Graph Structure Learning

Dirty entity resolution (ER), which identifies records referring to the same real-world entity from a single, messy dataset, is a fundamental task in data management and mining. However, the dominant blocking-matching-clustering paradigm for ER suffers from critical flaws. Its cascaded, decoupled workflow essentially produces a static, sparse graph plagued by missing edges (due to blocking failures) and noisy links (due to matching errors), causing error propagation and yielding suboptimal clusters, particularly when rigid transitivity is imposed in the clustering. We contend that matching and clustering are fundamentally synergistic, both optimizing for the construction of an ideal entity graph. Building upon this insight, we propose Alper, a unified framework that integrates these steps into an iterative probabilistic label propagation process over a global, evolving graph. Unlike disjoint blocking, Alper refines the graph structure and labels dynamically by adaptively integrating "weak but cheap" signals from graph propagation with "strong but expensive" LLM-based pairwise queries. For higher cost-effectiveness, we formulate the signal selection as a constrained optimization problem maximizing cumulative marginal gain under a query budget, solved via our greedy algorithm with provable theoretical guarantees. Our extensive experiments over eight benchmark datasets demonstrate that Alper is consistently superior to state-of-the-art cascaded pipelines.

Medical time series are central to healthcare, enabling continuous monitoring and supporting timely clinical decisions. Despite recent progress, existing methods struggle to jointly model local-global dynamics and handle nonstationarities like baseline drift, while often failing to capture latent channel interactions. To address these challenges, we propose MedMamba, an end-to-end architecture that integrates state space models with domain-specific inductive biases. Specifically, MedMamba first employs multi-scale convolutional embeddings to capture discriminative local morphology. Second, to mitigate nonstationarity, we introduce a tri-branch differential state space encoder that processes raw, temporal-difference, and frequency-domain views, fusing them to emphasize informative patterns while suppressing drift. Furthermore, to uncover latent channel correlations, we design a spatial graph Mamba module that learns a directed dependency structure regularized toward sparsity and acyclicity, which obviates the need for predefined graphs. Extensive experiments on five real-world datasets demonstrate that MedMamba achieves state-of-the-art performance while maintaining linear computational complexity, and ablation studies validate each component's contribution.Code is available at https://github.com/zhangda1018/MedMamba.

Hypergraphs have the capacity to capture higher-dimensional relationships among entities across various domains, making them a subject of growing interest within the research community for understanding the structure and dynamics of complex systems. However, a key challenge is the derivation of hypergraph representations from time series data in situations where the structure of the hypergraph is limited or absent. In this study, we propose a model that constructs a dynamic hypergraph representation for multivariate time series without relying on prior knowledge of the data. This is achieved by applying community detection to the time series and transforming the resulting communities, obtained through an attention mechanism, into a hypergraph using a clique-based technique. Hypergraph representations are derived from different time series datasets, and the resulting hypergraphs are then used by a Dynamic Hypergraph Attention Convolution Network (DHACN) for multivariate time series predictions. This research advances the field of hypergraph representation by introducing a novel approach that is better suited to uncover high-order relationships without prior knowledge.

Spectral clustering largely depends on the affinity graph, yet constructing a graph that preserves reliable local connectivity while adapting to heterogeneous data structures remains challenging. Existing granular-ball-based spectral clustering methods usually reduce graph complexity by using coarse-grained representatives. However, the learned local regions are often treated as graph nodes or anchors, and their structural information is not sufficiently used to regularize the original sample-level graph. To address this issue, this paper proposes a Minimum Description Length based Granular-Ball Tree-Regularized Spectral Clustering method, termed MDL-GBTRSC. The proposed method constructs a granular-ball tree through local MDL model selection, with reciprocal neighborhood continuity used to discourage splits that break reliable local connections. The stable leaf balls obtained from the tree provide coding-scale information for regularizing the sample-level affinity graph. In addition, a shared-neighbor bridge code is introduced to adjust weak local bridge relations without requiring an additional user-specified threshold. In this way, MDL-GBTRSC connects interpretable local representation learning with affinity graph construction in a unified spectral clustering framework. Experiments on real and synthetic datasets show that MDL-GBTRSC achieves the best average ARI and NMI under the adopted fixed-configuration protocol compared with classical spectral clustering baselines and representative granular-ball, micro-cluster, and anchor-based methods.

