README.md

metadata

title: HistAgent Chat
emoji: 🧬
colorFrom: indigo
colorTo: red
sdk: gradio
sdk_version: 5.44.1
app_file: app.py
pinned: false
license: other
models:
  - Qwen/Qwen3-8B
  - Qwen/Qwen3-Embedding-8B
datasets:
  - wli13/HistAgent-data
tags:
  - histopathology
  - spatial-transcriptomics
  - biology
  - chat
  - retrieval

HistAgent Chat

HistAgent Chat answers questions about selected tissue spots using ranked genes, cell-state estimates, functional programs and spatial context contained in a structured evidence card.

The online demonstration uses Qwen3-8B with the HistAgent evidence-card schema, system policy and evidence constraints. The interface therefore describes the language-model component as adapted Qwen3-8B. It does not expose chain-of-thought and is intended for research use.

The Atlas Explorer tab searches a balanced public index of 100,000 measured ST spots using 4,096-dimensional Qwen3-Embedding-8B vectors and cosine similarity. The demonstration index and checksum manifest are published in the HistAgent public evidence-bank release. The manuscript analyses use the complete 2.23-million-spot evidence bank.