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jiosephlee/intern-s1-mini-context-conditioned-molecule-transfer-v10-3-tdc-v2-hp-bioavailability-ma-best

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Intern-S1-mini context-conditioned molecule transfer V10.3 TDC-v2-HP — Oral bioavailability

Validation-selected checkpoint from the direct-inclusive TDC-v2-HP Oral bioavailability run. This was the best held-out macro-F1@5 result among the indirect-only and Starling-direct TDC variants.

Provenance

—Base model: jiosephlee/Intern-S1-mini-lm
—Base model revision: fcb667c380ae01f57693a45b4b5c2d331052a107
—Training dataset: jiosephlee/context-conditioned-molecule-transfer-v10.3-tdc-v2-hp-bioavailability-ma-mixed-continuous-intern
—Dataset revision: 9db99d12536f5dbb3d906ab90e5acff1b036405c
—Training data: 49,224 direct records, including TDC and Starling direct data, plus 49,224 indirect records
—Training configuration: 10 scheduled epochs, seed 42, soft-target loss, 8 GPUs, device batch size 4, gradient accumulation 4, Flash Attention 2, BFD packing, and padding-free training
—Selection metric: validation knn_binary_macro_f1_at_5
—Selected optimizer step: 80
—Selected validation macro-F1@5: 0.6297
—Training was intentionally stopped at step 202 of 440; this repository contains the saved step-80 validation-selected checkpoint.
—Training run
—Held-out model/Morgan comparison

Held-out test comparison

Ranker	Macro-F1@3	Macro-F1@5	Spearman@3	Top-1 hit@3
Model	0.5657	0.5657	0.5774	0.7266
Morgan vanilla	0.5987	0.5060	-0.0207	0.9297
Morgan weighted	0.6169	0.5439	-0.0142	0.9219

Checkpoint selection and the TDC-variant comparison use macro-F1@5. All model and Morgan test metrics are available in the linked W&B evaluation run.

The repository contains the full Transformers checkpoint and tokenizer files. metric.json is the complete validation-selection record stored with the checkpoint.