| --- |
| pretty_name: MolP2SBench |
| license: cc-by-4.0 |
| language: |
| - en |
| size_categories: |
| - 1K<n<10K |
| tags: |
| - chemistry |
| - molecular-discovery |
| - property-to-structure |
| - benchmark |
| - arxiv:2610.12522 |
| configs: |
| - config_name: dipole |
| default: true |
| data_files: |
| - split: correct |
| path: data/dipole/correct.jsonl |
| - split: shuffled |
| path: data/dipole/shuffled.jsonl |
| - split: counterfactual |
| path: data/dipole/counterfactual.jsonl |
| - config_name: gap |
| data_files: |
| - split: correct |
| path: data/gap/correct.jsonl |
| - split: shuffled |
| path: data/gap/shuffled.jsonl |
| - split: counterfactual |
| path: data/gap/counterfactual.jsonl |
| - config_name: infrared |
| data_files: |
| - split: correct |
| path: data/infrared/correct.jsonl |
| - split: shuffled |
| path: data/infrared/shuffled.jsonl |
| - split: counterfactual |
| path: data/infrared/counterfactual.jsonl |
| - config_name: raman |
| data_files: |
| - split: correct |
| path: data/raman/correct.jsonl |
| - split: shuffled |
| path: data/raman/shuffled.jsonl |
| - split: counterfactual |
| path: data/raman/counterfactual.jsonl |
| - config_name: ultraviolet_visible |
| data_files: |
| - split: correct |
| path: data/ultraviolet_visible/correct.jsonl |
| - split: shuffled |
| path: data/ultraviolet_visible/shuffled.jsonl |
| - split: counterfactual |
| path: data/ultraviolet_visible/counterfactual.jsonl |
| - config_name: proton_nmr_peaks |
| data_files: |
| - split: correct |
| path: data/proton_nmr_peaks/correct.jsonl |
| - split: shuffled |
| path: data/proton_nmr_peaks/shuffled.jsonl |
| - split: counterfactual |
| path: data/proton_nmr_peaks/counterfactual.jsonl |
| - config_name: proton_nmr_integration |
| data_files: |
| - split: correct |
| path: data/proton_nmr_integration/correct.jsonl |
| - split: shuffled |
| path: data/proton_nmr_integration/shuffled.jsonl |
| - split: counterfactual |
| path: data/proton_nmr_integration/counterfactual.jsonl |
| - config_name: proton_nmr_atom |
| data_files: |
| - split: correct |
| path: data/proton_nmr_atom/correct.jsonl |
| - split: shuffled |
| path: data/proton_nmr_atom/shuffled.jsonl |
| - split: counterfactual |
| path: data/proton_nmr_atom/counterfactual.jsonl |
| - config_name: carbon_nmr_peaks |
| data_files: |
| - split: correct |
| path: data/carbon_nmr_peaks/correct.jsonl |
| - split: shuffled |
| path: data/carbon_nmr_peaks/shuffled.jsonl |
| - split: counterfactual |
| path: data/carbon_nmr_peaks/counterfactual.jsonl |
| - config_name: carbon_nmr_degeneracy |
| data_files: |
| - split: correct |
| path: data/carbon_nmr_degeneracy/correct.jsonl |
| - split: shuffled |
| path: data/carbon_nmr_degeneracy/shuffled.jsonl |
| - split: counterfactual |
| path: data/carbon_nmr_degeneracy/counterfactual.jsonl |
| - config_name: carbon_nmr_atom |
| data_files: |
| - split: correct |
| path: data/carbon_nmr_atom/correct.jsonl |
| - split: shuffled |
| path: data/carbon_nmr_atom/shuffled.jsonl |
| - split: counterfactual |
| path: data/carbon_nmr_atom/counterfactual.jsonl |
| - config_name: electronic |
| data_files: |
| - split: correct |
| path: data/electronic/correct.jsonl |
| - split: shuffled |
| path: data/electronic/shuffled.jsonl |
| - split: counterfactual |
| path: data/electronic/counterfactual.jsonl |
| - config_name: magnetic_resonance |
| data_files: |
| - split: correct |
| path: data/magnetic_resonance/correct.jsonl |
| - split: shuffled |
| path: data/magnetic_resonance/shuffled.jsonl |
| - split: counterfactual |
| path: data/magnetic_resonance/counterfactual.jsonl |
| - config_name: vibrational |
| data_files: |
| - split: correct |
| path: data/vibrational/correct.jsonl |
| - split: shuffled |
| path: data/vibrational/shuffled.jsonl |
| - split: counterfactual |
| path: data/vibrational/counterfactual.jsonl |
| - config_name: all_properties |
| data_files: |
| - split: correct |
| path: data/all_properties/correct.jsonl |
| - split: shuffled |
| path: data/all_properties/shuffled.jsonl |
| - split: counterfactual |
| path: data/all_properties/counterfactual.jsonl |
| - config_name: dipole_labels |
| data_files: |
| - split: correct |
| path: data/dipole/correct.labels.jsonl |
| - split: shuffled |
| path: data/dipole/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/dipole/counterfactual.labels.jsonl |
| - config_name: gap_labels |
| data_files: |
| - split: correct |
| path: data/gap/correct.labels.jsonl |
| - split: shuffled |
| path: data/gap/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/gap/counterfactual.labels.jsonl |
| - config_name: infrared_labels |
| data_files: |
| - split: correct |
| path: data/infrared/correct.labels.jsonl |
| - split: shuffled |
| path: data/infrared/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/infrared/counterfactual.labels.jsonl |
| - config_name: raman_labels |
| data_files: |
| - split: correct |
| path: data/raman/correct.labels.jsonl |
