Daily Papers

Managing the response to natural disasters effectively can considerably mitigate their devastating impact. This work explores the potential of using supervised hybrid quantum machine learning to optimize emergency evacuation plans for cars during natural disasters. The study focuses on earthquake emergencies and models the problem as a dynamic computational graph where an earthquake damages an area of a city. The residents seek to evacuate the city by reaching the exit points where traffic congestion occurs. The situation is modeled as a shortest-path problem on an uncertain and dynamically evolving map. We propose a novel hybrid supervised learning approach and test it on hypothetical situations on a concrete city graph. This approach uses a novel quantum feature-wise linear modulation (FiLM) neural network parallel to a classical FiLM network to imitate Dijkstra's node-wise shortest path algorithm on a deterministic dynamic graph. Adding the quantum neural network in parallel increases the overall model's expressivity by splitting the dataset's harmonic and non-harmonic features between the quantum and classical components. The hybrid supervised learning agent is trained on a dataset of Dijkstra's shortest paths and can successfully learn the navigation task. The hybrid quantum network improves over the purely classical supervised learning approach by 7% in accuracy. We show that the quantum part has a significant contribution of 45.(3)% to the prediction and that the network could be executed on an ion-based quantum computer. The results demonstrate the potential of supervised hybrid quantum machine learning in improving emergency evacuation planning during natural disasters.

DL compiler's primary function is to translate DNN programs written in high-level DL frameworks such as PyTorch and TensorFlow into portable executables. These executables can then be flexibly executed by the deployed host programs. However, existing DL compilers rely on a tracing mechanism, which involves feeding a runtime input to a neural network program and tracing the program execution paths to generate the computational graph necessary for compilation. Unfortunately, this mechanism falls short when dealing with modern dynamic neural networks (DyNNs) that possess varying computational graphs depending on the inputs. Consequently, conventional DL compilers struggle to accurately compile DyNNs into executable code. To address this limitation, we propose \tool, a general approach that enables any existing DL compiler to successfully compile DyNNs. \tool tackles the dynamic nature of DyNNs by introducing a compilation mechanism that redistributes the control and data flow of the original DNN programs during the compilation process. Specifically, \tool develops program analysis and program transformation techniques to convert a dynamic neural network into multiple sub-neural networks. Each sub-neural network is devoid of conditional statements and is compiled independently. Furthermore, \tool synthesizes a host module that models the control flow of the DyNNs and facilitates the invocation of the sub-neural networks. Our evaluation demonstrates the effectiveness of \tool, achieving a 100\% success rate in compiling all dynamic neural networks. Moreover, the compiled executables generated by \tool exhibit significantly improved performance, running between 1.12times and 20.21times faster than the original DyNNs executed on general-purpose DL frameworks.

Dynamic shape computations have become critical in modern machine learning workloads, especially in emerging large language models. The success of these models has driven demand for deploying them to a diverse set of backend environments. In this paper, we present Relax, a compiler abstraction for optimizing end-to-end dynamic machine learning workloads. Relax introduces first-class symbolic shape annotations to track dynamic shape computations globally across the program. It also introduces a cross-level abstraction that encapsulates computational graphs, loop-level tensor programs, and library calls in a single representation to enable cross-level optimizations. We build an end-to-end compilation framework using the proposed approach to optimize dynamic shape models. Experimental results on large language models show that Relax delivers performance competitive with state-of-the-art hand-optimized systems across platforms and enables deployment of emerging dynamic models to a broader set of environments, including mobile phones, embedded devices, and web browsers.

This work presents dyGRASS, an efficient dynamic algorithm for spectral sparsification of large undirected graphs that undergo streaming edge insertions and deletions. At its core, dyGRASS employs a random-walk-based method to efficiently estimate node-to-node distances in both the original graph (for decremental update) and its sparsifier (for incremental update). For incremental updates, dyGRASS enables the identification of spectrally critical edges among the updates to capture the latest structural changes. For decremental updates, dyGRASS facilitates the recovery of important edges from the original graph back into the sparsifier. To further enhance computational efficiency, dyGRASS employs a GPU-based non-backtracking random walk scheme that allows multiple walkers to operate simultaneously across various target updates. This parallelization significantly improves both the performance and scalability of the proposed dyGRASS framework. Our comprehensive experimental evaluations reveal that dyGRASS achieves approximately a 10x speedup compared to the state-of-the-art incremental sparsification (inGRASS) algorithm while eliminating the setup overhead and improving solution quality in incremental spectral sparsification tasks. Moreover, dyGRASS delivers high efficiency and superior solution quality for fully dynamic graph sparsification, accommodating both edge insertions and deletions across a diverse range of graph instances originating from integrated circuit simulations, finite element analysis, and social networks.

Learning editable high-resolution scene representations for dynamic scenes is an open problem with applications across the domains from autonomous driving to creative editing - the most successful approaches today make a trade-off between editability and supporting scene complexity: neural atlases represent dynamic scenes as two deforming image layers, foreground and background, which are editable in 2D, but break down when multiple objects occlude and interact. In contrast, scene graph models make use of annotated data such as masks and bounding boxes from autonomous-driving datasets to capture complex 3D spatial relationships, but their implicit volumetric node representations are challenging to edit view-consistently. We propose Neural Atlas Graphs (NAGs), a hybrid high-resolution scene representation, where every graph node is a view-dependent neural atlas, facilitating both 2D appearance editing and 3D ordering and positioning of scene elements. Fit at test-time, NAGs achieve state-of-the-art quantitative results on the Waymo Open Dataset - by 5 dB PSNR increase compared to existing methods - and make environmental editing possible in high resolution and visual quality - creating counterfactual driving scenarios with new backgrounds and edited vehicle appearance. We find that the method also generalizes beyond driving scenes and compares favorably - by more than 7 dB in PSNR - to recent matting and video editing baselines on the DAVIS video dataset with a diverse set of human and animal-centric scenes. Project Page: https://princeton-computational-imaging.github.io/nag/

Advancement in finite element methods have become essential in various disciplines, and in particular for Computational Fluid Dynamics (CFD), driving research efforts for improved precision and efficiency. While Convolutional Neural Networks (CNNs) have found success in CFD by mapping meshes into images, recent attention has turned to leveraging Graph Neural Networks (GNNs) for direct mesh processing. This paper introduces a novel model merging Self-Attention with Message Passing in GNNs, achieving a 15\% reduction in RMSE on the well known flow past a cylinder benchmark. Furthermore, a dynamic mesh pruning technique based on Self-Attention is proposed, that leads to a robust GNN-based multigrid approach, also reducing RMSE by 15\%. Additionally, a new self-supervised training method based on BERT is presented, resulting in a 25\% RMSE reduction. The paper includes an ablation study and outperforms state-of-the-art models on several challenging datasets, promising advancements similar to those recently achieved in natural language and image processing. Finally, the paper introduces a dataset with meshes larger than existing ones by at least an order of magnitude. Code and Datasets will be released at https://github.com/DonsetPG/multigrid-gnn.

Temporal Graph Neural Networks have garnered substantial attention for their capacity to model evolving structural and temporal patterns while exhibiting impressive performance. However, it is known that these architectures are encumbered by issues that constrain their performance, such as over-squashing and over-smoothing. Meanwhile, Transformers have demonstrated exceptional computational capacity to effectively address challenges related to long-range dependencies. Consequently, we introduce Todyformer-a novel Transformer-based neural network tailored for dynamic graphs. It unifies the local encoding capacity of Message-Passing Neural Networks (MPNNs) with the global encoding of Transformers through i) a novel patchifying paradigm for dynamic graphs to improve over-squashing, ii) a structure-aware parametric tokenization strategy leveraging MPNNs, iii) a Transformer with temporal positional-encoding to capture long-range dependencies, and iv) an encoding architecture that alternates between local and global contextualization, mitigating over-smoothing in MPNNs. Experimental evaluations on public benchmark datasets demonstrate that Todyformer consistently outperforms the state-of-the-art methods for downstream tasks. Furthermore, we illustrate the underlying aspects of the proposed model in effectively capturing extensive temporal dependencies in dynamic graphs.

While complex simulations of physical systems have been widely used in engineering and scientific computing, lowering their often prohibitive computational requirements has only recently been tackled by deep learning approaches. In this paper, we present GraphSplineNets, a novel deep-learning method to speed up the forecasting of physical systems by reducing the grid size and number of iteration steps of deep surrogate models. Our method uses two differentiable orthogonal spline collocation methods to efficiently predict response at any location in time and space. Additionally, we introduce an adaptive collocation strategy in space to prioritize sampling from the most important regions. GraphSplineNets improve the accuracy-speedup tradeoff in forecasting various dynamical systems with increasing complexity, including the heat equation, damped wave propagation, Navier-Stokes equations, and real-world ocean currents in both regular and irregular domains.

Long-document QA presents challenges with large-scale text and long-distance dependencies. Recent advances in Large Language Models (LLMs) enable entire documents to be processed in a single pass. However, their computational cost is significantly high. Retrieval-Augmented Generation (RAG) methods split text into smaller chunks, but they often yield inferior results and may lose global context. Recent approaches that integrate LLMs into RAG via iterative summarization either underutilize LLM capabilities or still incur high computational costs. In this paper, we combine the high accuracy of LLMs with the efficiency of RAG and propose LLM-Guided Dynamic Progress Control with Attention-Based Hierarchical Weighted Graph (PECAN). Our method introduces two key improvements: (1) LLM-Guided Dynamic Progress Control: We leverage LLMs to dynamically control the retrieval process, adjusting the amount of retrieved information based on different queries to achieve a better balance of effectiveness and efficiency. (2) Attention-Guided Retrieval: We propose a novel retrieval method that constructs a hierarchical graph where edges are derived by LLM attention weights. Experimental results demonstrate that PECAN achieves LLM-level performance while maintaining computational complexity comparable to that of RAG methods on two single-document and two multi-document QA datasets.

Anomaly detection aims to identify deviations from normal patterns within data. This task is particularly crucial in dynamic graphs, which are common in applications like social networks and cybersecurity, due to their evolving structures and complex relationships. Although recent deep learning-based methods have shown promising results in anomaly detection on dynamic graphs, they often lack of generalizability. In this study, we propose GeneralDyG, a method that samples temporal ego-graphs and sequentially extracts structural and temporal features to address the three key challenges in achieving generalizability: Data Diversity, Dynamic Feature Capture, and Computational Cost. Extensive experimental results demonstrate that our proposed GeneralDyG significantly outperforms state-of-the-art methods on four real-world datasets.

Deep graph clustering has recently received significant attention due to its ability to enhance the representation learning capabilities of models in unsupervised scenarios. Nevertheless, deep clustering for temporal graphs, which could capture crucial dynamic interaction information, has not been fully explored. It means that in many clustering-oriented real-world scenarios, temporal graphs can only be processed as static graphs. This not only causes the loss of dynamic information but also triggers huge computational consumption. To solve the problem, we propose a general framework for deep Temporal Graph Clustering called TGC, which introduces deep clustering techniques to suit the interaction sequence-based batch-processing pattern of temporal graphs. In addition, we discuss differences between temporal graph clustering and static graph clustering from several levels. To verify the superiority of the proposed framework TGC, we conduct extensive experiments. The experimental results show that temporal graph clustering enables more flexibility in finding a balance between time and space requirements, and our framework can effectively improve the performance of existing temporal graph learning methods. The code is released: https://github.com/MGitHubL/Deep-Temporal-Graph-Clustering.

Accurate and efficient physical simulations are essential in science and engineering, yet traditional numerical solvers face significant challenges in computational cost when handling simulations across dynamic scenarios involving complex geometries, varying boundary/initial conditions, and diverse physical parameters. While deep learning offers promising alternatives, existing methods often struggle with flexibility and generalization, particularly on unstructured meshes, which significantly limits their practical applicability. To address these challenges, we propose PhysGTO, an efficient Graph-Transformer Operator for learning physical dynamics through explicit manifold embeddings in both physical and latent spaces. In the physical space, the proposed Unified Graph Embedding module aligns node-level conditions and constructs sparse yet structure-preserving graph connectivity to process heterogeneous inputs. In the latent space, PhysGTO integrates a lightweight flux-oriented message-passing scheme with projection-inspired attention to capture local and global dependencies, facilitating multilevel interactions among complex physical correlations. This design ensures linear complexity relative to the number of mesh points, reducing both the number of trainable parameters and computational costs in terms of floating-point operations (FLOPs), and thereby allowing efficient inference in real-time applications. We introduce a comprehensive benchmark spanning eleven datasets, covering problems with unstructured meshes, transient flow dynamics, and large-scale 3D geometries. PhysGTO consistently achieves state-of-the-art accuracy while significantly reducing computational costs, demonstrating superior flexibility, scalability, and generalization in a wide range of simulation tasks.

