Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material discovery. For these scientific problems, molecules serve as the fundamental building blocks, and machine learning has emerged as a highly effective and powerful tool for modeling their geometric structures. Nevertheless, due to the rapidly evolving process of the field and the knowledge gap between science (e.g., physics, chemistry, & biology) and machine learning communities, a benchmarking study on geometrical representation for such data has not been conducted. To address such an issue, in this paper, we first provide a unified view of the current symmetry-informed geometric methods, classifying them into three main categories: invariance, equivariance with spherical frame basis, and equivariance with vector frame basis. Then we propose a platform, coined Geom3D, which enables benchmarking the effectiveness of geometric strategies. Geom3D contains 16 advanced symmetry-informed geometric representation models and 14 geometric pretraining methods over 46 diverse datasets, including small molecules, proteins, and crystalline materials. We hope that Geom3D can, on the one hand, eliminate barriers for machine learning researchers interested in exploring scientific problems; and, on the other hand, provide valuable guidance for researchers in computational chemistry, structural biology, and materials science, aiding in the informed selection of representation techniques for specific applications. The source code is available on the GitHub repository.

Recent advancements in conversational large language models (LLMs), such as ChatGPT, have demonstrated remarkable promise in various domains, including drug discovery. However, existing works mainly focus on investigating the capabilities of conversational LLMs on chemical reaction and retrosynthesis. While drug editing, a critical task in the drug discovery pipeline, remains largely unexplored. To bridge this gap, we propose ChatDrug, a framework to facilitate the systematic investigation of drug editing using LLMs. ChatDrug jointly leverages a prompt module, a retrieval and domain feedback (ReDF) module, and a conversation module to streamline effective drug editing. We empirically show that ChatDrug reaches the best performance on 33 out of 39 drug editing tasks, encompassing small molecules, peptides, and proteins. We further demonstrate, through 10 case studies, that ChatDrug can successfully identify the key substructures (e.g., the molecule functional groups, peptide motifs, and protein structures) for manipulation, generating diverse and valid suggestions for drug editing. Promisingly, we also show that ChatDrug can offer insightful explanations from a domain-specific perspective, enhancing interpretability and enabling informed decision-making. This research sheds light on the potential of ChatGPT and conversational LLMs for drug editing. It paves the way for a more efficient and collaborative drug discovery pipeline, contributing to the advancement of pharmaceutical research and development.

Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e.g., SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks.

Molecular representation pretraining is critical in various applications for drug and material discovery due to the limited number of labeled molecules, and most existing work focuses on pretraining on 2D molecular graphs. However, the power of pretraining on 3D geometric structures has been less explored. This is owing to the difficulty of finding a sufficient proxy task that can empower the pretraining to effectively extract essential features from the geometric structures. Motivated by the dynamic nature of 3D molecules, where the continuous motion of a molecule in the 3D Euclidean space forms a smooth potential energy surface, we propose GeoSSL, a 3D coordinate denoising pretraining framework to model such an energy landscape. Further by leveraging an SE(3)-invariant score matching method, we propose GeoSSL-DDM in which the coordinate denoising proxy task is effectively boiled down to denoising the pairwise atomic distances in a molecule. Our comprehensive experiments confirm the effectiveness and robustness of our proposed method.

Distribution shift is a major challenge in machine learning, as models often perform poorly during the test stage if the test distribution differs from the training distribution. In this paper, we focus on domain shifts, which occur when the model is applied to new domains that are different from the ones it was trained on, and propose a new approach called D^3G. Unlike previous approaches that aim to learn a single model that is domain invariant, D^3G learns domain-specific models by leveraging the relations among different domains. Concretely, D^3G learns a set of training-domain-specific functions during the training stage and reweights them based on domain relations during the test stage. These domain relations can be directly derived or learned from fixed domain meta-data. Under mild assumptions, we theoretically proved that using domain relations to reweight training-domain-specific functions achieves stronger generalization compared to averaging them. Empirically, we evaluated the effectiveness of D^3G using both toy and real-world datasets for tasks such as temperature regression, land use classification, and molecule-protein interaction prediction. Our results showed that D^3G consistently outperformed state-of-the-art methods, with an average improvement of 10.6% in performance.

