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152a1c3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 | # MolP2SBench
MolP2SBench
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.
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
The task is defined on molecular graphs and shown as SMILES. A connected
functional group is replaced by a mask token. The system receives:
- the masked SMILES and mask metadata
- a short list of completed candidate SMILES, all valid on that scaffold
- the properties listed for that directory
It returns one candidate index. The closed comparison supplies that task
text only: no tools, and no web search or literature retrieval.
| 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` |
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.
The returned object matches the prompt:
```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.
| 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 |
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
Exact match on the correct-property view is not evidence that the property
was used. The same scaffolds are released under three views:
| 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 |
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.
A use claim needs a shuffle drop and a donor-directed counterfactual flip,
scoped to one model and one property.
## Environment
Loading and scoring use Python 3.9 or newer and the standard library.
```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
Score one property and one view at a time. The prediction file is JSONL,
one object per line:
| 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. |
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. |