Recent years have witnessed significant progress in the field of neural surface reconstruction. While the extensive focus was put on volumetric and implicit approaches, a number of works have shown that explicit graphics primitives such as point clouds can significantly reduce computational complexity, without sacrificing the reconstructed surface quality. However, less emphasis has been put on modeling dynamic surfaces with point primitives. In this work, we present a dynamic point field model that combines the representational benefits of explicit point-based graphics with implicit deformation networks to allow efficient modeling of non-rigid 3D surfaces. Using explicit surface primitives also allows us to easily incorporate well-established constraints such as-isometric-as-possible regularisation. While learning this deformation model is prone to local optima when trained in a fully unsupervised manner, we propose to additionally leverage semantic information such as keypoint dynamics to guide the deformation learning. We demonstrate our model with an example application of creating an expressive animatable human avatar from a collection of 3D scans. Here, previous methods mostly rely on variants of the linear blend skinning paradigm, which fundamentally limits the expressivity of such models when dealing with complex cloth appearances such as long skirts. We show the advantages of our dynamic point field framework in terms of its representational power, learning efficiency, and robustness to out-of-distribution novel poses.

The takeaway recommendation system aims to recommend users' future takeaway purchases based on their historical purchase behaviors, thereby improving user satisfaction and boosting merchant sales. Existing methods focus on incorporating auxiliary information or leveraging knowledge graphs to alleviate the sparsity issue of user purchase sequences. However, two main challenges limit the performance of these approaches: (1) capturing dynamic user preferences on complex geospatial information and (2) efficiently integrating spatial-temporal knowledge from both graphs and sequence data with low computational costs. In this paper, we propose a novel spatial-temporal knowledge distillation model for takeaway recommendation (STKDRec) based on the two-stage training process. Specifically, during the first pre-training stage, a spatial-temporal knowledge graph (STKG) encoder is trained to extract high-order spatial-temporal dependencies and collaborative associations from the STKG. During the second spatial-temporal knowledge distillation (STKD) stage, a spatial-temporal Transformer (ST-Transformer) is employed to comprehensively model dynamic user preferences on various types of fine-grained geospatial information from a sequential perspective. Furthermore, the STKD strategy is introduced to transfer graph-based spatial-temporal knowledge to the ST-Transformer, facilitating the adaptive fusion of rich knowledge derived from both the STKG and sequence data while reducing computational overhead. Extensive experiments on three real-world datasets show that STKDRec significantly outperforms the state-of-the-art baselines.

We propose DyGFormer, a new Transformer-based architecture for dynamic graph learning. DyGFormer is conceptually simple and only needs to learn from nodes' historical first-hop interactions by: (1) a neighbor co-occurrence encoding scheme that explores the correlations of the source node and destination node based on their historical sequences; (2) a patching technique that divides each sequence into multiple patches and feeds them to Transformer, allowing the model to effectively and efficiently benefit from longer histories. We also introduce DyGLib, a unified library with standard training pipelines, extensible coding interfaces, and comprehensive evaluating protocols to promote reproducible, scalable, and credible dynamic graph learning research. By performing exhaustive experiments on thirteen datasets for dynamic link prediction and dynamic node classification tasks, we find that DyGFormer achieves state-of-the-art performance on most of the datasets, demonstrating its effectiveness in capturing nodes' correlations and long-term temporal dependencies. Moreover, some results of baselines are inconsistent with previous reports, which may be caused by their diverse but less rigorous implementations, showing the importance of DyGLib. All the used resources are publicly available at https://github.com/yule-BUAA/DyGLib.

Networks have become indispensable and ubiquitous structures in many fields to model the interactions among different entities, such as friendship in social networks or protein interactions in biological graphs. A major challenge is to understand the structure and dynamics of these systems. Although networks evolve through time, most existing graph representation learning methods target only static networks. Whereas approaches have been developed for the modeling of dynamic networks, there is a lack of efficient continuous time dynamic graph representation learning methods that can provide accurate network characterization and visualization in low dimensions while explicitly accounting for prominent network characteristics such as homophily and transitivity. In this paper, we propose the Piecewise-Velocity Model (PiVeM) for the representation of continuous-time dynamic networks. It learns dynamic embeddings in which the temporal evolution of nodes is approximated by piecewise linear interpolations based on a latent distance model with piecewise constant node-specific velocities. The model allows for analytically tractable expressions of the associated Poisson process likelihood with scalable inference invariant to the number of events. We further impose a scalable Kronecker structured Gaussian Process prior to the dynamics accounting for community structure, temporal smoothness, and disentangled (uncorrelated) latent embedding dimensions optimally learned to characterize the network dynamics. We show that PiVeM can successfully represent network structure and dynamics in ultra-low two-dimensional spaces. It outperforms relevant state-of-art methods in downstream tasks such as link prediction. In summary, PiVeM enables easily interpretable dynamic network visualizations and characterizations that can further improve our understanding of the intrinsic dynamics of time-evolving networks.

We introduce a novel masked pre-training technique for graph neural networks (GNNs) applied to computational fluid dynamics (CFD) problems. By randomly masking up to 40\% of input mesh nodes during pre-training, we force the model to learn robust representations of complex fluid dynamics. We pair this masking strategy with an asymmetric encoder-decoder architecture and gated multi-layer perceptrons to further enhance performance. The proposed method achieves state-of-the-art results on seven CFD datasets, including a new challenging dataset of 3D intracranial aneurysm simulations with over 250,000 nodes per mesh. Moreover, it significantly improves model performance and training efficiency across such diverse range of fluid simulation tasks. We demonstrate improvements of up to 60\% in long-term prediction accuracy compared to previous best models, while maintaining similar computational costs. Notably, our approach enables effective pre-training on multiple datasets simultaneously, significantly reducing the time and data required to achieve high performance on new tasks. Through extensive ablation studies, we provide insights into the optimal masking ratio, architectural choices, and training strategies.

Modeling dynamic graphs, such as those found in social networks, recommendation systems, and e-commerce platforms, is crucial for capturing evolving relationships and delivering relevant insights over time. Traditional approaches primarily rely on graph neural networks with temporal components or sequence generation models, which often focus narrowly on the historical context of target nodes. This limitation restricts the ability to adapt to new and emerging patterns in dynamic graphs. To address this challenge, we propose a novel framework, Retrieval-Augmented Generation for Dynamic Graph modeling (RAG4DyG), which enhances dynamic graph predictions by incorporating contextually and temporally relevant examples from broader graph structures. Our approach includes a time- and context-aware contrastive learning module to identify high-quality demonstrations and a graph fusion strategy to effectively integrate these examples with historical contexts. The proposed framework is designed to be effective in both transductive and inductive scenarios, ensuring adaptability to previously unseen nodes and evolving graph structures. Extensive experiments across multiple real-world datasets demonstrate the effectiveness of RAG4DyG in improving predictive accuracy and adaptability for dynamic graph modeling. The code and datasets are publicly available at https://github.com/YuxiaWu/RAG4DyG.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

Dynamic graph clustering aims to detect and track time-varying clusters in dynamic graphs, revealing the evolutionary mechanisms of complex real-world dynamic systems. Matrix factorization-based methods are promising approaches for this task; however, these methods often struggle with scalability and can be time-consuming when applied to large-scale dynamic graphs. Moreover, they tend to lack robustness and are vulnerable to real-world noisy data. To address these issues, we make three key contributions. First, to improve scalability, we propose temporal separated matrix factorization, where a single matrix is divided into multiple smaller matrices for independent factorization, resulting in faster computation. Second, to improve robustness, we introduce bi-clustering regularization, which jointly optimizes graph embedding and clustering, thereby filtering out noisy features from the graph embeddings. Third, to further enhance effectiveness and efficiency, we propose selective embedding updating, where we update only the embeddings of dynamic nodes while the embeddings of static nodes are fixed among different timestamps. Experimental results on six synthetic and five real-world benchmarks demonstrate the scalability, robustness and effectiveness of our proposed method. Source code is available at https://github.com/Clearloveyuan/DyG-MF.

Embodied AI agents that search for objects in large environments such as households often need to make efficient decisions by predicting object locations based on partial information. We pose this as a new type of link prediction problem: link prediction on partially observable dynamic graphs. Our graph is a representation of a scene in which rooms and objects are nodes, and their relationships are encoded in the edges; only parts of the changing graph are known to the agent at each timestep. This partial observability poses a challenge to existing link prediction approaches, which we address. We propose a novel state representation -- Scene Graph Memory (SGM) -- with captures the agent's accumulated set of observations, as well as a neural net architecture called a Node Edge Predictor (NEP) that extracts information from the SGM to search efficiently. We evaluate our method in the Dynamic House Simulator, a new benchmark that creates diverse dynamic graphs following the semantic patterns typically seen at homes, and show that NEP can be trained to predict the locations of objects in a variety of environments with diverse object movement dynamics, outperforming baselines both in terms of new scene adaptability and overall accuracy. The codebase and more can be found at https://www.scenegraphmemory.com.

We present a unified representation for actionable spatial perception: 3D Dynamic Scene Graphs. Scene graphs are directed graphs where nodes represent entities in the scene (e.g. objects, walls, rooms), and edges represent relations (e.g. inclusion, adjacency) among nodes. Dynamic scene graphs (DSGs) extend this notion to represent dynamic scenes with moving agents (e.g. humans, robots), and to include actionable information that supports planning and decision-making (e.g. spatio-temporal relations, topology at different levels of abstraction). Our second contribution is to provide the first fully automatic Spatial PerceptIon eNgine(SPIN) to build a DSG from visual-inertial data. We integrate state-of-the-art techniques for object and human detection and pose estimation, and we describe how to robustly infer object, robot, and human nodes in crowded scenes. To the best of our knowledge, this is the first paper that reconciles visual-inertial SLAM and dense human mesh tracking. Moreover, we provide algorithms to obtain hierarchical representations of indoor environments (e.g. places, structures, rooms) and their relations. Our third contribution is to demonstrate the proposed spatial perception engine in a photo-realistic Unity-based simulator, where we assess its robustness and expressiveness. Finally, we discuss the implications of our proposal on modern robotics applications. 3D Dynamic Scene Graphs can have a profound impact on planning and decision-making, human-robot interaction, long-term autonomy, and scene prediction. A video abstract is available at https://youtu.be/SWbofjhyPzI

Unsupervised representation learning for dynamic graphs has attracted a lot of research attention in recent years. Compared with static graph, the dynamic graph is a comprehensive embodiment of both the intrinsic stable characteristics of nodes and the time-related dynamic preference. However, existing methods generally mix these two types of information into a single representation space, which may lead to poor explanation, less robustness, and a limited ability when applied to different downstream tasks. To solve the above problems, in this paper, we propose a novel disenTangled representation learning framework for discrete-time Dynamic graphs, namely DyTed. We specially design a temporal-clips contrastive learning task together with a structure contrastive learning to effectively identify the time-invariant and time-varying representations respectively. To further enhance the disentanglement of these two types of representation, we propose a disentanglement-aware discriminator under an adversarial learning framework from the perspective of information theory. Extensive experiments on Tencent and five commonly used public datasets demonstrate that DyTed, as a general framework that can be applied to existing methods, achieves state-of-the-art performance on various downstream tasks, as well as be more robust against noise.

We present the Evolving Graph Fourier Transform (EFT), the first invertible spectral transform that captures evolving representations on temporal graphs. We motivate our work by the inadequacy of existing methods for capturing the evolving graph spectra, which are also computationally expensive due to the temporal aspect along with the graph vertex domain. We view the problem as an optimization over the Laplacian of the continuous time dynamic graph. Additionally, we propose pseudo-spectrum relaxations that decompose the transformation process, making it highly computationally efficient. The EFT method adeptly captures the evolving graph's structural and positional properties, making it effective for downstream tasks on evolving graphs. Hence, as a reference implementation, we develop a simple neural model induced with EFT for capturing evolving graph spectra. We empirically validate our theoretical findings on a number of large-scale and standard temporal graph benchmarks and demonstrate that our model achieves state-of-the-art performance.

Key graph-based problems play a central role in understanding network topology and uncovering patterns of similarity in homogeneous and temporal data. Such patterns can be revealed by analyzing communities formed by nodes, which in turn can be effectively modeled through temporal k-cores. This paper introduces a novel decentralized and incremental algorithm for computing the core decomposition of temporal networks. Decentralized solutions leverage the ability of network nodes to communicate and coordinate locally, addressing complex problems in a scalable, adaptive, and timely manner. By leveraging previously computed coreness values, our approach significantly reduces the activation of nodes and the volume of message exchanges when the network changes over time. This enables scalability with only a minimal trade-off in precision. Experimental evaluations on large real-world networks under varying levels of dynamism demonstrate the efficiency of our solution compared to a state-of-the-art approach, particularly in terms of active nodes, communication overhead, and convergence speed.

