Graph Diffusion

Inverse kinematics (IK) is a fundamental problem in robotics, requiring the generation of joint configurations that satisfy target end-effector poses. Existing approaches often struggle to generalize across diverse robot morphologies and to effectively model the multi-modal nature of IK, particularly in articulated systems with multiple kinematic branches. In this work, we propose GraphDiff-IK, a structure-aware graph diffusion framework for inverse kinematics. Specifically, we represent the robot as a kinematic graph constructed from the robot URDF, where nodes correspond to actuated joints and edges encode kinematic dependencies. Building upon this representation, we formulate IK as a conditional graph diffusion process that directly generates joint configurations on the robot graph. To better capture structural dependencies in articulated systems, we further introduce a structure-aware graph reasoning framework with hierarchical stage-wise message passing and torso-aware conditioning for multi-branch robots. In addition, we incorporate noisy forward kinematics feedback and task-space supervision to improve geometric consistency during denoising. The proposed framework provides a unified formulation that naturally supports single-arm robots, dual-arm systems, and articulated robots with torso or waist structures. Extensive experiments on diverse robotic platforms demonstrate that the proposed method achieves accurate and stable IK performance while preserving the ability to generate multiple feasible solutions for redundant robotic systems.

Graph Neural Networks (GNNs) have emerged as a cornerstone of deep learning, with most existing methods rooted in graph signal processing and diffusion equations to model message passing. However, these approaches inherently suffer from the oversmoothing problem, where node features become indistinguishable as the network depth increases. Inspired by the Navier Stokes equations, we introduce Graph Navier Stokes Networks (GNSN), a novel architecture that transcends conventional diffusion-based message passing by incorporating convection into graph structures. GNSN defines a dynamic velocity field on the graph to govern convection, enabling more efficient and direct message propagation. By adaptively balancing convection and diffusion, GNSN is able to efficiently handle datasets with varying levels of homophily. Extensive evaluations across twelve real-world datasets demonstrate that GNSN consistently outperforms state-of-the-art baselines in classification accuracy. Moreover, experimental results further emphasize its effectiveness in alleviating the oversmoothing problem.

Deep generative models have emerged as state-of-the-art for solving inverse problems, but applying them to inverse problems for PDEs, like electrical impedance tomography (EIT) remains challenging. Because physical domains are naturally discretized as unstructured meshes rather than regular grids, standard convolutional architectures are often inadequate. In this paper, we propose a novel framework that extends diffusion posterior sampling (DPS) to graph-structured data. We develop an unconditional score-based diffusion model directly on a 2D triangular mesh to learn an accurate prior over the physical solution space. Furthermore, we introduce a regularized variant, RDPS, which incorporates explicit regularization terms, such as total variation and generalized Tikhonov, to complement the implicit diffusion prior and mitigate severe ill-posedness. Extensive experiments on synthetic and real 2D EIT datasets demonstrate that RDPS produces stable, physically plausible reconstructions. Our approach generalizes well to out-of-distribution inclusion geometries, is highly robust to measurement noise, and outperforms current state-of-the-art solvers (e.g., GPnP-BM3D, DP-SGS) in reconstruction accuracy and artifact reduction.

Deep Graph Neural Networks (GNNs) are essential for capturing complex dependencies in graph-structured data. However, scaling GNNs to depth remains challenging, as stacking layers leads to representation collapse and diminishing sensitivity due to repeated aggregation. While Neural Sheaf Diffusion (NSD) provides strong theoretical guarantees against such collapse, these guarantees do not translate to practice: as depth increases, the disagreement signal of the sheaf Laplacian vanishes, limiting the contribution of deeper layers. We identify mechanisms that hinder NSD effectiveness at depth and propose \emph{Deep Neural Sheaf Diffusion} (DNSD), which replaces the sheaf Laplacian with a sheaf adjacency operator to maintain informative signals across layers. This is complemented by normalization, odd nonlinearities, and gating. To provide a principled explanation of the expected performance improvement, we contrast sheaf diffusion to graph attention mechanisms, highlighting that DNSD replaces scalar attention scores with matrix-valued edge functions and normalizes node representations rather than attention scores. We demonstrate empirically that DNSD effectively utilizes deep aggregation in graph tasks, outperforming GNN and NSD baselines with up to 30pp accuracy on synthetic long-range datasets, and consistently outperforming them on real-world benchmarks. These results position sheaf-based architectures as a promising building block for graph foundation models by supporting effective deep architectures.

