diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..5a9d51a5fb4af428c19fc14991a42b91836efa54 --- /dev/null +++ b/README.md @@ -0,0 +1,85 @@ +--- +license: cc-by-nd-4.0 +tags: +- TFBS +- transcription-factor +- genomics +- mixture-of-experts +- DNA +library_name: pytorch +pretty_name: ENCODE-TFBS Heterogeneous Mixture-of-Experts checkpoints +datasets: +- Lab-Rasool/ENCODE-TFBS +--- + +# ENCODE-TFBS — Heterogeneous Mixture-of-Experts checkpoints + +Trained model checkpoints for **robust transcription-factor binding-site (TFBS) prediction with a +heterogeneous Mixture-of-Experts (MoE)**. A dense, soft MoE gates over per-expert *embeddings* from a +heterogeneous expert zoo (modified-DeepBIND **ConvNet** + **DeepSEA** + **DanQ**, each probed to a +common 32-dim embedding), which improves **out-of-distribution (OOD)** generalization to unseen +transcription factors. + +These weights back the paper *"Robust Transcription Factor Binding Site Prediction and Explainability +Using a Heterogeneous Mixture of Experts Architecture."* Code, training and evaluation pipeline: +**https://github.com/lab-rasool/TFBS**. Training/eval data: **[Lab-Rasool/ENCODE-TFBS](https://huggingface.co/datasets/Lab-Rasool/ENCODE-TFBS)**. + +## Headline result (genomic, fair-negative protocol, 7 training factors) + +Feeding the unchanged embedding-gating MoE a heterogeneous expert pool beats a fine-tuned DNABERT-6 +baseline on the motif-bearing OOD strata, averaged over seeds 0/1/42: + +| Model | OOD AUC (mean ± std) | +|---|---| +| **HetMoE (this work)** | **0.821 ± 0.005** | +| DNABERT-6 | 0.799 ± 0.008 | + +Margin **+0.022**. Per-seed: seed 42 → 0.827, seed 0 → 0.818, seed 1 → 0.819. + +## Repository contents + +``` +experts/.pth 7 ConvNet experts (modified DeepBIND), one per training TF +hyperparams/.pth per-expert hyperparameters (reproduce training without Optuna) +moe/moe_model.pth homogeneous ConvNet-only MoE gate (+ moe_model_config.pth) +zoo/seed{0,1,42}/ heterogeneous zoo probes — DeepSEA_.pth, DanQ_.pth + (E=32 FeatureProbeExpert heads over frozen DeepSEA/DanQ trunks) +``` + +The genomic HetMoE for a given seed is the **21-expert** pool: the 7 `experts/` ConvNets plus the +14 `zoo/seed/` DeepSEA + DanQ probes, with the `MixtureOfExperts` gate applied unchanged over the +concatenated 32-dim embeddings. Only the three paper seeds (0, 1, 42) are published here. + +**Transcription factors.** Training: `ARID3A, FOXM1, GATA3, JUND, MAX, GABPA, SP1`. OOD evaluation is +stratified into within-family, cross-family (e.g. CTCF, STAT3), cell-line-transfer, and a separately +reported non-motif appendix — see `tfbs/constants.py` in the code repo. + +## Usage + +Install the `tfbs` package and load with the provided classes (`map_location` handles CPU-only nodes): + +```python +from huggingface_hub import hf_hub_download +import torch +from tfbs.models import ConvNet, MixtureOfExperts # pip install -e . from github.com/lab-rasool/TFBS + +ckpt = hf_hub_download("Lab-Rasool/ENCODE-TFBS", "experts/GATA3.pth") +state = torch.load(ckpt, map_location="cpu", weights_only=True) +``` + +See the GitHub repo's README and `experiments/hetmoe/` for the full caching + gating pipeline that +rebuilds the heterogeneous MoE from these checkpoints. DNABERT-6 features are derived on the fly from +`zhihan1996/DNA_bert_6`; no BERT weights are stored here. + +## Reproducibility + +The ConvNet conv bias (`wRect`) is a saved `nn.Parameter` and expert order is pinned to +`tfbs.constants.TRAIN_TFS`, so re-running evaluation from these checkpoints is byte-identical on a +given machine (minor device-numerics differences may remain across machines). + +## License + +`cc-by-nd-4.0`, matching the [ENCODE-TFBS dataset](https://huggingface.co/datasets/Lab-Rasool/ENCODE-TFBS). +The underlying ENCODE data are from the ENCODE Project. + + diff --git a/experts/ARID3A.pth b/experts/ARID3A.pth new file mode 100644 index 0000000000000000000000000000000000000000..6d9dbfdb1c80ecb24cf6bc26aa1c9598f5e44772 --- /dev/null +++ b/experts/ARID3A.pth @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4efd60a57c44b1e64843e95edb2e11cc165cde205130e8e9c6cf39161ccf8055 +size 14015 diff --git a/experts/FOXM1.pth b/experts/FOXM1.pth new file mode 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