Hanchen Wang

Hanchen Wang, Jean Kaddour, Shengchao Liu et al. · stanford

Graph Self-Supervised Learning (GSSL) provides a robust pathway for acquiring embeddings without expert labelling, a capability that carries profound implications for molecular graphs due to the staggering number of potential molecules and the high cost of obtaining labels. However, GSSL methods are designed not for optimisation within a specific domain but rather for transferability across a variety of downstream tasks. This broad applicability complicates their evaluation. Addressing this challenge, we present "Molecular Graph Representation Evaluation" (MOLGRAPHEVAL), generating detailed profiles of molecular graph embeddings with interpretable and diversified attributes. MOLGRAPHEVAL offers a suite of probing tasks grouped into three categories: (i) generic graph, (ii) molecular substructure, and (iii) embedding space properties. By leveraging MOLGRAPHEVAL to benchmark existing GSSL methods against both current downstream datasets and our suite of tasks, we uncover significant inconsistencies between inferences drawn solely from existing datasets and those derived from more nuanced probing. These findings suggest that current evaluation methodologies fail to capture the entirety of the landscape.

Fang Wu, Haokai Zhao, Da Xing et al.

Diffusion models have achieved remarkable success across a wide range of generative tasks, yet their training paradigm largely treats injected noise as uniformly informative. In this work, we challenge this assumption and introduce NoiseRater, a meta-learning framework for instance-level noise valuation in diffusion model training. We propose a parametric noise rater that assigns importance scores to individual noise realizations conditioned on data and timestep, enabling adaptive reweighting of the training objective. The rater is trained via bilevel optimization to improve downstream validation performance after inner-loop diffusion updates. To enable efficient deployment, we further design a decoupled two-stage pipeline that transitions from soft weighting during meta-training to hard noise selection during standard training. Extensive experiments on FFHQ and ImageNet demonstrate that not all noise samples contribute equally, and that prioritizing informative noise improves both training efficiency and generation quality. Our results establish noise valuation as a complementary and previously underexplored axis for improving diffusion model training. Our code is available at: https://anonymous.4open.science/r/NoiseRater-DEB116.

Jianke Yu, Hanchen Wang, Chen Chen et al.

Graph Neural Networks (GNNs) are vital in data science but are increasingly susceptible to adversarial attacks. To help researchers develop more robust GNN models, it's essential to focus on designing strong attack models as foundational benchmarks and guiding references. Among adversarial attacks, gray-box poisoning attacks are noteworthy due to their effectiveness and fewer constraints. These attacks exploit GNNs' need for retraining on updated data, thereby impacting their performance by perturbing these datasets. However, current research overlooks the real-world scenario of incomplete graphs. To address this gap, we introduce the Robust Incomplete Deep Attack Framework (RIDA). It is the first algorithm for robust gray-box poisoning attacks on incomplete graphs. The approach innovatively aggregates distant vertex information and ensures powerful data utilization. Extensive tests against 9 SOTA baselines on 3 real-world datasets demonstrate that RIDA's superiority in handling incompleteness and high attack performance on the incomplete graph.

Tianyu Liu, Simeng Han, Xiao Luo et al.

Large language models (LLMs) and large multimodal models (LMMs) promise to accelerate biomedical discovery, yet their reliability remains unclear. We introduce ARIEL (AI Research Assistant for Expert-in-the-Loop Learning), an open-source evaluation and optimization framework that pairs a curated multimodal biomedical corpus with expert-vetted tasks to probe two capabilities: full-length article summarization and fine-grained figure interpretation. Using uniform protocols and blinded PhD-level evaluation, we find that state-of-the-art models generate fluent but incomplete summaries, whereas LMMs struggle with detailed visual reasoning. We later observe that prompt engineering and lightweight fine-tuning substantially improve textual coverage, and a compute-scaled inference strategy enhances visual question answering. We build an ARIEL agent that integrates textual and visual cues, and we show it can propose testable mechanistic hypotheses. ARIEL delineates current strengths and limitations of foundation models, and provides a reproducible platform for advancing trustworthy AI in biomedicine.

Hanchen Wang, Defu Lian, Ying Zhang et al.

Entity interaction prediction is essential in many important applications such as chemistry, biology, material science, and medical science. The problem becomes quite challenging when each entity is represented by a complex structure, namely structured entity, because two types of graphs are involved: local graphs for structured entities and a global graph to capture the interactions between structured entities. We observe that existing works on structured entity interaction prediction cannot properly exploit the unique graph of graphs model. In this paper, we propose a Graph of Graphs Neural Network, namely GoGNN, which extracts the features in both structured entity graphs and the entity interaction graph in a hierarchical way. We also propose the dual-attention mechanism that enables the model to preserve the neighbor importance in both levels of graphs. Extensive experiments on real-world datasets show that GoGNN outperforms the state-of-the-art methods on two representative structured entity interaction prediction tasks: chemical-chemical interaction prediction and drug-drug interaction prediction. Our code is available at Github.

