Metadata harmonization from biological datasets with language models
All datasets used in this study, including training, validation, and test splits, are available via the Netrias Hugging Face organization. This includes datasets for the cancer and alcohol-bacteria mix domains used to develop and evaluate harmonization models. Experiment results are provided in the Supplementary Materials. We also share one representative GPT-2 Large cancer model and five GPT-2 Large models trained on different alcohol-bacteria domain mixtures: (100/0, 75/25, 50/50, 25/75, 0/100). All resources are released under the Apache 2.0 license to support reproducibility and reuse.
Authors
- Mohammed Eslami (ORCID: https://orcid.org/0000-0001-5488-1542)
- Patrick Boutet
- Alexander Verbitsky
Institutions
- Maryland Department of Natural Resources (US)
Publication Details
- Journal
- Bioinformatics Advances
- Published
- 2024-12-26
- DOI
- https://doi.org/10.1093/bioadv/vbaf241
- Citations
- 1
- Primary Topic
- Biomedical Text Mining and Ontologies
- Type
- article
- Field-Weighted Citation Impact
- 0.23
Funders
- National Institutes of Health
- Advanced Research Projects Agency
- National Cancer Institute
- Center for Biomedical Informatics and Information Technology, National Cancer Institute