| - split: shuffled |
| path: data/raman/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/raman/counterfactual.labels.jsonl |
| - config_name: ultraviolet_visible_labels |
| data_files: |
| - split: correct |
| path: data/ultraviolet_visible/correct.labels.jsonl |
| - split: shuffled |
| path: data/ultraviolet_visible/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/ultraviolet_visible/counterfactual.labels.jsonl |
| - config_name: proton_nmr_peaks_labels |
| data_files: |
| - split: correct |
| path: data/proton_nmr_peaks/correct.labels.jsonl |
| - split: shuffled |
| path: data/proton_nmr_peaks/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/proton_nmr_peaks/counterfactual.labels.jsonl |
| - config_name: proton_nmr_integration_labels |
| data_files: |
| - split: correct |
| path: data/proton_nmr_integration/correct.labels.jsonl |
| - split: shuffled |
| path: data/proton_nmr_integration/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/proton_nmr_integration/counterfactual.labels.jsonl |
| - config_name: proton_nmr_atom_labels |
| data_files: |
| - split: correct |
| path: data/proton_nmr_atom/correct.labels.jsonl |
| - split: shuffled |
| path: data/proton_nmr_atom/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/proton_nmr_atom/counterfactual.labels.jsonl |
| - config_name: carbon_nmr_peaks_labels |
| data_files: |
| - split: correct |
| path: data/carbon_nmr_peaks/correct.labels.jsonl |
| - split: shuffled |
| path: data/carbon_nmr_peaks/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/carbon_nmr_peaks/counterfactual.labels.jsonl |
| - config_name: carbon_nmr_degeneracy_labels |
| data_files: |
| - split: correct |
| path: data/carbon_nmr_degeneracy/correct.labels.jsonl |
| - split: shuffled |
| path: data/carbon_nmr_degeneracy/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/carbon_nmr_degeneracy/counterfactual.labels.jsonl |
| - config_name: carbon_nmr_atom_labels |
| data_files: |
| - split: correct |
| path: data/carbon_nmr_atom/correct.labels.jsonl |
| - split: shuffled |
| path: data/carbon_nmr_atom/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/carbon_nmr_atom/counterfactual.labels.jsonl |
| - config_name: electronic_labels |
| data_files: |
| - split: correct |
| path: data/electronic/correct.labels.jsonl |
| - split: shuffled |
| path: data/electronic/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/electronic/counterfactual.labels.jsonl |
| - config_name: magnetic_resonance_labels |
| data_files: |
| - split: correct |
| path: data/magnetic_resonance/correct.labels.jsonl |
| - split: shuffled |
| path: data/magnetic_resonance/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/magnetic_resonance/counterfactual.labels.jsonl |
| - config_name: vibrational_labels |
| data_files: |
| - split: correct |
| path: data/vibrational/correct.labels.jsonl |
| - split: shuffled |
| path: data/vibrational/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/vibrational/counterfactual.labels.jsonl |
| - config_name: all_properties_labels |
| data_files: |
| - split: correct |
| path: data/all_properties/correct.labels.jsonl |
| - split: shuffled |
| path: data/all_properties/shuffled.labels.jsonl |
| - split: counterfactual |
| path: data/all_properties/counterfactual.labels.jsonl |
| --- |
| # MolP2SBench |
|
|
| **Can a language model use molecular properties to recover a missing structural fragment?** |
| MolP2SBench presents a masked molecular scaffold and two to four valid candidate structures. Controlled changes to the supplied properties test whether predictions respond to the evidence. |
|
|
| [Paper](https://arxiv.org/abs/2610.12522) · [Code and original release](https://github.com/DUAL-Xiao/MolP2SBench) · [RSI4Science usage guide](https://rsi4science.org/use/molp2s/) |
|
|
| ## Load a task view |
|
|
| The task and label configurations can be loaded separately: |
|
|
| ```python |
| from datasets import load_dataset |
| |
| repo = "Joshua1998/MolP2SBench" |
| tasks = load_dataset(repo, "dipole", split="correct") |
| labels = load_dataset(repo, "dipole_labels", split="correct") |
| |
| # Give the model task fields only. Join labels by record_id when scoring. |
| answers = {row["record_id"]: row["label"] for row in labels} |
| print(tasks[0]) |
| ``` |
|
|
| Task files and answer files remain separate. The answer is a zero-based index into `candidate_completed_smiles`; there is no reference reasoning trace. Labels are public, so this release is not a sealed evaluation set. |
|
|
| ## Contents |
|
|
| | Property configurations | What is supplied | |
| |---|---| |
| | `dipole`, `gap` | Dipole magnitude; HOMO–LUMO gap | |
| | `infrared`, `raman`, `ultraviolet_visible` | Vibrational and electronic spectral evidence | |
| | `proton_nmr_peaks`, `proton_nmr_integration`, `proton_nmr_atom` | Three representations of proton magnetic-shielding information | |
