t2know-biobert: BioBERT span classifier (flat, multi-label BIO)

Baseline model trained on the T2KNOW corpus (Huntington's disease abstracts, 40 UMLS-derived labels, nested and same-span multi-label entities). Three training seeds are provided in seed_12345/, seed_23456/ and seed_34567/.

• Base model: dmis-lab/biobert-base-cased-v1.1
• Corpus: T2KNOW v1.0.1 (Zenodo DOI: 10.5281/zenodo.23801223)
• Paper: under review; the citation will be added on publication.
• Code: release archive code/ (Zenodo DOI above)

Usage

The checkpoint uses the custom BertForSpanClassification head from the release code (code/flat_baselines/modeling.py); it cannot be loaded with a stock AutoModel head. Decode with logit_threshold=0.5 and start_confidence=0.9 (decoding.json), which were selected on the validation split.

Training data

Trained on the T2KNOW v1.0 document-disjoint train split (validation split for model selection). The v1.0 sentence-level split files contained duplicated sentence records; the corrected release v1.0.1 removes them without changing any annotation. No source text is included in this repository.

Test results

Overlap-aware scores from the official T2KNOW evaluator (partial span matches count half) on the de-duplicated T2KNOW v1.0.1 test split (151 documents, 1,413 sentences, 12,579 entities). Predictions are the archived outputs of these checkpoints.

Seed	Precision	Recall	F1
12345	0.5233	0.7396	0.6130
23456	0.5309	0.7383	0.6177
34567	0.5323	0.7289	0.6153

Mean F1 over the three seeds: 0.6153 (population std 0.0019).

Limitations

Scores measure agreement with the T2KNOW annotation layer (expert-checked, single annotator, see the paper), not semantic correctness. Very-low-support labels are unreliable.

Licence

Apache License 2.0, following the base model: BioBERT is released under Apache 2.0 (https://github.com/dmis-lab/biobert, LICENSE; the Hugging Face model page carries no licence tag). T2KNOW annotations used for training are MIT-licensed; no third-party source text is included.

Repository: https://huggingface.co/edugredu/t2know-biobert