Complete analysis pipeline and per-dataset results for the revised version of BIOINF-2026-2348. Includes: (1) unified per-layer probing of ESM-2 650M and SaProt_650M_AF2 on all 63 ProteinGym substitution datasets under three feature arms (masked wild-type, unmasked wild-type, mutant) and four train-test splits (random, ProteinGym-official modulo and contiguous, position-grouped); (2) a random-position lookup control showing random-split probing performance is largely position memorization; (3) multi-scale pooling benchmarks with per-fold-trained attention; (4) fp32 logit lens scoring validated against the official logits pathway; (5) layer-wise cosine and linear CKA similarity analyses; (6) TOST equivalence tests, and (7) Foldseek 3Di structure tokens for 62 datasets. Also includes the reproduction record of the withdrawn fp16 lens curves. Code MIT; results CC-BY-4.0.
Yutao Guo, Zihan Zhang, Xuezhou Zhao et al.· Zenodo (CERN European Organi...· 0 citations
Complete analysis pipeline and per-dataset results for the revised version of BIOINF-2026-2348. Includes: (1) unified per-layer probing of ESM-2 650M and SaProt_650M_AF2 on all 63 ProteinGym substitution datasets under three feature arms (masked wild-type, unmasked wild-type, mutant) and four train-test splits (random, ProteinGym-official modulo and contiguous, position-grouped); (2) a random-position lookup control showing random-split probing performance is largely position memorization; (3) multi-scale pooling benchmarks with per-fold-trained attention; (4) fp32 logit lens scoring validated against the official logits pathway; (5) layer-wise cosine and linear CKA similarity analyses; (6) TOST equivalence tests, and (7) Foldseek 3Di structure tokens for 62 datasets. Also includes the reproduction record of the withdrawn fp16 lens curves. Code MIT; results CC-BY-4.0.
Yutao Guo, Zihan Zhang, Xuezhou Zhao et al.· Zenodo (CERN European Organi...· 0 citations
Complete analysis pipeline and per-dataset results for the revised version of BIOINF-2026-2348. Includes: (1) unified per-layer probing of ESM-2 650M and SaProt_650M_AF2 on all 63 ProteinGym substitution datasets under three feature arms (masked wild-type, unmasked wild-type, mutant) and four train-test splits (random, ProteinGym-official modulo and contiguous, position-grouped); (2) a random-position lookup control showing random-split probing performance is largely position memorization; (3) multi-scale pooling benchmarks with per-fold-trained attention; (4) fp32 logit lens scoring validated against the official logits pathway; (5) layer-wise cosine and linear CKA similarity analyses; (6) TOST equivalence tests, and (7) Foldseek 3Di structure tokens for 62 datasets. Also includes the reproduction record of the withdrawn fp16 lens curves. Code MIT; results CC-BY-4.0.
Yutao Guo, Zihan Zhang, Xuezhou Zhao et al.· Zenodo (CERN European Organi...· 0 citations
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