James J. Lu

Chenqing Hua, Jiarui Lu, Yong Liu et al.

The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interaction prediction, primarily from a binding perspective, focusing on creating ideal lock-and-key models. However, these methods can fall short for enzyme-substrate interactions, where perfect binding models are rare, and induced fit states are more common. To address this, we shift to a functional perspective for enzyme design, where the enzyme function is defined by the reaction it catalyzes. Here, we introduce \textsc{GENzyme}, a \textit{de novo} enzyme design model that takes a catalytic reaction as input and generates the catalytic pocket, full enzyme structure, and enzyme-substrate binding complex. \textsc{GENzyme} is an end-to-end, three-staged model that integrates (1) a catalytic pocket generation and sequence co-design module, (2) a pocket inpainting and enzyme inverse folding module, and (3) a binding and screening module to optimize and predict enzyme-substrate complexes. The entire design process is driven by the catalytic reaction being targeted. This reaction-first approach allows for more accurate and biologically relevant enzyme design, potentially surpassing structure-based and binding-focused models in creating enzymes capable of catalyzing specific reactions. We provide \textsc{GENzyme} code at https://github.com/WillHua127/GENzyme.

Xiaoyin Chen, Jiarui Lu, Minsu Kim et al. · mila

Reinforcement learning (RL) has proven effective for fine-tuning large language models (LLMs), significantly enhancing their reasoning abilities in domains such as mathematics and code generation. A crucial factor influencing RL fine-tuning success is the training curriculum: the order in which training problems are presented. While random curricula serve as common baselines, they remain suboptimal; manually designed curricula often rely heavily on heuristics, and online filtering methods can be computationally prohibitive. To address these limitations, we propose Self-Evolving Curriculum (SEC), an automatic curriculum learning method that learns a curriculum policy concurrently with the RL fine-tuning process. Our approach formulates curriculum selection as a non-stationary Multi-Armed Bandit problem, treating each problem category (e.g., difficulty level or problem type) as an individual arm. We leverage the absolute advantage from policy gradient methods as a proxy measure for immediate learning gain. At each training step, the curriculum policy selects categories to maximize this reward signal and is updated using the TD(0) method. Across three distinct reasoning domains: planning, inductive reasoning, and mathematics, our experiments demonstrate that SEC significantly improves models' reasoning capabilities, enabling better generalization to harder, out-of-distribution test problems. Additionally, our approach achieves better skill balance when fine-tuning simultaneously on multiple reasoning domains. These findings highlight SEC as a promising strategy for RL fine-tuning of LLMs.