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.

Dingmin Wang, Shengchao Liu, Hanchen Wang et al. · stanford

Graph Neural Networks (GNNs) are effective tools for graph representation learning. Most GNNs rely on a recursive neighborhood aggregation scheme, named message passing, thereby their theoretical expressive power is limited to the first-order Weisfeiler-Lehman test (1-WL). An effective approach to this challenge is to explicitly retrieve some annotated examples used to enhance GNN models. While retrieval-enhanced models have been proved to be effective in many language and vision domains, it remains an open question how effective retrieval-enhanced GNNs are when applied to graph datasets. Motivated by this, we want to explore how the retrieval idea can help augment the useful information learned in the graph neural networks, and we design a retrieval-enhanced scheme called GRAPHRETRIEVAL, which is agnostic to the choice of graph neural network models. In GRAPHRETRIEVAL, for each input graph, similar graphs together with their ground-true labels are retrieved from an existing database. Thus they can act as a potential enhancement to complete various graph property predictive tasks. We conduct comprehensive experiments over 13 datasets, and we observe that GRAPHRETRIEVAL is able to reach substantial improvements over existing GNNs. Moreover, our empirical study also illustrates that retrieval enhancement is a promising remedy for alleviating the long-tailed label distribution problem.

Changhao Jiang, Jiahao Chen, Zhenghao Xiang et al.

Recent commercial systems such as Suno demonstrate strong capabilities in long-form song generation, while academic research remains largely non-reproducible due to the lack of publicly available training data, hindering fair comparison and progress. To this end, we release a fully open-source system for long-form song generation with fine-grained style conditioning, including a licensed synthetic dataset, training and evaluation pipelines, and Muse, an easy-to-deploy song generation model. The dataset consists of 116k fully licensed synthetic songs with automatically generated lyrics and style descriptions paired with audio synthesized by SunoV5. We train Muse via single-stage supervised finetuning of a Qwen-based language model extended with discrete audio tokens using MuCodec, without task-specific losses, auxiliary objectives, or additional architectural components. Our evaluations find that although Muse is trained with a modest data scale and model size, it achieves competitive performance on phoneme error rate, text--music style similarity, and audio aesthetic quality, while enabling controllable segment-level generation across different musical structures. All data, model weights, and training and evaluation pipelines will be publicly released, paving the way for continued progress in controllable long-form song generation research. The project repository is available at https://github.com/yuhui1038/Muse.

Peng Jin, Yinan Feng, Shihang Feng et al.

This paper investigates the impact of big data on deep learning models to help solve the full waveform inversion (FWI) problem. While it is well known that big data can boost the performance of deep learning models in many tasks, its effectiveness has not been validated for FWI. To address this gap, we present an empirical study that investigates how deep learning models in FWI behave when trained on OpenFWI, a collection of large-scale, multi-structural, synthetic datasets published recently. In particular, we train and evaluate the FWI models on a combination of 10 2D subsets in OpenFWI that contain 470K pairs of seismic data and velocity maps in total. Our experiments demonstrate that training on the combined dataset yields an average improvement of 13.03% in MAE, 7.19% in MSE and 1.87% in SSIM compared to each split dataset, and an average improvement of 28.60%, 21.55% and 8.22% in the leave-one-out generalization test. We further demonstrate that model capacity needs to scale in accordance with data size for optimal improvement, where our largest model yields an average improvement of 20.06%, 13.39% and 0.72% compared to the smallest one.

Bian Li, Hanchen Wang, Shihang Feng et al.

In the study of subsurface seismic imaging, solving the acoustic wave equation is a pivotal component in existing models. The advancement of deep learning enables solving partial differential equations, including wave equations, by applying neural networks to identify the mapping between the inputs and the solution. This approach can be faster than traditional numerical methods when numerous instances are to be solved. Previous works that concentrate on solving the wave equation by neural networks consider either a single velocity model or multiple simple velocity models, which is restricted in practice. Instead, inspired by the idea of operator learning, this work leverages the Fourier neural operator (FNO) to effectively learn the frequency domain seismic wavefields under the context of variable velocity models. We also propose a new framework paralleled Fourier neural operator (PFNO) for efficiently training the FNO-based solver given multiple source locations and frequencies. Numerical experiments demonstrate the high accuracy of both FNO and PFNO with complicated velocity models in the OpenFWI datasets. Furthermore, the cross-dataset generalization test verifies that PFNO adapts to out-of-distribution velocity models. Moreover, PFNO has robust performance in the presence of random noise in the labels. Finally, PFNO admits higher computational efficiency on large-scale testing datasets than the traditional finite-difference method. The aforementioned advantages endow the FNO-based solver with the potential to build powerful models for research on seismic waves.

