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Jun Pang

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8 papers

1 author row

TMLR Journal 2025 Journal Article

KAGNNs: Kolmogorov-Arnold Networks meet Graph Learning

Roman Bresson
Giannis Nikolentzos
George Panagopoulos
Michail Chatzianastasis
Jun Pang
Michalis Vazirgiannis

In recent years, Graph Neural Networks (GNNs) have become the de facto tool for learning node and graph representations. Most GNNs typically consist of a sequence of neighborhood aggregation (a.k.a., message-passing) layers, within which the representation of each node is updated based on those of its neighbors. The most expressive message-passing GNNs can be obtained through the use of the sum aggregator and of MLPs for feature transformation, thanks to their universal approximation capabilities. However, the limitations of MLPs recently motivated the introduction of another family of universal approximators, called Kolmogorov-Arnold Networks (KANs) which rely on a different representation theorem. In this work, we compare the performance of KANs against that of MLPs on graph learning tasks. We implement three new KAN-based GNN layers, inspired respectively by the GCN, GAT and GIN layers. We evaluate two different implementations of KANs using two distinct base families of functions, namely B-splines and radial basis functions. We perform extensive experiments on node classification, link prediction, graph classification and graph regression datasets. Our results indicate that KANs are on-par with or better than MLPs on all tasks studied in this paper. We also show that the size and training speed of RBF-based KANs is only marginally higher than for MLPs, making them viable alternatives. Code available at https://github.com/RomanBresson/KAGNN.

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IJCAI Conference 2025 Conference Paper

PAMol: Pocket-Aware Drug Design Method with Hypergraph Representation of Protein Pocket Structure and Feature Fusion

Xiaoli Lin
Xiongwei Liao
Jun Pang
Bo Li
Xiaolong Zhang

Efficient generation of targeted drug molecules is crucial in the field of drug discovery. Most existing methods neglect the high-order information in the structure of protein pockets, limiting the performance of generated drug molecules. This paper proposes a pocket-aware drug design framework, namely PAMol, constructing the hypergraph to represent the spatial structure of protein pockets, effectively capturing high-order relations and neighborhood information within the pocket structures. This framework also fuses different modal embeddings from proteins and molecules, to generate high-quality molecules. In addition, a conditional molecule generation module uses the high-order structural information in protein pockets as constraints to more accurately generate molecules for specific targets. The performance of PAMol has been assessed by analyzing generated molecules in terms of vina score, high affinity, QED, SA, LogP, Lipinski, diversity, and time. Experimental results demonstrate the potential of PAMol for targeted drug design. The source code is available at https: //github. com/YICHUANSYQ/PAMol. git.

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TMLR Journal 2025 Journal Article

Spurious Privacy Leakage in Neural Networks

Chenxiang Zhang
Jun Pang
Sjouke Mauw

Neural networks trained on real-world data often exhibit biases while simultaneously being vulnerable to privacy attacks aimed at extracting sensitive information. Despite extensive research on each problem individually, their intersection remains poorly understood. In this work, we investigate the privacy impact of spurious correlation bias. We introduce _spurious privacy leakage_, a phenomenon in which spurious groups are significantly more vulnerable to privacy attacks than non-spurious groups. We observe that privacy disparity between groups increases in tasks with simpler objectives (e.g. fewer classes) due to spurious features. Counterintuitively, we demonstrate that spurious robust methods, designed to reduce spurious bias, fail to mitigate privacy disparity. Our analysis reveals that this occurs because robust methods can reduce reliance on spurious features for prediction, but do not prevent their memorization during training. Finally, we systematically compare the privacy of different model architectures trained with spurious data, demonstrating that, contrary to previous work, architectural choice can affect privacy evaluation.

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NeurIPS Conference 2024 Conference Paper

Benchmarking Structural Inference Methods for Interacting Dynamical Systems with Synthetic Data

Aoran Wang
Tsz Pan Tong
Andrzej Mizera
Jun Pang

Understanding complex dynamical systems begins with identifying their topological structures, which expose the organization of the systems. This requires robust structural inference methods that can deduce structure from observed behavior. However, existing methods are often domain-specific and lack a standardized, objective comparison framework. We address this gap by benchmarking 13 structural inference methods from various disciplines on simulations representing two types of dynamics and 11 interaction graph models, supplemented by a biological experimental dataset to mirror real-world application. We evaluated the methods for accuracy, scalability, robustness, and sensitivity to graph properties. Our findings indicate that deep learning methods excel with multi-dimensional data, while classical statistics and information theory based approaches are notably accurate and robust. Additionally, performance correlates positively with the graph's average shortest path length. This benchmark should aid researchers in selecting suitable methods for their specific needs and stimulate further methodological innovation.

