Spatiotemporal graph neural networks (ST-GNNs) are powerful tools for modeling spatial and temporal data dependencies. However, their applications have been limited primarily to small-scale datasets because of memory constraints. While distributed training offers a solution, current frameworks lack support for spatiotemporal models and overlook the properties of spatiotemporal data. Informed by a scaling study on a large-scale workload, we present PyTorch Geometric Temporal Index (PGT-I), an extension to PyTorch Geometric Temporal that integrates distributed data parallel training and two novel strategies: index-batching and distributed-index-batching. Our index techniques exploit spatiotemporal structure to construct snapshots dynamically at runtime, significantly reducing memory overhead, while distributed-index-batching extends this approach by enabling scalable processing across multiple GPUs. Our techniques enable the first-ever training of an ST-GNN on the entire PeMS dataset without graph partitioning, reducing peak memory usage by up to 89\% and achieving up to a 13.1x speedup over standard DDP with 128 GPUs.
Graph neural networks (GNNs) are powerful tools for solving graph-related problems. Distributed GNN frameworks and systems enhance the scalability of GNNs and accelerate model training, yet most are optimized for node classification. Their performance on link prediction remains underexplored. This paper demystifies distributed training of GNNs for link prediction by investigating the issue of performance degradation when each worker trains a GNN on its assigned partitioned subgraph without having access to the entire graph. We discover that the main sources of the issue come from not only the information loss caused by graph partitioning but also the ways of drawing negative samples during model training. While sharing the complete graph information with each worker resolves the issue and preserves link prediction accuracy, it incurs a high communication cost. We propose SpLPG, which effectively leverages graph sparsification to mitigate the issue of performance degradation at a reduced communication cost. Experiment results on several public real-world datasets demonstrate the effectiveness of SpLPG, which reduces the communication overhead by up to about 80% while mostly preserving link prediction accuracy.
Large-scale atomistic simulations are essential to bridge computational materials and chemistry to realistic materials and drug discovery applications. In the past few years, rapid developments of machine learning interatomic potentials (MLIPs) have offered a solution to scale up quantum mechanical calculations. Parallelizing these interatomic potentials across multiple devices poses a challenging, but promising approach to further extending simulation scales to real-world applications. In this work, we present DistMLIP, an efficient distributed inference platform for MLIPs based on zero-redundancy, graph-level parallelization. In contrast to conventional space-partitioning parallelization, DistMLIP enables efficient MLIP parallelization through graph partitioning, allowing multi-device inference on flexible MLIP model architectures like multi-layer graph neural networks. DistMLIP presents an easy-to-use, flexible, plug-in interface that enables distributed inference of pre-existing MLIPs. We demonstrate DistMLIP on four widely used and state-of-the-art MLIPs: CHGNet, MACE, TensorNet, and eSEN. We show that existing foundational potentials can perform near-million-atom calculations at the scale of a few seconds on 8 GPUs with DistMLIP.
Superpixel segmentation is a foundation for many higher-level computer vision tasks, such as image segmentation, object recognition, and scene understanding. Existing graph-based superpixel segmentation methods typically concentrate on the relationships between a given pixel and its directly adjacent pixels while overlooking the influence of non-adjacent pixels. These approaches do not fully leverage the global information in the graph, leading to suboptimal segmentation quality. To address this limitation, we present SIT-HSS, a hierarchical superpixel segmentation method based on structural information theory. Specifically, we first design a novel graph construction strategy that incrementally explores the pixel neighborhood to add edges based on 1-dimensional structural entropy (1D SE). This strategy maximizes the retention of graph information while avoiding an overly complex graph structure. Then, we design a new 2D SE-guided hierarchical graph partitioning method, which iteratively merges pixel clusters layer by layer to reduce the graph's 2D SE until a predefined segmentation scale is achieved. Experimental results on three benchmark datasets demonstrate that the SIT-HSS performs better than state-of-the-art unsupervised superpixel segmentation algorithms. The source code is available at \url{https://github.com/SELGroup/SIT-HSS}.