Shihang Feng, Hanchen Wang, Chengyuan Deng et al.

Elastic geophysical properties (such as P- and S-wave velocities) are of great importance to various subsurface applications like CO$_2$ sequestration and energy exploration (e.g., hydrogen and geothermal). Elastic full waveform inversion (FWI) is widely applied for characterizing reservoir properties. In this paper, we introduce $\mathbf{\mathbb{E}^{FWI}}$, a comprehensive benchmark dataset that is specifically designed for elastic FWI. $\mathbf{\mathbb{E}^{FWI}}$ encompasses 8 distinct datasets that cover diverse subsurface geologic structures (flat, curve, faults, etc). The benchmark results produced by three different deep learning methods are provided. In contrast to our previously presented dataset (pressure recordings) for acoustic FWI (referred to as OpenFWI), the seismic dataset in $\mathbf{\mathbb{E}^{FWI}}$ has both vertical and horizontal components. Moreover, the velocity maps in $\mathbf{\mathbb{E}^{FWI}}$ incorporate both P- and S-wave velocities. While the multicomponent data and the added S-wave velocity make the data more realistic, more challenges are introduced regarding the convergence and computational cost of the inversion. We conduct comprehensive numerical experiments to explore the relationship between P-wave and S-wave velocities in seismic data. The relation between P- and S-wave velocities provides crucial insights into the subsurface properties such as lithology, porosity, fluid content, etc. We anticipate that $\mathbf{\mathbb{E}^{FWI}}$ will facilitate future research on multiparameter inversions and stimulate endeavors in several critical research topics of carbon-zero and new energy exploration. All datasets, codes and relevant information can be accessed through our website at https://efwi-lanl.github.io/

Haoran Li, Shulun Chen, Shaoyuan Sun et al.

As large language model (LLM)-based multi-agent systems scale to handle increasingly complex tasks, balancing structural stability and dynamic adaptability becomes increasingly challenging. Existing systems typically adopt either structure-centric methods, committing to structures determined upfront that limit fine-grained control, or orchestration-centric methods, adapting decisions dynamically while leaving coordination structure implicit and unstable. To address this challenge, we revisit multi-agent coordination from a probabilistic perspective, casting it as posterior inference over the joint distribution of structure and orchestration. We introduce MACA, an automated coordination framework that learns a task- and budget-conditioned structural prior over agent participation and interactions. This prior guides a policy-based orchestration as an approximation to posterior inference, enabling efficient solutions with fine-grained control. Across benchmarks, MACA outperforms adaptive multi-agent baselines by an average of 8.42% while using 43.19% fewer tokens. Further investigation reveals that joint adaptation of structure and orchestration suppresses redundant interactions, converging coordination toward task-effective execution.

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.

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.

Yuxin Jin, Siyuan Zhang, Hanchen Wang et al.

Large language model (LLM)-based agents have demonstrated strong capabilities in complex reasoning and problem solving through multi-step interactions, yet most deployed agents remain behaviorally static, with knowledge acquired during execution rarely translating into systematic improvement over time. In response, a growing line of work on self-evolving agents explores how agents can improve through experience during deployment, but most existing approaches either rely on ad hoc reflection limited to single-task correction or adopt unstructured memory that accumulates fragmented experience with delayed usability. To address this limitation, we introduce EXG, an experience graph framework for self-evolving agents that explicitly organizes accumulated successes and failures into a structured, relational representation. EXG is the first experience graph designed for self-evolving agents, supporting both online, real-time graph growth during execution for immediate cross-task experience reuse, and offline reuse of a consolidated experience graph as an external memory module. This design also enables EXG to serve as a plug-and-play component for existing self-evolving agents, organizing prior experience into a unified experience graph and improving both solution quality and resource efficiency as deployment progresses. Extensive experiments across code generation and reasoning benchmarks show that EXG attains more favorable performance-efficiency trade-offs than reflection- and memory-based baselines in both online and offline evaluations. Our results suggest that structuring experience as a graph provides a principled foundation for scalable and transferable self-evolving agent behavior.

