Bo Qiang

RuiKang OuYang, Bo Qiang, José Miguel Hernández-Lobato

Developing an efficient sampler capable of generating independent and identically distributed (IID) samples from a Boltzmann distribution is a crucial challenge in scientific research, e.g. molecular dynamics. In this work, we intend to learn neural samplers given energy functions instead of data sampled from the Boltzmann distribution. By learning the energies of the noised data, we propose a diffusion-based sampler, Noised Energy Matching, which theoretically has lower variance and more complexity compared to related works. Furthermore, a novel bootstrapping technique is applied to NEM to balance between bias and variance. We evaluate NEM and BNEM on a 2-dimensional 40 Gaussian Mixture Model (GMM) and a 4-particle double-well potential (DW-4). The experimental results demonstrate that BNEM can achieve state-of-the-art performance while being more robust.

Ningfeng Liu, Jie Yu, Siyu Xiu et al.

Molecular generation, an essential method for identifying new drug structures, has been supported by advancements in machine learning and computational technology. However, challenges remain in multi-objective generation, model adaptability, and practical application in drug discovery. In this study, we developed a versatile 'plug-in' molecular generation model that incorporates multiple objectives related to target affinity, drug-likeness, and synthesizability, facilitating its application in various drug development contexts. We improved the Particle Swarm Optimization (PSO) in the context of drug discoveries, and identified PSO-ENP as the optimal variant for multi-objective molecular generation and optimization through comparative experiments. The model also incorporates a novel target-ligand affinity predictor, enhancing the model's utility by supporting three-dimensional information and improving synthetic feasibility. Case studies focused on generating and optimizing drug-like big marine natural products were performed, underscoring PSO-ENP's effectiveness and demonstrating its considerable potential for practical drug discovery applications.