Recent studies have highlighted significant fairness issues in Graph Transformer (GT) models, particularly against subgroups defined by sensitive features. Additionally, GTs are computationally intensive and memory-demanding, limiting their application to large-scale graphs. Our experiments demonstrate that graph partitioning can enhance the fairness of GT models while reducing computational complexity. To understand this improvement, we conducted a theoretical investigation into the root causes of fairness issues in GT models. We found that the sensitive features of higher-order nodes disproportionately influence lower-order nodes, resulting in sensitive feature bias. We propose Fairness-aware scalable GT based on Graph Partitioning (FairGP), which partitions the graph to minimize the negative impact of higher-order nodes. By optimizing attention mechanisms, FairGP mitigates the bias introduced by global attention, thereby enhancing fairness. Extensive empirical evaluations on six real-world datasets validate the superior performance of FairGP in achieving fairness compared to state-of-the-art methods. The codes are available at https://github.com/LuoRenqiang/FairGP.
Epidemic prediction is of practical significance in public health, enabling early intervention, resource allocation, and strategic planning. However, privacy concerns often hinder the sharing of health data among institutions, limiting the development of accurate prediction models. In this paper, we develop a general privacy-preserving framework for node-level epidemic prediction on networks based on federated learning (FL). We frame the spatio-temporal spread of epidemics across multiple data-isolated subnetworks, where each node state represents the aggregate epidemic severity within a community. Then, both the pure temporal LSTM model and the spatio-temporal model i.e., Spatio-Temporal Graph Attention Network (STGAT) are proposed to address the federated epidemic prediction. Extensive experiments are conducted on various epidemic processes using a practical airline network, offering a comprehensive assessment of FL efficacy under diverse scenarios. By introducing the efficacy energy metric to measure system robustness under various client configurations, we systematically explore key factors influencing FL performance, including client numbers, aggregation strategies, graph partitioning, missing infectious reports. Numerical results manifest that STGAT excels in capturing spatio-temporal dependencies in dynamic processes whereas LSTM performs well in simpler pattern. Moreover, our findings highlight the importance of balancing feature consistency and volume uniformity among clients, as well as the prediction dilemma between information richness and intrinsic stochasticity of dynamic processes. This study offers practical insights into the efficacy of FL scenario in epidemic management, demonstrates the potential of FL to address broader collective dynamics.
The features of self-supervised vision transformers (ViTs) contain strong semantic and positional information relevant to downstream tasks like object localization and segmentation. Recent works combine these features with traditional methods like clustering, graph partitioning or region correlations to achieve impressive baselines without finetuning or training additional networks. We leverage upsampled features from ViT networks (e.g DINOv2) in two workflows: in a clustering based approach for object localization and segmentation, and paired with standard classifiers in weakly supervised materials segmentation. Both show strong performance on benchmarks, especially in weakly supervised segmentation where the ViT features capture complex relationships inaccessible to classical approaches. We expect the flexibility and generalizability of these features will both speed up and strengthen materials characterization, from segmentation to property-prediction.
Graph partitioning (GP) is a classic problem that divides the node set of a graph into densely-connected blocks. Following the IEEE HPEC Graph Challenge and recent advances in pre-training techniques (e.g., large-language models), we propose PR-GPT (Pre-trained & Refined Graph ParTitioning) based on a novel pre-training & refinement paradigm. We first conduct the offline pre-training of a deep graph learning (DGL) model on small synthetic graphs with various topology properties. By using the inductive inference of DGL, one can directly generalize the pre-trained model (with frozen model parameters) to large graphs and derive feasible GP results. We also use the derived partition as a good initialization of an efficient GP method (e.g., InfoMap) to further refine the quality of partitioning. In this setting, the online generalization and refinement of PR-GPT can not only benefit from the transfer ability regarding quality but also ensure high inference efficiency without re-training. Based on a mechanism of reducing the scale of a graph to be processed by the refinement method, PR-GPT also has the potential to support streaming GP. Experiments on the Graph Challenge benchmark demonstrate that PR-GPT can ensure faster GP on large-scale graphs without significant quality degradation, compared with running a refinement method from scratch. We will make our code public at https://github.com/KuroginQin/PRGPT.