Shaozhen Ma, Wei Huang, Hanchen Wang et al.

Conditional generative models, particularly diffusion-based methods, have recently been applied to graph prediction by modeling the target as a conditional distribution given the input graph, yielding competitive results compared to deterministic predictor. However, existing diffusion-based prediction methods typically require expensive iterative denoising at inference and often suffer from unstable sampling, which motivates recent efforts to reduce inference denoising steps and enable stable sampling via techniques such as consistency training. Despite this progress, we find that existing consistency training methods for graph prediction could potentially fall into a shortcut solution: the model may attempt to satisfy the self-consistency constraint by ignoring the noisy target (i.e., assigning it negligible weight), ultimately collapsing into a purely deterministic predictor. To mitigate such shortcut solution, we propose GCCM, a graph contrastive consistency model that goes beyond isolated pairwise matching between the same target at different noise levels by introducing negative pairs into a contrastive consistency objective. This adds an additional separation requirement, making the shortcut solution no longer trivially sufficient to satisfy the proposed objective. Moreover, we apply feature perturbation to the input node/edge features to break identical conditioning on the input graph, so that the shortcut no longer yields the same predictions across noise levels and becomes less attractive. Extensive experiments on benchmark datasets demonstrate that GCCM mitigates the shortcut solution and yields consistent performance improvements in graph prediction compared to deterministic predictors.

Runze Li, Hanchen Wang, Wenjie Zhang et al.

Multivariate time series imputation is fundamental in applications such as healthcare, traffic forecasting, and biological modeling, where sensor failures and irregular sampling lead to pervasive missing values. However, existing Transformer- and diffusion-based models lack explicit inductive biases and frequency awareness, limiting their generalization under structured missing patterns and distribution shifts. We propose FADTI, a diffusion-based framework that injects frequency-informed feature modulation via a learnable Fourier Bias Projection (FBP) module and combines it with temporal modeling through self-attention and gated convolution. FBP supports multiple spectral bases, enabling adaptive encoding of both stationary and non-stationary patterns. This design injects frequency-domain inductive bias into the generative imputation process. Experiments on multiple benchmarks, including a newly introduced biological time series dataset, show that FADTI consistently outperforms state-of-the-art methods, particularly under high missing rates. Code is available at https://anonymous.4open.science/r/TimeSeriesImputation-52BF

Yi Sheng, Hanchen Wang, Yipei Liu et al.

Ultrasound computed tomography (USCT) is a promising technique that achieves superior medical imaging reconstruction resolution by fully leveraging waveform information, outperforming conventional ultrasound methods. Despite its advantages, high-quality USCT reconstruction relies on extensive data acquisition by a large number of transducers, leading to increased costs, computational demands, extended patient scanning times, and manufacturing complexities. To mitigate these issues, we propose a new USCT method called APS-USCT, which facilitates imaging with sparse data, substantially reducing dependence on high-cost dense data acquisition. Our APS-USCT method consists of two primary components: APS-wave and APS-FWI. The APS-wave component, an encoder-decoder system, preprocesses the waveform data, converting sparse data into dense waveforms to augment sample density prior to reconstruction. The APS-FWI component, utilizing the InversionNet, directly reconstructs the speed of sound (SOS) from the ultrasound waveform data. We further improve the model's performance by incorporating Squeeze-and-Excitation (SE) Blocks and source encoding techniques. Testing our method on a breast cancer dataset yielded promising results. It demonstrated outstanding performance with an average Structural Similarity Index (SSIM) of 0.8431. Notably, over 82% of samples achieved an SSIM above 0.8, with nearly 61% exceeding 0.85, highlighting the significant potential of our approach in improving USCT image reconstruction by efficiently utilizing sparse data.

