como-ocsr 1.2.1

COMO: Closed-loop Optical Molecule recOgnition with Minimum Risk Training

COMO

COMO (Closed-loop Optical Molecule recOgnition) is a deep learning framework that recognizes chemical structure diagrams from images and predicts SMILES strings with atom-level coordinates and bond matrices. It uses Minimum Risk Training (MRT) to directly optimize molecular-level, non-differentiable objectives.

Installation

pip install como-ocsr

Quick Start

import como

# Load a model checkpoint (on GPU 0)
model = como.load_model("path/to/checkpoint.pth", device="cuda:0")

# Predict SMILES from a single image
smiles = como.predict(model, "molecule.png")
print(smiles)  # "CC(=O)O"

# Batch prediction on a specific GPU
smiles_list = como.predict_batch(model, ["mol1.png", "mol2.png"], device="cuda:1")

# Evaluate on a benchmark (single GPU by default)
metrics = como.evaluate(
    model,
    benchmark_dir="benchmark/USPTO/",
    csv_path="benchmark/USPTO.csv",
)
print(f"Exact Match: {metrics['postprocess/exact_match_acc']:.2%}")

# Multi-GPU, multi-benchmark evaluation
benchmarks = [
    {"name": "USPTO", "benchmark_dir": "benchmark/USPTO/",
     "csv_path": "benchmark/USPTO.csv"},
    {"name": "CLEF",  "benchmark_dir": "benchmark/CLEF/",
     "csv_path": "benchmark/CLEF_corrected.csv"},
]
results = como.evaluate_benchmarks(model, benchmarks, gpus="0,1,2,3")
for name, m in results.items():
    print(f"{name}: {m['postprocess/exact_match_acc']:.2%}")

API Reference

GPU Selection

All functions accept a device parameter for single-GPU usage:

model = como.load_model("checkpoint.pth", device="cuda:0")
como.predict(model, "img.png", device="cuda:1")
como.predict_batch(model, [...], device="cuda:2")

For evaluation (which uses multi-GPU internally via mp.spawn), use the gpus parameter:

Function	GPU control
load_model	device="cuda:0"
predict	device="cuda:0"
predict_batch	device="cuda:0"
evaluate	gpus="0" (default), gpus="0,1,2", gpus=None (all)
evaluate_benchmarks	gpus="0" (default), gpus="0,1,2", gpus=None (all)

---

como.load_model(checkpoint_path, device="cuda", **kwargs)

Load a COMO model from a .pth checkpoint. Returns a :class:ComoModel instance in evaluation mode.

Parameter	Type	Default	Description
checkpoint_path	str	required	Path to .pth checkpoint
device	str	"cuda"	"cuda", "cuda:0", or "cpu"

Returns: ComoModel

---

como.predict(model, image, *, beam_size=1, max_len=500, smiles_mode="postprocess", device=None)

Predict the SMILES string for a single molecular image.

Parameter	Type	Default	Description
model	ComoModel	required	A loaded model
image	str / np.ndarray / PIL.Image / torch.Tensor	required	Input image (file path, array, PIL, or preprocessed tensor)
beam_size	int	1	Beam width (1 = greedy, 3 = beam search)
max_len	int	500	Maximum number of tokens to generate
smiles_mode	str or None	"postprocess"	"postprocess" (best quality), "graph", "decoder", or None (raw result dict)
device	str or None	None	Optional device override (e.g. "cuda:1")

Returns:

• str — predicted SMILES string (if smiles_mode is not None)
• dict — full result dict with keys tokens, symbols, coords, bond_mat, decode_smiles, success (if smiles_mode=None)

---

como.predict_batch(model, images, *, beam_size=1, max_len=500, smiles_mode="postprocess", device=None)

Batch prediction on a single GPU.

Parameter	Type	Default	Description
model	ComoModel	required	A loaded model
images	list	required	List of file paths, NumPy arrays, PIL Images, or tensors
beam_size	int	1	Beam width (1 = greedy, recommended for batch)
max_len	int	500	Maximum tokens per image
smiles_mode	str or None	"postprocess"	SMILES reconstruction mode
device	str or None	None	Optional device override

Returns:

• list[str] — predicted SMILES for each image (if smiles_mode is not None)
• list[dict] — raw result dicts (if smiles_mode=None)

---

como.evaluate(model, benchmark_dir, csv_path, *, beam_size=1, postproc_workers=32, tautomer_standardize=True, gpus="0")

Evaluate on a single benchmark dataset. Returns a flat dict of metrics.

