PanMET
PanMET is a genome-aware foundation-model framework for RNA sequencing and DNA methylation. It combines independently pretrained modality towers, leakage-free cross-modal alignment, and masked bidirectional cross-modal reconstruction.
This repository contains the retained canonical model weights in the safe,
tensor-only safetensors format:
| Directory | Contents |
|---|---|
rna_stage_a/ |
RNA tower and training/configuration metadata |
methylation_stage_a/ |
Methylation tower, projection head, and metadata |
stage_b/ |
Leakage-free cross-modal alignment model |
stage_c/ |
Final fusion model and RNA/methylation reconstruction decoders |
The original training checkpoints contained optimizer and scheduler state.
Those training-only objects are intentionally excluded. Patient split
manifests are also excluded. manifest.json records SHA-256 hashes for every
source checkpoint and exported artifact, and every exported tensor was checked
for exact equality after serialization.
Loading weights
PanMET uses a custom PyTorch architecture from the
PanMET source repository. Download a
component and load its state dictionary with safetensors:
from huggingface_hub import hf_hub_download
from safetensors.torch import load_file
path = hf_hub_download(
repo_id="alexalexak/PanMET",
filename="stage_c/model.safetensors",
)
state_dict = load_file(path, device="cpu")
model.load_state_dict(state_dict, strict=True)
Stage C reconstruction uses stage_c/rna_decoder.safetensors and
stage_c/methylation_decoder.safetensors in addition to the Stage C model.
Architecture construction, preprocessing, and inference adapters are provided
in the source repository.
Model inputs
- RNA sequencing: 9,721 genomically ordered genes
- DNA methylation: 27,183 ordered CpG islands in 65 chromosome-aware chunks
Input feature identity, order, and preprocessing must match the training caches. The model is intended for research use and is not a clinical device.
Citation
The PanMET manuscript is in preparation. Citation information will be updated when it becomes available.