Shuvom Sadhuka, Drew Prinster, Clara Fannjiang et al.

Agentic AI systems execute a sequence of actions, such as reasoning steps or tool calls, in response to a user prompt. To evaluate the success of their trajectories, researchers have developed verifiers, such as LLM judges and process-reward models, to score the quality of each action in an agent's trajectory. Although these heuristic scores can be informative, there are no guarantees of correctness when used to decide whether an agent will yield a successful output. Here, we introduce e-valuator, a method to convert any black-box verifier score into a decision rule with provable control of false alarm rates. We frame the problem of distinguishing successful trajectories (that is, a sequence of actions that will lead to a correct response to the user's prompt) and unsuccessful trajectories as a sequential hypothesis testing problem. E-valuator builds on tools from e-processes to develop a sequential hypothesis test that remains statistically valid at every step of an agent's trajectory, enabling online monitoring of agents over arbitrarily long sequences of actions. Empirically, we demonstrate that e-valuator provides greater statistical power and better false alarm rate control than other strategies across six datasets and three agents. We additionally show that e-valuator can be used for to quickly terminate problematic trajectories and save tokens. Together, e-valuator provides a lightweight, model-agnostic framework that converts verifier heuristics into decisions rules with statistical guarantees, enabling the deployment of more reliable agentic systems.

Hanchen Wang, Yixuan Wu, Yinan Feng et al.

Prostate cancer is one of the most common and lethal cancers among men, making its early detection critically important. Although ultrasound imaging offers greater accessibility and cost-effectiveness compared to MRI, traditional transrectal ultrasound methods suffer from low sensitivity, especially in detecting anteriorly located tumors. Ultrasound computed tomography provides quantitative tissue characterization, but its clinical implementation faces significant challenges, particularly under anatomically constrained limited-angle acquisition conditions specific to prostate imaging. To address these unmet needs, we introduce OpenPros, the first large-scale benchmark dataset explicitly developed for limited-view prostate USCT. Our dataset includes over 280,000 paired samples of realistic 2D speed-of-sound (SOS) phantoms and corresponding ultrasound full-waveform data, generated from anatomically accurate 3D digital prostate models derived from real clinical MRI/CT scans and ex vivo ultrasound measurements, annotated by medical experts. Simulations are conducted under clinically realistic configurations using advanced finite-difference time-domain and Runge-Kutta acoustic wave solvers, both provided as open-source components. Through comprehensive baseline experiments, we demonstrate that state-of-the-art deep learning methods surpass traditional physics-based approaches in both inference efficiency and reconstruction accuracy. Nevertheless, current deep learning models still fall short of delivering clinically acceptable high-resolution images with sufficient accuracy. By publicly releasing OpenPros, we aim to encourage the development of advanced machine learning algorithms capable of bridging this performance gap and producing clinically usable, high-resolution, and highly accurate prostate ultrasound images. The dataset is publicly accessible at https://open-pros.github.io/.

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.

Nikita Makarov, Maria Bordukova, Lena Voith von Voithenberg et al.

Precision oncology requires forecasting clinical events and trajectories, yet modeling sparse, multi-modal clinical time series remains a critical challenge. We introduce TwinWeaver, an open-source framework that serializes longitudinal patient histories into text, enabling unified event prediction as well as forecasting with large language models, and use it to build Genie Digital Twin (GDT) on 93,054 patients across 20 cancer types. In benchmarks, GDT significantly reduces forecasting error, achieving a median Mean Absolute Scaled Error (MASE) of 0.87 compared to 0.97 for the strongest time-series baseline (p<0.001). Furthermore, GDT improves risk stratification, achieving an average concordance index (C-index) of 0.703 across survival, progression, and therapy switching tasks, surpassing the best baseline of 0.662. GDT also generalizes to out-of-distribution clinical trials, matching trained baselines at zero-shot and surpassing them with fine-tuning, achieving a median MASE of 0.75-0.88 and outperforming the strongest baseline in event prediction with an average C-index of 0.672 versus 0.648. Finally, TwinWeaver enables an interpretable clinical reasoning extension, providing a scalable and transparent foundation for longitudinal clinical modeling.