We present an approach to modifying Transformer architectures by integrating graph-aware relational reasoning into the attention mechanism, merging concepts from graph neural networks and language modeling. Building on the inherent connection between attention and graph theory, we reformulate the Transformer's attention mechanism as a graph operation and propose Graph-Aware Isomorphic Attention. This method leverages advanced graph modeling strategies, including Graph Isomorphism Networks (GIN) and Principal Neighborhood Aggregation (PNA), to enrich the representation of relational structures. Our approach captures complex dependencies and generalizes across tasks, as evidenced by a reduced generalization gap and improved learning performance. Additionally, we expand the concept of graph-aware attention to introduce Sparse GIN-Attention, a fine-tuning approach that employs sparse GINs. By interpreting attention matrices as sparse adjacency graphs, this technique enhances the adaptability of pre-trained foundational models with minimal computational overhead, endowing them with graph-aware capabilities. Sparse GIN-Attention fine-tuning achieves improved training dynamics and better generalization compared to alternative methods like low-rank adaption (LoRA). We discuss latent graph-like structures within traditional attention mechanisms, offering a new lens through which Transformers can be understood. By evolving Transformers as hierarchical GIN models for relational reasoning. This perspective suggests profound implications for foundational model development, enabling the design of architectures that dynamically adapt to both local and global dependencies. Applications in bioinformatics, materials science, language modeling, and beyond could benefit from this synthesis of relational and sequential data modeling, setting the stage for interpretable and generalizable modeling strategies.

Learning to simulate complex physical systems from data has emerged as a promising way to overcome the limitations of traditional numerical solvers, which often require prohibitive computational costs for high-fidelity solutions. Recent Graph Neural Simulators (GNSs) accelerate simulations by learning dynamics on graph-structured data, yet often struggle to capture long-range interactions and suffer from error accumulation under autoregressive rollouts. To address these challenges, we propose Information-preserving Graph Neural Simulators (IGNS), a graph-based neural simulator built on the principles of Hamiltonian dynamics. This structure guarantees preservation of information across the graph, while extending to port-Hamiltonian systems allows the model to capture a broader class of dynamics, including non-conservative effects. IGNS further incorporates a warmup phase to initialize global context, geometric encoding to handle irregular meshes, and a multi-step training objective that facilitates PDE matching, where the trajectory produced by integrating the port-Hamiltonian core aligns with the ground-truth trajectory, thereby reducing rollout error. To evaluate these properties systematically, we introduce new benchmarks that target long-range dependencies and challenging external forcing scenarios. Across all tasks, IGNS consistently outperforms state-of-the-art GNSs, achieving higher accuracy and stability under challenging and complex dynamical systems. Our project page: https://thobotics.github.io/neural_pde_matching.

Many-shot in-context learning has recently shown promise as an alternative to finetuning, with the major advantage that the same model can be served for multiple tasks. However, this shifts the computational burden from training-time to inference-time, making deployment of many-shot ICL challenging to justify in-practice. This cost is further increased if a custom demonstration set is retrieved for each inference example. We present Dynamic Block-Sparse Attention, a training-free framework for retrieval-based many-shot in-context learning. By combining carefully designed block-sparse attention and retrieval of cached groups of demonstrations, we achieve comparable per-example latency to finetuning while maintaining on average >95% of the best method's accuracy across strong ICL and finetuning baselines. We hope that this will further enable the deployment of many-shot ICL at scale.

Current paradigms for code verification rely heavily on external mechanisms-such as execution-based unit tests or auxiliary LLM judges-which are often labor-intensive or limited by the judging model's own capabilities. This raises a fundamental, yet unexplored question: Can an LLM's functional correctness be assessed purely from its internal computational structure? Our primary objective is to investigate whether the model's neural dynamics encode internally decodable signals that are predictive of logical validity during code generation. Inspired by mechanistic interpretability, we propose to treat code verification as a mechanistic diagnostic task, mapping the model's explicit algorithmic trajectory into line-level attribution graphs. By decomposing complex residual flows, we aim to identify the structural signatures that distinguish sound reasoning from logical failure within the model's internal circuits. Analysis across Python, C++, and Java confirms that intrinsic correctness signals are robust across diverse syntaxes. Topological features from these internal graphs predict correctness more reliably than surface heuristics and enable targeted causal interventions to fix erroneous logic. These findings establish internal introspection as a decodable property for verifying generated code. Our code is at https:// github.com/bruno686/CodeCircuit.

This work studies a central extremal graph theory problem inspired by a 1975 conjecture of Erdos, which aims to find graphs with a given size (number of nodes) that maximize the number of edges without having 3- or 4-cycles. We formulate this problem as a sequential decision-making problem and compare AlphaZero, a neural network-guided tree search, with tabu search, a heuristic local search method. Using either method, by introducing a curriculum -- jump-starting the search for larger graphs using good graphs found at smaller sizes -- we improve the state-of-the-art lower bounds for several sizes. We also propose a flexible graph-generation environment and a permutation-invariant network architecture for learning to search in the space of graphs.

Developing models capable of complex, multi-step reasoning is a central goal in artificial intelligence. While representing problems as graphs is a powerful approach, Graph Neural Networks (GNNs) are fundamentally constrained by their message-passing mechanism, which imposes a local bottleneck that limits global, holistic reasoning. We argue that dynamic programming (DP), which solves problems by iteratively refining a global state, offers a more powerful and suitable learning paradigm. We introduce FloydNet, a new architecture that embodies this principle. In contrast to local message passing, FloydNet maintains a global, all-pairs relationship tensor and learns a generalized DP operator to progressively refine it. This enables the model to develop a task-specific relational calculus, providing a principled framework for capturing long-range dependencies. Theoretically, we prove that FloydNet achieves 3-WL (2-FWL) expressive power, and its generalized form aligns with the k-FWL hierarchy. FloydNet demonstrates state-of-the-art performance across challenging domains: it achieves near-perfect scores (often >99\%) on the CLRS-30 algorithmic benchmark, finds exact optimal solutions for the general Traveling Salesman Problem (TSP) at rates significantly exceeding strong heuristics, and empirically matches the 3-WL test on the BREC benchmark. Our results establish this learned, DP-style refinement as a powerful and practical alternative to message passing for high-level graph reasoning.

A k-clique is a dense graph, consisting of k fully-connected nodes, that finds numerous applications, such as community detection and network analysis. In this paper, we study a new problem, that finds a maximum set of disjoint k-cliques in a given large real-world graph with a user-defined fixed number k, which can contribute to a good performance of teaming collaborative events in online games. However, this problem is NP-hard when k geq 3, making it difficult to solve. To address that, we propose an efficient lightweight method that avoids significant overheads and achieves a k-approximation to the optimal, which is equipped with several optimization techniques, including the ordering method, degree estimation in the clique graph, and a lightweight implementation. Besides, to handle dynamic graphs that are widely seen in real-world social networks, we devise an efficient indexing method with careful swapping operations, leading to the efficient maintenance of a near-optimal result with frequent updates in the graph. In various experiments on several large graphs, our proposed approaches significantly outperform the competitors by up to 2 orders of magnitude in running time and 13.3\% in the number of computed disjoint k-cliques, which demonstrates the superiority of the proposed approaches in terms of efficiency and effectiveness.

Many real-world systems exhibit temporal, dynamic behaviors, which are captured as time series of complex agent interactions. To perform temporal reasoning, current methods primarily encode temporal dynamics through simple sequence-based models. However, in general these models fail to efficiently capture the full spectrum of rich dynamics in the input, since the dynamics is not uniformly distributed. In particular, relevant information might be harder to extract and computing power is wasted for processing all individual timesteps, even if they contain no significant changes or no new information. Here we propose TimeGraphs, a novel approach that characterizes dynamic interactions as a hierarchical temporal graph, diverging from traditional sequential representations. Our approach models the interactions using a compact graph-based representation, enabling adaptive reasoning across diverse time scales. Adopting a self-supervised method, TimeGraphs constructs a multi-level event hierarchy from a temporal input, which is then used to efficiently reason about the unevenly distributed dynamics. This construction process is scalable and incremental to accommodate streaming data. We evaluate TimeGraphs on multiple datasets with complex, dynamic agent interactions, including a football simulator, the Resistance game, and the MOMA human activity dataset. The results demonstrate both robustness and efficiency of TimeGraphs on a range of temporal reasoning tasks. Our approach obtains state-of-the-art performance and leads to a performance increase of up to 12.2% on event prediction and recognition tasks over current approaches. Our experiments further demonstrate a wide array of capabilities including zero-shot generalization, robustness in case of data sparsity, and adaptability to streaming data flow.

Human beings primarily understand the world through concepts (e.g., dog), abstract mental representations that structure perception, reasoning, and learning. However, how large language models (LLMs) acquire, retain, and forget such concepts during continual pretraining remains poorly understood. In this work, we study how individual concepts are acquired and forgotten, as well as how multiple concepts interact through interference and synergy. We link these behavioral dynamics to LLMs' internal Concept Circuits, computational subgraphs associated with specific concepts, and incorporate Graph Metrics to characterize circuit structure. Our analysis reveals: (1) LLMs concept circuits provide a non-trivial, statistically significant signal of concept learning and forgetting; (2) Concept circuits exhibit a stage-wise temporal pattern during continual pretraining, with an early increase followed by gradual decrease and stabilization; (3) concepts with larger learning gains tend to exhibit greater forgetting under subsequent training; (4) semantically similar concepts induce stronger interference than weakly related ones; (5) conceptual knowledge differs in their transferability, with some significantly facilitating the learning of others. Together, our findings offer a circuit-level view of concept learning dynamics and inform the design of more interpretable and robust concept-aware training strategies for LLMs.

This paper presents a methodology to learn surrogate models of steady state fluid dynamics simulations on meshed domains, based on Implicit Neural Representations (INRs). The proposed models can be applied directly to unstructured domains for different flow conditions, handle non-parametric 3D geometric variations, and generalize to unseen shapes at test time. The coordinate-based formulation naturally leads to robustness with respect to discretization, allowing an excellent trade-off between computational cost (memory footprint and training time) and accuracy. The method is demonstrated on two industrially relevant applications: a RANS dataset of the two-dimensional compressible flow over a transonic airfoil and a dataset of the surface pressure distribution over 3D wings, including shape, inflow condition, and control surface deflection variations. On the considered test cases, our approach achieves a more than three times lower test error and significantly improves generalization error on unseen geometries compared to state-of-the-art Graph Neural Network architectures. Remarkably, the method can perform inference five order of magnitude faster than the high fidelity solver on the RANS transonic airfoil dataset. Code is available at https://gitlab.isae-supaero.fr/gi.catalani/aero-nepf

Real-world networks, with their evolving relations, are best captured as temporal graphs. However, existing software libraries are largely designed for static graphs where the dynamic nature of temporal graphs is ignored. Bridging this gap, we introduce TGX, a Python package specially designed for analysis of temporal networks that encompasses an automated pipeline for data loading, data processing, and analysis of evolving graphs. TGX provides access to eleven built-in datasets and eight external Temporal Graph Benchmark (TGB) datasets as well as any novel datasets in the .csv format. Beyond data loading, TGX facilitates data processing functionalities such as discretization of temporal graphs and node subsampling to accelerate working with larger datasets. For comprehensive investigation, TGX offers network analysis by providing a diverse set of measures, including average node degree and the evolving number of nodes and edges per timestamp. Additionally, the package consolidates meaningful visualization plots indicating the evolution of temporal patterns, such as Temporal Edge Appearance (TEA) and Temporal Edge Trafficc (TET) plots. The TGX package is a robust tool for examining the features of temporal graphs and can be used in various areas like studying social networks, citation networks, and tracking user interactions. We plan to continuously support and update TGX based on community feedback. TGX is publicly available on: https://github.com/ComplexData-MILA/TGX.

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at https://github.com/IBM/EvolveGCN.