Surgical instrument segmentation (SIS) on endoscopic images stands as a long-standing and essential task in the context of computer-assisted interventions for boosting minimally invasive surgery. Given the recent surge of deep learning methodologies and their data-hungry nature, training a neural predictive model based on massive expert-curated annotations has been dominating and served as an off-the-shelf approach in the field, which could, however, impose prohibitive burden to clinicians for preparing fine-grained pixel-wise labels corresponding to the collected surgical video frames. In this work, we propose an unsupervised method by reframing the video frame segmentation as a graph partitioning problem and regarding image pixels as graph nodes, which is significantly different from the previous efforts. A self-supervised pre-trained model is firstly leveraged as a feature extractor to capture high-level semantic features. Then, Laplacian matrixs are computed from the features and are eigendecomposed for graph partitioning. On the "deep" eigenvectors, a surgical video frame is meaningfully segmented into different modules such as tools and tissues, providing distinguishable semantic information like locations, classes, and relations. The segmentation problem can then be naturally tackled by applying clustering or threshold on the eigenvectors. Extensive experiments are conducted on various datasets (e.g., EndoVis2017, EndoVis2018, UCL, etc.) for different clinical endpoints. Across all the challenging scenarios, our method demonstrates outstanding performance and robustness higher than unsupervised state-of-the-art (SOTA) methods. The code is released at https://github.com/MingyuShengSMY/GraphClusteringSIS.git.
The aim in many sciences is to understand the mechanisms that underlie the observed distribution of variables, starting from a set of initial hypotheses. Causal discovery allows us to infer mechanisms as sets of cause and effect relationships in a generalized way -- without necessarily tailoring to a specific domain. Causal discovery algorithms search over a structured hypothesis space, defined by the set of directed acyclic graphs, to find the graph that best explains the data. For high-dimensional problems, however, this search becomes intractable and scalable algorithms for causal discovery are needed to bridge the gap. In this paper, we define a novel causal graph partition that allows for divide-and-conquer causal discovery with theoretical guarantees. We leverage the idea of a superstructure -- a set of learned or existing candidate hypotheses -- to partition the search space. We prove under certain assumptions that learning with a causal graph partition always yields the Markov Equivalence Class of the true causal graph. We show our algorithm achieves comparable accuracy and a faster time to solution for biologically-tuned synthetic networks and networks up to ${10^4}$ variables. This makes our method applicable to gene regulatory network inference and other domains with high-dimensional structured hypothesis spaces.
This paper proposes a problem-independent GRASP metaheuristic using the random-key optimizer (RKO) paradigm. GRASP (greedy randomized adaptive search procedure) is a metaheuristic for combinatorial optimization that repeatedly applies a semi-greedy construction procedure followed by a local search procedure. The best solution found over all iterations is returned as the solution of the GRASP. Continuous GRASP (C-GRASP) is an extension of GRASP for continuous optimization in the unit hypercube. A random-key optimizer (RKO) uses a vector of random keys to encode a solution to a combinatorial optimization problem. It uses a decoder to evaluate a solution encoded by the vector of random keys. A random-key GRASP is a C-GRASP where points in the unit hypercube are evaluated employing a decoder. We describe random key GRASP consisting of a problem-independent component and a problem-dependent decoder. As a proof of concept, the random-key GRASP is tested on five NP-hard combinatorial optimization problems: traveling salesman problem, tree of hubs location problem, Steiner triple covering problem, node capacitated graph partitioning problem, and job sequencing and tool switching problem.
Computation graphs are Directed Acyclic Graphs (DAGs) where the nodes correspond to mathematical operations and are used widely as abstractions in optimizations of neural networks. The device placement problem aims to identify optimal allocations of those nodes to a set of (potentially heterogeneous) devices. Existing approaches rely on two types of architectures known as grouper-placer and encoder-placer, respectively. In this work, we bridge the gap between encoder-placer and grouper-placer techniques and propose a novel framework for the task of device placement, relying on smaller computation graphs extracted from the OpenVINO toolkit. The framework consists of five steps, including graph coarsening, node representation learning and policy optimization. It facilitates end-to-end training and takes into account the DAG nature of the computation graphs. We also propose a model variant, inspired by graph parsing networks and complex network analysis, enabling graph representation learning and jointed, personalized graph partitioning, using an unspecified number of groups. To train the entire framework, we use reinforcement learning using the execution time of the placement as a reward. We demonstrate the flexibility and effectiveness of our approach through multiple experiments with three benchmark models, namely Inception-V3, ResNet, and BERT. The robustness of the proposed framework is also highlighted through an ablation study. The suggested placements improve the inference speed for the benchmark models by up to 58.2% over CPU execution and by up to 60.24% compared to other commonly used baselines.