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NeurIPS Conference 2024 Conference Paper

Structural Inference of Dynamical Systems with Conjoined State Space Models

Aoran Wang
Jun Pang

This paper introduces SICSM, a novel structural inference framework that integrates Selective State Space Models (selective SSMs) with Generative Flow Networks (GFNs) to handle the challenges posed by dynamical systems with irregularly sampled trajectories and partial observations. By utilizing the robust temporal modeling capabilities of selective SSMs, our approach learns input-dependent transition functions that adapt to non-uniform time intervals, thereby enhancing the accuracy of structural inference. By aggregating dynamics across diverse temporal dependencies and channeling them into the GFN, the SICSM adeptly approximates the posterior distribution of the system's structure. This process not only enables precise inference of complex interactions within partially observed systems but also ensures the seamless integration of prior knowledge, enhancing the model’s accuracy and robustness. Extensive evaluations on sixteen diverse datasets demonstrate that SICSM outperforms existing methods, particularly in scenarios characterized by irregular sampling and incomplete observations, which highlight its potential as a reliable tool for scientific discovery and system diagnostics in disciplines that demand precise modeling of complex interactions.

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NeurIPS Conference 2022 Conference Paper

Iterative Structural Inference of Directed Graphs

Aoran Wang
Jun Pang

In this paper, we propose a variational model, iterative Structural Inference of Directed Graphs (iSIDG), to infer the existence of directed interactions from observational agents’ features over a time period in a dynamical system. First, the iterative process in our model feeds the learned interactions back to encourage our model to eliminate indirect interactions and to emphasize directional representation during learning. Second, we show that extra regularization terms in the objective function for smoothness, connectiveness, and sparsity prompt our model to infer a more realistic structure and to further eliminate indirect interactions. We evaluate iSIDG on various datasets including biological networks, simulated fMRI data, and physical simulations to demonstrate that our model is able to precisely infer the existence of interactions, and is significantly superior to baseline models.

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TMLR Journal 2022 Journal Article

Simplifying Node Classification on Heterophilous Graphs with Compatible Label Propagation

Zhiqiang Zhong
Sergei Ivanov
Jun Pang

Graph Neural Networks (GNNs) have been predominant for graph learning tasks; however, recent studies showed that a well-known graph algorithm, Label Propagation (LP), combined with a shallow neural network can achieve comparable performance to GNNs in semi-supervised node classification on graphs with high homophily. In this paper, we show that this approach falls short on graphs with low homophily, where nodes often connect to the nodes of the opposite classes. To overcome this, we carefully design a combination of a base predictor with LP algorithm that enjoys a closed-form solution as well as convergence guarantees. Our algorithm first learns the class compatibility matrix and then aggregates label predictions using LP algorithm weighted by class compatibilities. On a wide variety of benchmarks, we show that our approach achieves the leading performance on graphs with various levels of homophily. Meanwhile, it has orders of magnitude fewer parameters and requires less execution time.

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TMLR Journal 2022 Journal Article

Unsupervised Network Embedding Beyond Homophily

Zhiqiang Zhong
Guadalupe Gonzalez
Daniele Grattarola
Jun Pang

Network embedding (NE) approaches have emerged as a predominant technique to represent complex networks and have benefited numerous tasks. However, most NE approaches rely on a homophily assumption to learn embeddings with the guidance of supervisory signals, leaving the unsupervised heterophilous scenario relatively unexplored. This problem becomes especially relevant in fields where a scarcity of labels exists. Here, we formulate the unsupervised NE task as an r-ego network discrimination problem and develop the SELENE framework for learning on networks with homophily and heterophily. Specifically, we design a dual-channel feature embedding pipeline to discriminate r-ego networks using node attributes and structural information separately. We employ heterophily adapted self-supervised learning objective functions to optimise the framework to learn intrinsic node embeddings. We show that SELENE's components improve the quality of node embeddings, facilitating the discrimination of connected heterophilous nodes. Comprehensive empirical evaluations on both synthetic and real-world datasets with varying homophily ratios validate the effectiveness of SELENE in homophilous and heterophilous settings showing an up to 12.52% clustering accuracy gain.

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