Relational prediction tasks are fundamental in many real-world applications, where data are naturally stored in relational databases (RDBs). Relational Deep Learning (RDL) addresses this problem by modeling RDBs as graphs and applying graph neural networks (GNNs) for end-to-end learning. However, the full-resolution property is commonly adopted as a design principle in graph construction for RDBs to preserve relational semantics, which leads most existing methods to rely on fixed graph structures. In this paper, we propose FROG, a Full-Resolution and Optimizable Graph Structure Learning} framework for RDL that formulates relational structure learning as a learnable table role modeling problem, allowing tables to contribute as nodes and edges in message passing. We further design role-driven message passing mechanisms to capture relational semantics, enabling joint optimization of graph structure and GNN representations. To ensure semantic consistency, we introduce functional dependency constraints that regularize representations across table and entity levels. Extensive experiments demonstrate that our method outperforms existing approaches and reveal how table roles impact downstream tasks, offering new insights into graph construction for RDL

This work addresses the problem of learning directed acyclic graphs (DAGs) from nodal observations generated by a linear structural equation model. DAG learning is a central task in signal processing, machine learning, and causal inference, but it remains challenging because acyclicity is a global combinatorial property. Continuous acyclicity constraints have led to important algorithmic advances by replacing the discrete DAG constraint with smooth equality constraints. However, existing formulations still involve difficult non-convex optimization landscapes and may suffer from degenerate first-order optimality conditions. Here, we restrict attention to DAGs with non-negative edge weights and exploit this additional structure to obtain a simpler characterization of acyclicity. Building on this characterization, we formulate a regularized non-negative DAG learning problem and develop an algorithm based on the method of multipliers. We further analyze the benign optimization landscape induced by non-negativity. In the population regime, we show that the true DAG is the unique global minimizer of the proposed augmented-Lagrangian formulation; moreover, the landscape contains no spurious interior stationary points, and the true DAG is the only acyclic KKT point. Numerical experiments on synthetic and real-world data show that the proposed method improves over state-of-the-art continuous DAG-learning alternatives.

Accurate estimation of plant skeletal structures (e.g., branching structures) from images is essential for smart agriculture and plant science. Unlike human skeletons with fixed topology, plant skeleton estimation presents a unique challenge, i.e., estimating arbitrary tree graphs from images. To address this problem, we introduce PlantPose, a universal plant skeleton estimator via tree-constrained graph generation. PlantPose combines learning-based graph generation with traditional graph algorithms to enforce tree constraints during the training loop. To enhance the model's generalization capability, we curate a large and diverse dataset comprising real-world and synthetic plant images, along with simplified representations (e.g., sketches and abstract drawings). This dataset enables the generalized model to adapt to diverse input styles and categories of plant images while preserving topological consistency. Our approach demonstrates robust and accurate plant skeleton estimation across multiple domains, including previously unseen out-of-domain scenarios. Further analyses highlight the method's strengths and limitations in handling complex, heterogeneous data distributions. All implementations and datasets are available at https://github.com/huntorochi/PlantPose/.

Coordination graphs are a central abstraction in cooperative multi-agent reinforcement learning (MARL), yet existing sparse-graph learners lack a theoretically grounded mechanism to decide which edges should exist and how much information each edge should carry. Current methods rely on heuristic criteria that offer no formal guarantee on the learned topology, and no principled way to allocate different communication capacities to structurally different agent relationships. To address this, we propose Heterogeneous Information-Bottleneck Coordination Graphs (HIBCG), which learns a group-aware sparse graph in which both edge existence and message capacity are theoretically justified. With the graph information bottleneck (GIB) serving as the underlying tool, HIBCG first constructs a group-aligned block-diagonal prior that provides a closed-form criterion for edge retention -- determining which edges should exist and at what density per group block -- and then controls per-agent feature bandwidth on the resulting topology, compressing messages to retain only task-relevant content. We prove that the group-aligned prior strictly tightens the variational bound on topology learning, that the objective decomposes per group block, enabling differential edge control, and that capacity allocation follows a water-filling principle.

