Protein contacts are already in the attention: a single-forward-pass alternative to the Categorical Jacobian

Protein language models learn transferable sequence representations. However, because they primarily model contextual dependencies along amino-acid sequences, their training objectives do not explicitly constrain the model to learn three-dimensional residue contacts formed after folding . Here, we introduce LC-SEPLM (Long-range Contact-supervised ESM Protein Language Model), which adapts ESM2 with LoRA and long-range residue-pair contact supervision while retaining sequence-only downstream inference. Pair-specific queries use cross-attention over the complete sequence to extract global sequence context associated with long-range spatial contacts. To expose the model to diverse structural information, we trained LC-SEPLM on 500,000 AlphaFold Swiss-Prot proteins. In downstream evaluation, LC-SEPLM improved all eight protein-level tasks relative to ESM2. The largest gain occurred in remote-homology recognition, where macro-F1 increased from 0.6122 to 0.6769 (+0.0647, or 6.47 percentage points). On the official ESM-S EC benchmark, LC-SEPLM also outperformed ESM-S with a maximum absolute gain of 0.1771. These results support residue-pair contact supervision as a bounded route for introducing structural information into protein sequence representations while preserving sequence-only inference.

Protein language models are trained primarily with masked language modeling (MLM), which predicts amino-acid identities at masked positions. We ask whether latent-space prediction can complement these token-level objectives under matched wall-clock budget. Across pretrained and random-init protein sequence encoders at 35--150M parameters, we find that the best protein-JEPA design is not all-position latent prediction but a variant: predicting latent targets only at masked positions, and retaining the MLM cross-entropy. We call this recipe masked-position MLM+JEPA. On a 16-task downstream suite (15 frozen linear probes plus SCOPe-40 zero-shot fold retrieval), under matched wall-clock budgets, this recipe wins more tasks than it loses against MLM-only continuation: 10 wins / 3 losses / 3 ties (hereafter W/L/T) on pretrained ESM2-35M, 11/2/3 on ESM2-150M while results in pretraining from scratch are mixed (6/8/2). Gains are seen for multiple models on 11 of 16 tasks, including stability, \b{eta}β\b{eta}-lactamase fitness, variant effect, intrinsic disorder, remote homology, enzyme classification, and SCOPe-40 fold retrieval. Tasks with more losses than wins are Fluorescence (TAPE) and Peptide-HLA Binding. All-position MLM+JEPA matches MLM-only overall but does not reproduce the masked-position gains. JEPA-only (no MLM) collapses in nearly every experiment. We conclude that JEPA, when combined with MLM, is competitive and can outperform pure MLM in pretraining and continued training, even under matched wall-clock budgets.

A companion paper studies when activation patching and weight-space ablation agree, inside an idealized model where a conditional computation is carried additively through a residual stream. For the one composition in that model where two carriers are architecturally dependent, an attention head and its own layer's normalization-MLP composition, it derives an exact first-order interaction formula, zero when only the MLP is ablated and second-order bounded when the head is also ablated. That result is confined to a single residual block and checked only on small transformers on a synthetic task. This paper extends the result past both limits. First, the interaction from ablating carriers spanning several layers decomposes exactly into same-block terms, one per touched layer, plus a cross-layer remainder on which the decomposition makes no claim of smallness. Second, we isolate that remainder exactly, for two layers, as a double integral of a mixed second derivative, and name the missing ingredient needed to bound it: a Jacobian bound for the attention sub-block. We derive this bound in closed form and verify it, without a single violation, against Qwen2.5-1.5B-Instruct's real weights, though we do not yet chain it across layers. We also give, in closed form, the curvature constant the companion paper's bound leaves unexhibited. Third, on that same model, we search for and find an emergent circuit for indirect object identification, never designed into it, using the original activation-patching method for this task, and test collapse, dissociation, and interaction on it. The result is mixed: a shared carrier emerges across all five tested instances, collapse and dissociation hold on most but not all, and a nonzero interaction is measurable on three of five, at layer pairs outside the same-block case the companion theorem covers.