Divin Yan

Shengchao Liu, Divin Yan, Weitao Du et al.

Artificial intelligence models have shown great potential in structure-based drug design, generating ligands with high binding affinities. However, existing models have often overlooked a crucial physical constraint: atoms must maintain a minimum pairwise distance to avoid separation violation, a phenomenon governed by the balance of attractive and repulsive forces. To mitigate such separation violations, we propose NucleusDiff. It models the interactions between atomic nuclei and their surrounding electron clouds by enforcing the distance constraint between the nuclei and manifolds. We quantitatively evaluate NucleusDiff using the CrossDocked2020 dataset and a COVID-19 therapeutic target, demonstrating that NucleusDiff reduces violation rate by up to 100.00% and enhances binding affinity by up to 22.16%, surpassing state-of-the-art models for structure-based drug design. We also provide qualitative analysis through manifold sampling, visually confirming the effectiveness of NucleusDiff in reducing separation violations and improving binding affinities.

Divin Yan, Lu Qi, Vincent Tao Hu et al.

Diffusion models have made significant advances recently in high-quality image synthesis and related tasks. However, diffusion models trained on real-world datasets, which often follow long-tailed distributions, yield inferior fidelity for tail classes. Deep generative models, including diffusion models, are biased towards classes with abundant training images. To address the observed appearance overlap between synthesized images of rare classes and tail classes, we propose a method based on contrastive learning to minimize the overlap between distributions of synthetic images for different classes. We show variants of our probabilistic contrastive learning method can be applied to any class conditional diffusion model. We show significant improvement in image synthesis using our loss for multiple datasets with long-tailed distribution. Extensive experimental results demonstrate that the proposed method can effectively handle imbalanced data for diffusion-based generation and classification models. Our code and datasets will be publicly available at https://github.com/yanliang3612/DiffROP.

Shengchao Liu, Weitao Du, Hannan Xu et al.

In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of improving the efficiency of MD simulations through better numerical methods and, more recently, by utilizing machine learning (ML) methods. Yet, challenges remain, such as accurate modeling of extended-timescale simulations. To address this issue, we propose NeuralMD, the first ML surrogate that can facilitate numerical MD and provide accurate simulations in protein-ligand binding dynamics. We propose a principled approach that incorporates a novel physics-informed multi-grained group symmetric framework. Specifically, we propose (1) the BindingNet model that satisfies group symmetry using vector frames and captures the multi-level protein-ligand interactions, and (2) an augmented neural differential equation solver that learns the trajectory under Newtonian mechanics. For the experiment, we design ten single-trajectory and three multi-trajectory binding simulation tasks. We demonstrate the efficiency and effectiveness of NeuralMD, achieving over 1K$\times$ speedup compared to standard numerical MD simulations. NeuralMD also outperforms all other ML approaches, achieving up to 15$\times$ reduction in reconstruction error and 70% increase in validity. Additionally, we qualitatively illustrate that the oscillations in the predicted trajectories align more closely with ground-truth dynamics than those of other machine-learning methods. We believe NeuralMD paves the foundation for a new research paradigm in simulating protein-ligand dynamics.

Shengzhong Zhang, Wenjie Yang, Yimin Zhang et al.

In this work, we discover a phenomenon of community bias amplification in graph representation learning, which refers to the exacerbation of performance bias between different classes by graph representation learning. We conduct an in-depth theoretical study of this phenomenon from a novel spectral perspective. Our analysis suggests that structural bias between communities results in varying local convergence speeds for node embeddings. This phenomenon leads to bias amplification in the classification results of downstream tasks. Based on the theoretical insights, we propose random graph coarsening, which is proved to be effective in dealing with the above issue. Finally, we propose a novel graph contrastive learning model called Random Graph Coarsening Contrastive Learning (RGCCL), which utilizes random coarsening as data augmentation and mitigates community bias by contrasting the coarsened graph with the original graph. Extensive experiments on various datasets demonstrate the advantage of our method when dealing with community bias amplification.