Sensor networks increasingly govern modern infrastructure, yet the data they lose are rarely missing in the uniform-random patterns assumed by standard imputation benchmarks. Loop detectors go offline during calibration, roadside cabinets silence clusters of nearby sensors, and newly installed instruments provide no history. Such failures create structured absences whose values are constrained by higher-order relations among groups of sensors, not merely by pairwise proximity. Existing low-rank and graph-based methods often miss this collective structure and can fail when missingness becomes coherent. We introduce Multi-Scale Hypergraph Laplacians (MSHL), a two-stage framework for learning higher-order structure from incomplete spatiotemporal observations. The Discovery stage builds a multi-scale hypergraph from complementary topology and residual-correlation evidence, with an observation-only selector that adapts to the supported interaction scale. The Refinement stage adds a small hypergraph-conditioned residual network that is safe by construction: it learns nonlinear corrections where informative residual features exist and defers to the linear estimate where they do not. We prove that MSHL represents group-conservation patterns inaccessible to pairwise graph priors, adapts to the best fixed scale up to a logarithmic factor, transfers this advantage to held-out imputation error, and admits a one-sided refinement guarantee. On two real traffic networks evaluated across scattered cell missingness, contiguous block outages, and whole-sensor blackouts at five rates, MSHL improves over a pairwise-graph baseline whenever higher-order structure is identifiable and otherwise matches it within sampling noise. The results point to a broader principle for reliable infrastructure learning: missing data should be treated not as isolated entries to fill, but as evidence of structure to discover.

The quality of graph-structured data is fundamental to the success of modern graph analysis techniques such as Graph Neural Networks (GNNs). However, real-world graph data is often suboptimal, suffering from issues such as noise and incomplete connections. Graph Structure Learning (GSL) has emerged as a promising technique that adaptively optimizes node connections. However, we observe that the effectiveness of GSL often comes at the cost of a dramatic expansion in edge count, resulting in significant storage and computational overhead. In this work, we reveal that this limitation stems from the prevalent use of similarity-based edge construction, which predominantly connects highly similar neighbors based on their embeddings, introducing substantial structure redundancy. To address this, we propose a novel Informative Graph Structure Learning method (InGSL), which jointly considers both similarity and diversity in edge construction by incorporating a mutual-information-guided learning strategy. Notably, InGSL serves as a plug-in module that can be seamlessly integrated into existing GSL frameworks. Through extensive experiments on six representative GSL methods, we demonstrate that InGSL achieves significant performance improvements at a reduced number of edges.

RSNet is an open-source R package that provides a resampling-based framework for robust and interpretable network inference, designed to address the limited-sample-size challenges common in high-dimensional data. It supports both the estimation of partial correlation networks modeled as Gaussian networks and conditional Gaussian Bayesian networks for mixed data types that combine continuous and discrete variables. The framework incorporates multiple resampling strategies, including bootstrap, subsampling, and cluster-based approaches, to accommodate both independent and correlated observations. To enhance interpretability, RSNet integrates graphlet-based topology analysis that captures higher-order connectivity and edge sign information, enabling single-node and subnetwork-level insights. Notably, RSNet is the first R package to efficiently construct signed graphlet degree vector matrices (GDVMs) in near-constant time for sparse networks, providing scalable analysis of higher-order network structure. Collectively, RSNet offers a versatile tool for statistically reliable and interpretable network inference in high-dimensional data.

