Conditioning Protein Generation via Hopfield Pattern Multiplicity

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arXiv:2603.20115v2 Announce Type: replace Abstract: Small protein-family alignments often contain a subset of interest but not enough labeled data to train a conditional generator. We condition a training-free stochastic-attention sampler by adding one multiplicity ratio to its logits. Increasing this ratio shifts generation from the full family toward the designated subset. For unit-norm memories, the resulting Boltzmann distribution is exactly a Gaussian mixture whose component weights are set by the multiplicities. This result separates exact conditioning in latent space from losses caused by sampling, PCA reconstruction, and sequence decoding. Across five Pfam families, attention followed the analytic target, but recovery of single-residue markers depended on how well PCA separated the designated and background sequences. A matched weighted profile HMM reproduced these markers more directly, while stochastic attention gave lower ESM2 pseudo-perplexity in the Kunitz comparison. Using a curated set of 23 omega-conotoxin sequences as the target subset produced diverse sequences that preserved the cysteine scaffold and Tyr13 and shifted other residues toward the designated set. These sequences are candidates for experimental testing; they do not establish binding.

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