README.md

---
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/<TF>.pth            7 ConvNet experts (modified DeepBIND), one per training TF
hyperparams/<TF>.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_<TF>.pth, DanQ_<TF>.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<N>/` 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.
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