Many complex systems can be modeled by temporal networks, whose organization often evolves through distinct structural phases. Detecting the change points that delimit these phases is both important and challenging. In this work, we extend the conditional entropy of heat diffusion from static graphs to temporal networks and study its properties. We provide an upper bound and explain how discrepancies from it arise from the presence of asymmetric temporal paths. Moreover, we show that this quantity is monotone in time, yielding an information-theoretic analog of the second law of thermodynamics for inhomogeneous diffusion on temporal networks. We then introduce a local version of conditional entropy, designed to probe diffusion over finite temporal windows, and show that it provides an informative signal for change-point detection in continuous-time temporal networks. We evaluate the proposed methodology on synthetic benchmarks, including comparative experiments with existing nonparametric baselines in the snapshot setting, and then apply it to a real-world temporal contact network from a French primary school. Finally, we show how to use detected change points to perform community detection on targeted sub-intervals, improving the quality and interpretability of the clustering results.

Neural Sheaf Diffusion (NSD) generalizes diffusion-based Graph Neural Networks by replacing scalar graph Laplacians with sheaf Laplacians whose learned restriction maps define a task-adapted geometry. While the diffusion limit of NSD is known to be the space of global sections, the representation-theoretic structure of this harmonic space remains largely implicit. We develop a quiver-theoretic interpretation of NSD by identifying cellular sheaves on graphs with representations of the associated incidence quiver. Under this correspondence, learned sheaf geometries become points in a finite-dimensional representation space. We show that direct-sum decompositions of the underlying incidence-quiver representation induce decompositions of the harmonic space reached in the diffusion limit. This gives an algebraic interpretation of oversmoothing as representation degeneration: learned sheaves may collapse toward low-complexity summands whose global sections fail to preserve discriminative information. Building on this viewpoint, we connect sheaf diffusion to stability and moment-map principles from Geometric Invariant Theory. We introduce moment-map-inspired regularizers that bias restriction maps toward balanced representation geometries, and identify a structural obstruction in equal-stalk architectures: when $d_v = d_e$, admissibility for learnable stability parameters forces the trivial all-object summand onto a stability wall. Non-uniform stalk dimensions remove this obstruction, making adaptive stability meaningful. Experiments on heterophilic benchmarks are consistent with this mechanism: breaking stalk symmetry can reduce variance or improve validation behavior, and adaptive stability becomes more effective in selected rectangular settings. Overall, our framework reframes oversmoothing as a degeneration phenomenon in the representation geometry underlying learned sheaf diffusion.

Despite the central role of sensor-derived measurements such as imaging traits and plasma biomarkers in biomedical research and clinical practice, existing generative models for disease prediction largely depend on event-level representations from hospital and registry data. Given the multi-factorial nature of human disease, the absence of explicit modeling of social determinants of health (SDoH), even in the limited form of ICD-coded proxies (chapters Z and V--Y in ICD-10), limits the capacity for personalized disease modeling and clinical decision support. To address this limitation, we propose a generative model with ICD-coded proxies of SDoH for \textit{in silico} modeling of disease reasoning, a conditioned latent diffusion framework that establishes the connection between multi-organ sensor data with tokenized healthcare events. Specifically, we introduce a novel geometric diffusion model to characterize the temporal evolution of complex data representation such as brain networks (region-to-region connectivity encoded in a graph), in parallel with diffusion models for tabular data from other organ systems. Together, we integrate the generative model with digitalized SDoH proxies (coined \modelname{}) for simulated intervention and reasoning of future disease trajectories. We conduct extensive experiments on the UK Biobank (UKB) dataset, which contains organ-specific imaging traits, including brain (44,834), heart (23,987), liver (28,722), and kidney (32,155), along with nearly 500k medical history sequences (age range: 25$\sim$89 years). Our \modelname{} achieves significant improvements over state-of-the-art human disease autoregressive models and imaging trait generative baselines.

Scene graphs (SGs) represent objects and their relationships as structured graphs, enabling applications in image generation, robotics, and 3D understanding. Recent work suggests that conditioning image generation on scene graphs improves compositional fidelity compared to text-only prompting. However, since users typically provide text rather than structured graphs, a key challenge is to generate scene graphs from natural language. Prior work on discrete diffusion has demonstrated success in generating generic graphs such as molecules and circuits, but fails to account for the hierarchical structure and strong dependencies between objects, edges, and relations in scene graphs. We address this limitation by introducing a dependency-aware, hierarchically constrained discrete diffusion model for scene graph generation. Our approach decouples structure and semantics across the forward and reverse processes, enabling the model to capture conditional dependencies. At inference time, we perform training-free conditioning to sample text-aligned scene graphs. We evaluate our method on standard SG benchmarks and demonstrate improvements over both continuous and discrete graph generation baselines across graph and layout metrics. When fed to downstream image generation, our approach yields improved compositional alignment compared to text-to-image models, particularly in multi-object scenarios.