Parameter	Type	Default	Description
model	ComoModel	required	A loaded model
benchmark_dir	str	required	Directory containing .png images
csv_path	str	required	CSV with columns image_id, SMILES
beam_size	int	1	Beam width for decoding
postproc_workers	int	32	Parallel workers for SMILES post-processing
tautomer_standardize	bool	True	Include tautomer-normalized exact match
gpus	str or None	"0"	GPU IDs ("0,1") or None for all

Returns: dict with the following keys:

Key	Type	Description
decoder/exact_match_acc	float	Exact match accuracy (decoder mode)
decoder/avg_tanimoto	float	Average Tanimoto similarity (decoder)
decoder/tautomer_match_acc	float	Tautomer-normalized exact match (decoder, if tautomer_standardize=True)
decoder/failed_predictions	int	Number of failed predictions (decoder)
decoder/valid	int	Number of chemically valid predictions (decoder)
decoder/total	int	Total benchmark samples
graph/exact_match_acc	float	Exact match accuracy (graph mode)
graph/avg_tanimoto	float	Average Tanimoto similarity (graph)
graph/tautomer_match_acc	float	Tautomer-normalized exact match (graph, if tautomer_standardize=True)
graph/failed_predictions	int	Number of failed predictions (graph)
graph/valid	int	Number of chemically valid predictions (graph)
graph/total	int	Total benchmark samples
postprocess/exact_match_acc	float	Exact match accuracy (postprocess mode, primary metric)
postprocess/avg_tanimoto	float	Average Tanimoto similarity (postprocess)
postprocess/tautomer_match_acc	float	Tautomer-normalized exact match (postprocess, if tautomer_standardize=True)
postprocess/failed_predictions	int	Number of failed predictions (postprocess)
postprocess/valid	int	Number of chemically valid predictions (postprocess)
postprocess/records_df	DataFrame	Per-image results with columns image_id, gt_smiles, pred_smiles, exact, tautomer, tanimoto
postprocess/total	int	Total benchmark samples
total	int	Total benchmark samples

---

como.evaluate_benchmarks(model, benchmarks, *, beam_size=1, postproc_workers=32, tautomer_standardize=True, gpus="0")

Evaluate on multiple benchmarks in one call. Returns a nested dict keyed by benchmark name.

Parameter	Type	Default	Description
model	ComoModel	required	A loaded model
benchmarks	list[dict]	required	Each dict has keys "name", "benchmark_dir", "csv_path"
beam_size	int	1	Beam width for decoding
postproc_workers	int	32	Parallel workers for SMILES post-processing
tautomer_standardize	bool	True	Include tautomer-normalized exact match
gpus	str or None	"0"	GPU IDs ("0,1") or None for all

Returns: dict[str, dict] — mapping from benchmark name to a metrics dict with the same structure as :func:evaluate. Example::

{
  "USPTO": {
    "postprocess/exact_match_acc": 0.934,
    "postprocess/avg_tanimoto": 0.987,
    ...
  },
  "CLEF": {
    "postprocess/exact_match_acc": 0.948,
    ...
  },
}

Example:

benchmarks = [
    {"name": "USPTO", "benchmark_dir": "data/benchmark/real/USPTO",
     "csv_path": "data/benchmark/real/USPTO.csv"},
    {"name": "CLEF",  "benchmark_dir": "data/benchmark/real/CLEF",
     "csv_path": "data/benchmark/real/CLEF_corrected.csv"},
]
results = como.evaluate_benchmarks(model, benchmarks, gpus="0,1")
for name, metrics in results.items():
    acc = metrics["postprocess/exact_match_acc"]
    tan = metrics["postprocess/avg_tanimoto"]
    print(f"{name}: Exact={acc:.2%}, Tanimoto={tan:.4f}")

---

como.canonicalize_smiles(smiles, *, ignore_chiral=False, ignore_cistrans=False, replace_rgroup=True)

Canonicalize a SMILES string using RDKit.