Optimization problems over dynamic networks have been extensively studied and widely used in the past decades to formulate numerous real-world problems. However, (1) traditional optimization-based approaches do not scale to large networks, and (2) the design of good heuristics or approximation algorithms often requires significant manual trial-and-error. In this work, we argue that data-driven strategies can automate this process and learn efficient algorithms without compromising optimality. To do so, we present network control problems through the lens of reinforcement learning and propose a graph network-based framework to handle a broad class of problems. Instead of naively computing actions over high-dimensional graph elements, e.g., edges, we propose a bi-level formulation where we (1) specify a desired next state via RL, and (2) solve a convex program to best achieve it, leading to drastically improved scalability and performance. We further highlight a collection of desirable features to system designers, investigate design decisions, and present experiments on real-world control problems showing the utility, scalability, and flexibility of our framework.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

This work presents a graph neural network (GNN) framework for solving the maximum independent set (MIS) problem, inspired by dynamic programming (DP). Specifically, given a graph, we propose a DP-like recursive algorithm based on GNNs that firstly constructs two smaller sub-graphs, predicts the one with the larger MIS, and then uses it in the next recursive call. To train our algorithm, we require annotated comparisons of different graphs concerning their MIS size. Annotating the comparisons with the output of our algorithm leads to a self-training process that results in more accurate self-annotation of the comparisons and vice versa. We provide numerical evidence showing the superiority of our method vs prior methods in multiple synthetic and real-world datasets.

Most graph neural network models learn embeddings of nodes in static attributed graphs for predictive analysis. Recent attempts have been made to learn temporal proximity of the nodes. We find that real dynamic attributed graphs exhibit complex co-evolution of node attributes and graph structure. Learning node embeddings for forecasting change of node attributes and birth and death of links over time remains an open problem. In this work, we present a novel framework called CoEvoGNN for modeling dynamic attributed graph sequence. It preserves the impact of earlier graphs on the current graph by embedding generation through the sequence. It has a temporal self-attention mechanism to model long-range dependencies in the evolution. Moreover, CoEvoGNN optimizes model parameters jointly on two dynamic tasks, attribute inference and link prediction over time. So the model can capture the co-evolutionary patterns of attribute change and link formation. This framework can adapt to any graph neural algorithms so we implemented and investigated three methods based on it: CoEvoGCN, CoEvoGAT, and CoEvoSAGE. Experiments demonstrate the framework (and its methods) outperform strong baselines on predicting an entire unseen graph snapshot of personal attributes and interpersonal links in dynamic social graphs and financial graphs.

We present DYMAG, a graph neural network based on a novel form of message aggregation. Standard message-passing neural networks, which often aggregate local neighbors via mean-aggregation, can be regarded as convolving with a simple rectangular waveform which is non-zero only on 1-hop neighbors of every vertex. Here, we go beyond such local averaging. We will convolve the node features with more sophisticated waveforms generated using dynamics such as the heat equation, wave equation, and the Sprott model (an example of chaotic dynamics). Furthermore, we use snapshots of these dynamics at different time points to create waveforms at many effective scales. Theoretically, we show that these dynamic waveforms can capture salient information about the graph including connected components, connectivity, and cycle structures even with no features. Empirically, we test DYMAG on both real and synthetic benchmarks to establish that DYMAG outperforms baseline models on recovery of graph persistence, generating parameters of random graphs, as well as property prediction for proteins, molecules and materials. Our code is available at https://github.com/KrishnaswamyLab/DYMAG.

Dynamic graph representation learning requires capturing both structural relationships and temporal evolution, yet existing approaches face a fundamental trade-off: attention-based methods achieve expressiveness at O(T^2) complexity, while recurrent architectures suffer from gradient pathologies and dense state storage. Spiking neural networks offer event-driven efficiency but remain limited by sequential propagation, binary information loss, and local aggregation that misses global context. We propose ChronoSpike, an adaptive spiking graph neural network that integrates learnable LIF neurons with per-channel membrane dynamics, multi-head attentive spatial aggregation on continuous features, and a lightweight Transformer temporal encoder, enabling both fine-grained local modeling and long-range dependency capture with linear memory complexity O(T cdot d). On three large-scale benchmarks, ChronoSpike outperforms twelve state-of-the-art baselines by 2.0% Macro-F1 and 2.4% Micro-F1 while achieving 3-10times faster training than recurrent methods with a constant 105K-parameter budget independent of graph size. We provide theoretical guarantees for membrane potential boundedness, gradient flow stability under contraction factor ρ< 1, and BIBO stability; interpretability analyses reveal heterogeneous temporal receptive fields and a learned primacy effect with 83-88% sparsity.

Symbolic world modeling requires inferring and representing an environment's transitional dynamics as an executable program. Prior work has focused on largely deterministic environments with abundant interaction data, simple mechanics, and human guidance. We address a more realistic and challenging setting, learning in a complex, stochastic environment where the agent has only "one life" to explore a hostile environment without human guidance. We introduce OneLife, a framework that models world dynamics through conditionally-activated programmatic laws within a probabilistic programming framework. Each law operates through a precondition-effect structure, activating in relevant world states. This creates a dynamic computation graph that routes inference and optimization only through relevant laws, avoiding scaling challenges when all laws contribute to predictions about a complex, hierarchical state, and enabling the learning of stochastic dynamics even with sparse rule activation. To evaluate our approach under these demanding constraints, we introduce a new evaluation protocol that measures (a) state ranking, the ability to distinguish plausible future states from implausible ones, and (b) state fidelity, the ability to generate future states that closely resemble reality. We develop and evaluate our framework on Crafter-OO, our reimplementation of the Crafter environment that exposes a structured, object-oriented symbolic state and a pure transition function that operates on that state alone. OneLife can successfully learn key environment dynamics from minimal, unguided interaction, outperforming a strong baseline on 16 out of 23 scenarios tested. We also test OneLife's planning ability, with simulated rollouts successfully identifying superior strategies. Our work establishes a foundation for autonomously constructing programmatic world models of unknown, complex environments.

Recent advances in neural algorithmic reasoning with graph neural networks (GNNs) are propped up by the notion of algorithmic alignment. Broadly, a neural network will be better at learning to execute a reasoning task (in terms of sample complexity) if its individual components align well with the target algorithm. Specifically, GNNs are claimed to align with dynamic programming (DP), a general problem-solving strategy which expresses many polynomial-time algorithms. However, has this alignment truly been demonstrated and theoretically quantified? Here we show, using methods from category theory and abstract algebra, that there exists an intricate connection between GNNs and DP, going well beyond the initial observations over individual algorithms such as Bellman-Ford. Exposing this connection, we easily verify several prior findings in the literature, produce better-grounded GNN architectures for edge-centric tasks, and demonstrate empirical results on the CLRS algorithmic reasoning benchmark. We hope our exposition will serve as a foundation for building stronger algorithmically aligned GNNs.

We present the Temporal Graph Benchmark (TGB), a collection of challenging and diverse benchmark datasets for realistic, reproducible, and robust evaluation of machine learning models on temporal graphs. TGB datasets are of large scale, spanning years in duration, incorporate both node and edge-level prediction tasks and cover a diverse set of domains including social, trade, transaction, and transportation networks. For both tasks, we design evaluation protocols based on realistic use-cases. We extensively benchmark each dataset and find that the performance of common models can vary drastically across datasets. In addition, on dynamic node property prediction tasks, we show that simple methods often achieve superior performance compared to existing temporal graph models. We believe that these findings open up opportunities for future research on temporal graphs. Finally, TGB provides an automated machine learning pipeline for reproducible and accessible temporal graph research, including data loading, experiment setup and performance evaluation. TGB will be maintained and updated on a regular basis and welcomes community feedback. TGB datasets, data loaders, example codes, evaluation setup, and leaderboards are publicly available at https://tgb.complexdatalab.com/.

Various human-designed prompt engineering techniques have been proposed to improve problem solvers based on Large Language Models (LLMs), yielding many disparate code bases. We unify these approaches by describing LLM-based agents as computational graphs. The nodes implement functions to process multimodal data or query LLMs, and the edges describe the information flow between operations. Graphs can be recursively combined into larger composite graphs representing hierarchies of inter-agent collaboration (where edges connect operations of different agents). Our novel automatic graph optimizers (1) refine node-level LLM prompts (node optimization) and (2) improve agent orchestration by changing graph connectivity (edge optimization). Experiments demonstrate that our framework can be used to efficiently develop, integrate, and automatically improve various LLM agents. The code can be found at https://github.com/metauto-ai/gptswarm.

As mathematical computing becomes more democratized in high-level languages, high-performance symbolic-numeric systems are necessary for domain scientists and engineers to get the best performance out of their machine without deep knowledge of code optimization. Naturally, users need different term types either to have different algebraic properties for them, or to use efficient data structures. To this end, we developed Symbolics.jl, an extendable symbolic system which uses dynamic multiple dispatch to change behavior depending on the domain needs. In this work we detail an underlying abstract term interface which allows for speed without sacrificing generality. We show that by formalizing a generic API on actions independent of implementation, we can retroactively add optimized data structures to our system without changing the pre-existing term rewriters. We showcase how this can be used to optimize term construction and give a 113x acceleration on general symbolic transformations. Further, we show that such a generic API allows for complementary term-rewriting implementations. We demonstrate the ability to swap between classical term-rewriting simplifiers and e-graph-based term-rewriting simplifiers. We showcase an e-graph ruleset which minimizes the number of CPU cycles during expression evaluation, and demonstrate how it simplifies a real-world reaction-network simulation to halve the runtime. Additionally, we show a reaction-diffusion partial differential equation solver which is able to be automatically converted into symbolic expressions via multiple dispatch tracing, which is subsequently accelerated and parallelized to give a 157x simulation speedup. Together, this presents Symbolics.jl as a next-generation symbolic-numeric computing environment geared towards modeling and simulation.

Multi-agent systems (MAS) based on Large Language Models (LLMs) have the potential to solve tasks that are beyond the reach of any single LLM. However, this potential can only be realized when the collaboration mechanism between agents is optimized. Specifically, optimizing the communication structure between agents is critical for fruitful collaboration. Most existing approaches rely on fixed topologies, pretrained graph generators, optimization over edges, or employ external LLM judges, thereby adding to the complexity. In this work, we introduce a response-conditioned framework that adapts communication on-the-fly. Agents independently generate responses to the user query and assess peer contributions using an approximation of the Shapley value. A directed acyclic graph (DAG) is then constructed to regulate the propagation of the responses among agents, which ensures stable and efficient message transmission from high-contributing agents to others. This graph is dynamically updated based on the agent responses from the previous collaboration round. Since the proposed framework enables the self-organization of agents without additional supervision or training, we refer to it as SelfOrg. The SelfOrg framework goes beyond task- and query-level optimization and takes into account the stochastic nature of agent responses. Experiments with both strong and weak LLM backends demonstrate robust performance, with significant gains in the weak regime where prior methods collapse. We also theoretically show that multiple agents increase the chance of correctness and that the correct responses naturally dominate the information flow.

The automated extraction of complete and precise road network graphs from remote sensing imagery remains a critical challenge in geospatial computer vision. Segmentation-based approaches, while effective in pixel-level recognition, struggle to maintain topology fidelity after vectorization postprocessing. Graph-growing methods build more topologically faithful graphs but suffer from computationally prohibitive iterative ROI cropping. Graph-generating methods first predict global static candidate road network vertices, and then infer possible edges between vertices. They achieve fast topology-aware inference, but limits the dynamic insertion of vertices. To address these challenges, we propose DeH4R, a novel hybrid model that combines graph-generating efficiency and graph-growing dynamics. This is achieved by decoupling the task into candidate vertex detection, adjacent vertex prediction, initial graph contruction, and graph expansion. This architectural innovation enables dynamic vertex (edge) insertions while retaining fast inference speed and enhancing both topology fidelity and spatial consistency. Comprehensive evaluations on CityScale and SpaceNet benchmarks demonstrate state-of-the-art (SOTA) performance. DeH4R outperforms the prior SOTA graph-growing method RNGDet++ by 4.62 APLS and 10.18 IoU on CityScale, while being approximately 10 times faster. The code will be made publicly available at https://github.com/7777777FAN/DeH4R.

The execution of graph algorithms using neural networks has recently attracted significant interest due to promising empirical progress. This motivates further understanding of how neural networks can replicate reasoning steps with relational data. In this work, we study the ability of transformer networks to simulate algorithms on graphs from a theoretical perspective. The architecture that we utilize is a looped transformer with extra attention heads that interact with the graph. We prove by construction that this architecture can simulate algorithms such as Dijkstra's shortest path algorithm, Breadth- and Depth-First Search, and Kosaraju's strongly connected components algorithm. The width of the network does not increase with the size of the input graph, which implies that the network can simulate the above algorithms for any graph. Despite this property, we show that there is a limit to simulation in our solution due to finite precision. Finally, we show a Turing Completeness result with constant width when the extra attention heads are utilized.