Namkyeong Lee, Yunhak Oh, Heewoong Noh et al.

Molecular Relational Learning (MRL) is a rapidly growing field that focuses on understanding the interaction dynamics between molecules, which is crucial for applications ranging from catalyst engineering to drug discovery. Despite recent progress, earlier MRL approaches are limited to using only the 2D topological structure of molecules, as obtaining the 3D interaction geometry remains prohibitively expensive. This paper introduces a novel 3D geometric pre-training strategy for MRL (3DMRL) that incorporates a 3D virtual interaction environment, overcoming the limitations of costly traditional quantum mechanical calculation methods. With the constructed 3D virtual interaction environment, 3DMRL trains 2D MRL model to learn the global and local 3D geometric information of molecular interaction. Extensive experiments on various tasks using real-world datasets, including out-of-distribution and extrapolation scenarios, demonstrate the effectiveness of 3DMRL, showing up to a 24.93% improvement in performance across 40 tasks. Our code is publicly available at https://github.com/Namkyeong/3DMRL.

Lincan Li, Hanchen Wang, Wenjie Zhang et al.

Spatial-Temporal Graph (STG) data is characterized as dynamic, heterogenous, and non-stationary, leading to the continuous challenge of spatial-temporal graph learning. In the past few years, various GNN-based methods have been proposed to solely focus on mimicking the relationships among node individuals of the STG network, ignoring the significance of modeling the intrinsic features that exist in STG system over time. In contrast, modern Selective State Space Models (SSSMs) present a new approach which treat STG Network as a system, and meticulously explore the STG system's dynamic state evolution across temporal dimension. In this work, we introduce Spatial-Temporal Graph Mamba (STG-Mamba) as the first exploration of leveraging the powerful selective state space models for STG learning by treating STG Network as a system, and employing the Spatial-Temporal Selective State Space Module (ST-S3M) to precisely focus on the selected STG latent features. Furthermore, to strengthen GNN's ability of modeling STG data under the setting of selective state space models, we propose Kalman Filtering Graph Neural Networks (KFGN) for dynamically integrate and upgrade the STG embeddings from different temporal granularities through a learnable Kalman Filtering statistical theory-based approach. Extensive empirical studies are conducted on three benchmark STG forecasting datasets, demonstrating the performance superiority and computational efficiency of STG-Mamba. It not only surpasses existing state-of-the-art methods in terms of STG forecasting performance, but also effectively alleviate the computational bottleneck of large-scale graph networks in reducing the computational cost of FLOPs and test inference time. The implementation code is available at: \url{https://github.com/LincanLi98/STG-Mamba}.

Chengyuan Deng, Shihang Feng, Hanchen Wang et al.

Full waveform inversion (FWI) is widely used in geophysics to reconstruct high-resolution velocity maps from seismic data. The recent success of data-driven FWI methods results in a rapidly increasing demand for open datasets to serve the geophysics community. We present OpenFWI, a collection of large-scale multi-structural benchmark datasets, to facilitate diversified, rigorous, and reproducible research on FWI. In particular, OpenFWI consists of 12 datasets (2.1TB in total) synthesized from multiple sources. It encompasses diverse domains in geophysics (interface, fault, CO2 reservoir, etc.), covers different geological subsurface structures (flat, curve, etc.), and contains various amounts of data samples (2K - 67K). It also includes a dataset for 3D FWI. Moreover, we use OpenFWI to perform benchmarking over four deep learning methods, covering both supervised and unsupervised learning regimes. Along with the benchmarks, we implement additional experiments, including physics-driven methods, complexity analysis, generalization study, uncertainty quantification, and so on, to sharpen our understanding of datasets and methods. The studies either provide valuable insights into the datasets and the performance, or uncover their current limitations. We hope OpenFWI supports prospective research on FWI and inspires future open-source efforts on AI for science. All datasets and related information can be accessed through our website at https://openfwi-lanl.github.io/

Hanchen Wang, Qi Liu, Xiangyu Yue et al.

