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

Institutions

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

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Metadata harmonization from biological datasets with language models

Mohammed Eslami, Patrick Boutet, Alexander Verbitsky
1 citations
Bioinformatics Advances
Biomedical Text Mining and Ontologies
0.23
article

Metadata harmonization from biological datasets with language models

Mohammed Eslami, Patrick Boutet, Alexander Verbitsky
article en
1 citations

Abstract

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.

Bioinformatics AdvancesVol. 5(1)
Maryland Department of Natural Resources (US)
National Institutes of Health, Advanced Research Projects Agency, National Cancer Institute, Center for Biomedical Informatics and Information Technology, National Cancer Institute
Openalex Percentile: Top 39%
Biomedical Text Mining and Ontologies
0.23
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.