Segmenting small and sparse structures in large-scale images is fundamentally constrained by voxel-level, lattice-bound computation and extreme class imbalance -- dense, full-resolution inference scales poorly and forces most pipelines to rely on fixed regionization or downsampling, coupling computational cost to image resolution and attenuating boundary evidence precisely where minority structures are most informative. We introduce SEMIR (Semantic Minor-Induced Representation Learning), a representation framework that decouples inference from the native grid by learning a task-adapted, topology-preserving latent graph representation with exact decoding. SEMIR transforms the underlying grid graph into a compact, boundary-aligned graph minor through parameterized edge contraction, node deletion, and edge deletion, while preserving an exact lifting map from minor predictions to lattice labels. Minor construction is formalized as a few-shot structure learning problem that replaces hand-tuned preprocessing with a boundary-alignment objective: minor parameters are learned by maximizing agreement between predicted boundary elements and target-specific semantic edges under a boundary Dice criterion, and the induced minor is annotated with scale- and rotation-robust geometric and intensity descriptors and supports efficient region-level inference via message passing on a graph neural network (GNN) with relational edge features. We benchmark SEMIR on three tumor segmentation datasets -- BraTS 2021, KiTS23, and LiTS -- where targets exhibit high structural variability and distributional uncertainty. SEMIR yields consistent improvements in minority-structure Dice at practical runtime. More broadly, SEMIR establishes a framework for learning task-adapted, topology-preserving latent representations with exact decoding for high-resolution structured visual data.

Citation graphs are fundamental tools for modeling scientific structure, but are often fragmented due to missing citations of scientifically connected articles. To address this issue, we propose a computationally efficient hybrid framework integrating citation topology with large language model (LLM)-based text similarity. Using 662,369 Web of Science publications in Mathematics and Operations Research & Management Science, we augment the original graph by adding semantic edges from small, disconnected components and weighting existing citations according to textual similarity. Semantic augmentation substantially reduces fragmentation while preserving disciplinary homogeneity. Compared to embedding-only clustering, cluster detection on augmented graphs using the Leiden algorithm retains structural interpretability while offering multi-scale organization. The method scales efficiently to large datasets and offers a practical strategy for strengthening citation-based indicators without collapsing disciplinary boundaries.

The high-dimensional features extracted from large-scale unlabeled data via various pretrained models with diverse architectures are referred to as heterogeneous multiview data. Most existing unsupervised transfer learning methods fail to faithfully recover intrinsic subspace structures when exploiting complementary information across multiple views. Therefore, a fundamental challenge involves constructing sparse similarity graphs that preserve these underlying subspace structures for achieving semantic alignment across heterogeneous views. In this paper, we propose a sparse attention graph learning (SAGL) method that learns subspace-preserving sparse attention graphs from heterogeneous multiview data. Specifically, we introduce a bilinear attention factorization scheme to capture asymmetric similarities among the high-dimensional features, which breaks the symmetry bottleneck that is inherent in the traditional representation learning techniques. A dynamic sparsity gating mechanism then predicts a feature-specific compression factor for adaptively controlling the topological contributions of neighbors. Furthermore, we employ a structured sparse projection via $α$-entmax to generate subspace-preserving sparse attention graphs for individual views. SAGL leverages these view-specific graphs to conduct sparse information aggregation, yielding discriminative representations for multiview learning tasks. In addition, we provide a rigorous theoretical analysis that bridges differentiable sparse attention and probability simplex constraints. Extensive experiments conducted on multiple benchmark datasets demonstrate that SAGL consistently outperforms the state-of-the-art unsupervised transfer learning approaches.

Vision state space models inherit the efficiency and long-range modeling ability of Mamba-style selective scans. However, their performance depends critically on the representation of two-dimensional visual features as one-dimensional token sequences. Existing scan operators range from predefined geometric traversals to dynamic coordinate-based samplers that reroute tokens through predicted offsets and interpolation. While effective, these mechanisms primarily adapt paths or sampling locations, rather than explicitly modeling which local patches should exchange information before global state-space mixing. This motivates a simple question: \emph{can graphs help vision state space models see better?} We introduce \textbf{GraphScan}, a graph-induced dynamic scanning operator for Vision SSMs. For each token, GraphScan constructs a spatially bounded local graph, learns feature-conditioned affinities with relative positional bias, and produces the output token by one-step message passing over its semantic neighborhood. The resulting tokens are locally grounded before being processed by the selective SSM for global aggregation. GraphScan preserves token count and linear scaling in image size, while replacing coordinate-conditioned interpolation with feature-conditioned semantic routing. Integrated into a hierarchical backbone, \textbf{GraphScan-Mamba} achieves state-of-the-art performance among Vision SSMs across image classification, object detection, instance segmentation, and semantic segmentation, with modest computational overhead. Our analysis further shows that GraphScan induces interpretable displacement fields over the token lattice, providing a semantic and spatially grounded view of dynamic scanning. These results suggest that future Vision SSMs should treat scanning not merely as geometric serialization, but as learned local semantic routing before global state-space modeling.

