arXiv:2507.17731v2 Announce Type: replace-cross Abstract: Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, catalysis discovery, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions. The corresponding curated resources are available at https://github.com/Violet24K/Awesome-Flow-Matching-Meets-Biology.

arXiv:2603.00117v2 Announce Type: replace-cross Abstract: Living organisms exhibit persistent autonomy through internally generated goals and self-sustaining behavioral organization, yet current embodied agents remain driven by externally scripted objectives. This dependence on predefined task specifications limits their capacity for long-term deployment in dynamic, unstructured environments where continuous human intervention is impractical. We propose that personality traits provide an intrinsic organizational principle for achieving persistent autonomy. Analogous to genotypic biases shaping biological behavioral tendencies, personalities enable agents to autonomously generate goals and sustain behavioral evolution without external supervision. To realize this, we develop PEPA, a three-layer cognitive architecture that operates through three interacting systems: Sys3 autonomously synthesizes personality-aligned goals and refines them via episodic memory and daily self-reflection; Sys2 performs deliberative reasoning to translate goals into executable action plans; Sys1 grounds the agent in sensorimotor interaction, executing actions and recording experiences. We validate the framework through real-world deployment on a quadruped robot in a multi-floor office building. Operating without reliance on fixed task specifications, the robot autonomously arbitrates between user requests and personality-driven motivations, navigating elevators and exploring environments accordingly. Quantitative analysis across five distinct personality prototypes demonstrates stable, trait-aligned behaviors. The results confirm that personality-driven cognitive architectures enable sustained autonomous operation characteristic of persistent embodied systems. Code and demo videos are available at https://sites.google.com/view/pepa-persistent/.