Parameter	Type	Default	Description
smiles	str	required	Input SMILES string
ignore_chiral	bool	False	Strip tetrahedral chirality before canonicalization
ignore_cistrans	bool	False	Strip cis–trans markers (/ and \) before canonicalization
replace_rgroup	bool	True	If True, replace R-group tokens (R, R1, X, Ar, …) with wildcard *

Returns: tuple[str, bool] — (canonical_smiles, ok) where ok is True if the SMILES is chemically valid and canonicalization succeeded.

---

como.canonicalize_tautomer(smiles)

Canonicalize a SMILES string via RDKit's TautomerEnumerator, normalizing different tautomeric forms (e.g., keto/enol, lactam/lactim) to the same canonical representation.

Parameter	Type	Default	Description
smiles	str	required	Input SMILES string

Returns: tuple[str, bool] — (tautomer_canonical_smiles, ok) where ok is False if the input SMILES is invalid or tautomer enumeration fails.

---

como._result_to_smiles(result, mode="postprocess")

Low-level: convert a raw prediction result dict (from :func:predict with smiles_mode=None) to a canonical SMILES string.

Parameter	Type	Default	Description
result	dict	required	Raw prediction dict with keys decode_smiles, symbols, coords, bond_mat, success
mode	str	"postprocess"	SMILES reconstruction mode

mode options:

Mode	Source	Chirality	Description
"decoder"	Decoder token sequence	✗	Raw decoder SMILES, no graph info used. Fastest but lowest quality.
"graph"	Predicted atoms + bonds	✓	Reconstructs SMILES entirely from predicted atom symbols, coordinates, and bond matrix. Chirality restored via _verify_chirality.
"postprocess"	Decoder + atoms + bonds	✓	Starts from decoder SMILES, replaces R-groups/abbreviations, restores chirality from predicted coordinates and bond matrix, then expands functional groups back. Best quality.

Returns: str or None — canonical SMILES string, or None if conversion fails.

Model Weights

Pre-trained model weights are available on HuggingFace:

Checkpoint	Reward Mode	Description
COMO_joint/tanimoto/final.pth	Tanimoto	Joint MLE+MRT (Tanimoto reward)
COMO_joint/edit_distance/final.pth	Edit Distance	Joint MLE+MRT (Edit Distance reward)
COMO_joint/visual/final.pth	Visual	Joint MLE+MRT (Visual reward)

Download from: https://huggingface.co/Keylab/COMO

Benchmark Datasets

Benchmark datasets (images + CSV ground truth) are available on HuggingFace Datasets:

Dataset	Images	Type
USPTO	~6K	Real patent images
USPTO-10K	~10K	Real patent images
CLEF	~5K	Real patent images
JPO	~3K	Real patent images
UOB	~4K	Real academic images
staker	~1K	Real images
acs	~2K	Real publication images
WildMol-10K	~10K	Real wild images
indigo	~8K	Synthetic (Indigo-rendered)
chemdraw	~8K	Synthetic (ChemDraw style)

Download from: https://huggingface.co/Keylab/COMO (see benchmarks/ folder)

Citation

If you use COMO in your research, please cite:

@article{lyu2026closed,
  title={COMO: Closed-Loop Optical Molecule Recognition with Minimum Risk Training},
  author={Lyu, Zhuoqi and Ke, Qing},
  journal={arXiv preprint arXiv:2604.23546},
  year={2026}
}

License

• Code (como/ package): MIT License
• Model Weights (.pth files): CC BY-NC 4.0 (non-commercial use only)
• Benchmark Datasets: collected from existing public OCSR benchmarks; please refer to their original sources for license and attribution:

Dataset	Source
USPTO, CLEF, JPO, UOB, Staker	Rajan et al., 2020, Xiong et al., 2023
Indigo, ChemDraw, ACS, Staker	Qian et al., 2023
USPTO-10K	Morin et al., 2023
WildMol-10K	Fang et al., 2025

See LICENSE for full terms.