Neural Flows efficiently model irregular multivariate time series by directly learning ODE solution trajectories with neural networks, bypassing step-by-step numerical solvers. Despite their efficiency, many existing approaches treat variables independently, leaving inter-variable interactions underexplored. Moreover, their one-step mapping makes interaction modeling inherently challenging, as it removes the iterative refinement of interactions during learning. To address this challenge, we propose one-step Graph-Structured Neural Flows (GSNF), which introduce two auxiliary-trajectory self-supervision strategies to strengthen interaction learning: (i) interaction-aware trajectory generation via re-initialization, which induces trajectory divergence to expose graph-induced interactions, with a theoretically derived lower bound on divergence; and (ii) reverse-time trajectory generation, which enforces forward-backward consistency to regularize graph learning, enabled by flow invertibility. Experiments on five real-world datasets show that GSNF achieves state-of-the-art classification performance with highly competitive training time and memory usage.

While Graph Neural Networks (GNNs) have demonstrated significant efficacy in node classification tasks, where predictions rely on local neighborhood information, the performance of GNNs often drops when prediction tasks depend on long-range interactions. These limitations are attributed to phenomena such as oversquashing, where structural bottlenecks restrict signal propagation across the network topology. To address this challenge, we introduce RAwR, a computationally efficient rewiring framework that augments the input graph with a quotient graph derived from equitable partitions. This approach facilitates accelerated communication between nodes that share identical structural roles, as identified by the Weisfeiler-Leman graph coloring, and thereby reduces the total effective resistance of the system. Furthermore, by employing an approximate definition of the equitable partition, RAwR enables a controllable reduction of the quotient graph, which, in its most condensed state, recovers the conventional Master Node rewiring technique. Empirical evaluations across a diverse suite of benchmarks -- including homophilic, heterophilic, and synthetic long-range datasets -- demonstrate that RAwR achieves state-of-the-art results. Our contribution is further supported by an analytical investigation using a teacher-student model of linear GNNs, which elucidates the theoretical foundations of role-based rewiring. This analysis leads to the formulation of Spectral Role Lift (SRL), a metric designed to identify the optimal approximate equitable partition for maximizing predictive performance.

Bilevel graph structure learning is widely understood to improve graph neural networks by jointly optimizing model parameters and a learned graph structure, with the resulting performance gain attributed to the rewired adjacency. We find that this attribution may be overstated: training-dynamics effects in the inner loop, rather than the rewiring itself, capture a substantial share of the gain. To establish this, we introduce frozen-$φ$, a control that freezes the graph while retaining the inner-loop training schedule. This decomposes the bilevel gain into an inner channel of $T$-step training dynamics with implicit gradient regularization and a graph channel of the graph rewiring itself. On spatio-temporal flow forecasting the inner channel matches or exceeds the full bilevel pipeline, accounting for 78-101% of the gain; on node classification it accounts for 37-44% under a Bernoulli edge-level parameterization. We also verify that classical spectral diagnostics can dissociate from task gain. We propose frozen-$φ$ as a standardized diagnostic for bilevel graph structure learning, with graph distillation as a method-agnostic complement. A three-precondition framework further predicts the sign of the bilevel gain on all six benchmarks.

Graph neural networks (GNNs) increasingly rely on sophisticated architectures and training procedures to achieve desirable properties such as high predictive performance, fairness, and robustness. However, these properties typically remain tied to the models that learn them, limiting their transferability to simpler models and downstream settings. We introduce model-to-data (M2D) distillation, a new distillation paradigm that transfers properties learned by a complex GNN teacher into graph data, enabling simpler models to recover them through standard training. M2D distillation explicitly trades model complexity for data complexity by jointly learning augmented node features and graph structure that encode the teacher's behavior. The resulting graph serves as a persistent medium for knowledge transfer and can be used with different downstream models. We show that M2D distillation enables simple GNNs to approximate the behavior of substantially more sophisticated teachers, including fairness-aware GNNs, Graph Attention Networks, and Graph Transformers, while maintaining comparable predictive performance and transferring desirable properties of the teacher.

