README.md

metadata

title: MarkushGlyph
emoji: 🧪
colorFrom: gray
colorTo: purple
sdk: gradio
sdk_version: 6.23.1
app_file: app.py
short_description: Extract Markush CXSMILES from chemical structure images
python_version: '3.12'
startup_duration_timeout: 30m

MarkushGlyph — Markush Structure Recognition

This Space demonstrates MarkushGlyph, a vision-language model (LoRA fine-tune of Qwen3.5-2B-Base) that converts images of patent Markush chemical structures into CXSMILES strings.

How it works

1. Upload an image of a chemical structure (Markush or ordinary molecule).
2. The model extracts the structure and returns it in the XML format <markush><cxsmi>...</cxsmi><stable>...</stable></markush>.
3. The CXSMILES core and stable-group definitions are displayed separately for easy copying.

Model

• Base model: Qwen/Qwen3.5-2B-Base
• LoRA adapter: EdisonScientific/MarkushGlyph (r=128, alpha=128)
• Code: github.com/EdisonScientific/glyph (Apache-2.0)

Example images

The example images are from the glyph repository (Apache-2.0 license):

• markush_m2s_13.png — a Markush structure crop from the M2S benchmark
• imatinib.png — the drug imatinib (C₂₉H₃₁N₇O)
• cholesterol_ester.png — a cholesterol ester structure