Model compression is essential in the deployment of large Computer Vision models on embedded devices. However, static optimization techniques (e.g. pruning, quantization, etc.) neglect the fact that different inputs have different complexities, thus requiring different amount of computations. Dynamic Neural Networks allow to condition the number of computations to the specific input. The current literature on the topic is very extensive and fragmented. We present a comprehensive survey that synthesizes and unifies existing Dynamic Neural Networks research in the context of Computer Vision. Additionally, we provide a logical taxonomy based on which component of the network is adaptive: the output, the computation graph or the input. Furthermore, we argue that Dynamic Neural Networks are particularly beneficial in the context of Sensor Fusion for better adaptivity, noise reduction and information prioritization. We present preliminary works in this direction. We complement this survey with a curated repository listing all the surveyed papers, each with a brief summary of the solution and the code base when available: https://github.com/DTU-PAS/awesome-dynn-for-cv .

For a broad range of research, governmental and commercial applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As social media data sets are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present a single-machine real-time system for large-scale graph processing that allows analysts to interactively explore graph structures. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates user similarities while being robust to noise and queryable in real-time. We achieve single machine real-time performance by compressing the neighbourhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e. communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetise their data, helping them to continue to provide free services that are valued by billions of people globally.

Mesh-based simulations are central to modeling complex physical systems in many disciplines across science and engineering. Mesh representations support powerful numerical integration methods and their resolution can be adapted to strike favorable trade-offs between accuracy and efficiency. However, high-dimensional scientific simulations are very expensive to run, and solvers and parameters must often be tuned individually to each system studied. Here we introduce MeshGraphNets, a framework for learning mesh-based simulations using graph neural networks. Our model can be trained to pass messages on a mesh graph and to adapt the mesh discretization during forward simulation. Our results show it can accurately predict the dynamics of a wide range of physical systems, including aerodynamics, structural mechanics, and cloth. The model's adaptivity supports learning resolution-independent dynamics and can scale to more complex state spaces at test time. Our method is also highly efficient, running 1-2 orders of magnitude faster than the simulation on which it is trained. Our approach broadens the range of problems on which neural network simulators can operate and promises to improve the efficiency of complex, scientific modeling tasks.

Graph representation learning is a fundamental task in various applications that strives to learn low-dimensional embeddings for nodes that can preserve graph topology information. However, many existing methods focus on static graphs while ignoring evolving graph patterns. Inspired by the success of graph convolutional networks(GCNs) in static graph embedding, we propose a novel k-core based temporal graph convolutional network, the CTGCN, to learn node representations for dynamic graphs. In contrast to previous dynamic graph embedding methods, CTGCN can preserve both local connective proximity and global structural similarity while simultaneously capturing graph dynamics. In the proposed framework, the traditional graph convolution is generalized into two phases, feature transformation and feature aggregation, which gives the CTGCN more flexibility and enables the CTGCN to learn connective and structural information under the same framework. Experimental results on 7 real-world graphs demonstrate that the CTGCN outperforms existing state-of-the-art graph embedding methods in several tasks, including link prediction and structural role classification. The source code of this work can be obtained from https://github.com/jhljx/CTGCN.

Dynamical systems with complex behaviours, e.g. immune system cells interacting with a pathogen, are commonly modelled by splitting the behaviour into different regimes, or modes, each with simpler dynamics, and then learning the switching behaviour from one mode to another. Switching Dynamical Systems (SDS) are a powerful tool that automatically discovers these modes and mode-switching behaviour from time series data. While effective, these methods focus on independent objects, where the modes of one object are independent of the modes of the other objects. In this paper, we focus on the more general interacting object setting for switching dynamical systems, where the per-object dynamics also depends on an unknown and dynamically changing subset of other objects and their modes. To this end, we propose a novel graph-based approach for switching dynamical systems, GRAph Switching dynamical Systems (GRASS), in which we use a dynamic graph to characterize interactions between objects and learn both intra-object and inter-object mode-switching behaviour. We introduce two new datasets for this setting, a synthesized ODE-driven particles dataset and a real-world Salsa Couple Dancing dataset. Experiments show that GRASS can consistently outperforms previous state-of-the-art methods.

We present FastRP, a scalable and performant algorithm for learning distributed node representations in a graph. FastRP is over 4,000 times faster than state-of-the-art methods such as DeepWalk and node2vec, while achieving comparable or even better performance as evaluated on several real-world networks on various downstream tasks. We observe that most network embedding methods consist of two components: construct a node similarity matrix and then apply dimension reduction techniques to this matrix. We show that the success of these methods should be attributed to the proper construction of this similarity matrix, rather than the dimension reduction method employed. FastRP is proposed as a scalable algorithm for network embeddings. Two key features of FastRP are: 1) it explicitly constructs a node similarity matrix that captures transitive relationships in a graph and normalizes matrix entries based on node degrees; 2) it utilizes very sparse random projection, which is a scalable optimization-free method for dimension reduction. An extra benefit from combining these two design choices is that it allows the iterative computation of node embeddings so that the similarity matrix need not be explicitly constructed, which further speeds up FastRP. FastRP is also advantageous for its ease of implementation, parallelization and hyperparameter tuning. The source code is available at https://github.com/GTmac/FastRP.

Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are essential, making prior methods potentially unsuitable in such contexts. Moreover, while trivial adaptations are available, empirical investigations reveal their limited efficacy as they do not properly model the interplay among graph components. To address this, we propose a joint score-based model of nodes and edges for graph generation that considers all graph components. Our approach offers two key novelties: (i) node and edge attributes are combined in an attention module that generates samples based on the two ingredients; and (ii) node, edge and adjacency information are mutually dependent during the graph diffusion process. We evaluate our method on challenging benchmarks involving real-world and synthetic datasets in which edge features are crucial. Additionally, we introduce a new synthetic dataset that incorporates edge values. Furthermore, we propose a novel application that greatly benefits from the method due to its nature: the generation of traffic scenes represented as graphs. Our method outperforms other graph generation methods, demonstrating a significant advantage in edge-related measures.

Dynamic graph learning methods have recently emerged as powerful tools for modelling relational data evolving through time. However, despite extensive benchmarking efforts, it remains unclear whether current Temporal Graph Neural Networks (TGNNs) effectively capture core temporal patterns such as periodicity, cause-and-effect, and long-range dependencies. In this work, we introduce the Temporal Graph Reasoning Benchmark (T-GRAB), a comprehensive set of synthetic tasks designed to systematically probe the capabilities of TGNNs to reason across time. T-GRAB provides controlled, interpretable tasks that isolate key temporal skills: counting/memorizing periodic repetitions, inferring delayed causal effects, and capturing long-range dependencies over both spatial and temporal dimensions. We evaluate 11 temporal graph learning methods on these tasks, revealing fundamental shortcomings in their ability to generalize temporal patterns. Our findings offer actionable insights into the limitations of current models, highlight challenges hidden by traditional real-world benchmarks, and motivate the development of architectures with stronger temporal reasoning abilities. The code for T-GRAB can be found at: https://github.com/alirezadizaji/T-GRAB.

Personalized PageRank (PPR) has enormous applications, such as link prediction and recommendation systems for social networks, which often require the fully PPR to be known. Besides, most of real-life graphs are edge-weighted, e.g., the interaction between users on the Facebook network. However, it is computationally difficult to compute the fully PPR, especially on large graphs, not to mention that most existing approaches do not consider the weights of edges. In particular, the existing approach cannot handle graphs with billion edges on a moderate-size cluster. To address this problem, this paper presents a novel study on the computation of fully edge-weighted PPR on large graphs using the distributed computing framework. Specifically, we employ the Monte Carlo approximation that performs a large number of random walks from each node of the graph, and exploits the parallel pipeline framework to reduce the overall running time of the fully PPR. Based on that, we develop several optimization techniques which (i) alleviate the issue of large nodes that could explode the memory space, (ii) pre-compute short walks for small nodes that largely speedup the computation of random walks, and (iii) optimize the amount of random walks to compute in each pipeline that significantly reduces the overhead. With extensive experiments on a variety of real-life graph datasets, we demonstrate that our solution is several orders of magnitude faster than the state-of-the-arts, and meanwhile, largely outperforms the baseline algorithms in terms of accuracy.

Graph neural networks are popular architectures for graph machine learning, based on iterative computation of node representations of an input graph through a series of invariant transformations. A large class of graph neural networks follow a standard message-passing paradigm: at every layer, each node state is updated based on an aggregate of messages from its neighborhood. In this work, we propose a novel framework for training graph neural networks, where every node is viewed as a player that can choose to either 'listen', 'broadcast', 'listen and broadcast', or to 'isolate'. The standard message propagation scheme can then be viewed as a special case of this framework where every node 'listens and broadcasts' to all neighbors. Our approach offers a more flexible and dynamic message-passing paradigm, where each node can determine its own strategy based on their state, effectively exploring the graph topology while learning. We provide a theoretical analysis of the new message-passing scheme which is further supported by an extensive empirical analysis on a synthetic dataset and on real-world datasets.

We present Marian, an efficient and self-contained Neural Machine Translation framework with an integrated automatic differentiation engine based on dynamic computation graphs. Marian is written entirely in C++. We describe the design of the encoder-decoder framework and demonstrate that a research-friendly toolkit can achieve high training and translation speed.

We present MiniTensor, an open source tensor operations library that focuses on minimalism, correctness, and performance. MiniTensor exposes a familiar PyTorch-like Python API while it executes performance critical code in a Rust engine. The core supports dense n dimensional tensors, broadcasting, reductions, matrix multiplication, reverse mode automatic differentiation, a compact set of neural network layers, and standard optimizers. In this paper, we describe the design of MiniTensor's architecture, including its efficient memory management, dynamic computation graph for gradients, and integration with Python via PyO3. We also compare the install footprint with PyTorch and TensorFlow to demonstrate that MiniTensor achieves a package size of only a few megabytes, several orders of magnitude smaller than mainstream frameworks, while preserving the essentials needed for research and development on CPUs. The repository can be found at https://github.com/neuralsorcerer/minitensor

Reasoning system dynamics is one of the most important analytical approaches for many scientific studies. With the initial state of a system as input, the recent graph neural networks (GNNs)-based methods are capable of predicting the future state distant in time with high accuracy. Although these methods have diverse designs in modeling the coordinates and interacting forces of the system, we show that they actually share a common paradigm that learns the integration of the velocity over the interval between the initial and terminal coordinates. However, their integrand is constant w.r.t. time. Inspired by this observation, we propose a new approach to predict the integration based on several velocity estimations with Newton-Cotes formulas and prove its effectiveness theoretically. Extensive experiments on several benchmarks empirically demonstrate consistent and significant improvement compared with the state-of-the-art methods.

Many graph algorithms can be viewed as sets of rules that are iteratively applied, with the number of iterations dependent on the size and complexity of the input graph. Existing machine learning architectures often struggle to represent these algorithmic decisions as discrete state transitions. Therefore, we propose a novel framework: GraphFSA (Graph Finite State Automaton). GraphFSA is designed to learn a finite state automaton that runs on each node of a given graph. We test GraphFSA on cellular automata problems, showcasing its abilities in a straightforward algorithmic setting. For a comprehensive empirical evaluation of our framework, we create a diverse range of synthetic problems. As our main application, we then focus on learning more elaborate graph algorithms. Our findings suggest that GraphFSA exhibits strong generalization and extrapolation abilities, presenting an alternative approach to represent these algorithms.

Dynamic programming (DP) algorithms for combinatorial optimization problems work with taking maximization, minimization, and classical addition in their recursion algorithms. The associated value functions correspond to convex polyhedra in the max plus semiring. Existing Neural Algorithmic Reasoning models, however, rely on softmax-normalized dot-product attention where the smooth exponential weighting blurs these sharp polyhedral structures and collapses when evaluated on out-of-distribution (OOD) settings. We introduce Tropical attention, a novel attention function that operates natively in the max-plus semiring of tropical geometry. We prove that Tropical attention can approximate tropical circuits of DP-type combinatorial algorithms. We then propose that using Tropical transformers enhances empirical OOD performance in both length generalization and value generalization, on algorithmic reasoning tasks, surpassing softmax baselines while remaining stable under adversarial attacks. We also present adversarial-attack generalization as a third axis for Neural Algorithmic Reasoning benchmarking. Our results demonstrate that Tropical attention restores the sharp, scale-invariant reasoning absent from softmax.

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.

This work proposes DyExpert, a dynamic graph model for cross-domain link prediction. It can explicitly model historical evolving processes to learn the evolution pattern of a specific downstream graph and subsequently make pattern-specific link predictions. DyExpert adopts a decode-only transformer and is capable of efficiently parallel training and inference by conditioned link generation that integrates both evolution modeling and link prediction. DyExpert is trained by extensive dynamic graphs across diverse domains, comprising 6M dynamic edges. Extensive experiments on eight untrained graphs demonstrate that DyExpert achieves state-of-the-art performance in cross-domain link prediction. Compared to the advanced baseline under the same setting, DyExpert achieves an average of 11.40% improvement Average Precision across eight graphs. More impressive, it surpasses the fully supervised performance of 8 advanced baselines on 6 untrained graphs.

