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Yongqiang Chen 0002

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7 papers

1 author row

ICML Conference 2025 Conference Paper

Hierarchical Graph Tokenization for Molecule-Language Alignment

Yongqiang Chen 0002
Quanming Yao
Juzheng Zhang
James Cheng
Yatao An Bian

Recently, there has been a surge of interest in extending the success of large language models (LLMs) from texts to molecules. Most existing approaches adopt a graph neural network to represent a molecule as a series of node tokens for molecule-language alignment, which, however, have overlooked the inherent hierarchical structures in molecules. Notably, higher-order molecular structures contain rich semantics of functional groups, which encode crucial biochemical functionalities of the molecules. We show that neglecting the hierarchical information in tokenization will lead to subpar molecule-language alignment and severe hallucination. To address this limitation, we propose HIerarchical GrapH Tokenization (HIGHT). HIGHT employs a hierarchical graph tokenizer that encodes the hierarchy of atom, motif, and molecular levels of informative tokens to improve the molecular perception of LLMs. HIGHT also adopts an augmented instruction tuning dataset, enriched with the hierarchical graph information, to further enhance the molecule-language alignment. Extensive experiments on 14 real-world benchmarks verify the effectiveness of HIGHT in reducing hallucination by 40%, and significant improvements in various molecule-language downstream tasks. The project is available at https: //higraphllm. github. io/.

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ICLR Conference 2025 Conference Paper

Learning Graph Invariance by Harnessing Spuriosity

Tianjun Yao
Yongqiang Chen 0002
Kai Hu 0010
Tongliang Liu
Kun Zhang 0001
Zhiqiang Shen

Recently, graph invariant learning has become the _de facto_ approach to tackle the Out-of-Distribution (OOD) generalization failure in graph representation learning. They generically follow the framework of invariant risk minimization to capture the invariance of graph data from different environments. Despite some success, it remains unclear to what extent existing approaches have captured invariant features for OOD generalization on graphs. In this work, we find that representative OOD methods such as IRM and VRex, and their variants on graph invariant learning may have captured a limited set of invariant features. To tackle this challenge, we propose $\texttt{LIRS}$, a novel learning framework designed to **L**earn graph **I**nvariance by **R**emoving **S**purious features. Different from most existing approaches that _directly_ learn the invariant features, $\texttt{LIRS}$ takes an _indirect_ approach by first learning the spurious features and then removing them from the ERM-learned features, which contains both spurious and invariant features. We demonstrate that learning the invariant graph features in an _indirect_ way can learn a more comprehensive set of invariant features. Moreover, our proposed method outperforms the second-best method by as much as 25.50% across all competitive baseline methods, highlighting its effectiveness in learning graph invariant features.

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ICML Conference 2024 Conference Paper

Empowering Graph Invariance Learning with Deep Spurious Infomax

Tianjun Yao
Yongqiang Chen 0002
Zhenhao Chen
Kai Hu 0010
Zhiqiang Shen
Kun Zhang 0001

Recently, there has been a surge of interest in developing graph neural networks that utilize the invariance principle on graphs to generalize the out-of-distribution (OOD) data. Due to the limited knowledge about OOD data, existing approaches often pose assumptions about the correlation strengths of the underlying spurious features and the target labels. However, this prior is often unavailable and will change arbitrarily in the real-world scenarios, which may lead to severe failures of the existing graph invariance learning methods. To bridge this gap, we introduce a novel graph invariance learning paradigm, which induces a robust and general inductive bias, which is built upon the observation that the infomax principle encourages learning spurious features regardless of spurious correlation strengths. We further propose the EQuAD framework that realizes this learning paradigm and employs tailored learning objectives that provably elicit invariant features by disentangling them from the spurious features learned through infomax. Notably, EQuAD shows stable and enhanced performance across different degrees of bias in synthetic datasets and challenging real-world datasets up to 31. 76%.

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ICLR Conference 2024 Conference Paper

Enhancing Neural Subset Selection: Integrating Background Information into Set Representations

Binghui Xie
Yatao An Bian
Kaiwen Zhou 0001
Yongqiang Chen 0002
Peilin Zhao
Bo Han 0003
Wei Meng 0001
James Cheng

Learning neural subset selection tasks, such as compound selection in AI-aided drug discovery, have become increasingly pivotal across diverse applications. The existing methodologies in the field primarily concentrate on constructing models that capture the relationship between utility function values and subsets within their respective supersets. However, these approaches tend to overlook the valuable information contained within the superset when utilizing neural networks to model set functions. In this work, we address this oversight by adopting a probabilistic perspective. Our theoretical findings demonstrate that when the target value is conditioned on both the input set and subset, it is essential to incorporate an invariant sufficient statistic of the superset into the subset of interest for effective learning. This ensures that the output value remains invariant to permutations of the subset and its corresponding superset, enabling identification of the specific superset from which the subset originated. Motivated by these insights, we propose a simple yet effective information aggregation module designed to merge the representations of subsets and supersets from a permutation invariance perspective. Comprehensive empirical evaluations across diverse tasks and datasets validate the enhanced efficacy of our approach over conventional methods, underscoring the practicality and potency of our proposed strategies in real-world contexts.

