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wli13/
HistAgent

peft

safetensors

computational-pathology

spatial-transcriptomics

prov-gigapath/prov-gigapath

adapter

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HistAgent

HistAgent is a visual-omics foundation model that generates ranked molecular readouts from routine H&E images. It combines a spot-centred image with surrounding tissue context and autoregressively predicts the top 50 genes for each location.

Model details

Property	Value
Base encoder	`prov-gigapath/prov-gigapath` tile encoder
Vision adaptation	LoRA, rank 16, alpha 32
Image inputs	Paired local and context H&E views
Decoder	Six-layer Transformer decoder, hidden size 512
Output	Ranked sequence of up to 50 genes
Vocabulary	44,538 genes plus four special tokens
Species conditioning	Human, mouse or unknown
Organ conditioning	32-entry training vocabulary

The repository contains only the trained LoRA parameters and HistAgent-specific modules. The frozen GigaPath base weights are loaded separately from the official gated repository.

Training data

The model was trained on 2.23 million paired H&E–ST locations from 936 human and mouse 10x Visium slides spanning 32 tissue categories. The release checkpoint corresponds to epoch 30 of the GigaPath training run.

Use

Install the accompanying code:

bash

git clone https://github.com/zipging/HistAgent.git
cd HistAgent
pip install -e .

Request access to Prov-GigaPath, set HF_TOKEN, and load the model:

python

from histagent import load_pretrained

model, tokenizer, config = load_pretrained("wli13/HistAgent", device="cuda")

See the GitHub repository for image preprocessing and ranked-gene inference examples.

Intended use and limitations

This model is intended for research on computational pathology and spatial molecular biology. It predicts rank-based molecular readouts rather than transcript counts. Performance can vary with tissue type, staining, scanner characteristics, image resolution and preprocessing. Predictions require independent biological validation and are not intended for clinical diagnosis or treatment decisions.

Citation

The HistAgent manuscript and citation will be added when publicly available.