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🧬 Biochemistry, Genetics and Molecular Biology

86 papers · page 2 of 2 · 26–86 · the most cited first · all shelves

Genes, proteins, cells and the chemistry of life.

 Papers

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  1. Nested Named Entity RecognitionJenny Rose Finkel, Christopher D. Manning2009 · 403 citations
  2. A Neural Layered Model for Nested Named Entity RecognitionMeizhi Ju, Makoto Miwa, Sophia Ananiadou2018 · 378 citations
  3. Temporal Annotation in the Clinical DomainWilliam F. Styler IV, Steven Bethard, Sean Finan, et al.2014 · 349 citations
  4. Lessons from Natural Language Inference in the Clinical DomainAlexey Romanov, Chaitanya Shivade2018 · 343 citations
  5. A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical LiteratureBenjamin Nye, Junyi Jessy Li, Roma Patel, et al.2018 · 293 citations
  6. Modeling Biological Processes for Reading ComprehensionJonathan Berant, Vivek Srikumar, Pei-Chun Chen, et al.2014 · 288 citations
  7. emrQA: A Large Corpus for Question Answering on Electronic Medical RecordsAnusri Pampari, Preethi Raghavan, Jennifer Liang, et al.2018 · 285 citations
  8. Weakly Supervised Learning for Hedge Classification in Scientific LiteratureBen Medlock, Ted Briscoe2007 · 266 citations
  9. An Analysis of Simple Data Augmentation for Named Entity RecognitionXiang Dai, Heike Adel2020 · 264 citations
  10. SemEval-2016 Task 12: Clinical TempEvalSteven Bethard, Guergana Savova, Wei-Te Chen, et al.2016 · 263 citations
  11. From Light to Rich ERE: Annotation of Entities, Relations, and EventsZhiyi Song, Ann Bies, Stephanie Strassel, et al.2015 · 263 citations
  12. Pretrained Language Models for Biomedical and Clinical Tasks: Understanding and Extending the State-of-the-ArtPatrick Lewis, Myle Ott, Jingfei Du, et al.2020 · 240 citations
  13. The BioScope corpus: annotation for negation, uncertainty and their scope in biomedical textsGyörgy Szarvas, Veronika Vincze, Richárd Farkas, et al.2008 · 240 citations
  14. Richer Event Description: Integrating event coreference with temporal, causal and bridging annotationTim O'Gorman, Kristin Wright-Bettner, Martha Palmer2016 · 223 citations
  15. Loosely Tree-Based Alignment for Machine TranslationDaniel Gildea2003 · 220 citations
  16. SciREX: A Challenge Dataset for Document-Level Information ExtractionSarthak Jain, Madeleine van Zuylen, Hannaneh Hajishirzi, et al.2020 · 217 citations
  17. Learning Word-Class Lattices for Definition and Hypernym ExtractionRoberto Navigli, Paola Velardi2010 · 201 citations
  18. Appendix F: MUC-7 Coreference Task Definition (version 3.0)Lynette Hirschman, Nancy Chinchor1998 · 186 citations
  19. Learning the Scope of Hedge Cues in Biomedical TextsRoser Morante, Walter Daelemans2009 · 175 citations
  20. Task-oriented Evaluation of Syntactic Parsers and Their RepresentationsYusuke Miyao, Rune Sætre, Kenji Sagae, et al.2008 · 129 citations
  21. Hedge Classification in Biomedical Texts with a Weakly Supervised Selection of KeywordsGyörgy Szarvas2008 · 107 citations
  22. Identifying the Information Structure of Scientific Abstracts: An Investigation of Three Different SchemesYufan Guo, Anna Korhonen, Maria Liakata, et al.2010 · 93 citations
  23. Statistical Anaphora Resolution in Biomedical TextsCaroline Gasperin, Ted Briscoe2008 · 66 citations
  24. A Linguistic Resource for Discovering Event Structures and Resolving Event CoreferenceCosmin Bejan, Sanda Harabagiu2008 · 64 citations
  25. The Arabic Ontology — An Arabic Wordnet with Ontologically Clean ContentMustafa Jarrar2021 · 61 citations
  26. Joint Event Trigger Identification and Event Coreference Resolution with Structured PerceptronJun Araki, Teruko Mitamura2015 · 56 citations
  27. Findings of the WMT 2019 Biomedical Translation Shared Task: Evaluation for MEDLINE Abstracts and Biomedical TerminologiesRachel Bawden, Kevin Bretonnel Cohen, Cristian Grozea, et al.2019 · 54 citations
  28. Overview of BioNLP 2011 Protein Coreference Shared TaskNgan Nguyen, Jin-Dong Kim, Jun'ichi Tsujii2011 · 32 citations
  29. ChEMU-Ref: A Corpus for Modeling Anaphora Resolution in the Chemical DomainBiaoyan Fang, Christian Druckenbrodt, Saber A Akhondi, et al.2021 · 27 citations
  30. The Taming of Reconcile as a Biomedical Coreference ResolverYoungjun Kim, Ellen Riloff, Nathan Gilbert2011 · 27 citations
  31. Pronominal and Sortal Anaphora Resolution for Biomedical LiteratureYu-Hsiang Lin, Tyne Liang2004 · 23 citations