Public attitudes toward artificial intelligence are heterogeneous, ordinally measured, and poorly captured by any single dependency graph. Existing ordinal structure learners assume a shared directed acyclic graph (DAG) across all respondents; recent heterogeneous ordinal graphical-model approaches focus on subgroup discovery rather than confirmatory cluster-specific DAG estimation; and latent profile analyses discard dependency structure entirely. We introduce a heterogeneous ordinal structure-learning framework combining monotone Gaussian score embedding, Bayesian nonparametric (BNP) complexity discovery via a truncated stick-breaking prior, and confirmatory fixed-K estimation with cluster-specific sparse DAG learning. The key methodological insight is a discovery-to-confirmation workflow: the nonparametric stage calibrates plausible archetype complexity, while inner-validated confirmatory refitting yields stable, interpretable structural estimates. On the 2024 Pew American Trends Panel AI attitudes survey, Wave 152 (W152) survey, (N = 4,788, 8 ordinal items), the confirmatory K*=5 model reduces holdout transformed-score mean squared error (MSE) by 25.8% over a single-graph baseline and by 4.6% over mixture-only clustering. A controlled tiered semi-synthetic benchmark calibrated to W152 structure validates recovery across difficulty regimes and transparently reveals failure modes under stress conditions.

Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the problem of learning the best polytree is NP-hard, we study which restrictions make it more tractable by considering for example in-degree bounds, properties of score functions measuring the quality of a polytree, and approximation algorithms. We devise an algorithm that finds the optimal polytree in time $O((2+ε)^n)$ for arbitrarily small $ε> 0$ and any constant in-degree bound $k$, improving over the fastest previously known algorithm of time complexity $O(3^n)$. We further give polynomial-time algorithms for finding a polytree whose score is within a factor of $k$ from the optimal one for arbitrary scores and a factor of $2$ for additive ones. Many of the results are complemented by (nearly) tight lower bounds for either the time complexity or the approximation factors.

Capturing semantic consistency among nodes is crucial for effective graph representation learning. Existing approaches typically rely on $k$-nearest neighbors ($k$NN) or other node-level full search algorithms (FSA) to mine semantic relationships via exhaustive pairwise similarity computation, which suffer from high computational complexity and rigid neighbor selection, limiting scalability and introducing noisy connections. In this paper, we propose the Semantic Consistency enhanced Graph Neural Network (SCGNN), a novel plug-and-play framework that leverages granular-ball computing (GBC) to efficiently capture semantic consistency in a scalable manner. Unlike node-level FSA methods, SCGNN models group-level semantic structure by adaptively partitioning nodes into granular balls, significantly reducing computational cost while improving robustness to noise. To effectively utilize the discovered group-level semantic consistency, we design a dual enhancement strategy. Specifically, (1) a structure enhancement module constructs an anchor-based graph structure, where each anchor is a virtual node representing the group-level semantic carried by a granular ball, then injecting group-level semantic information into the graph structure; and (2) a supervision enhancement module performs label consistency checking (LCC) by combining GBC predictions with model-generated pseudo-labels, thereby producing more reliable supervision signals. SCGNN is compatible with various GNN backbones. During the forward propagation of SCGNN, the vanilla graph and the augment graph are jointly encoded, and their predictions are fused; during the backpropagation, the supervision enhancement module provides enhanced supervision signals to guide parameter updates.

Electroencephalogram (EEG) signals are vital for automated seizure detection, but their inherent noise makes robust representation learning challenging. Existing graph construction methods, whether correlation-based or learning-based, often generate redundant or irrelevant edges due to the noisy nature of EEG data. This significantly impairs the quality of graph representation and limits downstream task performance. Motivated by the remarkable reasoning and contextual understanding capabilities of large language models (LLMs), we explore the idea of using LLMs as graph edge refiners. Specifically, we propose a two-stage framework: we first verify that LLM-based edge refinement can effectively identify and remove redundant connections, leading to significant improvements in seizure detection accuracy and more meaningful graph structures. Building on this insight, we further develop a robust solution where the initial graph is constructed using a Transformer-based edge predictor and multilayer perceptron, assigning probability scores to potential edges and applying a threshold to determine their existence. The LLM then acts as an edge set refiner, making informed decisions based on both textual and statistical features of node pairs to validate the remaining connections. Extensive experiments on TUSZ dataset demonstrate that our LLM-refined graph learning framework not only enhances task performance but also yields cleaner and more interpretable graph representations.

