LOGICA adds context to pretrained biological LMs via logit-space contrastive alignment with gated adapters, improving AUC on held-out drug-resistance mutation ranking from ~0.55 to ~0.65 while preserving token likelihoods.
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A policy network learns to choose unmasking order in masked diffusion by reweighting the loss, outperforming random and heuristic baselines on ordering-sensitive tasks.
Screening of 52,000 bioRxiv preprints finds dual-use-adjacent content routinely present in open titles and abstracts, often exceeding risk thresholds.
STOMP extends direct preference optimization to the multi-objective setting via smooth Tchebysheff scalarization and standardization of observed rewards, achieving highest hypervolume in eight of nine protein engineering evaluations.
AlphaEvolve is an LLM-orchestrated evolutionary coding agent that discovered a 4x4 complex matrix multiplication algorithm using 48 scalar multiplications, the first improvement over Strassen's algorithm in 56 years, plus optimizations for Google data centers and hardware.
ESM2 predicts N-terminal methionine via retrieval of a positional prior from the BOS token through distributed attention circuits rather than direct recognition, revealed by a norm-direction decomposition of rotary attention scores.
ALL-FEM fine-tunes LLMs on a corpus of verified FEniCS scripts and uses multi-agent workflows to automate finite element code generation, achieving 71.79% success on 39 benchmarks across elasticity, flow, and coupled problems.
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Retrieval and competition: how a protein foundation model starts a protein
ESM2 predicts N-terminal methionine via retrieval of a positional prior from the BOS token through distributed attention circuits rather than direct recognition, revealed by a norm-direction decomposition of rotary attention scores.