| # MolP2SBench |
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|
| MolP2SBench |
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|
| Usual molecular benchmarks give a complete structure and ask for a property. |
| MolP2SBench studies the inverse problem: a fragment of the molecule is |
| hidden, and the system must decide which chemically valid completion fits the |
| remaining graph and the supplied physical evidence. |
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|
| The work is a test of property-grounded completion. A high recovery rate can |
| come from valence, common functional-group templates, or SMILES familiarity. |
| The released views ask a narrower question: when several completions are |
| already valid on the same scaffold, does the supplied property change the |
| selection in the direction the evidence implies? |
|
|
| ## Task |
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|
| The task is defined on molecular graphs and shown as SMILES. A connected |
| functional group is replaced by a mask token. The system receives: |
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|
| - the masked SMILES and mask metadata |
| - a short list of completed candidate SMILES, all valid on that scaffold |
| - the properties listed for that directory |
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|
| It returns one candidate index. The closed comparison supplies that task |
| text only: no tools, and no web search or literature retrieval. |
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|
| | Artifact | Path | |
| | ------------- | ----------------------------------------------------------- | |
| | Single-property prompt | `prompts/single_property_system.txt`, `prompts/single_property_user.txt` | |
| | Bundle prompt | `prompts/property_bundle_system.txt`, `prompts/property_bundle_user.txt` | |
| | All-properties prompt | `prompts/all_properties_system.txt`, `prompts/all_properties_user.txt` | |
| | Tasks | `data/<property>/{correct,shuffled,counterfactual}.jsonl` | |
| | Labels | `data/<property>/{correct,shuffled,counterfactual}.labels.jsonl` | |
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| Each task line is one JSON object with `record_id`, `masked_smiles`, `mask`, |
| `properties`, and `candidate_completed_smiles`. The answer is not in that |
| object. It is the sibling file `<condition>.labels.jsonl`. A label line has |
| `record_id` and `label`. `label` is the 0-based index of the target |
| candidate. |
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| The returned object matches the prompt: |
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|
| ```json |
| { |
| "record_id": "<input record_id>", |
| "selected_candidate_index": 0, |
| "reasoning": "<concise justification>" |
| } |
| ``` |
|
|
| `selected_candidate_index` is a 0-based index into |
| `candidate_completed_smiles`, in the order given. |
|
|
| Single-property directories carry one representation. A bundle carries one |
| family. `all_properties` carries seven properties: the dipole norm, the gap, |
| infrared, Raman, ultraviolet–visible, proton NMR with integration, and |
| carbon NMR with degeneracy. |
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|
| | Directory | Property | |
| | ------------------------ | ------------------------------------------------------------------------- | |
| | `dipole` | Dipole moment, Euclidean norm | |
| | `gap` | Gap between the highest occupied and lowest unoccupied molecular orbitals | |
| | `infrared` | Infrared spectrum | |
| | `raman` | Raman spectrum | |
| | `ultraviolet_visible` | Ultraviolet–visible excitations | |
| | `proton_nmr_peaks` | Proton NMR, peaks only | |
| | `proton_nmr_integration` | Proton NMR, peaks with integration | |
| | `proton_nmr_atom` | Proton NMR, atom-wise | |
| | `carbon_nmr_peaks` | Carbon NMR, peaks only | |
| | `carbon_nmr_degeneracy` | Carbon NMR, peaks with degeneracy | |
| | `carbon_nmr_atom` | Carbon NMR, atom-wise | |
| | `electronic` | Dipole norm, gap, and ultraviolet–visible | |
| | `magnetic_resonance` | Proton NMR with integration, and carbon NMR with degeneracy | |
| | `vibrational` | Infrared and Raman spectra | |
| | `all_properties` | The seven properties listed above | |
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|
| Correct and shuffled files have 136 records each. Counterfactual files have |
| 240 records for dipole, infrared, Raman, ultraviolet–visible, `electronic`, |
| `vibrational`, and `all_properties`. They have 258 records for the gap, each |
| NMR representation, and `magnetic_resonance`. |
|
|
| ## Views |
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|
| Exact match on the correct-property view is not evidence that the property |
| was used. The same scaffolds are released under three views: |
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|
| | View | File | What is supplied | What it tests | |
| | ----------------------- | ---------------------- | ------------------------------------------------------------- | ----------------------------------------------- | |
| | Correct property | `correct.jsonl` | The property of the source molecule | Recovery under the matched property | |
| | Shuffled property | `shuffled.jsonl` | The same property type, taken from a different molecule | Whether the value is read or ignored | |
| | Counterfactual property | `counterfactual.jsonl` | The property of another valid completion on the same scaffold | Whether the choice moves toward that completion | |
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| Correct and shuffled views of a property share `record_id` and the candidate |
| list. The shuffled file changes the property, not the answer index. A |
| structure-only comparison uses that same masked graph and candidate list |
| with the property omitted. The prompt states that case: if no property is |
| supplied, use only the structural context. |
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|
| A use claim needs a shuffle drop and a donor-directed counterfactual flip, |
| scoped to one model and one property. |
|
|
| ## Environment |
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|
| Loading and scoring use Python 3.9 or newer and the standard library. |
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|
| ```bash |
| python3 scripts/build_tasks.py |
| python3 scripts/score_tasks.py \ |
| --property dipole \ |
| --condition correct \ |
| --predictions predictions.jsonl |
| ``` |
|
|
| `scripts/build_tasks.py` loads every task file and prints the record counts. |
| `scripts/score_tasks.py` compares one prediction file with the label file |
| for that property and view. `--property` is a directory name from the table |
| above. `--condition` is `correct`, `shuffled`, or `counterfactual`. |
|
|
| ## Trajectory |
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| Score one property and one view at a time. The prediction file is JSONL, |
| one object per line: |
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|
| | Field | Contents | |
| | -------------------------- | ----------------------------------------------------------------------- | |
| | `record_id` | Task id | |
| | `selected_candidate_index` | 0-based index into `candidate_completed_smiles` | |
| | `reasoning` | Justification. The scorer does not read this field. | |
| | `invalid` | `true` when the submission does not parse. Omit the index on that line. | |
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| A missing record, a line marked invalid, or an index outside the candidate |
| list counts as incorrect. A duplicate `record_id` is rejected. The scorer |
| prints the hit count, the number of tasks, the accuracy, and the counts of |
| missing, invalid, and out-of-range lines. |
