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Zhaojie Chai

Zhaojie Chai contributes to research discovery and scholarly infrastructure.

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Published work

3 published item(s)

preprint2026arXiv

GRAFT-ATHENA: Self-Improving Agentic Teams for Autonomous Discovery and Evolutionary Numerical Algorithms

Scientific discovery can be modeled as a sequence of probabilistic decisions that map physical problems to numerical solutions. Recent agentic AI systems automate individual scientific tasks by orchestrating LLM-driven planners, solvers, and evaluators. Each method is a combination of methodological actions, with many viable combinations for any given problem and structural dependencies between choices. However, existing frameworks treat each problem in isolation, with no shared substrate to accumulate methodological experience across domains. Here we show that GRAFT-ATHENA, a self-improving agentic framework, learns from past problems and autonomously expands its own action space across diverse domains. GRAFT (Graph Reduction to Adaptive Factored Trees) projects combinatorial decision spaces into factored probabilistic trees in which each method is a single path, taking the parameter footprint from exponential to linear. In the lineage of classical Bayesian networks, the factorization is an $I$-map of the policy, and the resulting paths embed as unique fingerprints in a metric space whose closeness lets each new problem learn from similar past ones. On canonical physics-informed machine learning (PIML) benchmarks, GRAFT-ATHENA improves over human and prior agentic baselines, and on production solvers, it tackles complex engineering problems such as reconstructing Mach-10 flow over the Apollo Command Module from a 1968 report and recovering shear-thinning blood-cell rheology. Notably, the system grows its own knowledge substrate, autonomously proposing regularization constraints for ill-posed inverse problems and discovering new numerical methods such as a spectral PINN with exponential convergence. These results provide a foundation for autonomous laboratories that grow more capable with every problem they solve.

preprint2020arXiv

A deep reinforcement learning model based on deterministic policy gradient for collective neural crest cell migration

Modeling cell interactions such as co-attraction and contact-inhibition of locomotion is essential for understanding collective cell migration. Here, we propose a novel deep reinforcement learning model for collective neural crest cell migration. We apply the deep deterministic policy gradient algorithm in association with a particle dynamics simulation environment to train agents to determine the migration path. Because of the different migration mechanisms of leader and follower neural crest cells, we train two types of agents (leaders and followers) to learn the collective cell migration behavior. For a leader agent, we consider a linear combination of a global task, resulting in the shortest path to the target source, and a local task, resulting in a coordinated motion along the local chemoattractant gradient. For a follower agent, we consider only the local task. First, we show that the self-driven forces learned by the leader cell point approximately to the placode, which means that the agent is able to learn to follow the shortest path to the target. To validate our method, we compare the total time elapsed for agents to reach the placode computed using the proposed method and the time computed using an agent-based model. The distributions of the migration time intervals calculated using the two methods are shown to not differ significantly. We then study the effect of co-attraction and contact-inhibition of locomotion to the collective leader cell migration. We show that the overall leader cell migration for the case with co-attraction is slower because the co-attraction mitigates the source-driven effect. In addition, we find that the leader and follower agents learn to follow a similar migration behavior as in experimental observations. Overall, our proposed method provides useful insight on how to apply reinforcement learning techniques to simulate collective cell migration.

preprint2020arXiv

Deep reinforcement learning with a particle dynamics environment applied to emergency evacuation of a room with obstacles

A very successful model for simulating emergency evacuation is the social-force model. At the heart of the model is the self-driven force that is applied to an agent and is directed towards the exit. However, it is not clear if the application of this force results in optimal evacuation, especially in complex environments with obstacles. Here, we develop a deep reinforcement learning algorithm in association with the social force model to train agents to find the fastest evacuation path. During training, we penalize every step of an agent in the room and give zero reward at the exit. We adopt the Dyna-Q learning approach. We first show that in the case of a room without obstacles the resulting self-driven force points directly towards the exit as in the social force model and that the median exit time intervals calculated using the two methods are not significantly different. Then, we investigate evacuation of a room with one obstacle and one exit. We show that our method produces similar results with the social force model when the obstacle is convex. However, in the case of concave obstacles, which sometimes can act as traps for agents governed purely by the social force model and prohibit complete room evacuation, our approach is clearly advantageous since it derives a policy that results in object avoidance and complete room evacuation without additional assumptions. We also study evacuation of a room with multiple exits. We show that agents are able to evacuate efficiently from the nearest exit through a shared network trained for a single agent. Finally, we test the robustness of the Dyna-Q learning approach in a complex environment with multiple exits and obstacles. Overall, we show that our model can efficiently simulate emergency evacuation in complex environments with multiple room exits and obstacles where it is difficult to obtain an intuitive rule for fast evacuation.