bionerd-re — C (BiomedBERT, BioRED typed relations)

BioNERD's own typed relation-extraction model "C": microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext (MIT) fine-tuned on the BioRED Train split (public domain) as an entity-marker sequence classifier.

• Input: text with [E1] … [/E1] and [E2] … [/E2] around the two arguments (the four marker tokens are in the tokenizer).
• Labels: 0 = None, then BioRED's eight types in this order: Association, Positive_Correlation, Negative_Correlation, Bind, Cotreatment, Comparison, Drug_Interaction, Conversion.
• Training: seed 13, lr 2e-5, batch 16, up to 5 epochs, max length 512, 2 negatives per positive; the best epoch on BioRED Dev typed F1 was kept.

No accuracy is claimed here. BioNERD shows its measured labels in the app's model catalog, each tied to this exact artefact.

File	sha256
config.json	6ac24d941178b632550aa2cb2c81594b9c88463bea01c32c5712064afbb23732
model.safetensors	7a96681585571fa82910d3e547bd71ff83eb5285c0859a37ae272116bbcca598
tokenizer_config.json	8b1605c818426817b2b46a1dbf23e834c7fc893a1a04cbda394382d719cb553a
tokenizer.json	8c801ddf1fd1e9591578b90b7e3fa2bc895d80af941ae967f1f1869ea75aaca4