Fine-Tuning Models for Biomedical Relation Extraction
Mirrored from arXiv — NLP / Computation & Language for archival readability. Support the source by reading on the original site.
Computer Science > Computation and Language
Title:Fine-Tuning Models for Biomedical Relation Extraction
Abstract:Next-Generation Sequencing has revolutionized the study of genetic mutations, enabling large-scale investigations into their roles in disease development. However, extracting meaningful insights from the vast amount of biomedical literature remains a complex challenge that cannot be addressed manually. In this paper, we present pre-trained models (PTMs) for the automatic extraction of relations from biomedical text, specifically targeting the variant-phenotype domain. Our evaluation on the SNPPhenA corpus demonstrates that fine-tuning small BERT-based models, particularly DeBERTa, yields strong performance, approaching the current state-of-the-art (SOTA). Additionally, our results indicate that carefully fine-tuning Google's Gemini Pro 1.0 outperforms the existing SOTA for both sentence-level tasks (where the model processes only the target sentence) and abstract-level tasks (where the model processes the entire abstract).
| Subjects: | Computation and Language (cs.CL) |
| Cite as: | arXiv:2609.20169 [cs.CL] |
| (or arXiv:2609.20169v1 [cs.CL] for this version) | |
| https://doi.org/10.48550/arXiv.2609.20169
arXiv-issued DOI via DataCite (pending registration)
|
Access Paper:
- View PDF
- TeX Source
References & Citations
Bookmark
Bibliographic and Citation Tools
Code, Data and Media Associated with this Article
Demos
Recommenders and Search Tools
arXivLabs: experimental projects with community collaborators
arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website.
Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them.
Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
More from arXiv — NLP / Computation & Language
-
A Mechanistic Study of AI-Text Detection Neurons in Frozen BERT: Sparse Probing and Activation Patching on RAID
Sep 28
-
Manifold Projection and Iterative Autoencoder Refinement for Masked Language Modeling
Sep 28
-
Not All Memories Are Equal: Hierarchical Collaborative Memory for Validity-Aware Retrieval in LLM Agents
Sep 28
-
Auditing and Repairing LLM-as-Judge Failures in a Production Text-to-SQL Pipeline
Sep 28
Discussion (0)
Sign in to join the discussion. Free account, 30 seconds — email code or GitHub.
Sign in →No comments yet. Sign in and be the first to say something.