arXiv:2603.06748v1 Announce Type: cross Abstract: Protein sequence design must balance designability, defined as the ability to recover a target backbone, with multiple, often competing, developability properties such as solubility, thermostability, and expression. Existing approaches address these properties through post hoc mutation, inference-time biasing, or retraining on property-specific subsets, yet they are target dependent and demand substantial domain expertise or careful hyperparameter tuning. In this paper, we introduce ProtAlign, a multi-objective preference alignment framework that fine-tunes pretrained inverse folding models to satisfy diverse developability objectives while preserving structural fidelity. ProtAlign employs a semi-online Direct Preference Optimization strategy with a flexible preference margin to mitigate conflicts among competing objectives and constructs preference pairs using in silico property predictors. Applied to the widely used ProteinMPNN backbone, the resulting model MoMPNN enhances developability without compromising designability across tasks including sequence design for CATH 4.3 crystal structures, de novo generated backbones, and real-world binder design scenarios, making it an appealing framework for practical protein sequence design.

arXiv:2506.06683v4 Announce Type: replace-cross Abstract: Dual-arm robots play a crucial role in improving efficiency and flexibility in complex multitasking scenarios. While existing methods have achieved promising results in task planning, they often fail to fully optimize task parallelism, limiting the potential of dual-arm collaboration. To address this issue, we propose RoboPARA, a novel large language model (LLM)-driven framework for dual-arm task parallelism planning. RoboPARA employs a two-stage process: (1) Dependency Graph-based Planning Candidates Generation, which constructs directed acyclic graphs (DAGs) to model task dependencies and eliminate redundancy, and (2) Graph Re-Traversal-based Dual-Arm Parallel Planning, which optimizes DAG traversal to maximize parallelism while maintaining task coherence. In addition, we introduce the Cross-Scenario Dual-Arm Parallel Task dataset (X-DAPT dataset), the first dataset specifically designed to evaluate dual-arm task parallelism across diverse scenarios and difficulty levels. Extensive experiments demonstrate that RoboPARA significantly outperforms existing planning methods, achieving higher efficiency and reliability, particularly in complex task combinations. Our code is publicly available at https://github.com/AiDuanshiying/RoboPARA.

arXiv:2602.19685v1 Announce Type: cross Abstract: Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, perturbation prediction requires mapping unpaired control and perturbed populations. Existing models address this by learning maps between distributions, but typically assume a single fixed response distribution when conditioned on observed cellular context (e.g., cell type) and the perturbation type. In reality, responses vary systematically due to unobservable latent factors such as microenvironmental fluctuations and complex batch effects, forming a manifold of possible distributions for the same observed conditions. To account for this variability, we introduce PerturbDiff, which shifts modeling from individual cells to entire distributions. By embedding distributions as points in a Hilbert space, we define a diffusion-based generative process operating directly over probability distributions. This allows PerturbDiff to capture population-level response shifts across hidden factors. Benchmarks on established datasets show that PerturbDiff achieves state-of-the-art performance in single-cell response prediction and generalizes substantially better to unseen perturbations. See our project page (https://katarinayuan.github.io/PerturbDiff-ProjectPage/), where code and data will be made publicly available (https://github.com/DeepGraphLearning/PerturbDiff).