Zhicheng Zhang

Mingyuan Zhang, Zhicheng Zhang, Hao Wu et al.

We present flow matching for reaction coordinates (FMRC), a novel deep learning algorithm designed to identify optimal reaction coordinates (RC) in biomolecular reversible dynamics. FMRC is based on the mathematical principles of lumpability and decomposability, which we reformulate into a conditional probability framework for efficient data-driven optimization using deep generative models. While FMRC does not explicitly learn the well-established transfer operator or its eigenfunctions, it can effectively encode the dynamics of leading eigenfunctions of the system transfer operator into its low-dimensional RC space. We further quantitatively compare its performance with several state-of-the-art algorithms by evaluating the quality of Markov state models (MSM) constructed in their respective RC spaces, demonstrating the superiority of FMRC in three increasingly complex biomolecular systems. In addition, we successfully demonstrated the efficacy of FMRC for bias deposition in the enhanced sampling of a simple model system. Finally, we discuss its potential applications in downstream applications such as enhanced sampling methods and MSM construction.

Yuan Bi, Cheng Qian, Zhicheng Zhang et al.

Ultrasound (US) has been widely used in daily clinical practice for screening internal organs and guiding interventions. However, due to the acoustic shadow cast by the subcutaneous rib cage, the US examination for thoracic application is still challenging. To fully cover and reconstruct the region of interest in US for diagnosis, an intercostal scanning path is necessary. To tackle this challenge, we present a reinforcement learning (RL) approach for planning scanning paths between ribs to monitor changes in lesions on internal organs, such as the liver and heart, which are covered by rib cages. Structured anatomical information of the human skeleton is crucial for planning these intercostal paths. To obtain such anatomical insight, an RL agent is trained in a virtual environment constructed using computational tomography (CT) templates with randomly initialized tumors of various shapes and locations. In addition, task-specific state representation and reward functions are introduced to ensure the convergence of the training process while minimizing the effects of acoustic attenuation and shadows during scanning. To validate the effectiveness of the proposed approach, experiments have been carried out on unseen CTs with randomly defined single or multiple scanning targets. The results demonstrate the efficiency of the proposed RL framework in planning non-shadowed US scanning trajectories in areas with limited acoustic access.