Key Point Analysis (KPA), the summarization of multiple arguments into a concise collection of key points, continues to be a significant and unresolved issue within the field of argument mining. Existing models adapt a two-stage pipeline of clustering arguments or generating key points for argument clusters. This approach rely on semantic similarity instead of measuring the existence of shared key points among arguments. Additionally, it only models the intra-cluster relationship among arguments, disregarding the inter-cluster relationship between arguments that do not share key points. To address these limitations, we propose a novel approach for KPA with pairwise generation and graph partitioning. Our objective is to train a generative model that can simultaneously provide a score indicating the presence of shared key point between a pair of arguments and generate the shared key point. Subsequently, to map generated redundant key points to a concise set of key points, we proceed to construct an arguments graph by considering the arguments as vertices, the generated key points as edges, and the scores as edge weights. We then propose a graph partitioning algorithm to partition all arguments sharing the same key points to the same subgraph. Notably, our experimental findings demonstrate that our proposed model surpasses previous models when evaluated on both the ArgKP and QAM datasets.
In this paper, we introduce VoteCut, an innovative method for unsupervised object discovery that leverages feature representations from multiple self-supervised models. VoteCut employs normalized-cut based graph partitioning, clustering and a pixel voting approach. Additionally, We present CuVLER (Cut-Vote-and-LEaRn), a zero-shot model, trained using pseudo-labels, generated by VoteCut, and a novel soft target loss to refine segmentation accuracy. Through rigorous evaluations across multiple datasets and several unsupervised setups, our methods demonstrate significant improvements in comparison to previous state-of-the-art models. Our ablation studies further highlight the contributions of each component, revealing the robustness and efficacy of our approach. Collectively, VoteCut and CuVLER pave the way for future advancements in image segmentation.
We consider the fundamental problem of decomposing a large-scale approximate nearest neighbor search (ANNS) problem into smaller sub-problems. The goal is to partition the input points into neighborhood-preserving shards, so that the nearest neighbors of any point are contained in only a few shards. When a query arrives, a routing algorithm is used to identify the shards which should be searched for its nearest neighbors. This approach forms the backbone of distributed ANNS, where the dataset is so large that it must be split across multiple machines. In this paper, we design simple and highly efficient routing methods, and prove strong theoretical guarantees on their performance. A crucial characteristic of our routing algorithms is that they are inherently modular, and can be used with any partitioning method. This addresses a key drawback of prior approaches, where the routing algorithms are inextricably linked to their associated partitioning method. In particular, our new routing methods enable the use of balanced graph partitioning, which is a high-quality partitioning method without a naturally associated routing algorithm. Thus, we provide the first methods for routing using balanced graph partitioning that are extremely fast to train, admit low latency, and achieve high recall. We provide a comprehensive evaluation of our full partitioning and routing pipeline on billion-scale datasets, where it outperforms existing scalable partitioning methods by significant margins, achieving up to 2.14x higher QPS at 90% recall$@10$ than the best competitor.
Conventional fair graph clustering methods face two primary challenges: i) They prioritize balanced clusters at the expense of cluster cohesion by imposing rigid constraints, ii) Existing methods of both individual and group-level fairness in graph partitioning mostly rely on eigen decompositions and thus, generally lack interpretability. To address these issues, we propose iFairNMTF, an individual Fairness Nonnegative Matrix Tri-Factorization model with contrastive fairness regularization that achieves balanced and cohesive clusters. By introducing fairness regularization, our model allows for customizable accuracy-fairness trade-offs, thereby enhancing user autonomy without compromising the interpretability provided by nonnegative matrix tri-factorization. Experimental evaluations on real and synthetic datasets demonstrate the superior flexibility of iFairNMTF in achieving fairness and clustering performance.
