Jingrui He

Yikun Ban, Jiaru Zou, Zihao Li et al.

Link prediction is a critical problem in graph learning with broad applications such as recommender systems and knowledge graph completion. Numerous research efforts have been directed at solving this problem, including approaches based on similarity metrics and Graph Neural Networks (GNN). However, most existing solutions are still rooted in conventional supervised learning, which makes it challenging to adapt over time to changing customer interests and to address the inherent dilemma of exploitation versus exploration in link prediction. To tackle these challenges, this paper reformulates link prediction as a sequential decision-making process, where each link prediction interaction occurs sequentially. We propose a novel fusion algorithm, PRB (PageRank Bandits), which is the first to combine contextual bandits with PageRank for collaborative exploitation and exploration. We also introduce a new reward formulation and provide a theoretical performance guarantee for PRB. Finally, we extensively evaluate PRB in both online and offline settings, comparing it with bandit-based and graph-based methods. The empirical success of PRB demonstrates the value of the proposed fusion approach. Our code is released at https://github.com/jiaruzouu/PRB.

Katherine Tieu, Dongqi Fu, Jun Wu et al.

In the era of foundation models, Out-of- Distribution (OOD) problems, i.e., the data discrepancy between the training environments and testing environments, hinder AI generalization. Further, relational data like graphs disobeying the Independent and Identically Distributed (IID) condition makes the problem more challenging, especially much harder when it is associated with time. Motivated by this, to realize the robust invariant learning over temporal graphs, we want to investigate what components in temporal graphs are most invariant and representative with respect to labels. With the Information Bottleneck (IB) method, we propose an error-bounded Invariant Link Selector that can distinguish invariant components and variant components during the training process to make the deep learning model generalizable for different testing scenarios. Besides deriving a series of rigorous generalizable optimization functions, we also equip the training with task-specific loss functions, e.g., temporal link prediction, to make pretrained models solve real-world application tasks like citation recommendation and merchandise recommendation, as demonstrated in our experiments with state-of-the-art (SOTA) methods. Our code is available at https://github.com/kthrn22/OOD-Linker.

Zihao Li, Zhichen Zeng, Xiao Lin et al.

Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions. The corresponding curated resources are available at https://github.com/Violet24K/Awesome-Flow-Matching-Meets-Biology.

Zihao Li, Dongqi Fu, Hengyu Liu et al.

Local clustering aims to find a compact cluster near the given starting instances. This work focuses on graph local clustering, which has broad applications beyond graphs because of the internal connectivities within various modalities. While most existing studies on local graph clustering adopt the discrete graph setting (i.e., unweighted graphs without self-loops), real-world graphs can be more complex. In this paper, we extend the non-approximating Andersen-Chung-Lang ("ACL") algorithm beyond discrete graphs and generalize its quadratic optimality to a wider range of graphs, including weighted, directed, and self-looped graphs and hypergraphs. Specifically, leveraging PageRank, we propose two algorithms: GeneralACL for graphs and HyperACL for hypergraphs. We theoretically prove that, under two mild conditions, both algorithms can identify a quadratically optimal local cluster in terms of conductance with at least 1/2 probability. On the property of hypergraphs, we address a fundamental gap in the literature by defining conductance for hypergraphs from the perspective of hypergraph random walks. Additionally, we provide experiments to validate our theoretical findings.

Jun Wu, Jingrui He

Transfer learning aims to transfer knowledge or information from a source domain to a relevant target domain. In this paper, we understand transfer learning from the perspectives of knowledge transferability and trustworthiness. This involves two research questions: How is knowledge transferability quantitatively measured and enhanced across domains? Can we trust the transferred knowledge in the transfer learning process? To answer these questions, this paper provides a comprehensive review of trustworthy transfer learning from various aspects, including problem definitions, theoretical analysis, empirical algorithms, and real-world applications. Specifically, we summarize recent theories and algorithms for understanding knowledge transferability under (within-domain) IID and non-IID assumptions. In addition to knowledge transferability, we review the impact of trustworthiness on transfer learning, e.g., whether the transferred knowledge is adversarially robust or algorithmically fair, how to transfer the knowledge under privacy-preserving constraints, etc. Beyond discussing the current advancements, we highlight the open questions and future directions for understanding transfer learning in a reliable and trustworthy manner.