  32. Cross-Document, Cross-Language Event Coreference Annotation Using Event HoppersZhiyi Song, Ann Bies, Justin Mott, et al.2018 · 18 citations
  33. An NP-Cluster Based Approach to Coreference ResolutionXiaofeng Yang, Jian Su, GuoDong Zhou, et al.2004 · 18 citations
  34. Coreference Resolution for the Biomedical Domain: A SurveyPengcheng Lu, Massimo Poesio2021 · 17 citations
  35. Al –-Khalil : The Arabic Linguistic Ontology ProjectHassina Aliane, Zaia Alimazighi, Ahmed Cherif Mazari2010 · 16 citations
  36. Exploiting Coreference Annotations for Text-to-Hypertext ConversionAnke Holler, Jan Frederik Maas, Angelika Storrer2004 · 16 citations
  37. Cross-document coreference: An approach to capturing coreference without contextKristin Wright-Bettner, Martha Palmer, Guergana Savova, et al.2019 · 15 citations
  38. Towards Cross-Domain PDTB-Style Discourse ParsingEvgeny Stepanov, Giuseppe Riccardi2014 · 15 citations
  39. New Arabic Medical Dataset for Diseases ClassificationJaafar Hammoud, Aleksandra Vatian, Natalia Dobrenko, et al.2021 · 14 citations
  40. Medical Term Extraction in an Arabic Medical CorpusDoaa Samy, Antonio Moreno-Sandoval, Conchi Bueno-Díaz, et al.2012 · 13 citations
  41. Towards Ontology Construction with Language ModelsMaurice Funk, Simon Hosemann, Jean Christoph Jung, et al.2023 · 12 citations
  42. Domain Adaptation of Coreference Resolution for Radiology ReportsEmilia Apostolova, Noriko Tomuro, Pattanasak Mongkolwat, et al.2012 · 12 citations
  43. SciCorp: A Corpus of English Scientific Articles Annotated for Information Status AnalysisIna Roesiger2016 · 11 citations
  44. Negation scope and spelling variation for text-mining of Danish electronic patient recordsCecilia Engel Thomas, Peter Bjødstrup Jensen, Thomas Werge, et al.2014 · 9 citations
  45. Developing an Arabic Infectious Disease Ontology to Include Non-Standard TerminologyLama Alsudias, Paul Rayson2020 · 5 citations
  46. Agent-Based Uncertainty Awareness Improves Automated Radiology Report Labeling with an Open-Source Large Language ModelHadas Ben-Atya, Naama Gavrielov, Zvi Badash, et al.2025 · 3 citations
  47. Automatic Suggestions Help Extending Eventive Ontology: A Case Study on SynSemClassJana Straková, Eva Fučíková, Zdenka Uresova, et al.2026 · 1 citation
  48. EPOP: A Benchmark Corpus for Assessing NLP Models on Structured Information Extraction in Plant HealthClaire Nedellec, Marine Courtin, Xinzhi Yao, et al.2026 · 1 citation
  49. Unsupervised Labelling of Mutation Triggers in WelshNicolás Gutiérrez-Rolón, Fernando Alva-Manchego2026 · 1 citation
  50. How to construct a multi-lingual domain ontologyNitsan Chrizman, Alon Itai2014 · 1 citation
  51. Effect of Out Of Vocabulary Terms on Inferring Eligibility Criteria for a Retrospective Study in Hebrew EHRRaphael Cohen, Michael Elhadad2013 · 1 citation
  52. A Dataset of Psychiatric Hospital Notes with Temporal Information AnnotationsTimothy A. Miller, Gaby Dinh, David Harris, et al.2026
  53. Extracting Medical Image-Related Entities from Spanish Electronic Health Records Using NER MethodsAlexander Platas, Marcos Merino, Elena Zotova, et al.2026
  54. JPPB: Automatic Construction of a Soft-Labeled Japanese Patient Phrase Bank for Symptom NormalizationTomohiro Nishiyama, Mana Kuramoto, Shoko Wakamiya, et al.2026
  55. MUC-4 Revisited: Document-level Event Analysis beyond Span-based ArgumentsHelene Bøsei Olsen, Erik Velldal, Lilja Øvrelid2026
  56. Towards Corpus-Based Population and Visualization of ISO 24617-8 Ontology (Short Paper)Maciej Ogrodniczuk, Dariusz Czerski2026
  57. Trustworthy NLP for Low-Resource Languages: Agent-Based Uncertainty Modeling for Hebrew Radiology Report StructuringHadas Ben Atya, Naama Gavrielov, Zvi Badash, et al.2026
  58. Building Patient Journeys in Hebrew: A Language Model for Clinical Timeline ExtractionKai Golan Hashiloni, Brenda Kasabe Nokai, Michal Shevach, et al.2025
  59. Hierarchical Section Matching Prediction (HSMP) BERT for Fine-Grained Extraction of Structured Data from Hebrew Free-Text Radiology Reports in Crohn's DiseaseZvi Badash; Hadas Ben-Atya; Naama Gavrielov; Liam Hazan; Gili Focht; Ruth Cytter-Kuint; Talar Hagopian; Dan Turner;, Moti Freiman2025
  60. Rdgai: Classifying transcriptional changes using Large Language Models with a test case from an Arabic Gospel traditionRobert Turnbull2025
  61. Using English for commonsense knowledgeAllan Ramsay, Debora Field2009

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