We propose the convergent graph solver (CGS), a deep learning method that learns iterative mappings to predict the properties of a graph system at its stationary state (fixed point) with guaranteed convergence. CGS systematically computes the fixed points of a target graph system and decodes them to estimate the stationary properties of the system without the prior knowledge of existing solvers or intermediate solutions. The forward propagation of CGS proceeds in three steps: (1) constructing the input dependent linear contracting iterative maps, (2) computing the fixed-points of the linear maps, and (3) decoding the fixed-points to estimate the properties. The contractivity of the constructed linear maps guarantees the existence and uniqueness of the fixed points following the Banach fixed point theorem. To train CGS efficiently, we also derive a tractable analytical expression for its gradient by leveraging the implicit function theorem. We evaluate the performance of CGS by applying it to various network-analytic and graph benchmark problems. The results indicate that CGS has competitive capabilities for predicting the stationary properties of graph systems, irrespective of whether the target systems are linear or non-linear. CGS also shows high performance for graph classification problems where the existence or the meaning of a fixed point is hard to be clearly defined, which highlights the potential of CGS as a general graph neural network architecture.

Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

Temporal hypergraphs provide a powerful paradigm for modeling time-dependent, higher-order interactions in complex systems. Representation learning for hypergraphs is essential for extracting patterns of the higher-order interactions that are critically important in real-world problems in social network analysis, neuroscience, finance, etc. However, existing methods are typically designed only for specific tasks or static hypergraphs. We present CAT-Walk, an inductive method that learns the underlying dynamic laws that govern the temporal and structural processes underlying a temporal hypergraph. CAT-Walk introduces a temporal, higher-order walk on hypergraphs, SetWalk, that extracts higher-order causal patterns. CAT-Walk uses a novel adaptive and permutation invariant pooling strategy, SetMixer, along with a set-based anonymization process that hides the identity of hyperedges. Finally, we present a simple yet effective neural network model to encode hyperedges. Our evaluation on 10 hypergraph benchmark datasets shows that CAT-Walk attains outstanding performance on temporal hyperedge prediction benchmarks in both inductive and transductive settings. It also shows competitive performance with state-of-the-art methods for node classification. (https://github.com/ubc-systopia/CATWalk)

Accurately predicting road networks from satellite images requires a global understanding of the network topology. We propose to capture such high-level information by introducing a graph-based framework that simulates the addition of sequences of graph edges using a reinforcement learning (RL) approach. In particular, given a partially generated graph associated with a satellite image, an RL agent nominates modifications that maximize a cumulative reward. As opposed to standard supervised techniques that tend to be more restricted to commonly used surrogate losses, these rewards can be based on various complex, potentially non-continuous, metrics of interest. This yields more power and flexibility to encode problem-dependent knowledge. Empirical results on several benchmark datasets demonstrate enhanced performance and increased high-level reasoning about the graph topology when using a tree-based search. We further highlight the superiority of our approach under substantial occlusions by introducing a new synthetic benchmark dataset for this task.

Causal discovery for dynamical systems poses a major challenge in fields where active interventions are infeasible. Most methods used to investigate these systems and their associated benchmarks are tailored to deterministic, low-dimensional and weakly nonlinear time-series data. To address these limitations, we present CausalDynamics, a large-scale benchmark and extensible data generation framework to advance the structural discovery of dynamical causal models. Our benchmark consists of true causal graphs derived from thousands of coupled ordinary and stochastic differential equations as well as two idealized climate models. We perform a comprehensive evaluation of state-of-the-art causal discovery algorithms for graph reconstruction on systems with noisy, confounded, and lagged dynamics. CausalDynamics consists of a plug-and-play, build-your-own coupling workflow that enables the construction of a hierarchy of physical systems. We anticipate that our framework will facilitate the development of robust causal discovery algorithms that are broadly applicable across domains while addressing their unique challenges. We provide a user-friendly implementation and documentation on https://kausable.github.io/CausalDynamics.

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

Graph Neural Networks have gained huge interest in the past few years. These powerful algorithms expanded deep learning models to non-Euclidean space and were able to achieve state of art performance in various applications including recommender systems and social networks. However, this performance is based on static graph structures assumption which limits the Graph Neural Networks performance when the data varies with time. Spatiotemporal Graph Neural Networks are extension of Graph Neural Networks that takes the time factor into account. Recently, various Spatiotemporal Graph Neural Network algorithms were proposed and achieved superior performance compared to other deep learning algorithms in several time dependent applications. This survey discusses interesting topics related to Spatiotemporal Graph Neural Networks, including algorithms, applications, and open challenges.

Large Language Models (LLMs) have demonstrated exceptional abilities in reasoning for task planning. However, challenges remain under-explored for parallel schedules. This paper introduces a novel paradigm, plan-over-graph, in which the model first decomposes a real-life textual task into executable subtasks and constructs an abstract task graph. The model then understands this task graph as input and generates a plan for parallel execution. To enhance the planning capability of complex, scalable graphs, we design an automated and controllable pipeline to generate synthetic graphs and propose a two-stage training scheme. Experimental results show that our plan-over-graph method significantly improves task performance on both API-based LLMs and trainable open-sourced LLMs. By normalizing complex tasks as graphs, our method naturally supports parallel execution, demonstrating global efficiency. The code and data are available at https://github.com/zsq259/Plan-over-Graph.

We revisit the structure learning problem for dynamic Bayesian networks and propose a method that simultaneously estimates contemporaneous (intra-slice) and time-lagged (inter-slice) relationships between variables in a time-series. Our approach is score-based, and revolves around minimizing a penalized loss subject to an acyclicity constraint. To solve this problem, we leverage a recent algebraic result characterizing the acyclicity constraint as a smooth equality constraint. The resulting algorithm, which we call DYNOTEARS, outperforms other methods on simulated data, especially in high-dimensions as the number of variables increases. We also apply this algorithm on real datasets from two different domains, finance and molecular biology, and analyze the resulting output. Compared to state-of-the-art methods for learning dynamic Bayesian networks, our method is both scalable and accurate on real data. The simple formulation and competitive performance of our method make it suitable for a variety of problems where one seeks to learn connections between variables across time.

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

Complex networks have become essential tools for understanding diverse phenomena in social systems, traffic systems, biomolecular systems, and financial systems. Identifying critical nodes is a central theme in contemporary research, serving as a vital bridge between theoretical foundations and practical applications. Nevertheless, the intrinsic complexity and structural heterogeneity characterizing real-world networks, with particular emphasis on dynamic and higher-order networks, present substantial obstacles to the development of universal frameworks for critical node identification. This paper provides a comprehensive review of critical node identification techniques, categorizing them into seven main classes: centrality, critical nodes deletion problem, influence maximization, network control, artificial intelligence, higher-order and dynamic methods. Our review bridges the gaps in existing surveys by systematically classifying methods based on their methodological foundations and practical implications, and by highlighting their strengths, limitations, and applicability across different network types. Our work enhances the understanding of critical node research by identifying key challenges, such as algorithmic universality, real-time evaluation in dynamic networks, analysis of higher-order structures, and computational efficiency in large-scale networks. The structured synthesis consolidates current progress and highlights open questions, particularly in modeling temporal dynamics, advancing efficient algorithms, integrating machine learning approaches, and developing scalable and interpretable metrics for complex systems.

Despite the successful application of Temporal Graph Networks (TGNs) for tasks such as dynamic node classification and link prediction, they still perform poorly on the task of dynamic node affinity prediction -- where the goal is to predict 'how much' two nodes will interact in the future. In fact, simple heuristic approaches such as persistent forecasts and moving averages over ground-truth labels significantly and consistently outperform TGNs. Building on this observation, we find that computing heuristics over messages is an equally competitive approach, outperforming TGN and all current temporal graph (TG) models on dynamic node affinity prediction. In this paper, we prove that no formulation of TGN can represent persistent forecasting or moving averages over messages, and propose to enhance the expressivity of TGNs by adding source-target identification to each interaction event message. We show that this modification is required to represent persistent forecasting, moving averages, and the broader class of autoregressive models over messages. Our proposed method, TGNv2, significantly outperforms TGN and all current TG models on all Temporal Graph Benchmark (TGB) dynamic node affinity prediction datasets.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.

Graphs can be used to represent and reason about systems and a variety of metrics have been devised to quantify their global characteristics. However, little is currently known about how to construct a graph or improve an existing one given a target objective. In this work, we formulate the construction of a graph as a decision-making process in which a central agent creates topologies by trial and error and receives rewards proportional to the value of the target objective. By means of this conceptual framework, we propose an algorithm based on reinforcement learning and graph neural networks to learn graph construction and improvement strategies. Our core case study focuses on robustness to failures and attacks, a property relevant for the infrastructure and communication networks that power modern society. Experiments on synthetic and real-world graphs show that this approach can outperform existing methods while being cheaper to evaluate. It also allows generalization to out-of-sample graphs, as well as to larger out-of-distribution graphs in some cases. The approach is applicable to the optimization of other global structural properties of graphs.

Machine learning on graphs has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To solve this critical challenge, automated machine learning (AutoML) on graphs which combines the strength of graph machine learning and AutoML together, is gaining attention from the research community. Therefore, we comprehensively survey AutoML on graphs in this paper, primarily focusing on hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We further overview libraries related to automated graph machine learning and in-depth discuss AutoGL, the first dedicated open-source library for AutoML on graphs. In the end, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive review of automated machine learning on graphs to the best of our knowledge.

Graph representations of programs are commonly a central element of machine learning for code research. We introduce an open source Python library python_graphs that applies static analysis to construct graph representations of Python programs suitable for training machine learning models. Our library admits the construction of control-flow graphs, data-flow graphs, and composite ``program graphs'' that combine control-flow, data-flow, syntactic, and lexical information about a program. We present the capabilities and limitations of the library, perform a case study applying the library to millions of competitive programming submissions, and showcase the library's utility for machine learning research.

Signed networks allow us to model conflicting relationships and interactions, such as friend/enemy and support/oppose. These signed interactions happen in real-time. Modeling such dynamics of signed networks is crucial to understanding the evolution of polarization in the network and enabling effective prediction of the signed structure (i.e., link signs and signed weights) in the future. However, existing works have modeled either (static) signed networks or dynamic (unsigned) networks but not dynamic signed networks. Since both sign and dynamics inform the graph structure in different ways, it is non-trivial to model how to combine the two features. In this work, we propose a new Graph Neural Network (GNN)-based approach to model dynamic signed networks, named SEMBA: Signed link's Evolution using Memory modules and Balanced Aggregation. Here, the idea is to incorporate the signs of temporal interactions using separate modules guided by balance theory and to evolve the embeddings from a higher-order neighborhood. Experiments on 4 real-world datasets and 4 different tasks demonstrate that SEMBA consistently and significantly outperforms the baselines by up to 80% on the tasks of predicting signs of future links while matching the state-of-the-art performance on predicting the existence of these links in the future. We find that this improvement is due specifically to the superior performance of SEMBA on the minority negative class.

Deploying dynamic heterogeneous graph embeddings in production faces key challenges of scalability, data freshness, and cold-start. This paper introduces a practical, two-stage solution that balances deep graph representation with low-latency incremental updates. Our framework combines HetSGFormer, a scalable graph transformer for static learning, with Incremental Locally Linear Embedding (ILLE), a lightweight, CPU-based algorithm for real-time updates. HetSGFormer captures global structure with linear scalability, while ILLE provides rapid, targeted updates to incorporate new data, thus avoiding costly full retraining. This dual approach is cold-start resilient, leveraging the graph to create meaningful embeddings from sparse data. On billion-scale graphs, A/B tests show HetSGFormer achieved up to a 6.11% lift in Advertiser Value over previous methods, while the ILLE module added another 3.22% lift and improved embedding refresh timeliness by 83.2%. Our work provides a validated framework for deploying dynamic graph learning in production environments.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

Temporal networks have been widely used to model real-world complex systems such as financial systems and e-commerce systems. In a temporal network, the joint neighborhood of a set of nodes often provides crucial structural information useful for predicting whether they may interact at a certain time. However, recent representation learning methods for temporal networks often fail to extract such information or depend on online construction of structural features, which is time-consuming. To address the issue, this work proposes Neighborhood-Aware Temporal network model (NAT). For each node in the network, NAT abandons the commonly-used one-single-vector-based representation while adopting a novel dictionary-type neighborhood representation. Such a dictionary representation records a downsampled set of the neighboring nodes as keys, and allows fast construction of structural features for a joint neighborhood of multiple nodes. We also design a dedicated data structure termed N-cache to support parallel access and update of those dictionary representations on GPUs. NAT gets evaluated over seven real-world large-scale temporal networks. NAT not only outperforms all cutting-edge baselines by averaged 1.2% and 4.2% in transductive and inductive link prediction accuracy, respectively, but also keeps scalable by achieving a speed-up of 4.1-76.7x against the baselines that adopt joint structural features and achieves a speed-up of 1.6-4.0x against the baselines that cannot adopt those features. The link to the code: https: //github.com/Graph-COM/Neighborhood-Aware-Temporal-Network.

