Publications

• On-the-fly Definition Augmentation of LLMs for Biomedical NER. Monica_Munnangi, Sergey Feldman, Byron C Wallace, Silvio Amir, Tom Hope and Aakanksha Naik. Proceedings of the North Americal Chapter of the Association for Computational Linguistics (NAACL), 2024.

• Infolossqa: Characterizing and recovering information loss in text simplification. Jan Trienes, Sebastian Joseph, Jörg Schlötterer, Christin Seifert, Kyle Lo, Wei Xu, Byron C Wallace, and Junyi Jessy Li. Proceedings of the Association for Computational Linguistics (ACL), 2024.

• FactPICO: Factuality Evaluation for Plain Language Summarization of Medical Evidence. Sebastian Antony Joseph, Lily Chen, Jan Trienes, Hannah Louisa Göke, Monika Coers, Wei Xu, Byron C Wallace, and Junyi Jessy Li. Proceedings of the Association for Computational Linguistics (ACL), 2024.

• Automatically Extracting Numerical Results from Randomized Controlled Trials with Large Language Models. Hye Sun Yun, Iain J. Marshall, Thomas Trikalinos and Byron C. Wallace. Proceedings of Machine Learning for Healthcare (MLHC), 2024.

• Jointly Extracting Interventions, Outcomes, and Findings from RCT Reports with LLMs. Somin Wadhwa, Jay DeYoung, Benjamin Nye, Silvio Amir, and Byron C. Wallace. Proceedings of Machine Learning for Healthcare (MLHC), 2023.

• Appraising the Potential Uses and Harms of LLMs for Medical Systematic Reviews. Hye Sun Yun, Iain J. Marshall, Thomas Trikalinos and Byron C. Wallace. Proceedings of Empirical Methods in Natural Language Processing (EMNLP), 2024.

• Revisiting Relation Extraction in the era of Large Language Models. Somin Wadhwa, Silvio Amir and Byron C. Wallace. Proceedings of the Association for Computational Linguistics (ACL), 2023.

• Overview of MSLR2022: A Shared Task on Multi-document Summarization for Literature Reviews. Proceedings of the Third Workshop on Scholarly Document Processing at International Conference on Computational Linguistics (COLING), 2023.

• RedHOT: A Corpus of Annotated Medical Questions, Experiences, and Claims on Social Media. Somin Wadhwa, Vivek Khetan, Silvio Amir, and Byron C. Wallace. Proceedings of the European Chapter of the Association for Computational Linguistics (EACL): Findings, 2023.

• Automatically Summarizing Evidence from Clinical Trials: A Prototype Highlighting Current Challenges. Sanjana Ramprasad, Denis Jered McInerney, Iain J. Marshall, and Byron C. Wallace. Proceedings of the European Chapter of the Association for Computational Linguistics (EACL): Demonstrations, 2023.

• Combining Feature and Instance Attribution to Detect Artifacts. Pouya Pezeshkpour, Sarthak Jain, Sameer Singh, and Byron C. Wallace. Proceedings of the Association for Computational Linguistics (ACL): Findings, 2022.

• Understanding Clinical Trial Reports: Extracting Medical Entities and Their Relations. Benjamin E. Nye, Jay DeYoung, Eric Lehman, Ani Nenkova, Iain J. Marshall, and Byron C. Wallace. AMIA Virtual Informatics Summit, 2021. Best Student-led Paper: https://www.amia.org/summit2021/award-winners.

• Biomedical Interpretable Entity Representations. Diego Garcia-Olano, Yasumasa Onoe, Ioana Baldini, Joydeep Ghosh, Byron C. Wallace and Kush Varzney. Proceedings of the Association for Computational Linguistics (ACL): Findings, 2021.

• Trialstreamer: a living, automatically updated database of clinical trial reports. Iain J. Marshall, Benjamin Nye, Joël Kuiper, Anna Noel-Storr, Rachel Marshall, Rory Maclean, Frank Soboczenski, Ani Nenkova, James Thomas, and Byron C. Wallace. Journal of the American Medical Informatics Association, 2020.

• Evidence Inference 2.0: More Data, Better Models. Jay DeYoung, Eric Lehman, Iain J. Marshall, and Byron C. Wallace. Proceedings of BioNLP (co-located with ACL), 2020.

• Semi-Automating Knowledge Base Construction for Cancer Genetics. Somin Wadhwa, Kanhua Yin, Kevin S. Hughes, and Byron C. Wallace. Proceedings of Automated Knowledge Base Construction (AKBC), 2020.

• Trialstreamer: Mapping and Browsing Medical Evidence in Real-Time. Benjamin E. Nye, Ani Nenkova, Iain J. Marshall, and Byron C. Wallace. Proceedings of the Association for Computational Linguistics (ACL): Systems Demonstrations, 2020.

• ERASER: A Benchmark to Evaluate Rationalized NLP Models. Jay DeYoung, Sarthak Jain, Nazneen Fatema Rajani, Eric Lehman, Caiming Xiong, Richard Socher, and Byron C. Wallace. Proceedings of the Association for Computational Linguistics (ACL), 2020.

• Learning to Faithfully Rationalize by Construction. Sarthak Jain, Sarah Wiegreffe, Yuval Pinter, and Byron C. Wallace. Proceedings of the Association for Computational Linguistics (ACL), 2020.

• Inferring Which Medical Treatments Work from Reports of Clinical Trials. Eric Lehman, Jay DeYoung, Regina Barzilay, and Byron C. Wallace. Proceedings of the North American Chapter of the Association for Computational Linguistics (NAACL), 2019.

Blog posts, &etc.

• All predictions from our trained evidence-inference model (for all trial reports in PubMed) are available in the Trialstreamer database: https://trialstreamer.robotreviewer.net/.

• Here is the Evidence Inference dataset/task website, which allows one to browse and download the collected data. We also provide pointers to starter code to begin working with the data and on the task, which is available in our GitHub repository.

• Here is a blog post describing the Evidence Inference task, and our initial models.

• Here is the website for the ERASER benchmark, which includes the Evidence Inference corpus and other datasets for which targets are accompanied by supporting snippets (rationales): http://www.eraserbenchmark.com/

• PI Wallace spoke about the overarching goal of automating biomedical evidence synthesis on the NLP Highlights podcast: https://soundcloud.com/nlp-highlights/86-nlp-for-evidence-based-medicine-with-byron-wallace.