arXiv:2606. 02386v1 Announce Type: new Abstract: Protein language models (PLMs) are passive oracles: they generate sequences in a single forward pass with no mechanism to consult external biophysical feedback or redirect generation when a candidate violates thermodynamic or structural constraints.
arXiv:2606. 18961v1 Announce Type: new Abstract: Protein language models (PLMs) have emerged as powerful tools for controllable biomolecular design, yet their post-training adaptation typically relies on costly wet-lab validation or curated preference datasets.
arXiv:2608. 12192v1 Announce Type: new Abstract: Foundation models for protein structure prediction remain unreliable on certain targets.
Oracle-limited molecular optimization gives reward only after a complete molecule is generated, while each rollout requires many local next-token decisions. This delayed-feedback interface makes molecular policy optimization myopic: an optimizer can learn that a molecule was good without knowing which intermediate actions made it good.
arXiv:2607. 26391v1 Announce Type: new Abstract: Oracle-limited molecular optimization gives reward only after a complete molecule is generated, while each rollout requires many local next-token decisions.
Protein language models (PLMs) have emerged as powerful tools for controllable biomolecular design, yet their post-training adaptation typically relies on costly wet-lab validation or curated preference datasets. To overcome this supervision bottleneck, we introduce unsupervised reward optimization of PLMs, a comprehensive framework for steerable protein generation without ground-truth labels.
arXiv:2606. 11256v1 Announce Type: cross Abstract: Designing molecules with target properties is most useful when candidate structures are accompanied by feasible synthetic routes.
Foundation models for protein structure prediction remain unreliable on certain targets. External oracles can flag and correct these failures, but biological oracles are expensive, making oracle budget a critical constraint.
arXiv:2607. 06987v1 Announce Type: new Abstract: Reinforcement learning (RL) has become the standard paradigm for enhancing the complex reasoning capabilities of large language models (LLMs).
arXiv:2607. 00531v1 Announce Type: cross Abstract: Scientific reasoning is an increasingly important capability of large language models, yet improving the robustness and efficiency of training such reasoning remains a key open challenge.
arXiv:2606. 08100v1 Announce Type: new Abstract: Multimodal $\Delta\Delta G$ predictors integrating protein language models with inverse-folding representations achieve strong in-distribution accuracy on the Megascale dataset but exhibit limited robustness on out-of-distribution (OOD) proteins, persistent forward-reverse bias on paired-mutation benchmarks, and under-representation of rare stabilizing mutations.
arXiv:2608. 17310v1 Announce Type: new Abstract: Reinforcement Learning (RL) has been promising in single-turn LLM fine-tuning.
arXiv:2608. 02641v1 Announce Type: cross Abstract: Large language models (LLMs) can translate natural-language optimization problems into solver-ready formulations, but direct code generation is brittle: schema, indexing, and semantic errors can cause compilation failures, infeasible models, or incorrect objectives, while iterative repair, search, and multi-agent workflows increase inference cost.