State-of-the-art neural algorithmic reasoners make use of message passing in graph neural networks (GNNs). But typical GNNs blur the distinction between the definition and invocation of the message function, forcing a node to send messages to its neighbours at every layer, synchronously. When applying GNNs to learn to execute dynamic programming algorithms, however, on most steps only a handful of the nodes would have meaningful updates to send. One, hence, runs the risk of inefficiencies by sending too much irrelevant data across the graph -- with many intermediate GNN steps having to learn identity functions. In this work, we explicitly separate the concepts of node state update and message function invocation. With this separation, we obtain a mathematical formulation that allows us to reason about asynchronous computation in both algorithms and neural networks.

The performance of an algorithm often critically depends on its parameter configuration. While a variety of automated algorithm configuration methods have been proposed to relieve users from the tedious and error-prone task of manually tuning parameters, there is still a lot of untapped potential as the learned configuration is static, i.e., parameter settings remain fixed throughout the run. However, it has been shown that some algorithm parameters are best adjusted dynamically during execution, e.g., to adapt to the current part of the optimization landscape. Thus far, this is most commonly achieved through hand-crafted heuristics. A promising recent alternative is to automatically learn such dynamic parameter adaptation policies from data. In this article, we give the first comprehensive account of this new field of automated dynamic algorithm configuration (DAC), present a series of recent advances, and provide a solid foundation for future research in this field. Specifically, we (i) situate DAC in the broader historical context of AI research; (ii) formalize DAC as a computational problem; (iii) identify the methods used in prior-art to tackle this problem; (iv) conduct empirical case studies for using DAC in evolutionary optimization, AI planning, and machine learning.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

We investigate novel random graph embeddings that can be computed in expected polynomial time and that are able to distinguish all non-isomorphic graphs in expectation. Previous graph embeddings have limited expressiveness and either cannot distinguish all graphs or cannot be computed efficiently for every graph. To be able to approximate arbitrary functions on graphs, we are interested in efficient alternatives that become arbitrarily expressive with increasing resources. Our approach is based on Lov\'asz' characterisation of graph isomorphism through an infinite dimensional vector of homomorphism counts. Our empirical evaluation shows competitive results on several benchmark graph learning tasks.

Estimating the structure of directed acyclic graphs (DAGs, also known as Bayesian networks) is a challenging problem since the search space of DAGs is combinatorial and scales superexponentially with the number of nodes. Existing approaches rely on various local heuristics for enforcing the acyclicity constraint. In this paper, we introduce a fundamentally different strategy: We formulate the structure learning problem as a purely continuous optimization problem over real matrices that avoids this combinatorial constraint entirely. This is achieved by a novel characterization of acyclicity that is not only smooth but also exact. The resulting problem can be efficiently solved by standard numerical algorithms, which also makes implementation effortless. The proposed method outperforms existing ones, without imposing any structural assumptions on the graph such as bounded treewidth or in-degree. Code implementing the proposed algorithm is open-source and publicly available at https://github.com/xunzheng/notears.

Given a massive graph, how can we exploit its hierarchical structure for concisely but exactly summarizing the graph? By exploiting the structure, can we achieve better compression rates than state-of-the-art graph summarization methods? The explosive proliferation of the Web has accelerated the emergence of large graphs, such as online social networks and hyperlink networks. Consequently, graph compression has become increasingly important to process such large graphs without expensive I/O over the network or to disk. Among a number of approaches, graph summarization, which in essence combines similar nodes into a supernode and describe their connectivity concisely, protrudes with several advantages. However, we note that it fails to exploit pervasive hierarchical structures of real-world graphs as its underlying representation model enforces supernodes to be disjoint. In this work, we propose the hierarchical graph summarization model, which is an expressive graph representation model that includes the previous one proposed by Navlakha et al. as a special case. The new model represents an unweighted graph using positive and negative edges between hierarchical supernodes, each of which can contain others. Then, we propose Slugger, a scalable heuristic for concisely and exactly representing a given graph under our new model. Slugger greedily merges nodes into supernodes while maintaining and exploiting their hierarchy, which is later pruned. Slugger significantly accelerates this process by sampling, approximation, and memoization. Our experiments on 16 real-world graphs show that Slugger is (a) Effective: yielding up to 29.6% more concise summary than state-of-the-art lossless summarization methods, (b) Fast: summarizing a graph with 0.8 billion edges in a few hours, and (c) Scalable: scaling linearly with the number of edges in the input graph.

Persistent homology, a technique from computational topology, has recently shown strong empirical performance in the context of graph classification. Being able to capture long range graph properties via higher-order topological features, such as cycles of arbitrary length, in combination with multi-scale topological descriptors, has improved predictive performance for data sets with prominent topological structures, such as molecules. At the same time, the theoretical properties of persistent homology have not been formally assessed in this context. This paper intends to bridge the gap between computational topology and graph machine learning by providing a brief introduction to persistent homology in the context of graphs, as well as a theoretical discussion and empirical analysis of its expressivity for graph learning tasks.

We study a class of optimization problems motivated by automating the design and update of AI systems like coding assistants, robots, and copilots. We propose an end-to-end optimization framework, Trace, which treats the computational workflow of an AI system as a graph akin to neural networks, based on a generalization of back-propagation. Optimization of computational workflows often involves rich feedback (e.g. console output or user's responses), heterogeneous parameters (e.g. prompts, hyper-parameters, codes), and intricate objectives (beyond maximizing a score). Moreover, its computation graph can change dynamically with the inputs and parameters. We frame a new mathematical setup of iterative optimization, Optimization with Trace Oracle (OPTO), to capture and abstract these properties so as to design optimizers that work across many domains. In OPTO, an optimizer receives an execution trace along with feedback on the computed output and updates parameters iteratively. Trace is the tool to implement OPTO in practice. Trace has a Python interface that efficiently converts a computational workflow into an OPTO instance using a PyTorch-like interface. Using Trace, we develop a general-purpose LLM-based optimizer called OptoPrime that can effectively solve OPTO problems. In empirical studies, we find that OptoPrime is capable of first-order numerical optimization, prompt optimization, hyper-parameter tuning, robot controller design, code debugging, etc., and is often competitive with specialized optimizers for each domain. We believe that Trace, OptoPrime and the OPTO framework will enable the next generation of interactive agents that automatically adapt using various kinds of feedback. Website: https://microsoft.github.io/Trace

Simulating physics using Graph Neural Networks (GNNs) is predominantly driven by message-passing architectures, which face challenges in scaling and efficiency, particularly in handling large, complex meshes. These architectures have inspired numerous enhancements, including multigrid approaches and K-hop aggregation (using neighbours of distance K), yet they often introduce significant complexity and suffer from limited in-depth investigations. In response to these challenges, we propose a novel Graph Transformer architecture that leverages the adjacency matrix as an attention mask. The proposed approach incorporates innovative augmentations, including Dilated Sliding Windows and Global Attention, to extend receptive fields without sacrificing computational efficiency. Through extensive experimentation, we evaluate model size, adjacency matrix augmentations, positional encoding and K-hop configurations using challenging 3D computational fluid dynamics (CFD) datasets. We also train over 60 models to find a scaling law between training FLOPs and parameters. The introduced models demonstrate remarkable scalability, performing on meshes with up to 300k nodes and 3 million edges. Notably, the smallest model achieves parity with MeshGraphNet while being 7times faster and 6times smaller. The largest model surpasses the previous state-of-the-art by 38.8\% on average and outperforms MeshGraphNet by 52\% on the all-rollout RMSE, while having a similar training speed. Code and datasets are available at https://github.com/DonsetPG/graph-physics.

In recent years, many large directed networks such as online social networks are collected with the help of powerful data engineering and data storage techniques. Analyses of such networks attract significant attention from both the academics and industries. However, analyses of large directed networks are often time-consuming and expensive because the complexities of a lot of graph algorithms are often polynomial with the size of the graph. Hence, sampling algorithms that can generate graphs preserving properties of original graph are of great importance because they can speed up the analysis process. We propose a promising framework to sample directed graphs: Construct a sample graph with linearly rescaled Joint Degree Matrix (JDM) and Degree Correlation Matrix (DCM). Previous work shows that graphs with the same JDM and DCM will have a range of very similar graph properties. We also conduct experiments on real-world datasets to show that the numbers of non-zero entries in JDM and DCM are quite small compared to the number of edges and nodes. Adopting this framework, we propose a novel graph sampling algorithm that can provably preserves in-degree and out-degree distributions, which are two most fundamental properties of a graph. We also prove the upper bound for deviations in the joint degree distribution and degree correlation distribution, which correspond to JDM and DCM. Besides, we prove that the deviations in these distributions are negatively correlated with the sparsity of the JDM and DCM. Considering that these two matrices are always quite sparse, we believe that proposed algorithm will have a better-than-theory performance on real-world large directed networks.

Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional 'Pre-train & Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates SIX pre-training methods and FIVE state-of-the-art graph prompt techniques, evaluated across FIFTEEN diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG.

Graphs have often been used to answer questions about the interaction between real-world entities by taking advantage of their capacity to represent complex topologies. Complex networks are known to be graphs that capture such non-trivial topologies; they are able to represent human phenomena such as epidemic processes, the dynamics of populations, and the urbanization of cities. The investigation of complex networks has been extrapolated to many fields of science, with particular emphasis on computing techniques, including artificial intelligence. In such a case, the analysis of the interaction between entities of interest is transposed to the internal learning of algorithms, a paradigm whose investigation is able to expand the state of the art in Computer Science. By exploring this paradigm, this thesis puts together complex networks and machine learning techniques to improve the understanding of the human phenomena observed in pandemics, pendular migration, and street networks. Accordingly, we contribute with: (i) a new neural network architecture capable of modeling dynamic processes observed in spatial and temporal data with applications in epidemics propagation, weather forecasting, and patient monitoring in intensive care units; (ii) a machine-learning methodology for analyzing and predicting links in the scope of human mobility between all the cities of Brazil; and, (iii) techniques for identifying inconsistencies in the urban planning of cities while tracking the most influential vertices, with applications over Brazilian and worldwide cities. We obtained results sustained by sound evidence of advances to the state of the art in artificial intelligence, rigorous formalisms, and ample experimentation. Our findings rely upon real-world applications in a range of domains, demonstrating the applicability of our methodologies.

Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or cannot sufficiently model the complex dependency between nodes and edges, which is crucial for generating real-world graphs such as molecules. To overcome such limitations, we propose a novel score-based generative model for graphs with a continuous-time framework. Specifically, we propose a new graph diffusion process that models the joint distribution of the nodes and edges through a system of stochastic differential equations (SDEs). Then, we derive novel score matching objectives tailored for the proposed diffusion process to estimate the gradient of the joint log-density with respect to each component, and introduce a new solver for the system of SDEs to efficiently sample from the reverse diffusion process. We validate our graph generation method on diverse datasets, on which it either achieves significantly superior or competitive performance to the baselines. Further analysis shows that our method is able to generate molecules that lie close to the training distribution yet do not violate the chemical valency rule, demonstrating the effectiveness of the system of SDEs in modeling the node-edge relationships. Our code is available at https://github.com/harryjo97/GDSS.

Graph Neural Networks (GNNs) have emerged as powerful tools for learning on graph-structured data, but often struggle to balance local and global information. While graph Transformers aim to address this by enabling long-range interactions, they often overlook the inherent locality and efficiency of Message Passing Neural Networks (MPNNs). We propose a new concept called fractal nodes, inspired by the fractal structure observed in real-world networks. Our approach is based on the intuition that graph partitioning naturally induces fractal structure, where subgraphs often reflect the connectivity patterns of the full graph. Fractal nodes are designed to coexist with the original nodes and adaptively aggregate subgraph-level feature representations, thereby enforcing feature similarity within each subgraph. We show that fractal nodes alleviate the over-squashing problem by providing direct shortcut connections that enable long-range propagation of subgraph-level representations. Experiment results show that our method improves the expressive power of MPNNs and achieves comparable or better performance to graph Transformers while maintaining the computational efficiency of MPNN by improving the long-range dependencies of MPNN.

