| # Restore consistent NMR peak-set encoding under batch padding |
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| You are repairing a scientific machine-learning workflow in the supplied |
| NMRTrans source snapshot. The workflow encodes 1H and 13C NMR peak sets into |
| continuous representations that a decoder consumes for molecular structure |
| elucidation. The required representation treats spectra as unordered peak sets |
| and uses permutation-equivariant attention blocks followed by |
| permutation-invariant pooling. |
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| Different compounds produce different numbers of observed peaks, so spectra |
| are batched by appending dummy padding rows up to a common length and |
| recording which rows are real observations. A user running this encoding |
| workflow reports that the encoded spectrum is not stable under this batching: |
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| - Encoding the same spectrum with a different number of appended padding |
| rows changes the produced representations, even though the observed peaks |
| are identical. |
| - In a padded batch, the pooled spectrum-level representation barely |
| responds when a real observed peak is moved to a different chemical shift. |
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| Both observations contradict the required set-encoding contract: the encoded |
| representation must be a function of the observed peaks alone, and |
| it must respond to chemically meaningful changes in those peaks. |
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| Inspect the complete source snapshot and run `python reproduce.py`. Repair the implementation so that the peak-set |
| encoders satisfy the documented contract for all valid inputs. The repair |
| must generalize to arbitrary spectra, peak counts, padding lengths, random |
| initializations, and encoder configurations; do not hard-code the public |
| fixtures, specific tensor values, or a particular padding length. |
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| Keep the overall architecture (the stacked ISAB encoder, the PMA pooling, |
| the learnable tokens, and the projection layers) and the existing function |
| signatures intact, and preserve the documented input feature layout for both |
| modalities. The public reproduction is only a small smoke diagnostic; use the |
| source call graph to determine the complete behavior that needs to be repaired. Do not use the network or add external data files. |
| Keep changes limited to the scientific implementation and any focused |
| comments that are necessary for a general fix. |
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