De novo molecular generation from tandem mass spectra is a challenging inverse problem whose core difficulty lies in the circular dependency between atom-level and bond-level reasoning: determining a bond's type requires knowing its endpoint atoms' chemical environment, yet an atom's environment is in turn defined by its incident bonds. Existing graph diffusion methods process atoms and bonds within a single computation stream, where atom-bond information synchronization can only occur implicitly across layers. We argue that this single-stream paradigm, rather than the choice of any particular aggregation kernel, is a key architectural bottleneck. We propose DualLGD (Dual-stream Line Graph Diffusion), which reformulates molecular graph denoising as the alternating solution of two coupled subproblems: atom-level reasoning and bond-level reasoning, each operating in its own dedicated representation space. The line graph provides a natural mathematical construction for the bond space, in which bond angles, dihedrals, conjugation chains, and rings correspond to local topological motifs between bonds. Incidence-constrained bidirectional cross-attention synchronizes the two streams at every layer, ensuring that each atom attends only to its incident bonds and vice versa, respecting the fundamental chemical principle that an atom's environment is determined by its bonding context. On the NPLIB1 and MassSpecGym benchmarks, DualLGD achieves top-1 accuracy of 34.37% and 23.89%, approximately $3\times$ the previous state of the art. Ablation studies confirm the architecture as the primary source of improvement: DualLGD without any pre-training already surpasses the previous best fully pretrained model.

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.

Diffusion-based voxel prior modelling is challenging for the reconstruction of large-scale 3D porous microstructures. Due to the demanding requirements for simultaneously modelling both the continuous pore morphology and the discrete pore-throat topology, the diffusion models require fully observed CT scans to provide topology-faithful priors, which results in an inherent trade-off among throughput, topological fidelity, and field of view in practical industrial applications. We propose GeoTopoDiff, a graph diffusion-based framework for reconstructing 3D porous microstructures from sparse CT slices. GeoTopoDiff transfers the learning of diffusion priors from a voxel-based space to a mixed graph state space, which simultaneously encompasses continuous pore geometry and discrete pore-throat topology. A topology-aware partial graph prior from sparsely observed CT slices is introduced to constrain the reverse denoising process. Experiments on anisotropic PTFE and Fontainebleau sandstone show that GeoTopoDiff reduces morphology-related errors by 19.8% and topology-sensitive transport errors by 36.5% on average. Our findings suggest that the mixed graph state space promotes the diffusion denoising process to reduce posterior uncertainty under a sparse observations. All models and code have been made publicly available to facilitate the exploration of diffusion models in the field of 3D porous microstructures simulation.

In wireless communications, recovering the optimal solution to the multiple-input multiple-output (MIMO) detection problem is NP-hard. Obtaining high-quality suboptimal solutions with a favorable performance-complexity trade-off is particularly challenging in under-determined systems with $N_t$ transmit antennas and $N_r < N_t$ receive antennas. Recent diffusion-based MIMO detectors have shown promise, but they require extensive sampling iterations at inference time, and their performance degrades in under-determined scenarios. We propose GD4, a graph-based discrete denoising diffusion method for MIMO detection. Unlike existing diffusion-based detectors that operate in a continuous relaxed space, GD4 performs denoising directly in the discrete symbol space and enables fast inference with one or a few denoising evaluations. Numerical results show that, under a similar inference-time compute budget, GD4 produces higher-quality suboptimal solutions than existing diffusion-based detectors and some widely used classical baseline including box-constrained Babai point and the $K$-best box-constrained randomized Klein-Babai point in both under-determined and overdetermined settings.

Standard diffusion models for graph generation typically rely on uniform time-stepping, an approach that overlooks the non-homogeneous dynamics of distributional evolution on complex manifolds. In this paper, we present an information-geometric framework that reinterprets the diffusion sampling trajectory as a parametric curve on a Riemannian manifold. Our key observation is that the Fisher-Rao metric provides a principled measure of the intrinsic distance. By analyzing this metric, we derive the Drift Variation Score (DVS), a geometry-aware indicator that quantifies the instantaneous rate of distributional change. Unlike prior heuristic-based adaptive samplers, our DVS solver enforces a constant informational speed on the statistical manifold, automatically maintaining a uniform rate of distributional change along the sampling trajectory. This equal arc-length strategy ensures that each discretization step contributes equally to the information speed. Theoretical analysis verifies that DVS characterizes the local stiffness of the sampling dynamics in the Fisher-Rao sense. Experimental results on molecule and social network generation show that DVS significantly improves structural fidelity and sampling efficiency. Code is at https://github.com/kunzhan/DVS