We describe a simple pre-training approach for point clouds. It works in three steps: 1. Mask all points occluded in a camera view; 2. Learn an encoder-decoder model to reconstruct the occluded points; 3. Use the encoder weights as initialisation for downstream point cloud tasks. We find that even when we construct a single pre-training dataset (from ModelNet40), this pre-training method improves accuracy across different datasets and encoders, on a wide range of downstream tasks. Specifically, we show that our method outperforms previous pre-training methods in object classification, and both part-based and semantic segmentation tasks. We study the pre-trained features and find that they lead to wide downstream minima, have high transformation invariance, and have activations that are highly correlated with part labels. Code and data are available at: https://github.com/hansen7/OcCo

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.

Chenyu Wang, Masatoshi Uehara, Yichun He et al.

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

Fang Wu, Weihao Xuan, Heli Qi et al.

Deep learning in \emph{de novo} protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries without explicitly reasoning about which residues or interactions are functionally essential. As a result, design decisions are entangled with continuous sampling dynamics, limiting interpretability, controllability, and systematic reuse of biochemical knowledge. We introduce \textbf{Proteo-R1}, a reasoning-guided protein design framework that explicitly decouples \emph{molecular understanding} from \emph{geometric generation}. Proteo-R1 adopts a dual-expert architecture in which a multimodal large language model (MLLM) serves as an \emph{understanding expert}, analyzing protein sequences, structures, and textual context to identify key functional residues that govern binding and specificity. These residue-level decisions are then passed as hard constraints to a separate diffusion-based \emph{generation expert}, which performs conditional co-design while respecting the fixed interaction anchors. This factorization mirrors how human experts approach molecular engineering: first, reasoning about critical interactions, then optimizing geometry subject to those constraints. By operationalizing reasoning as explicit residue-level commitments rather than latent textual guidance, Proteo-R1 achieves stable, interpretable, and modular integration of LLM reasoning with state-of-the-art geometric generative models. Code, data, and demos are available at https://smiles724.github.io/r1/.

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.

Junhuan Yang, Hanchen Wang, Yi Sheng et al.

Full-waveform inversion (FWI) plays a vital role in geoscience to explore the subsurface. It utilizes the seismic wave to image the subsurface velocity map. As the machine learning (ML) technique evolves, the data-driven approaches using ML for FWI tasks have emerged, offering enhanced accuracy and reduced computational cost compared to traditional physics-based methods. However, a common challenge in geoscience, the unprivileged data, severely limits ML effectiveness. The issue becomes even worse during model pruning, a step essential in geoscience due to environmental complexities. To tackle this, we introduce the EdGeo toolkit, which employs a diffusion-based model guided by physics principles to generate high-fidelity velocity maps. The toolkit uses the acoustic wave equation to generate corresponding seismic waveform data, facilitating the fine-tuning of pruned ML models. Our results demonstrate significant improvements in SSIM scores and reduction in both MAE and MSE across various pruning ratios. Notably, the ML model fine-tuned using data generated by EdGeo yields superior quality of velocity maps, especially in representing unprivileged features, outperforming other existing methods.

Wei Huang, Hanchen Wang, Dong Wen et al.

The Graph Edit Distance (GED) problem, which aims to compute the minimum number of edit operations required to transform one graph into another, is a fundamental challenge in graph analysis with wide-ranging applications. However, due to its NP-hard nature, traditional A* approaches often suffer from scalability issue, making them computationally intractable for large graphs. Many recent deep learning frameworks address GED by formulating it as a regression task, which, while efficient, fails to recover the edit path -- a central interest in GED. Furthermore, recent hybrid approaches that combine deep learning with traditional methods to recover the edit path often yield poor solution quality. These methods also struggle to generate candidate solutions in parallel, resulting in increased running times.In this paper, we present a novel approach, DiffGED, that leverages generative diffusion model to solve GED and recover the corresponding edit path. Specifically, we first generate multiple diverse node matching matrices in parallel through a diffusion-based graph matching model. Next, node mappings are extracted from each generated matching matrices in parallel, and each extracted node mapping can be simply transformed into an edit path. Benefiting from the generative diversity provided by the diffusion model, DiffGED is less likely to fall into local sub-optimal solutions, thereby achieving superior overall solution quality close to the exact solution. Experimental results on real-world datasets demonstrate that DiffGED can generate multiple diverse edit paths with exceptionally high accuracy comparable to exact solutions while maintaining a running time shorter than most of hybrid approaches.

