Published November 12, 2023 | Version v1
Conference proceeding Open

Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models

Creators

  • 1. National Library of Medicine, National Institutes of Health, Bethesda, MD
  • 2. Department of Computer & Information Sciences, University of Delaware, Newark, DE
  • 3. Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
  • 4. Cedar Sinai, Los Angeles, CA
  • 5. The MITRE Corporation, Bedford, Massachusetts
  • 6. Barcelona Supercomputing Center, Barcelona

Description

Table of Contents 

1. The BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models. Islamaj et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

Track 1: BioRED (Biomedical Relation Extraction Dataset)

2. BioRED (biomedical relation extraction dataset) Track Overview at BioCreative VIII. Islamaj et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

3. The corpus of the BioRED Track at BioCreative VIII. Islamaj et al.  Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

4. BioRED task DUTIR-901 submission: Enhancing Biomedical Document-Level Relation Extraction through Multi-Task Method. Li et al.  Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

5. BIT.UA at Biocreative VIII track 1: A joint model for relation classification and novelty detection. Almeida et al.  Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

6. Probability model with Ensemble learning and Data augmentation for named entity recognition (NER) and relation extraction (RE) tasks. Phan et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

7. BioRED task NCU-IISR submission: Preprocessing-Robust Ensemble Learning Approach for Biomedical Relation Extraction. Meesawad et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

8. Exploring Biomedical Relation Extraction through ChatGPT Augmentation and Dual Training. Yu et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

9. UIUC-BioNLP @ BioCreative VIII BioRED Track. Sarol et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

10. TTI-COIN at BioCreative VIII Track 1. Matsubara et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

11. An End-to-End Approach for Asserted Named Entity Recognition and Relationship Extraction in Biomedical Text. Salem et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

12. BioRED track lasigeBioTM submission: Relation Extraction using Domain Ontologies with BioRED. Conceição et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

13. EMBRE Entity-aware Masking for Biomedical Relation Extraction. Li et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

14. Assessing the state of the art in biomedical relation extraction: evaluating ChatGPT, PubMedBERT and BioREx for the BioRED track at BioCreative VIII. Lai et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

Track 2: SympTEMIST (Symptom TExt Mining Shared Task)

15. Overview of SympTEMIST at BioCreative VIII: corpus, guidelines and evaluation of systems for the detection and normalization of symptoms, signs and findings from text. Lima-López et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

16. HPI-DHC @ BC8 SympTEMIST Track: Detection and Normalization of Symptom Mentions with SpanMarker and xMEN. Borchert et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

17. Team BIT.UA @ BC8 SympTEMIST Track: A Two-Step Pipeline for Discovering and Normalizing Clinical Symptoms in Spanish. Jonker et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

18. Team Fusion@SU @ BC8 SympTEMIST track: Transformer-based Approach for Symptom Recognition and Linking. Grazhdanski et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

19. FRE @ BC8 SympTEMIST track: Named Entity Recognition. Martínez et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

20. PicusLab @ BC8 SympTEMIST track: Disambiguating Entity Linking Candidates with Question Answering. Cirillo et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

21. IIC/UC3M @ BC8 SympTEMIST track: RigoBERTa and Domain Adaptation for SympTEMIST Subtask1. García-Subies et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

22. ICB-UMA at BioCreative VIII @ AMIA 2023 Task 2 SYMPTEMIST (Symptom TExt Mining Shared Task). Gallego et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

23. Fine-Tuned Large Language Models for Symptom Recognition from Spanish Clinical Text. Shaaban et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

24. Symptom normalization using unsupervised learning and text similarity. Kavak et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

25. An exploratory approach to the SympTEMIST challenge. Castaño et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

Track 3: Phenotype normalization (genetic conditions in pediatric patients)

26. BioCreative VIII – Task 3: Genetic Phenotype Normalization from Dysmorphology Physical Examinations. Weissenbacher et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

27. UTH-Olympia@BC8 Track 3: Adapting GPT-4 for Entity Extraction and Normalizing Responses to Detect Key Findings in Dysmorphology Physical Examination Observations. Soysal et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

28. DUTIR-BioNLP@BC8 Track 3: Genetic Phenotype Extraction and Normalization with Biomedical Pre-trained Language Models. Qi et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

29. KU AIGEN ICL EDI@BC8 Track 3: Advancing Phenotype Named Entity Recognition and Normalization for Dysmorphology Physical Examination Reports. Kim et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

30. DiscHPO@BC8 Track 3: Recognising and Normalising Continuous and Discontinuous Genetic Phenotypes Using T5 Variants and Sentence-Transformers Models. Alhassan et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

31. IKMLab@BC8 Track 3: Sequence Tagging for Position-Aware Human Phenotype Extraction with Pre-trained Language Models. Lin et al. Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, XX-XX. PDF

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