arXiv:2306.13732v2 Announce Type: replace Abstract: We study a class of reinforcement learning (RL) tasks where the objective of the agent is to accomplish temporally extended goals. In this setting, a common approach is to represent the tasks as deterministic finite automata (DFA) and integrate them into the state-space for RL algorithms. However, while these machines model the reward function, they often overlook the causal knowledge about the environment. To address this limitation, we propose the Temporal-Logic-based Causal Diagram (TL-CD) in RL, which captures the temporal causal relationships between different properties of the environment. We exploit the TL-CD to devise an RL algorithm in which an agent requires significantly less exploration of the environment. To this end, based on a TL-CD and a task DFA, we identify configurations where the agent can determine the expected rewards early during an exploration. Through a series of case studies, we demonstrate the benefits of using TL-CDs, particularly the faster convergence of the algorithm to an optimal policy due to reduced exploration of the environment.

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.