Guangxin Su, Hanchen Wang, Jianwei Wang et al.

Large Language Models (LLMs) have achieved remarkable success in natural language processing through strong semantic understanding and generation. However, their black-box nature limits structured and multi-hop reasoning. In contrast, Text-Attributed Graphs (TAGs) provide explicit relational structures enriched with textual context, yet often lack semantic depth. Recent research shows that combining LLMs and TAGs yields complementary benefits: enhancing TAG representation learning and improving the reasoning and interpretability of LLMs. This survey provides the first systematic review of LLM--TAG integration from an orchestration perspective. We introduce a novel taxonomy covering two fundamental directions: LLM for TAG, where LLMs enrich graph-based tasks, and TAG for LLM, where structured graphs improve LLM reasoning. We categorize orchestration strategies into sequential, parallel, and multi-module frameworks, and discuss advances in TAG-specific pretraining, prompting, and parameter-efficient fine-tuning. Beyond methodology, we summarize empirical insights, curate available datasets, and highlight diverse applications across recommendation systems, biomedical analysis, and knowledge-intensive question answering. Finally, we outline open challenges and promising research directions, aiming to guide future work at the intersection of language and graph learning.

Han Chen, Hanchen Wang, Hongmei Chen et al.

The advancement of graph-based malware analysis is critically limited by the absence of large-scale datasets that capture the inherent hierarchical structure of software. Existing methods often oversimplify programs into single level graphs, failing to model the crucial semantic relationship between high-level functional interactions and low-level instruction logic. To bridge this gap, we introduce \dataset, the largest public hierarchical graph dataset for malware analysis, comprising over \textbf{200M} Control Flow Graphs (CFGs) nested within \textbf{595K} Function Call Graphs (FCGs). This two-level representation preserves structural semantics essential for building robust detectors resilient to code obfuscation and malware evolution. We demonstrate HiGraph's utility through a large-scale analysis that reveals distinct structural properties of benign and malicious software, establishing it as a foundational benchmark for the community. The dataset and tools are publicly available at https://higraph.org.

Hanchen Wang, Ying Zhang, Lu Qin et al.

Subgraph matching is a fundamental problem in various fields that use graph structured data. Subgraph matching algorithms enumerate all isomorphic embeddings of a query graph q in a data graph G. An important branch of matching algorithms exploit the backtracking search approach which recursively extends intermediate results following a matching order of query vertices. It has been shown that the matching order plays a critical role in time efficiency of these backtracking based subgraph matching algorithms. In recent years, many advanced techniques for query vertex ordering (i.e., matching order generation) have been proposed to reduce the unpromising intermediate results according to the preset heuristic rules. In this paper, for the first time we apply the Reinforcement Learning (RL) and Graph Neural Networks (GNNs) techniques to generate the high-quality matching order for subgraph matching algorithms. Instead of using the fixed heuristics to generate the matching order, our model could capture and make full use of the graph information, and thus determine the query vertex order with the adaptive learning-based rule that could significantly reduces the number of redundant enumerations. With the help of the reinforcement learning framework, our model is able to consider the long-term benefits rather than only consider the local information at current ordering step.Extensive experiments on six real-life data graphs demonstrate that our proposed matching order generation technique could reduce up to two orders of magnitude of query processing time compared to the state-of-the-art algorithms.

Xiang Bai, Hanchen Wang, Liya Ma et al.

Artificial intelligence (AI) provides a promising substitution for streamlining COVID-19 diagnoses. However, concerns surrounding security and trustworthiness impede the collection of large-scale representative medical data, posing a considerable challenge for training a well-generalised model in clinical practices. To address this, we launch the Unified CT-COVID AI Diagnostic Initiative (UCADI), where the AI model can be distributedly trained and independently executed at each host institution under a federated learning framework (FL) without data sharing. Here we show that our FL model outperformed all the local models by a large yield (test sensitivity /specificity in China: 0.973/0.951, in the UK: 0.730/0.942), achieving comparable performance with a panel of professional radiologists. We further evaluated the model on the hold-out (collected from another two hospitals leaving out the FL) and heterogeneous (acquired with contrast materials) data, provided visual explanations for decisions made by the model, and analysed the trade-offs between the model performance and the communication costs in the federated training process. Our study is based on 9,573 chest computed tomography scans (CTs) from 3,336 patients collected from 23 hospitals located in China and the UK. Collectively, our work advanced the prospects of utilising federated learning for privacy-preserving AI in digital health.

