Molecular representation learning (MRL) has gained tremendous attention due to its critical role in learning from limited supervised data for applications like drug design. In most MRL methods, molecules are treated as 1D sequential tokens or 2D topology graphs, limiting their ability to incorporate 3D information for downstream tasks and, in particular, making it almost impossible for 3D geometry prediction/generation. In this paper, we propose a universal 3D MRL framework, called Uni-Mol, that significantly enlarges the representation ability and application scope of MRL schemes. Uni-Mol contains two pretrained models with the same SE(3) Transformer architecture: a molecular model pretrained by 209M molecular conformations; a pocket model pretrained by 3M candidate protein pocket data. Besides, Uni-Mol contains several finetuning strategies to apply the pretrained models to various downstream tasks. By properly incorporating 3D information, Uni-Mol outperforms SOTA in 14/15 molecular property prediction tasks. Moreover, Uni-Mol achieves superior performance in 3D spatial tasks, including protein-ligand binding pose prediction, molecular conformation generation, etc. The code, model, and data are made publicly available at https://github.com/dptech-corp/Uni-Mol.

Graph neural networks (GNNs) have emerged as a powerful tool for effectively mining and learning from graph-structured data, with applications spanning numerous domains. However, most research focuses on static graphs, neglecting the dynamic nature of real-world networks where topologies and attributes evolve over time. By integrating sequence modeling modules into traditional GNN architectures, dynamic GNNs aim to bridge this gap, capturing the inherent temporal dependencies of dynamic graphs for a more authentic depiction of complex networks. This paper provides a comprehensive review of the fundamental concepts, key techniques, and state-of-the-art dynamic GNN models. We present the mainstream dynamic GNN models in detail and categorize models based on how temporal information is incorporated. We also discuss large-scale dynamic GNNs and pre-training techniques. Although dynamic GNNs have shown superior performance, challenges remain in scalability, handling heterogeneous information, and lack of diverse graph datasets. The paper also discusses possible future directions, such as adaptive and memory-enhanced models, inductive learning, and theoretical analysis.

Personalized PageRank (PPR) is a traditional measure for node proximity on large graphs. For a pair of nodes $\boldsymbol{s}$ and $\boldsymbol{t}$ , the PPR value ${\boldsymbol{\pi }_{s}(t)}$ equals the probability that an $\boldsymbol{\alpha }$ -discounted random walk from $\boldsymbol{s}$ terminates at $\boldsymbol{t}$ and reflects the importance between $\boldsymbol{s}$ and $\boldsymbol{t}$ in a bidirectional way. As a generalization of Google's celebrated PageRank centrality, PPR has been extensively studied and has found multifaceted applications in many fields, such as network analysis, graph mining, and graph machine learning. Despite numerous studies devoted to PPR over the decades, efficient computation of PPR remains a challenging problem, and there is a dearth of systematic summaries and comparisons of existing algorithms. In this paper, we recap several frequently used techniques for PPR computation and conduct a comprehensive survey of various recent PPR algorithms from an algorithmic perspective. We classify these approaches based on the types of queries they address and review their methodologies and contributions. We also discuss some representative algorithms for computing PPR on dynamic graphs and in parallel or distributed environments.

The matching between trajectories and locations, called Trajectory-to-Location join (TL-Join), is fundamental functionality in spatiotemporal data management. Given a set of trajectories, a set of locations, and a threshold θ, the TL-Join finds all (trajectory, location) pairs from the two sets with spatiotemporal correlation above θ. This join targets diverse applications, including location recommendation, event tracking, and trajectory activity analyses. We address three challenges in relation to the TL-Join: how to define the spatiotemporal correlation between trajectories and locations, how to prune the search space effectively when computing the join, and how to perform the computation in parallel. Specifically, we define new metrics to measure the spatiotemporal correlation between trajectories and locations. We develop a novel parallel collaborative (PCol) search method based on a divide-and-conquer strategy. For each location, we retrieve the trajectories with high spatiotemporal correlation to, and then we merge the results. An upper bound on the spatiotemporal correlation and a heuristic scheduling strategy are developed to prune the search space. The trajectory searches from different locations are independent and are performed in parallel, and the result merging cost is independent of the degree of parallelism. Studies of the performance of the developed algorithms using large spatiotemporal data sets are reported.

Integrating scientific principles into machine learning models to enhance their predictive performance and generalizability is a central challenge in the development of AI for Science. Herein, we introduce Uni-pK _a, a novel framework that successfully incorporates thermodynamic principles into machine learning modeling, achieving high-precision predictions of acid dissociation constants (pK _a), a crucial task in the rational design of drugs and catalysts, as well as a modeling challenge in computational physical chemistry for small organic molecules. Uni-pK _a utilizes a comprehensive free energy model to represent molecular protonation equilibria accurately. It features a structure enumerator that reconstructs molecular configurations from pK _a data, coupled with a neural network that functions as a free energy predictor, ensuring high-throughput, data-driven prediction while preserving thermodynamic consistency. Employing a pretraining-finetuning strategy with both predicted and experimental pK _a data, Uni-pK _a not only achieves state-of-the-art accuracy in chemoinformatics but also shows comparable precision to quantum mechanics-based methods.

Given a social network G with n nodes and m edges, a positive integer k , and a cascade model C , the influence maximization (IM) problem asks for k nodes in G such that the expected number of nodes influenced by the k nodes under cascade model C is maximized. The state-of-the-art approximate solutions run in O(k(n+m) log n/ ε ² ) expected time while returning a (1 - 1/ e - ε) approximate solution with at least 1 - 1/ n probability. A key phase of these IM algorithms is the random reverse reachable (RR) set generation, and this phase significantly affects the efficiency and scalability of the state-of-the-art IM algorithms. In this article, we present a study on this key phase and propose an efficient random RR set generation algorithm under IC model. With the new algorithm, we show that the expected running time of existing IM algorithms under IC model can be improved to O(k ċ n log n ċ ² ), when for any node v , the total weight of its incoming edges is no larger than a constant. For the general IC model where the weights are skewed, we present a sampling algorithm SKIP. To the best of our knowledge, it is the first index-free algorithm that achieves the optimal time complexity of the sorted subset sampling problem. Moreover, existing approximate IM algorithms suffer from scalability issues in high influence networks where the size of random RR sets is usually quite large. We tackle this challenging issue by reducing the average size of random RR sets without sacrificing the approximation guarantee. The proposed solution is orders of magnitude faster than states of the art as shown in our experiment. Besides, we investigate the issues of forward propagation and derive its time complexity with our proposed subset sampling techniques. We also present a heuristic condition to indicate when the forward propagation approach should be utilized to estimate the expected influence of a given seed set.