Graph-based Retrieval-Augmented Generation (RAG) systems leverage interconnected knowledge structures to capture complex relationships that flat retrieval struggles with, enabling multi-hop reasoning. Yet most existing graph-based methods suffer from (i) heuristic designs lacking theoretical guarantees for subgraph quality or relevance and/or (ii) the use of static exploration strategies that ignore the query's holistic meaning, retrieving neighborhoods or communities regardless of intent. We propose Query-Aware Flow Diffusion RAG (QAFD-RAG), a training-free framework that dynamically adapts graph traversal to each query's holistic semantics. The central innovation is query-aware traversal: during graph exploration, edges are dynamically weighted by how well their endpoints align with the query's embedding, guiding flow along semantically relevant paths while avoiding structurally connected but irrelevant regions. These query-specific reasoning subgraphs enable the first statistical guarantees for query-aware graph retrieval, showing that QAFD-RAG recovers relevant subgraphs with high probability under mild signal-to-noise conditions. The algorithm converges exponentially fast, with complexity scaling with the retrieved subgraph size rather than the full graph. Experiments on question answering and text-to-SQL tasks demonstrate consistent improvements over state-of-the-art graph-based RAG methods.

Knowledge Graphs (KGs) are composed of triples, and the goal of Knowledge Graph Completion (KGC) is to infer the missing factual triples. Traditional KGC tasks predict missing elements in a triple given one or two of its elements. As a more realistic task, the Triple Set Prediction (TSP) task aims to infer the set of missing triples conditioned only on the observed knowledge graph, without assuming any partial information about the missing triples. Existing TSP methods predict the set of missing triples in a triple-by-triple manner, falling short in capturing the dependencies among the predicted triples to ensure consistency. To address this issue, we propose a novel discrete diffusion model termed DiffTSP that treats TSP as a generative task. DiffTSP progressively adds noise to the KG through a discrete diffusion process, achieved by masking relational edges. The reverse process then gradually recovers the complete KG conditioned on the incomplete graph. To this end, we design a structure-aware denoising network that integrates a relational context encoder with a relational graph diffusion transformer for knowledge graph generation. DiffTSP can generate the complete set of triples in a one-pass manner while ensuring the dependencies among the predicted triples. Our approach achieves state-of-the-art performance on three public datasets. Code: https://github.com/ADMIS-TONGJI/DiffTSP.

Influence maximization (IM) is a fundamental problem in complex network analysis, with a wide range of real-world applications. To date, existing approaches to influential node identification in IM have predominantly relied on standard graphs, failing to capture higher-order intrinsic interactions embedded in many real-world systems. Hypergraphs can be employed to better capture higher-order interactions. However, using hypergraphs may lead to an excessively large search space and increased complexity in modeling cascading dynamics, making it challenging to accurately identify influential nodes. Therefore, in this study, we propose a new hypergraph-modeled IM method, based on the Discrete Particle Swarm Optimization algorithm and the threshold model. In the proposed method, a particle (i.e., a candidate solution) represents the selection information of seed nodes, and the fitness function is designed to accurately and efficiently evaluate the influence of seed nodes via a two-layer local influence approximation. We also propose a degree-based initialization strategy to improve the quality of initial solutions and develop rules for updating particles' velocity and position, incorporated with a local search to drive particles toward better solutions. Experimental results demonstrate that the proposed method outperforms baseline methods on both synthetic and real-world hypergraphs. In addition, ablation studies validate the effectiveness of both the local search and the initialization strategies.

Graph Neural Networks (GNNs) conventionally rely on standard Laplacian or adjacency matrices for structural message passing. In this work, we substitute the traditional Laplacian with a Doubly Stochastic graph Matrix (DSM), derived from the inverse of the modified Laplacian, to naturally encode continuous multi-hop proximity and strict local centrality. To overcome the intractable $O(n^3)$ complexity of exact matrix inversion, we first utilize a truncated Neumann series to scalably approximate the DSM, which serves as the foundation for our proposed DsmNet. Furthermore, because algebraic truncation inherently causes probability mass leakage, we introduce DsmNet-compensate. This variant features a mathematically rigorous Residual Mass Compensation mechanism that analytically re-injects the truncated tail mass into self-loops, strictly restoring row-stochasticity and structural dominance. Extensive theoretical and empirical analyses demonstrate that our decoupled architectures operate efficiently in $O(K|E|)$ time and effectively mitigate over-smoothing by bounding Dirichlet energy decay, providing robust empirical validation on homophilic benchmarks. Finally, we establish the theoretical boundaries of the DSM on heterophilic topologies and demonstrate its versatility as a continuous structural encoding for Graph Transformers.

