ESMFold2: expose MSA inference-diversity options#3
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…mask) Port the MSA inference-time diversity feature to the esmfold2 model: - modeling_esmfold2_common.py: add maybe_subsample_msa and maybe_apply_msa_column_masking helpers (operate on [B, depth, L] encoder inputs, always keep query row 0). - modeling_esmfold2.py + modeling_esmfold2_experimental.py: new forward kwargs msa_max_depth (1024) / msa_column_mask_rate (0.1) / msa_subsample_at_inference (True). Column masking is applied once before the recycling loop (shared across loops); row subsampling is drawn fresh per loop inside the loop, matching the pro-msa setup. Defaults are hardcoded in the public signatures (not model config), so these are pure inference-time knobs. The diffusion sampler / num_sampling_steps schedule is untouched. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
imathur1
approved these changes
Jun 5, 2026
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What does this PR do?
Port the MSA inference-time diversity feature to the esmfold2 model:
Defaults are hardcoded in the public signatures (not model config), so these are pure inference-time knobs. The diffusion sampler / num_sampling_steps schedule is untouched.
Fixes #
absence of inference-time diversity knobs in implementation
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