We explore the downstream task performances for graph neural network (GNN) self-supervised learning (SSL) methods trained on subgraphs extracted from relational databases (RDBs). Intuitively, this joint use of SSL and GNNs should allow to leverage more of the available data, which could translate to better results. However, we found that naively porting contrastive SSL techniques can cause ``negative transfer'': linear evaluation on fixed representations from a pretrained model performs worse than on representations from the randomly-initialized model. Based on the conjecture that contrastive SSL conflicts with the message passing layers of the GNN, we propose InfoNode: a contrastive loss aiming to maximize the mutual information between a node's initial- and final-layer representation. The primary empirical results support our conjecture and the effectiveness of InfoNode.

Graph neural networks (GNNs) have been shown to possess strong representation power, which can be exploited for downstream prediction tasks on graph-structured data, such as molecules and social networks. They typically learn representations by aggregating information from the K-hop neighborhood of individual vertices or from the enumerated walks in the graph. Prior studies have demonstrated the effectiveness of incorporating weighting schemes into GNNs; however, this has been primarily limited to K-hop neighborhood GNNs so far. In this paper, we aim to extensively analyze the effect of incorporating weighting schemes into walk-aggregating GNNs. Towards this objective, we propose a novel GNN model, called AWARE, that aggregates information about the walks in the graph using attention schemes in a principled way to obtain an end-to-end supervised learning method for graph-level prediction tasks. We perform theoretical, empirical, and interpretability analyses of AWARE. Our theoretical analysis provides the first provable guarantees for weighted GNNs, demonstrating how the graph information is encoded in the representation, and how the weighting schemes in AWARE affect the representation and learning performance. We empirically demonstrate the superiority of AWARE over prior baselines in the domains of molecular property prediction (61 tasks) and social networks (4 tasks). Our interpretation study illustrates that AWARE can successfully learn to capture the important substructures of the input graph.

Over the last decade, there has been significant progress in the field of machine learning for de novo drug design, particularly in deep generative models. However, current generative approaches exhibit a significant challenge as they do not ensure that the proposed molecular structures can be feasibly synthesized nor do they provide the synthesis routes of the proposed small molecules, thereby seriously limiting their practical applicability. In this work, we propose a novel forward synthesis framework powered by reinforcement learning (RL) for de novo drug design, Policy Gradient for Forward Synthesis (PGFS), that addresses this challenge by embedding the concept of synthetic accessibility directly into the de novo drug design system. In this setup, the agent learns to navigate through the immense synthetically accessible chemical space by subjecting commercially available small molecule building blocks to valid chemical reactions at every time step of the iterative virtual multi-step synthesis process. The proposed environment for drug discovery provides a highly challenging test-bed for RL algorithms owing to the large state space and high-dimensional continuous action space with hierarchical actions. PGFS achieves state-of-the-art performance in generating structures with high QED and penalized clogP. Moreover, we validate PGFS in an in-silico proof-of-concept associated with three HIV targets. Finally, we describe how the end-to-end training conceptualized in this study represents an important paradigm in radically expanding the synthesizable chemical space and automating the drug discovery process.

Several recent works have aimed to explain why severely overparameterized models, generalize well when trained by Stochastic Gradient Descent (SGD). The emergent consensus explanation has two parts: the first is that there are "no bad local minima", while the second is that SGD performs implicit regularization by having a bias towards low complexity models. We revisit both of these ideas in the context of image classification with common deep neural network architectures. Our first finding is that there exist bad global minima, i.e., models that fit the training set perfectly, yet have poor generalization. Our second finding is that given only unlabeled training data, we can easily construct initializations that will cause SGD to quickly converge to such bad global minima. For example, on CIFAR, CINIC10, and (Restricted) ImageNet, this can be achieved by starting SGD at a model derived by fitting random labels on the training data: while subsequent SGD training (with the correct labels) will reach zero training error, the resulting model will exhibit a test accuracy degradation of up to 40% compared to training from a random initialization. Finally, we show that regularization seems to provide SGD with an escape route: once heuristics such as data augmentation are used, starting from a complex model (adversarial initialization) has no effect on the test accuracy.

Distributed model training suffers from communication overheads due to frequent gradient updates transmitted between compute nodes. To mitigate these overheads, several studies propose the use of sparsified stochastic gradients. We argue that these are facets of a general sparsification method that can operate on any possible atomic decomposition. Notable examples include element-wise, singular value, and Fourier decompositions. We present ATOMO, a general framework for atomic sparsification of stochastic gradients. Given a gradient, an atomic decomposition, and a sparsity budget, ATOMO gives a random unbiased sparsification of the atoms minimizing variance. We show that recent methods such as QSGD and TernGrad are special cases of ATOMO, and that sparsifiying the singular value decomposition of neural networks gradients, rather than their coordinates, can lead to significantly faster distributed training.