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: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:2605. 00182v3 Announce Type: replace Abstract: Proteins are shaped by gradual evolution under biophysical and functional constraints.
arXiv:2507. 08920v4 Announce Type: replace-cross Abstract: We introduce AMix-1, a powerful protein foundation model built on Bayesian Flow Networks and empowered by a systematic training methodology, encompassing pretraining scaling laws, emergent capability analysis, in-context learning mechanism, and test-time scaling algorithm.
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:2603. 14717v2 Announce Type: replace Abstract: Generating novel protein sequences that respect a family's statistical constraints typically requires training deep generative models on thousands to millions of examples.
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:2605. 01625v3 Announce Type: replace Abstract: Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology.
arXiv:2602. 22822v3 Announce Type: replace Abstract: Tandem mass spectrometry (MS/MS) is central to small molecule identification, but current deep learning systems for spectrum prediction still remain difficult to evaluate and deploy in practice.
arXiv:2505. 20346v3 Announce Type: replace-cross Abstract: Function-guided protein design is a crucial task with significant applications in drug discovery and enzyme engineering.
arXiv:2509. 09371v2 Announce Type: replace-cross Abstract: Distributionally robust optimization (DRO) protects statistical learning against distributional shifts by optimizing the worst-case performance over a set of perturbed distributions.
arXiv:2607. 28553v1 Announce Type: new Abstract: Predicting the 3D structures of atomic systems is fundamental to advancing material science and drug discovery.
arXiv:2607. 22314v1 Announce Type: new Abstract: Multiple Sequence Alignments (MSAs) provide protein language models with explicit evolutionary context, but their large depth makes subsampling unavoidable under limited token budgets.