Deep spectral methods reframe the image decomposition process as a graph partitioning task by extracting features using self-supervised learning and utilizing the Laplacian of the affinity matrix to obtain eigensegments. However, instance segmentation has received less attention compared to other tasks within the context of deep spectral methods. This paper addresses the fact that not all channels of the feature map extracted from a self-supervised backbone contain sufficient information for instance segmentation purposes. In fact, Some channels are noisy and hinder the accuracy of the task. To overcome this issue, this paper proposes two channel reduction modules: Noise Channel Reduction (NCR) and Deviation-based Channel Reduction (DCR). The NCR retains channels with lower entropy, as they are less likely to be noisy, while DCR prunes channels with low standard deviation, as they lack sufficient information for effective instance segmentation. Furthermore, the paper demonstrates that the dot product, commonly used in deep spectral methods, is not suitable for instance segmentation due to its sensitivity to feature map values, potentially leading to incorrect instance segments. A new similarity metric called Bray-Curtis over Chebyshev (BoC) is proposed to address this issue. It takes into account the distribution of features in addition to their values, providing a more robust similarity measure for instance segmentation. Quantitative and qualitative results on the Youtube-VIS2019 dataset highlight the improvements achieved by the proposed channel reduction methods and the use of BoC instead of the conventional dot product for creating the affinity matrix. These improvements are observed in terms of mean Intersection over Union and extracted instance segments, demonstrating enhanced instance segmentation performance. The code is available on: https://github.com/farnooshar/SpecUnIIS
We present a novel local improvement scheme for the perfectly balanced graph partitioning problem. This scheme encodes local searches that are not restricted to a balance constraint into a model allowing us to find combinations of these searches maintaining balance by applying a negative cycle detection algorithm. We combine this technique with an algorithm to balance unbalanced solutions and integrate it into a parallel multi-level evolutionary algorithm, KaFFPaE, to tackle the problem. Overall, we obtain a system that is fast on the one hand and on the other hand is able to improve or reproduce most of the best known perfectly balanced partitioning results ever reported in the literature.
We present a novel distributed evolutionary algorithm, KaFFPaE, to solve the Graph Partitioning Problem, which makes use of KaFFPa (Karlsruhe Fast Flow Partitioner). The use of our multilevel graph partitioner KaFFPa provides new effective crossover and mutation operators. By combining these with a scalable communication protocol we obtain a system that is able to improve the best known partitioning results for many inputs in a very short amount of time. For example, in Walshaw's well known benchmark tables we are able to improve or recompute 76% of entries for the tables with 1%, 3% and 5% imbalance.
There is a considerable body of work on data cleaning which employs various principles to rectify erroneous data and transform a dirty dataset into a cleaner one. One of prevalent approaches is probabilistic methods, including Bayesian methods. However, existing probabilistic methods often assume a simplistic distribution (e.g., Gaussian distribution), which is frequently underfitted in practice, or they necessitate experts to provide a complex prior distribution (e.g., via a programming language). This requirement is both labor-intensive and costly, rendering these methods less suitable for real-world applications. In this paper, we propose BClean, a Bayesian Cleaning system that features automatic Bayesian network construction and user interaction. We recast the data cleaning problem as a Bayesian inference that fully exploits the relationships between attributes in the observed dataset and any prior information provided by users. To this end, we present an automatic Bayesian network construction method that extends a structure learning-based functional dependency discovery method with similarity functions to capture the relationships between attributes. Furthermore, our system allows users to modify the generated Bayesian network in order to specify prior information or correct inaccuracies identified by the automatic generation process. We also design an effective scoring model (called the compensative scoring model) necessary for the Bayesian inference. To enhance the efficiency of data cleaning, we propose several approximation strategies for the Bayesian inference, including graph partitioning, domain pruning, and pre-detection. By evaluating on both real-world and synthetic datasets, we demonstrate that BClean is capable of achieving an F-measure of up to 0.9 in data cleaning, outperforming existing Bayesian methods by 2% and other data cleaning methods by 15%.