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ICML Conference 2024 Conference Paper

How Interpretable Are Interpretable Graph Neural Networks?

Yongqiang Chen 0002
Yatao An Bian
Bo Han 0003
James Cheng

Interpretable graph neural networks (XGNNs ) are widely adopted in various scientific applications involving graph-structured data. Existing XGNNs predominantly adopt the attention-based mechanism to learn edge or node importance for extracting and making predictions with the interpretable subgraph. However, the representational properties and limitations of these methods remain inadequately explored. In this work, we present a theoretical framework that formulates interpretable subgraph learning with the multilinear extension of the subgraph distribution, coined as subgraph multilinear extension (SubMT). Extracting the desired interpretable subgraph requires an accurate approximation of SubMT, yet we find that the existing XGNNs can have a huge gap in fitting SubMT. Consequently, the SubMT approximation failure will lead to the degenerated interpretability of the extracted subgraphs. To mitigate the issue, we design a new XGNN architecture called Graph Multilinear neT (GMT), which is provably more powerful in approximating SubMT. We empirically validate our theoretical findings on a number of graph classification benchmarks. The results demonstrate that GMT outperforms the state-of-the-art up to 10% in terms of both interpretability and generalizability across 12 regular and geometric graph benchmarks.

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ICLR Conference 2023 Conference Paper

Pareto Invariant Risk Minimization: Towards Mitigating the Optimization Dilemma in Out-of-Distribution Generalization

Yongqiang Chen 0002
Kaiwen Zhou 0001
Yatao An Bian
Binghui Xie
Bingzhe Wu
Yonggang Zhang 0003
Kaili Ma 0001
Han Yang 0002

Recently, there has been a growing surge of interest in enabling machine learning systems to generalize well to Out-of-Distribution (OOD) data. Most efforts are devoted to advancing optimization objectives that regularize models to capture the underlying invariance; however, there often are compromises in the optimization process of these OOD objectives: i) Many OOD objectives have to be relaxed as penalty terms of Empirical Risk Minimization (ERM) for the ease of optimization, while the relaxed forms can weaken the robustness of the original objective; ii) The penalty terms also require careful tuning of the penalty weights due to the intrinsic conflicts between ERM and OOD objectives. Consequently, these compromises could easily lead to suboptimal performance of either the ERM or OOD objective. To address these issues, we introduce a multi-objective optimization (MOO) perspective to understand the OOD optimization process, and propose a new optimization scheme called PAreto Invariant Risk Minimization (PAIR). PAIR improves the robustness of OOD objectives by cooperatively optimizing with other OOD objectives, thereby bridging the gaps caused by the relaxations. Then PAIR approaches a Pareto optimal solution that trades off the ERM and OOD objectives properly. Extensive experiments on challenging benchmarks, WILDS, show that PAIR alleviates the compromises and yields top OOD performances.

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ICLR Conference 2022 Conference Paper

Understanding and Improving Graph Injection Attack by Promoting Unnoticeability

Yongqiang Chen 0002
Han Yang 0002
Yonggang Zhang 0003
Kaili Ma 0001
Tongliang Liu
Bo Han 0003
James Cheng

Recently Graph Injection Attack (GIA) emerges as a practical attack scenario on Graph Neural Networks (GNNs), where the adversary can merely inject few malicious nodes instead of modifying existing nodes or edges, i.e., Graph Modification Attack (GMA). Although GIA has achieved promising results, little is known about why it is successful and whether there is any pitfall behind the success. To understand the power of GIA, we compare it with GMA and find that GIA can be provably more harmful than GMA due to its relatively high flexibility. However, the high flexibility will also lead to great damage to the homophily distribution of the original graph, i.e., similarity among neighbors. Consequently, the threats of GIA can be easily alleviated or even prevented by homophily-based defenses designed to recover the original homophily. To mitigate the issue, we introduce a novel constraint – homophily unnoticeability that enforces GIA to preserve the homophily, and propose Harmonious Adversarial Objective (HAO) to instantiate it. Extensive experiments verify that GIA with HAO can break homophily-based defenses and outperform previous GIA attacks by a significant margin. We believe our methods can serve for a more reliable evaluation of the robustness of GNNs.

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