Heterogeneous graphs with heterophily have emerged as a powerful abstraction for modeling complex real-world systems, where nodes of different types and labels interact in diverse and often non-homophilous ways. Despite recent advances, robust representation learning for such graphs remains largely unexplored, particularly in the presence of noisy or misleading connectivity. In this work, we investigate this problem and identify structural noise as a critical challenge that significantly degrades model performance. To address this issue, we propose a unified framework, Heterogeneous Graph Unified Learning (HGUL), which jointly handles heterophily and noisy graph structures. The framework consists of three complementary modules: a kNN-based graph construction module that recovers reliable local neighborhoods, a graph structure learning module that adaptively refines the adjacency by filtering noisy edges, and a heterogeneous affinity learning module that captures class-level relationships via an extended affinity matrix derived from a polynomial graph kernel. Extensive experiments on multiple datasets demonstrate that HGUL consistently outperforms existing methods on clean graphs and maintains strong robustness under varying levels of structural noise. The results further underscore the importance of jointly modeling heterophily and noise in heterogeneous graph learning.

We aim to learn a sparse and connected graph from sparse data, where the number of observations K can be substantially smaller than the signal dimension N for signals x in R^N, and the underlying distribution is unknown. In this severely ill-posed setting, we incorporate Fiedler number (the second eigenvalue of the graph Laplacian matrix that quantifies connectedness) as a robust regularization term in the sparse graph learning objective. We first develop a greedy algorithm that iteratively selects one edge globally for weakening/removal to reduce the objective, leveraging eigenvalue perturbation theorems that bound the adverse effect of an edge change to the Fiedler number. Next, we design a parallel variant, based on the Cheeger's inequality, that recursively partitions an input graph into two sub-graphs using an approximate Cheeger cut to distributedly find an optimal edge. Simulation experiments show that Fiedler number maximization robustifies sparse graph estimates, outperforming previous sparse graph learning algorithms.

Graph neural ordinary differential equations (Graph ODEs) extend graph learning from discrete message-passing layers to continuous-time representation flows. While it supports adaptive long-range propagation, we show that Graph ODEs with strictly positive irreducible mixing operators face an inherent \emph{monostability trap}: in the long-time regime, information leakage is unavoidable and the dynamics converge to a single global consensus attractor. We propose the \textbf{Hysteresis Graph ODE (HGODE)}, which couples feature evolution with a latent topological potential driven by a learned pairwise force. A double-well edge potential and bipolarized gate allow edge states to polarize into connected or insulated phases while preserving differentiability. We provide asymptotic analysis of the collapse mechanism and the proposed hysteretic topology dynamics, and validate HGODE on theory-driven synthetic diagnostics and real-world graph benchmarks.

Lattice Hamiltonian systems underpin models across condensed matter, nonlinear optics, and biophysics, yet learning their dynamics from data is obstructed by two unknowns: the interaction topology and whether node dynamics are homogeneous. Existing graph-based approaches either assume the graph is given or, as in $α$-separable graph Hamiltonian network, infer it only for separable Hamiltonians with homogeneous node dynamics. We introduce the Hamiltonian Graph Inference Network (HGIN), which jointly recovers the interaction graph and predicts long-time trajectories from state data alone, for both separable and non-separable Hamiltonians and under heterogeneous node dynamics. HGIN couples a structure-learning module -- a learnable weighted adjacency matrix trained under a Hamilton's-equations loss -- with a trajectory-prediction module that partitions edges into physically distinct subgraphs via $k$-means clustering, assigning each subgraph its own encoder and thereby breaking the parameter-sharing bottleneck of conventional GNNs. On three benchmarks -- a Klein--Gordon lattice with long-range interactions and two discrete nonlinear Schrödinger lattices (homogeneous and heterogeneous) -- HGIN reduces long-time energy prediction error and trajectory prediction error by six to thirteen orders of magnitude relative to baselines. A symmetry argument on the Hamiltonian loss further shows that the learned weights encode the parity of the underlying pair potential, yielding an interpretable readout of the system's interaction structure.