| | `carbon_nmr_peaks`, `carbon_nmr_degeneracy`, `carbon_nmr_atom` | Three representations of carbon magnetic-shielding information | |
| | `electronic`, `magnetic_resonance`, `vibrational` | Property-family bundles | |
| | `all_properties` | Seven property types together | |
|
|
| Each configuration has three condition views, exposed as Hugging Face split names: |
|
|
| | View | Evidence | Evaluation purpose | |
| |---|---|---| |
| | `correct` | Properties associated with the source structure | Recovery with matched evidence | |
| | `shuffled` | Properties from another molecule, with the original label retained | Sensitivity to disrupted property–structure pairing | |
| | `counterfactual` | Properties of another valid completion on the same scaffold | Recovery directed toward the donor completion | |
|
|
| These are **paired experimental conditions, not independent train/validation/test partitions**. Each channel has 136 correct and 136 shuffled records. Counterfactual views contain 240 or 258 records, depending on the channel. There are 7,824 task rows across all views and channels; repeated views are not additional independent molecules. Every task configuration has a corresponding `<configuration>_labels` configuration. |
|
|
| ## Fields and scoring |
|
|
| Tasks contain `record_id`, `masked_smiles`, `mask`, `properties`, and `candidate_completed_smiles`. Property metadata records units and representations; NMR fields describe calculated magnetic shieldings, not a general set of experimental chemical shifts. Answer files contain `record_id` and `label`. |
|
|
| The original prompts and Python scorer are included. Run from a downloaded repository snapshot: |
|
|
| ```bash |
| python scripts/score_tasks.py --property dipole --condition correct --predictions predictions.jsonl |
| ``` |
|
|
| The scorer reports exact-match outcomes and invalid or missing predictions. It does not score free-text reasoning, infer why a model failed, or implement the paper's family-weighted PGR/CFR metrics. See `SOURCE_README.md` for the original prediction schema and protocol. |
|
|
| ## Using the data for improvement research |
|
|
| Compare outcomes by property and evidence condition to form testable hypotheses about evidence use. A change in one answer is not a diagnosis of an internal reasoning mechanism. Evaluate revisions on independent molecular families under matched budgets; the views here do not supply an independent held-out split. This release supports diagnostics and experiments, and does not establish that recursive self-improvement or open-ended molecular discovery has been achieved. |
|
|
| ## Source and permissions |
|
|
| The data, prompts and scripts are copied without changes from GitHub commit `1ede82bf68f634097b296b1937d66a9b04bbf269`. `source-manifest.json` records their SHA-256 hashes. Dataset construction and preprocessing are described in the linked paper. The upstream sources retain their respective terms: |
|
|
| - **QM9**: HOMO–LUMO gaps; [data record](https://figshare.com/articles/dataset/Data_for_6095_constitutional_isomers_of_C7H10O2/1057646), CC0. |
| - **QM9S**: dipole, IR, Raman and UV–Vis properties; [data record](https://figshare.com/articles/dataset/QM9S_dataset/24235333), CC BY 4.0; [source article](https://doi.org/10.1038/s43588-023-00550-y). |
| - **QM9NMR**: gas-phase computed magnetic shieldings; [data record](https://doi.org/10.17172/NOMAD/2021.10.16-1), CC BY 4.0; [project and citation information](https://moldis-group.github.io/qm9nmr/). |
|
|
| This mirror preserves the released task payloads and does not redistribute the complete upstream databases. The benchmark constructs masked-scaffold candidate-selection tasks and condition-specific property views from those sources; the upstream measurements and calculations are not newly generated here. |
|
|
| The MolP2SBench benchmark data, task formulations, prompts and accompanying documentation in this release are licensed under [Creative Commons Attribution 4.0 International (CC BY 4.0)](https://creativecommons.org/licenses/by/4.0/). Reuse and adaptation, including commercial use, are permitted with attribution, a link to the license and an indication of changes. See `LICENSE`. |
|
|
| The upstream data retain the terms listed above; this release does not impose new restrictions on CC0 material. Please credit MolP2SBench and the relevant upstream sources when reusing their material. The original Python scripts in `scripts/` are included unchanged for reference; this data license does not assign them a software license. |
|
|
| ## Citation |
|
|
| ```bibtex |
| @misc{xie2026molp2sbench, |
| title={MolP2SBench: Do LLMs Really Reason from Molecular Properties to Structure?}, |
| author={Yuhang Xie and Zhiyi Shi and Zeyi Zhang and Zhisheng Qi and Yushun Dong and Yu Wang and Xiongye Xiao}, |
| year={2026}, |
| eprint={2610.12522}, |
| archivePrefix={arXiv}, |
| primaryClass={physics.chem-ph}, |
| url={https://arxiv.org/abs/2610.12522} |
| } |
| ``` |
|
|