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

We introduce fast algorithms for correlation clustering with respect to the Min Max objective that provide constant factor approximations on complete graphs. Our algorithms are the first purely combinatorial approximation algorithms for this problem. We construct a novel semi-metric on the set of vertices, which we call the correlation metric, that indicates to our clustering algorithms whether pairs of nodes should be in the same cluster. The paper demonstrates empirically that, compared to prior work, our algorithms sacrifice little in the objective quality to obtain significantly better run-time. Moreover, our algorithms scale to larger networks that are effectively intractable for known algorithms.

Large Language Models (LLMs) have demonstrated impressive reasoning capabilities, yet their performance is highly dependent on the prompting strategy and model scale. While reinforcement learning and fine-tuning have been deployed to boost reasoning, these approaches incur substantial computational and data overhead. In this work, we introduce Adaptive Graph of Thoughts (AGoT), a dynamic, graph-based inference framework that enhances LLM reasoning solely at test time. Rather than relying on fixed-step methods like Chain of Thought (CoT) or Tree of Thoughts (ToT), AGoT recursively decomposes complex queries into structured subproblems, forming an dynamic directed acyclic graph (DAG) of interdependent reasoning steps. By selectively expanding only those subproblems that require further analysis, AGoT unifies the strengths of chain, tree, and graph paradigms into a cohesive framework that allocates computation where it is most needed. We validate our approach on diverse benchmarks spanning multi-hop retrieval, scientific reasoning, and mathematical problem-solving, achieving up to 46.2% improvement on scientific reasoning tasks (GPQA) - comparable to gains achieved through computationally intensive reinforcement learning approaches and outperforming state-of-the-art iterative approaches. These results suggest that dynamic decomposition and structured recursion offer a scalable, cost-effective alternative to post-training modifications, paving the way for more robust, general-purpose reasoning in LLMs.

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

Layer-wise Relevance Propagation (LRP) provides principled attribution for neural networks through conservation properties and foundations in Deep Taylor Decomposition. However, existing implementations operate at the module level, requiring architecture-specific propagation rules and modifications. These limit the generality of target model and sustainability of implementations as architectures evolve. We introduce DynamicLRP, a model-agnostic LRP framework operating at the tensor operation level. By decomposing attribution to individual operations within computation graphs and introducing a novel mechanism for deferred activation resolution, named the Promise System, our approach achieves true architecture agnosticity while maintaining LRP's theoretical guarantees. This design operates independently of backpropagation machinery, enabling operation on arbitrary computation graphs without model modification and side-by-side execution with gradient backpropagation. Being based on computation graphs, this method is theoretically extensible to other deep learning libraries that support auto-differentiation. We demonstrate faithfulness matching or exceeding specialized implementations (1.77 vs 1.69 ABPC on VGG, equivalent performance on ViT, 93.70\% and 95.06\% top-1 attribution accuracy for explaining RoBERTa-large and Flan-T5-large answers on SQuADv2, respectively) while maintaining practical efficiency on models with hundreds of millions of parameters. We achieved 99.92\% node coverage across 31,465 computation graph nodes from 15 diverse architectures, including state-space models (Mamba), audio transformers (Whisper), and multimodal systems (DePlot) without any model-specific code with rules for 47 fundamental operations implemented. Our operation-level decomposition and Promise System establish a sustainable, extensible foundation for LRP across evolving architectures.

In the graph node embedding problem, embedding spaces can vary significantly for different data types, leading to the need for different GNN model types. In this paper, we model the embedding update of a node feature as a Hamiltonian orbit over time. Since the Hamiltonian orbits generalize the exponential maps, this approach allows us to learn the underlying manifold of the graph in training, in contrast to most of the existing literature that assumes a fixed graph embedding manifold with a closed exponential map solution. Our proposed node embedding strategy can automatically learn, without extensive tuning, the underlying geometry of any given graph dataset even if it has diverse geometries. We test Hamiltonian functions of different forms and verify the performance of our approach on two graph node embedding downstream tasks: node classification and link prediction. Numerical experiments demonstrate that our approach adapts better to different types of graph datasets than popular state-of-the-art graph node embedding GNNs. The code is available at https://github.com/zknus/Hamiltonian-GNN.

While Graph Neural Networks have gained popularity in multiple domains, graph-structured input remains a major challenge due to (a) over-smoothing, (b) noisy neighbours (heterophily), and (c) the suspended animation problem. To address all these problems simultaneously, we propose a novel graph neural network FDGATII, inspired by attention mechanism's ability to focus on selective information supplemented with two feature preserving mechanisms. FDGATII combines Initial Residuals and Identity Mapping with the more expressive dynamic self-attention to handle noise prevalent from the neighbourhoods in heterophilic data sets. By using sparse dynamic attention, FDGATII is inherently parallelizable in design, whist efficient in operation; thus theoretically able to scale to arbitrary graphs with ease. Our approach has been extensively evaluated on 7 datasets. We show that FDGATII outperforms GAT and GCN based benchmarks in accuracy and performance on fully supervised tasks, obtaining state-of-the-art results on Chameleon and Cornell datasets with zero domain-specific graph pre-processing, and demonstrate its versatility and fairness.

Large Language Model (LLM)-based agents have demonstrated remarkable effectiveness. However, their performance can be compromised in data science scenarios that require real-time data adjustment, expertise in optimization due to complex dependencies among various tasks, and the ability to identify logical errors for precise reasoning. In this study, we introduce the Data Interpreter, a solution designed to solve with code that emphasizes three pivotal techniques to augment problem-solving in data science: 1) dynamic planning with hierarchical graph structures for real-time data adaptability;2) tool integration dynamically to enhance code proficiency during execution, enriching the requisite expertise;3) logical inconsistency identification in feedback, and efficiency enhancement through experience recording. We evaluate the Data Interpreter on various data science and real-world tasks. Compared to open-source baselines, it demonstrated superior performance, exhibiting significant improvements in machine learning tasks, increasing from 0.86 to 0.95. Additionally, it showed a 26% increase in the MATH dataset and a remarkable 112% improvement in open-ended tasks. The solution will be released at https://github.com/geekan/MetaGPT.

Motivated by applications in chemistry and other sciences, we study the expressive power of message-passing neural networks for geometric graphs, whose node features correspond to 3-dimensional positions. Recent work has shown that such models can separate generic pairs of non-isomorphic geometric graphs, though they may fail to separate some rare and complicated instances. However, these results assume a fully connected graph, where each node possesses complete knowledge of all other nodes. In contrast, often, in application, every node only possesses knowledge of a small number of nearest neighbors. This paper shows that generic pairs of non-isomorphic geometric graphs can be separated by message-passing networks with rotation equivariant features as long as the underlying graph is connected. When only invariant intermediate features are allowed, generic separation is guaranteed for generically globally rigid graphs. We introduce a simple architecture, EGENNET, which achieves our theoretical guarantees and compares favorably with alternative architecture on synthetic and chemical benchmarks. Our code is available at https://github.com/yonatansverdlov/E-GenNet.

We present a new class of fast polylog-linear algorithms based on the theory of structured matrices (in particular low displacement rank) for integrating tensor fields defined on weighted trees. Several applications of the resulting fast tree-field integrators (FTFIs) are presented, including (a) approximation of graph metrics with tree metrics, (b) graph classification, (c) modeling on meshes, and finally (d) Topological Transformers (TTs) (Choromanski et al., 2022) for images. For Topological Transformers, we propose new relative position encoding (RPE) masking mechanisms with as few as three extra learnable parameters per Transformer layer, leading to 1.0-1.5%+ accuracy gains. Importantly, most of FTFIs are exact methods, thus numerically equivalent to their brute-force counterparts. When applied to graphs with thousands of nodes, those exact algorithms provide 5.7-13x speedups. We also provide an extensive theoretical analysis of our methods.

Acceleration of graph applications on GPUs has found large interest due to the ubiquitous use of graph processing in various domains. The inherent irregularity in graph applications leads to several challenges for parallelization. A key challenge, which we address in this paper, is that of load-imbalance. If the work-assignment to threads uses node-based graph partitioning, it can result in skewed task-distribution, leading to poor load-balance. In contrast, if the work-assignment uses edge-based graph partitioning, the load-balancing is better, but the memory requirement is relatively higher. This makes it unsuitable for large graphs. In this work, we propose three techniques for improved load-balancing of graph applications on GPUs. Each technique brings in unique advantages, and a user may have to employ a specific technique based on the requirement. Using Breadth First Search and Single Source Shortest Paths as our processing kernels, we illustrate the effectiveness of each of the proposed techniques in comparison to the existing node-based and edge-based mechanisms.

Large language models (LLMs) have achieved remarkable performance in various evaluation benchmarks. However, concerns are raised about potential data contamination in their considerable volume of training corpus. Moreover, the static nature and fixed complexity of current benchmarks may inadequately gauge the advancing capabilities of LLMs. In this paper, we introduce DyVal, a general and flexible protocol for dynamic evaluation of LLMs. Based on our framework, we build graph-informed DyVal by leveraging the structural advantage of directed acyclic graphs to dynamically generate evaluation samples with controllable complexities. DyVal generates challenging evaluation sets on reasoning tasks including mathematics, logical reasoning, and algorithm problems. We evaluate various LLMs ranging from Flan-T5-large to GPT-3.5-Turbo and GPT-4. Experiments show that LLMs perform worse in DyVal-generated evaluation samples with different complexities, highlighting the significance of dynamic evaluation. We also analyze the failure cases and results of different prompting methods. Moreover, DyVal-generated samples are not only evaluation sets, but also helpful data for fine-tuning to improve the performance of LLMs on existing benchmarks. We hope that DyVal can shed light on future evaluation research of LLMs. Code is available at: https://github.com/microsoft/promptbench.

The structure learning problem consists of fitting data generated by a Directed Acyclic Graph (DAG) to correctly reconstruct its arcs. In this context, differentiable approaches constrain or regularize the optimization problem using a continuous relaxation of the acyclicity property. The computational cost of evaluating graph acyclicity is cubic on the number of nodes and significantly affects scalability. In this paper we introduce COSMO, a constraint-free continuous optimization scheme for acyclic structure learning. At the core of our method, we define a differentiable approximation of an orientation matrix parameterized by a single priority vector. Differently from previous work, our parameterization fits a smooth orientation matrix and the resulting acyclic adjacency matrix without evaluating acyclicity at any step. Despite the absence of explicit constraints, we prove that COSMO always converges to an acyclic solution. In addition to being asymptotically faster, our empirical analysis highlights how COSMO performance on graph reconstruction compares favorably with competing structure learning methods.

Hypergraphs are a powerful abstraction for representing higher-order interactions between entities of interest. To exploit these relationships in making downstream predictions, a variety of hypergraph neural network architectures have recently been proposed, in large part building upon precursors from the more traditional graph neural network (GNN) literature. Somewhat differently, in this paper we begin by presenting an expressive family of parameterized, hypergraph-regularized energy functions. We then demonstrate how minimizers of these energies effectively serve as node embeddings that, when paired with a parameterized classifier, can be trained end-to-end via a supervised bilevel optimization process. Later, we draw parallels between the implicit architecture of the predictive models emerging from the proposed bilevel hypergraph optimization, and existing GNN architectures in common use. Empirically, we demonstrate state-of-the-art results on various hypergraph node classification benchmarks. Code is available at https://github.com/yxzwang/PhenomNN.

Attention mechanisms have been widely used to capture long-range dependencies among nodes in Graph Transformers. Bottlenecked by the quadratic computational cost, attention mechanisms fail to scale in large graphs. Recent improvements in computational efficiency are mainly achieved by attention sparsification with random or heuristic-based graph subsampling, which falls short in data-dependent context reasoning. State space models (SSMs), such as Mamba, have gained prominence for their effectiveness and efficiency in modeling long-range dependencies in sequential data. However, adapting SSMs to non-sequential graph data presents a notable challenge. In this work, we introduce Graph-Mamba, the first attempt to enhance long-range context modeling in graph networks by integrating a Mamba block with the input-dependent node selection mechanism. Specifically, we formulate graph-centric node prioritization and permutation strategies to enhance context-aware reasoning, leading to a substantial improvement in predictive performance. Extensive experiments on ten benchmark datasets demonstrate that Graph-Mamba outperforms state-of-the-art methods in long-range graph prediction tasks, with a fraction of the computational cost in both FLOPs and GPU memory consumption. The code and models are publicly available at https://github.com/bowang-lab/Graph-Mamba.