/rdagent/scenarios/finetune/datasets/chemcot

language, license, tags, size_categories, task_categories

language	license	tags	size_categories	task_categories
en	mit	chemistry chain-of-thought molecular-reasoning	10K<n<100K	text-generation question-answering

ChemCoT Dataset

Chemical reasoning dataset with Chain-of-Thought annotations from ChemCoTBench.

Repository: OpenMol/ChemCoTDataset

Overview

The ChemCoTDataset provides ~23K high-quality chain-of-thought samples for training chemical reasoning models. CoT annotations were distilled from state-of-the-art reasoning models (Gemini-2.5-pro, DeepSeek-R1, Claude-3.7-sonnet-thinking) and validated by 13 chemistry PhD candidates with >90% accuracy.

Dataset Scale

Category	Subtasks	Samples
mol_und	fg_count, ring_count, ring_system_scaffold, Murcko_scaffold	6,319
mol_edit	add, delete, sub	4,497
mol_opt	drd, gsk, jnk, qed, solubility, logp	5,587
rxn	fs_by_product, fs_major_product, rcr	6,820
Total	16 subtasks	23,223

Tasks

1. Molecular Understanding (mol_und)

Subtask	Description
fg_count	Functional group counting
ring_count	Ring counting
Murcko_scaffold	Murcko scaffold extraction
ring_system_scaffold	Ring system scaffold extraction

Metrics: MAE for counting, Tanimoto similarity for scaffold extraction

2. Molecular Editing (mol_edit)

Subtask	Description
add	Add functional groups to molecules
delete	Delete functional groups from molecules
sub	Substitute functional groups in molecules

Metrics: Pass@1 (validity and instruction matching)

3. Molecular Optimization (mol_opt)

Subtask	Description
logp	LogP (lipophilicity) optimization
solubility	Aqueous solubility optimization
qed	QED (drug-likeness) optimization
drd	DRD2 binding affinity optimization
gsk	GSK3-beta binding affinity optimization
jnk	JNK3 binding affinity optimization

Metrics: Mean improvement rate, Success rate

4. Reaction Prediction (rxn)

Subtask	Description
fs	Forward synthesis (major product + by-product prediction)
rcr	Reaction Condition Recommendation (catalyst prediction)

Metrics: Top-1 accuracy, Fingerprint similarity

Data Format

Field	Type	Description
id	string	Unique sample identifier
query	string	The chemical problem/question
task	string	Task category (mol_und, mol_edit, mol_opt, rxn)
subtask	string	Specific subtask name
struct_cot	string	Structured chain-of-thought reasoning
raw_cot	string	Raw chain-of-thought annotation
meta	object	Additional metadata

CoT Quality Assessment

IMPORTANT: Distilled CoT may require domain refinement.

Dimension	Value
baseline_quality	medium-high
task_type	chemistry
polish_difficulty	medium

Baseline: CoT distilled from Gemini-2.5-pro/DeepSeek-R1/Claude, validated by 13 chemistry PhD candidates (>90% accuracy). Paper notes: "distillation strategy falters in chemistry" - consider expert refinement for optimal results.

License

MIT License