. “PEDL: Extracting protein-protein associations using deep language models and distant supervision.” Int. Conf. on Intelligent Systems in Molecular Biology 2020 [paper] [code]


L. Weber, P. Minervini, J. Münchmeyer, U. Leser and T. Rocktäschel. “NLProlog: Reasoning with Weak Unification for Question Answering in Natural Language.” ACL 2019, Florence, Italy [paper] [code]

L. Weber*, J. Münchmeyer*, T. Rocktäschel, M. Habibi and U. Leser. “HUNER: Improving Biomedical NER with Pretraining.” Bioinformatics (accepted) [paper][code] *:Equal contribution

K. Shi, S. Schellenberger, L. Weber, P. Wiedemann, F. Michler, T. Steigleder, A. Malessa, F. Lurz, C. Ostgathe, R. Weigel, and A. Koelpin. “Segmentation of Radar-Recorded Heart Sound Signals Using Bidirectional LSTM Networks.” 41st IEEE International Engineering in Medicine and Biology Conference, Berlin, Germany, 2019

M. Sänger*, L. Weber*, M. Kittner*, U. Leser. “Classifying German Animal Experiment Summaries with Multi-lingual BERT at CLEF eHealth 2019 Task 1.” CLEF Working Papers. *:Equal contribution [code] 1st rank out of 6 participating teams in the CLEF eHealth Multilingual Information Extraction Competition


M. Habibi, L. Weber, M. Neves, D. L. Wiegandt, and U. Leser. “Deep learning with word embeddings improves biomedical named entity recognition.” Bioinformatics 33, no. 14 (2017): i37-i48. [paper] [code]

C. Benzmüller, L. Weber, and B. Woltzenlogel Paleo. “Computer-assisted analysis of the Anderson–Hájek ontological controversy.” Logica Universalis 11, no. 1 (2017): 139-151. [paper]