README.md

metadata

pretty_name: Glyph Datasets
license: apache-2.0
language:
  - en
task_categories:
  - image-to-text
size_categories:
  - 100K<n<1M
tags:
  - chemistry
  - cheminformatics
  - ocsr
  - markush
  - chemical-structure-recognition
  - smiles
  - cxsmiles
configs:
  - config_name: markush-train
    data_files:
      - split: train
        path: markush/train.jsonl

glyph-datasets

Data artifacts for Glyph — chemical-structure transcription with two models: OCSRGlyph (molecule image → SMILES) and MarkushGlyph (patent Markush image → CXSMILES + R-group table). This repository holds the training indices, training metadata, and the frozen self-contained evaluation benchmarks that the glyph package auto-downloads.

• Code: EdisonScientific/glyph (GitHub)
• Weights: EdisonScientific/OCSRGlyph, EdisonScientific/MarkushGlyph
• License: Apache-2.0. See License.
• Citation: TBD — the BibTeX entry and arXiv identifier will be added on release. See Citation.

Redistribution classes

Artifacts fall into three classes; every subdirectory README.md / *.provenance.json sidecar records the class per file.

• (a) Referenced upstream — pulled from the pinned public source at load time and not re-hosted here (the raw OCSR training images, the MolNexTR CSVs, the raw Markush source images).
• (b) Transformed metadata — derived label / index / subset files (SMILES + relative paths, the mined adjacent_ring subset, the flat Markush training index). These carry no upstream image bytes.
• (c) Embedded copies — the frozen self-contained eval parquets, which do embed the benchmark images and labels so glyph … eval runs with no local reconstruction: the 5,719 OCSR benchmark images (ocsr/uspto_ocsr_benchmark.parquet) and the 1,055 Markush eval images (878 + 103 + 74 across the three markush-eval/* parquets). These images are public-domain USPTO patent depictions / the pinned public MarkushGrapher-2 benchmark; they are re-hosted only inside these frozen benchmark copies.

Artifact map

Path	Rows	Class	Purpose
ocsr/uspto_ocsr_5719_complete.csv	5,719	(b)	USPTO-OCSR-5719 complete labels (label sidecar).
ocsr/uspto_ocsr_benchmark.parquet	5,719	(c)	Frozen self-contained OCSR benchmark (images + labels embedded); the file glyph ocsr eval downloads.
ocsr/adjacent_ring.csv	64,752	(b)	This work: pure-logic mined subset of PubChem-1M (OCSR enrichment).
ocsr/stereo_200k/{train,val}.csv	200,000 / 2,000	(b)	Stereo-200K SMILES + relative image paths (images re-fetched).
ocsr/stereo_200k_white/{train,val}.csv	200,000 / 2,000	(b)	White-cropped Stereo-200K variant (this work's preprocessing).
ocsr/ocsrglyph-recipe.json	—	—	OCSRGlyph training recipe (hyperparameters).
markush/train.jsonl	263,158	(b)	Frozen flat MarkushGlyph training index (exact order, repeats intact).
markush/manifest.json	—	—	Flat-index metadata (schema, counts, source revisions, integrity).
markush-eval/ip5m/ip5m_benchmark.parquet	878	(c)	Frozen self-contained IP5-M eval benchmark (images embedded).
markush-eval/ip5m/ds4sd_mg2_predictions_878.jsonl	878	(b)	DS4SD MarkushGrapher-2's own IP5-M eval output: ground truth + MG2 baseline.
markush-eval/m2s/m2s_benchmark.parquet	103	(c)	Frozen self-contained M2S eval benchmark (images embedded).
markush-eval/m2s/ds4sd_mg2_gt_103.jsonl	103	(b)	Derived M2S ground truth for the official DS4SD scorer.
markush-eval/uspto_markush/uspto_markush_benchmark.parquet	74	(c)	Frozen self-contained USPTO-Markush eval benchmark (images embedded).
markush-eval/uspto_markush/ds4sd_mg2_gt_74.jsonl	74	(b)	Derived USPTO-Markush ground truth for the official DS4SD scorer.

Every data artifact has a companion *.provenance.json (source repo + pinned revision, transformation, counts, integrity hash). Row counts are data rows; each CSV also carries a 1-line header.

Per-artifact schemas

OCSR

• uspto_ocsr_5719_complete.csv — image_id, smiles, source_of_label.
• uspto_ocsr_benchmark.parquet — id, image (struct<bytes, path>), mol, smiles, selfies, inchi, source_of_label; image bytes present for all 5,719 rows, zero null SMILES.
• adjacent_ring.csv — pubchem_cid, InChI, SMILES, num_atoms.
• stereo_200k/*.csv, stereo_200k_white/*.csv — SMILES, file_path (relative image path; images re-fetched from Robert-zwr/Stereo-200k).

Markush

• train.jsonl — one JSON object per line: source, source_id, images (list of images/<source>/train/<source_id>.png), messages (a user + assistant chat turn). See manifest.json for the full contract, per-source counts, and source revisions.

Markush eval

• *_benchmark.parquet — id, image (struct<bytes, path>), benchmark, record (record is the JSON of the prepared eval row); image bytes present for all rows.
• ip5m/ds4sd_mg2_predictions_878.jsonl — id, cxsmiles (MG2 baseline prediction), cxsmiles_opt, gt_cxsmiles (DS4SD ground truth; 8 unparseable rows kept as null), gt_cxsmiles_opt.
• m2s/ds4sd_mg2_gt_103.jsonl, uspto_markush/ds4sd_mg2_gt_74.jsonl — id, gt_cxsmiles, gt_cxsmiles_opt (derived ground truth; no MG2 baseline column, since no DS4SD model run is published for these two benchmarks).

Usage

The glyph package resolves these artifacts automatically — no manual huggingface-cli step.

# OCSR headline: the benchmark parquet auto-downloads from this repo.
uv run glyph ocsr eval --checkpoint EdisonScientific/OCSRGlyph --output uspto5719.json

# Markush: the self-contained benchmark auto-downloads; STEP 2 auto-pulls the
# matching ground truth from markush-eval/<name>/.
uv run glyph markush eval benchmark --benchmark ip5m \
    --checkpoint EdisonScientific/MarkushGlyph --base-model Qwen/Qwen3.5-2B-Base \
    --output preds.json
tools/mg2_scorer/score_benchmark.sh --benchmark ip5m --input-json preds.json

# Markush training: the flat index auto-downloads with hub:markush/train.jsonl.
uv run python -m glyph.markush.train.sft \
    --config configs/ablations/ocsr-as-markush-fraction/sft_2b_markush_ocsr5pct.yaml \
    --data-path hub:markush/train.jsonl

See the code repository's REPRODUCE.md for the exact commands, expected counts, pinned revisions, and both Markush scoring contracts.

License

Apache-2.0 (same as the code repository). Each referenced upstream source keeps its own license — see the per-subdirectory README.md and *.provenance.json sidecars for attribution (PubChem, MolNexTR, MolSight/Stereo-200K, MolScribe, hheiden/USPTO_OCSR_benchmark, docling-project/MarkushGrapher-Datasets and -2-Datasets, UniParser/MolParser-7M). The embedded benchmark images are public-domain USPTO patent depictions / the pinned public MarkushGrapher-2 benchmark.

Citation

TBD. This data accompanies the paper Chemical Structure Transcription Across Molecules; the BibTeX entry and arXiv identifier will be added on release.