Feihao Fang

Zihao Li, Zhichen Zeng, Xiao Lin et al.

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, 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.

Zihao Li, Jiaru Zou, Feihao Fang et al.

Agentic large language model systems have demonstrated strong capabilities. However, their reliance on language as the universal interface fundamentally limits their applicability to many real-world problems, especially in scientific domains where domain-specific foundation models have been developed to address specialized tasks beyond natural language. In this work, we introduce Eywa, a heterogeneous agentic framework designed to extend language-centric systems to a broader class of scientific foundation models. The key idea of Eywa is to augment domain-specific foundation models with a language-model-based reasoning interface, enabling language models to guide inference over non-linguistic data modalities. This design allows predictive foundation models, which are typically optimized for specialized data and tasks, to participate in higher-level reasoning and decision-making processes within agentic systems. Eywa can serve as a drop-in replacement for a single-agent pipeline (EywaAgent) or be integrated into existing multi-agent systems by replacing traditional agents with specialized agents (EywaMAS). We further investigate a planning-based orchestration framework in which a planner dynamically coordinates traditional agents and Eywa agents to solve complex tasks across heterogeneous data modalities (EywaOrchestra). We evaluate Eywa across a diverse set of scientific domains spanning physical, life, and social sciences. Experimental results demonstrate that Eywa improves performance on tasks involving structured and domain-specific data, while reducing reliance on language-based reasoning through effective collaboration with specialized foundation models.

Feihao Fang, My T. Thai, Yuanyuan Lei

Large Language Models (LLMs) still struggle with multi-step logical reasoning. Existing approaches either purely refine the reasoning chain in natural language form or attach a symbolic solver as an external module. In this work, we instead ask whether LLMs contain a shared internal logical subspace that simultaneously aligns natural-language and symbolic-language views of the reasoning process. Our hypothesis is that this logical subspace captures logical reasoning capabilities in LLMs that are shared across views while remaining independent of surface forms. To verify this, we employ Canonical Correlation Analysis on the paired residual activations from natural-language and symbolic-language reasoning chains, learning a low-dimensional subspace with maximum cross-view correlation. Furthermore, we design a training-free approach that steers LLMs reasoning chain along this logical subspace, thereby leveraging the complementary reasoning signals from both views. Experiments on four logical reasoning benchmarks demonstrate the effectiveness of our approach, improving accuracy by up to 11 percentage points and generalizing well on out-of-domain problems.