MarkushGlyph

Installing the code

The commands below use the glyph package. Install it from the code repository:

git clone https://github.com/EdisonScientific/glyph
cd glyph
uv venv && uv sync --extra markush # or: pip install -e ".[markush]"

See the repo's README.md (quickstart + inference) and REPRODUCE.md (frozen eval contract).

Markush chemical structure recognition: image -> CXSMILES. A LoRA adapter (r=128, alpha=128) over Qwen/Qwen3.5-2B-Base.

Results - IP5-M (n=878, official DS4SD paired scoring contract)

System	Accuracy
MarkushGrapher-2 (baseline)	467/878 = 53.19%
MarkushGlyph - greedy	511/878 = 58.20%
MarkushGlyph - MV@8	532/878 = 60.59%

Usage

python -m glyph.markush.eval.fast_eval \
 --checkpoint EdisonScientific/MarkushGlyph --base-model Qwen/Qwen3.5-2B-Base --eval-data <eval_ip5m.jsonl> ...

Scored with the pinned DS4SD get_scores (official contract). See the code repository's REPRODUCE.md.

License: pending. Citation: to be added on publication.