Yang Song

Qi Yan, Zhengyang Liang, Yang Song et al. · stanford

Diffusion models based on permutation-equivariant networks can learn permutation-invariant distributions for graph data. However, in comparison to their non-invariant counterparts, we have found that these invariant models encounter greater learning challenges since 1) their effective target distributions exhibit more modes; 2) their optimal one-step denoising scores are the score functions of Gaussian mixtures with more components. Motivated by this analysis, we propose a non-invariant diffusion model, called $\textit{SwinGNN}$, which employs an efficient edge-to-edge 2-WL message passing network and utilizes shifted window based self-attention inspired by SwinTransformers. Further, through systematic ablations, we identify several critical training and sampling techniques that significantly improve the sample quality of graph generation. At last, we introduce a simple post-processing trick, $\textit{i.e.}$, randomly permuting the generated graphs, which provably converts any graph generative model to a permutation-invariant one. Extensive experiments on synthetic and real-world protein and molecule datasets show that our SwinGNN achieves state-of-the-art performances. Our code is released at https://github.com/qiyan98/SwinGNN.

Minkai Xu, Lantao Yu, Yang Song et al.

Predicting molecular conformations from molecular graphs is a fundamental problem in cheminformatics and drug discovery. Recently, significant progress has been achieved with machine learning approaches, especially with deep generative models. Inspired by the diffusion process in classical non-equilibrium thermodynamics where heated particles will diffuse from original states to a noise distribution, in this paper, we propose a novel generative model named GeoDiff for molecular conformation prediction. GeoDiff treats each atom as a particle and learns to directly reverse the diffusion process (i.e., transforming from a noise distribution to stable conformations) as a Markov chain. Modeling such a generation process is however very challenging as the likelihood of conformations should be roto-translational invariant. We theoretically show that Markov chains evolving with equivariant Markov kernels can induce an invariant distribution by design, and further propose building blocks for the Markov kernels to preserve the desirable equivariance property. The whole framework can be efficiently trained in an end-to-end fashion by optimizing a weighted variational lower bound to the (conditional) likelihood. Experiments on multiple benchmarks show that GeoDiff is superior or comparable to existing state-of-the-art approaches, especially on large molecules.

Yang Ma, Chaoyi Zhang, Mariano Cabezas et al.

Multiple sclerosis (MS) is a chronic inflammatory and degenerative disease of the central nervous system, characterized by the appearance of focal lesions in the white and gray matter that topographically correlate with an individual patient's neurological symptoms and signs. Magnetic resonance imaging (MRI) provides detailed in-vivo structural information, permitting the quantification and categorization of MS lesions that critically inform disease management. Traditionally, MS lesions have been manually annotated on 2D MRI slices, a process that is inefficient and prone to inter-/intra-observer errors. Recently, automated statistical imaging analysis techniques have been proposed to detect and segment MS lesions based on MRI voxel intensity. However, their effectiveness is limited by the heterogeneity of both MRI data acquisition techniques and the appearance of MS lesions. By learning complex lesion representations directly from images, deep learning techniques have achieved remarkable breakthroughs in the MS lesion segmentation task. Here, we provide a comprehensive review of state-of-the-art automatic statistical and deep-learning MS segmentation methods and discuss current and future clinical applications. Further, we review technical strategies, such as domain adaptation, to enhance MS lesion segmentation in real-world clinical settings.