Predictive machine learning models generally excel on in-distribution data, but their performance degrades on out-of-distribution (OOD) inputs. Reliable deployment therefore requires robust OOD detection, yet this is particularly challenging for irregular 3D graphs that combine continuous geometry with categorical identities and are unordered by construction. Here, we present a probabilistic OOD detection framework for complex 3D graph data built on a diffusion model that learns a density of the training distribution in a fully unsupervised manner. A key ingredient we introduce is a unified continuous diffusion over both 3D coordinates and discrete features: categorical identities are embedded in a continuous space and trained with cross-entropy, while the corresponding diffusion score is obtained analytically via posterior-mean interpolation from predicted class probabilities. This yields a single self-consistent probability-flow ODE (PF-ODE) that produces per-sample log-likelihoods, providing a principled typicality score for distribution shift. We validate the approach on protein-ligand complexes and construct strict OOD datasets by withholding entire protein families from training. PF-ODE likelihoods identify held-out families as OOD and correlate strongly with prediction errors of an independent binding-affinity model (GEMS), enabling a priori reliability estimates on new complexes. Beyond scalar likelihoods, we show that multi-scale PF-ODE trajectory statistics - including path tortuosity, flow stiffness, and vector-field instability - provide complementary OOD information. Modeling the joint distribution of these trajectory features yields a practical, high-sensitivity detector that improves separation over likelihood-only baselines, offering a label-free OOD quantification workflow for geometric deep learning.

Urban sensor networks need forecasts that are accurate, carry useful uncertainty, and refresh fast enough to act on as new readings arrive. These goals conflict: deterministic models give no distribution, while diffusion forecasters model uncertainty but denoise from pure noise over many steps. We present Double-Diffusion, which integrates a closed-form graph-heat prior into a denoising diffusion model. The prior is a parameter-free low-pass forecast over the sensor graph, and it serves two roles: it is the residual target the model generates, and it conditions the denoiser. The reverse process therefore starts near the prior and denoises a short warm-started chain instead of synthesizing from pure noise; the name denotes this composition, a graph diffusion feeding a denoising diffusion. A compact denoiser, DD-Net, is trained as a Denoising Diffusion Probabilistic Model (DDPM) in the Resfusion warm-start formulation, so generation refines the prior over a short truncated chain rather than synthesizing from pure noise; a graph-spectral read-out of the prior residual sets its switchable spatial filter per domain from training data alone. On four real-world air quality and traffic networks, Double-Diffusion attains the best CRPS of all probabilistic methods on every dataset and stays competitive in point accuracy with the strongest baselines, at a fraction of the sampling cost of from-noise diffusion. The code is available at: https://github.com/teddyicare/Double-Diffusion

Diffusion models have demonstrated remarkable generative capabilities in continuous data domains such as images and videos. Recently, discrete graph diffusion models (DGDMs) have extended this success to graph generation, achieving state-of-the-art performance. However, deploying DGDMs in safety-critical applications, such as drug discovery, poses significant risks without a thorough understanding of their security vulnerabilities. In this work, we conduct the first study of backdoor attacks on DGDMs, a potent threat that manipulates both the training and generation phases of graph diffusion. We begin by formalizing the threat model and then design a backdoor attack that enables the compromised model to: 1) generate high-quality, benign graphs when the backdoor is not activated, 2) produce effective, stealthy, and persistent backdoored graphs when triggered, and 3) preserve fundamental graph properties (permutation equivariance and exchangeability) even under attack. We validate 1) and 2) empirically, both with and without backdoor defenses, and support 3) through theoretical analysis inspired by prior work.

Vertex-level clustering for directed graphs (digraphs) remains challenging as edge directionality breaks the key assumptions underlying popular spectral methods, which also incur the overhead of eigen-decomposition. This paper proposes Parametrized Power-Iteration Clustering (ParPIC), a random-walk-based clustering method for weakly connected digraphs. This builds over the Power-Iteration Clustering paradigm, which uses the rows of the iterated diffusion operator as a data embedding. ParPIC has three important features: the use of parametrized reversible random walk operators, the automatic tuning of the diffusion time, and the efficient truncation of the final embedding, which produces low-dimensional data representations and reduces complexity. Empirical results on synthetic and real-world graphs demonstrate that ParPIC achieves competitive clustering accuracy with improved scalability relative to spectral and teleportation-based methods.