Graph Neural Networks (GNNs) have demonstrated impressive performance in learning representations from graph-structured data. However, their message-passing mechanism inherently relies on the assumption of label consistency among connected nodes, limiting their applicability to low-homophily settings. Moreover, since message passing operates as a hierarchical diffusion process, GNNs face challenges in capturing long-range dependencies. As network depth increases, the structural noise along heterophilic edges tends to be amplified, resulting in over-smoothing. This issue becomes especially prominent in highly heterophilic graphs, where the propagation of inconsistent semantics across the topology continually exacerbates misaggregation. To address this issue, we propose a novel framework named Layer Embedding Deep Fusion Graph Neural Network (LEDF-GNN). Specifically, we design a Layer Embedding Deep Fusion (LEDF) operator that nonlinearly fuses multi-layer embeddings to capture inter-layer dependencies and effectively alleviate deep propagation degradation. Meanwhile, to mitigate structural heterophily, LEDF-GNN employs a Dual-Topology Parallel Strategy (DTPS) that simultaneously leverages the original and reconstructed topologies, allowing for adaptive structure-semantics co-optimization under diverse homophily conditions. Extensive semi-supervised classification experiments on the citation and image benchmarks demonstrate that, under both homophilic and heterophilic settings, LEDF-GNN consistently outperforms state-of-the-art baselines, validating its effectiveness and generalization capability across diverse graph types.

We study the problem of learning an unknown graph via group queries on node subsets, where each query reports whether at least one edge is present among the queried nodes. In general, learning arbitrary graphs with $n$ nodes and $k$ edges is hard in the non-adaptive setting, requiring $Ω\big(\min\{k^2\log n,\,n^2\}\big)$ tests even when a small error probability is allowed. We focus on learning Erdős--Rényi (ER) graphs $G\sim\mathrm{ER}(n,q)$ in the non-adaptive setting, where the expected number of edges is $\bar{k}=q\binom{n}{2}$, and we aim to design an efficient testing--decoding scheme, namely, a non-adaptive test design together with a decoding algorithm, achieving asymptotically vanishing error probability. Prior work (Li--Fresacher--Scarlett, NeurIPS 2019) presents a testing--decoding scheme that attains an order-optimal number of tests $O(\bar{k}\log n)$ but incurs $Ω(n^2)$ decoding time, whereas their proposed sublinear-time algorithm incurs an extra $(\log \bar{k})(\log n)$ factor in the number of tests. We extend the binary splitting approach, recently developed for non-adaptive group testing, to the ER graph learning setting, and prove that the edge set can be recovered with high probability using $O(\bar{k}\log n)$ tests while attaining decoding time $O(\bar{k}^{1+δ}\log n)$ for any fixed $δ>0$.

We study the design of interventions for causal discovery in simple structural causal models whose causal graphs are directed mixed graphs (DMGs) that may contain directed cycles and bidirected edges representing latent confounding. In such case, observational conditional-independence (CI) information may not identify even the graph skeleton, while CI alone cannot generally detect a bidirected edge coexisting with a directed edge. To this end, we propose a stage-wise framework based on tailored separating systems. Separating-system interventions first recover descendant relations and strongly connected components (SCCs). The SCCs are then ordered by ancestry, and an SCC-Anc separating system recovers the directed subgraph. Given this subgraph, further systems use CI tests interpreted through $d$- or $σ$-separation to recover non-adjacent bidirected edges, whose endpoints share no directed edge, and do-see comparisons to recover those coexisting with exactly one directed edge. Under our assumptions, the framework recovers the directed subgraph and every bidirected edge except double-adjacent ones, whose endpoints are connected by a directed edge in each direction. We develop algorithms for unrestricted and $M$-bounded settings, with each experiment targeting at most $M$ variables in the latter. For recovering the directed subgraph and non-adjacent bidirected edges, our upper bounds on the number and maximum size of experiments match corresponding worst-case lower bounds up to logarithmic factors.