Weiyang Liu, Zhen Liu, Hanchen Wang et al.

In this paper, we consider the problem of iterative machine teaching, where a teacher provides examples sequentially based on the current iterative learner. In contrast to previous methods that have to scan over the entire pool and select teaching examples from it in each iteration, we propose a label synthesis teaching framework where the teacher randomly selects input teaching examples (e.g., images) and then synthesizes suitable outputs (e.g., labels) for them. We show that this framework can avoid costly example selection while still provably achieving exponential teachability. We propose multiple novel teaching algorithms in this framework. Finally, we empirically demonstrate the value of our framework.

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.

Tariq Alkhalifah, Hanchen Wang, Oleg Ovcharenko

Among the biggest challenges we face in utilizing neural networks trained on waveform data (i.e., seismic, electromagnetic, or ultrasound) is its application to real data. The requirement for accurate labels forces us to develop solutions using synthetic data, where labels are readily available. However, synthetic data often do not capture the reality of the field/real experiment, and we end up with poor performance of the trained neural network (NN) at the inference stage. We describe a novel approach to enhance supervised training on synthetic data with real data features (domain adaptation). Specifically, for tasks in which the absolute values of the vertical axis (time or depth) of the input data are not crucial, like classification, or can be corrected afterward, like velocity model building using a well-log, we suggest a series of linear operations on the input so the training and application data have similar distributions. This is accomplished by applying two operations on the input data to the NN model: 1) The crosscorrelation of the input data (i.e., shot gather, seismic image, etc.) with a fixed reference trace from the same dataset. 2) The convolution of the resulting data with the mean (or a random sample) of the autocorrelated data from another domain. In the training stage, the input data are from the synthetic domain and the auto-correlated data are from the real domain, and random samples from real data are drawn at every training epoch. In the inference/application stage, the input data are from the real subset domain and the mean of the autocorrelated sections are from the synthetic data subset domain. Example applications on passive seismic data for microseismic event source location determination and active seismic data for predicting low frequencies are used to demonstrate the power of this approach in improving the applicability of trained models to real data.

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}

Hanchen Wang, Defu Lian, Ying Zhang et al.

Recently, there have been some breakthroughs in graph analysis by applying the graph neural networks (GNNs) following a neighborhood aggregation scheme, which demonstrate outstanding performance in many tasks. However, we observe that the parameters of the network and the embedding of nodes are represented in real-valued matrices in existing GNN-based graph embedding approaches which may limit the efficiency and scalability of these models. It is well-known that binary vector is usually much more space and time efficient than the real-valued vector. This motivates us to develop a binarized graph neural network to learn the binary representations of the nodes with binary network parameters following the GNN-based paradigm. Our proposed method can be seamlessly integrated into the existing GNN-based embedding approaches to binarize the model parameters and learn the compact embedding. Extensive experiments indicate that the proposed binarized graph neural network, namely BGN, is orders of magnitude more efficient in terms of both time and space while matching the state-of-the-art performance.

Hanchen Wang, Nina Grgic-Hlaca, Preethi Lahoti et al.

The notion of individual fairness requires that similar people receive similar treatment. However, this is hard to achieve in practice since it is difficult to specify the appropriate similarity metric. In this work, we attempt to learn such similarity metric from human annotated data. We gather a new dataset of human judgments on a criminal recidivism prediction (COMPAS) task. By assuming the human supervision obeys the principle of individual fairness, we leverage prior work on metric learning, evaluate the performance of several metric learning methods on our dataset, and show that the learned metrics outperform the Euclidean and Precision metric under various criteria. We do not provide a way to directly learn a similarity metric satisfying the individual fairness, but to provide an empirical study on how to derive the similarity metric from human supervisors, then future work can use this as a tool to understand human supervision.