Yichun He | Searcharxiv

arXiv2025

Human-AI Co-Embodied Intelligence for Scientific Experimentation and Manufacturing

Scientific experimentation and manufacturing rely on prolonged protocol development and complex, multi-step implementation, which require continuous human expertise for precise execution and decision-making, limiting interpretability and scalability. Here, we introduce human-artificial intelligence (AI) co-embodied intelligence, a new form of physical AI that unites human researchers, agentic AI, and wearable hardware. In this paradigm, humans provide precise execution, while agentic AI contributes contextual reasoning, adaptive planning, and analysis. The wearable interface continuously captures experimentation and manufacturing, facilitating seamless communication between humans and AI. We instantiate this paradigm in a microfabrication cleanroom, leading to the agentic-physical experimentation (APEX) system which understands fabrication procedure with accuracy 51% higher than state-of-the-art multimodal large language models/vision language models (LLMs/VLMs), detects and corrects fabrication errors in real-time, and transfers procedural expertise to novice users. Critically, APEX system enables the co-development of fabrication protocols in cleanrooms, overcoming the incompatibility of elastomeric materials in standard microfabrication processes and enabling previously unattainable fabrication outcomes, as demonstrated by the wafer-scale realization of brain-level soft neural probe capable of single-unit-resolution neural recording. These results establish the human-AI co-embodied intelligence that extends agentic reasoning beyond computation into the physical domain, transforming scientific experimentation and manufacturing into autonomous, traceable, interpretable and scalable processes.

cs.AI↗

arXiv2024

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

cs.LG↗