Zijie Li

Yuyang Wang, Zijie Li, Amir Barati Farimani

Graph neural networks (GNNs), which are capable of learning representations from graphical data, are naturally suitable for modeling molecular systems. This review introduces GNNs and their various applications for small organic molecules. GNNs rely on message-passing operations, a generic yet powerful framework, to update node features iteratively. Many researches design GNN architectures to effectively learn topological information of 2D molecule graphs as well as geometric information of 3D molecular systems. GNNs have been implemented in a wide variety of molecular applications, including molecular property prediction, molecular scoring and docking, molecular optimization and de novo generation, molecular dynamics simulation, etc. Besides, the review also summarizes the recent development of self-supervised learning for molecules with GNNs.

Zijie Li, Henry Li, Yichun Shi et al.

Diffusion models have gained tremendous success in text-to-image generation, yet still lag behind with visual understanding tasks, an area dominated by autoregressive vision-language models. We propose a large-scale and fully end-to-end diffusion model for multi-modal understanding and generation that significantly improves on existing diffusion-based multimodal models, and is the first of its kind to support the full suite of vision-language modeling capabilities. Inspired by the multimodal diffusion transformer (MM-DiT) and recent advances in discrete diffusion language modeling, we leverage a cross-modal maximum likelihood estimation framework that simultaneously trains the conditional likelihoods of both images and text jointly under a single loss function, which is back-propagated through both branches of the diffusion transformer. The resulting model is highly flexible and capable of a wide range of tasks including image generation, captioning, and visual question answering. Our model attained competitive performance compared to recent unified image understanding and generation models, demonstrating the potential of multimodal diffusion modeling as a promising alternative to autoregressive next-token prediction models.

Zijie Li, Anthony Zhou, Saurabh Patil et al. · cmu

Accurate weather forecasting is crucial in various sectors, impacting decision-making processes and societal events. Data-driven approaches based on machine learning models have recently emerged as a promising alternative to numerical weather prediction models given their potential to capture physics of different scales from historical data and the significantly lower computational cost during the prediction stage. Renowned for its state-of-the-art performance across diverse domains, the Transformer model has also gained popularity in machine learning weather prediction. Yet applying Transformer architectures to weather forecasting, particularly on a global scale is computationally challenging due to the quadratic complexity of attention and the quadratic increase in spatial points as resolution increases. In this work, we propose a factorized-attention-based model tailored for spherical geometries to mitigate this issue. More specifically, it utilizes multi-dimensional factorized kernels that convolve over different axes where the computational complexity of the kernel is only quadratic to the axial resolution instead of overall resolution. The deterministic forecasting accuracy of the proposed model on $1.5^\circ$ and 0-7 days' lead time is on par with state-of-the-art purely data-driven machine learning weather prediction models. We also showcase the proposed model holds great potential to push forward the Pareto front of accuracy-efficiency for Transformer weather models, where it can achieve better accuracy with less computational cost compared to Transformer based models with standard attention.

Zehua Zhang, Zijie Li, Amir Barati Farimani

We propose a mask pretraining method for Graph Neural Networks (GNNs) to improve their performance on fitting potential energy surfaces, particularly in water systems. GNNs are pretrained by recovering spatial information related to masked-out atoms from molecules, then transferred and finetuned on atomic forcefields. Through such pretraining, GNNs learn meaningful prior about structural and underlying physical information of molecule systems that are useful for downstream tasks. From comprehensive experiments and ablation studies, we show that the proposed method improves the accuracy and convergence speed compared to GNNs trained from scratch or using other pretraining techniques such as denoising. On the other hand, our pretraining method is suitable for both energy-centric and force-centric GNNs. This approach showcases its potential to enhance the performance and data efficiency of GNNs in fitting molecular force fields.