Yun-Hao Cao, Jianxin Wu, Hanchen Wang et al.

The random subspace method, known as the pillar of random forests, is good at making precise and robust predictions. However, there is not a straightforward way yet to combine it with deep learning. In this paper, we therefore propose Neural Random Subspace (NRS), a novel deep learning based random subspace method. In contrast to previous forest methods, NRS enjoys the benefits of end-to-end, data-driven representation learning, as well as pervasive support from deep learning software and hardware platforms, hence achieving faster inference speed and higher accuracy. Furthermore, as a non-linear component to be encoded into Convolutional Neural Networks (CNNs), NRS learns non-linear feature representations in CNNs more efficiently than previous higher-order pooling methods, producing good results with negligible increase in parameters, floating point operations (FLOPs) and real running time. Compared with random subspaces, random forests and gradient boosting decision trees (GBDTs), NRS achieves superior performance on 35 machine learning datasets. Moreover, on both 2D image and 3D point cloud recognition tasks, integration of NRS with CNN architectures achieves consistent improvements with minor extra cost. Code is available at https://github.com/CupidJay/NRS_pytorch.

Guangxin Su, Yifan Zhu, Wenjie Zhang et al.

Graph representation learning, involving both node features and graph structures, is crucial for real-world applications but often encounters pervasive noise. State-of-the-art methods typically address noise by focusing separately on node features with large language models (LLMs) and on graph structures with graph structure learning models (GSLMs). In this paper, we introduce LangGSL, a robust framework that integrates the complementary strengths of pre-trained language models and GSLMs to jointly enhance both node feature and graph structure learning. In LangGSL, we first leverage LLMs to filter noise in the raw data and extract valuable cleaned information as features, enhancing the synergy of downstream models. During the mutual learning phase in LangGSL, the core idea is to leverage the relatively small language model (LM) to process local attributes and generate reliable pseudo-labels and informative node embeddings, which are then integrated into the GSLM's prediction phase. This approach enriches the global context and enhances overall performance. Meanwhile, GSLM refines the evolving graph structure constructed from the LM's output, offering updated labels back to the LM as additional guidance, thus facilitating a more effective mutual learning process. The LM and GSLM work synergistically, complementing each other's strengths and offsetting weaknesses within a variational information-maximizing framework, resulting in enhanced node features and a more robust graph structure. Extensive experiments on diverse graph datasets of varying scales and across different task scenarios demonstrate the scalability and effectiveness of the proposed approach.

Shengchao Liu, Chengpeng Wang, Jiarui Lu et al.

Deep generative models (DGMs) have been widely developed for graph data. However, much less investigation has been carried out on understanding the latent space of such pretrained graph DGMs. These understandings possess the potential to provide constructive guidelines for crucial tasks, such as graph controllable generation. Thus in this work, we are interested in studying this problem and propose GraphCG, a method for the unsupervised discovery of steerable factors in the latent space of pretrained graph DGMs. We first examine the representation space of three pretrained graph DGMs with six disentanglement metrics, and we observe that the pretrained representation space is entangled. Motivated by this observation, GraphCG learns the steerable factors via maximizing the mutual information between semantic-rich directions, where the controlled graph moving along the same direction will share the same steerable factors. We quantitatively verify that GraphCG outperforms four competitive baselines on two graph DGMs pretrained on two molecule datasets. Additionally, we qualitatively illustrate seven steerable factors learned by GraphCG on five pretrained DGMs over five graph datasets, including two for molecules and three for point clouds.

Shengchao Liu, Hanchen Wang, Weiyang Liu et al.

Molecular graph representation learning is a fundamental problem in modern drug and material discovery. Molecular graphs are typically modeled by their 2D topological structures, but it has been recently discovered that 3D geometric information plays a more vital role in predicting molecular functionalities. However, the lack of 3D information in real-world scenarios has significantly impeded the learning of geometric graph representation. To cope with this challenge, we propose the Graph Multi-View Pre-training (GraphMVP) framework where self-supervised learning (SSL) is performed by leveraging the correspondence and consistency between 2D topological structures and 3D geometric views. GraphMVP effectively learns a 2D molecular graph encoder that is enhanced by richer and more discriminative 3D geometry. We further provide theoretical insights to justify the effectiveness of GraphMVP. Finally, comprehensive experiments show that GraphMVP can consistently outperform existing graph SSL methods.

Mohammadreza Noormandipour, Hanchen Wang

In this work, we propose a parameterised quantum circuit learning approach to point set matching problem. In contrast to previous annealing-based methods, we propose a quantum circuit-based framework whose parameters are optimised via descending the gradients w.r.t a kernel-based loss function. We formulate the shape matching problem into a distribution learning task; that is, to learn the distribution of the optimal transformation parameters. We show that this framework is able to find multiple optimal solutions for symmetric shapes and is more accurate, scalable and robust than the previous annealing-based method. Code, data and pre-trained weights are available at the project page: \href{https://hansen7.github.io/qKC}{https://hansen7.github.io/qKC}