Traditional query answering over knowledge graphs -- or broadly over relational data -- is one of the most fundamental problems in data management. Motivated by the incompleteness of modern knowledge graphs, a new setup for query answering has emerged, where the goal is to predict answers that do not necessarily appear in the knowledge graph, but are present in its completion. In this work, we propose AnyCQ, a graph neural network model that can classify answers to any conjunctive query on any knowledge graph, following training. At the core of our framework lies a graph neural network model trained using a reinforcement learning objective to answer Boolean queries. Our approach and problem setup differ from existing query answering studies in multiple dimensions. First, we focus on the problem of query answer classification: given a query and a set of possible answers, classify these proposals as true or false relative to the complete knowledge graph. Second, we study the problem of query answer retrieval: given a query, retrieve an answer to the query relative to the complete knowledge graph or decide that no correct solutions exist. Trained on simple, small instances, AnyCQ can generalize to large queries of arbitrary structure, reliably classifying and retrieving answers to samples where existing approaches fail, which is empirically validated on new and challenging benchmarks. Furthermore, we demonstrate that our AnyCQ models effectively transfer to out-of-distribution knowledge graphs, when equipped with a relevant link predictor, highlighting their potential to serve as a general engine for query answering.
The capability of generating high-quality source code using large language models (LLMs) reduces software development time and costs. However, they often introduce security vulnerabilities due to training on insecure open-source data. This highlights the need for ensuring secure and functional code generation. This paper introduces PromSec, an algorithm for prom optimization for secure and functioning code generation using LLMs. In PromSec, we combine 1) code vulnerability clearing using a generative adversarial graph neural network, dubbed as gGAN, to fix and reduce security vulnerabilities in generated codes and 2) code generation using an LLM into an interactive loop, such that the outcome of the gGAN drives the LLM with enhanced prompts to generate secure codes while preserving their functionality. Introducing a new contrastive learning approach in gGAN, we formulate code-clearing and generation as a dual-objective optimization problem, enabling PromSec to notably reduce the number of LLM inferences. PromSec offers a cost-effective and practical solution for generating secure, functional code. Extensive experiments conducted on Python and Java code datasets confirm that PromSec effectively enhances code security while upholding its intended functionality. Our experiments show that while a state-of-the-art approach fails to address all code vulnerabilities, PromSec effectively resolves them. Moreover, PromSec achieves more than an order-of-magnitude reduction in operation time, number of LLM queries, and security analysis costs. Furthermore, prompts optimized with PromSec for a certain LLM are transferable to other LLMs across programming languages and generalizable to unseen vulnerabilities in training. This study is a step in enhancing the trustworthiness of LLMs for secure and functional code generation, supporting their integration into real-world software development.
Ensuring the security of cloud environments is imperative for sustaining organizational growth and operational efficiency. As the ubiquity of cloud services continues to rise, the inevitability of cyber threats underscores the importance of preemptive detection. This paper introduces a pioneering time-based embedding approach for Cloud Services Graph-based Anomaly Detection (CS-GAD), utilizing a Graph Neural Network (GNN) to discern anomalous user behavior during interactions with cloud services. Our method employs a dynamic tripartite graph representation to encapsulate the evolving interactions among cloud services, users, and their activities over time. Leveraging GNN models in each time frame, our approach generates a graph embedding wherein each user is assigned a score based on their historical activity, facilitating the identification of unusual behavior. Results demonstrate a notable reduction in false positive rates (2-9%) compared to prevailing methods, coupled with a commendable true positive rate (100%). The contributions of this work encompass early detection capabilities, a low false positive rate, an innovative tripartite graph representation incorporating action types, the introduction of a new cloud services dataset featuring various user attacks, and an open-source implementation for community collaboration in advancing cloud service security.
Graph neural networks (GNNs) are a type of neural network capable of learning on graph-structured data. However, training GNNs on large-scale graphs is challenging due to iterative aggregations of high-dimensional features from neighboring vertices within sparse graph structures combined with neural network operations. The sparsity of graphs frequently results in suboptimal memory access patterns and longer training time. Graph reordering is an optimization strategy aiming to improve the graph data layout. It has shown to be effective to speed up graph analytics workloads, but its effect on the performance of GNN training has not been investigated yet. The generalization of reordering to GNN performance is nontrivial, as multiple aspects must be considered: GNN hyper-parameters such as the number of layers, the number of hidden dimensions, and the feature size used in the GNN model, neural network operations, large intermediate vertex states, and GPU acceleration. In our work, we close this gap by performing an empirical evaluation of 12 reordering strategies in two state-of-the-art GNN systems, PyTorch Geometric and Deep Graph Library. Our results show that graph reordering is effective in reducing training time for CPU- and GPU-based training, respectively. Further, we find that GNN hyper-parameters influence the effectiveness of reordering, that reordering metrics play an important role in selecting a reordering strategy, that lightweight reordering performs better for GPU-based than for CPU-based training, and that invested reordering time can in many cases be amortized.
Incomplete LU factorizations of sparse matrices are widely used as preconditioners in Krylov subspace methods to speed up solving linear systems. Unfortunately, computing the preconditioner itself can be time-consuming and sensitive to hyper-parameters. Instead, we replace the hand-engineered algorithm with a graph neural network that is trained to approximate the matrix factorization directly. To apply the output of the neural network as a preconditioner, we propose an output activation function that guarantees that the predicted factorization is invertible. Further, applying a graph neural network architecture allows us to ensure that the output itself is sparse which is desirable from a computational standpoint. We theoretically analyze and empirically evaluate different loss functions to train the learned preconditioners and show their effectiveness in decreasing the number of GMRES iterations and improving the spectral properties on synthetic data. The code is available at https://github.com/paulhausner/neural-incomplete-factorization.
Graph neural networks have become the default choice by practitioners for graph learning tasks such as graph classification and node classification. Nevertheless, popular graph neural network models still struggle to capture higher-order information, i.e., information that goes \emph{beyond} pairwise interactions. Recent work has shown that persistent homology, a tool from topological data analysis, can enrich graph neural networks with topological information that they otherwise could not capture. Calculating such features is efficient for dimension 0 (connected components) and dimension 1 (cycles). However, when it comes to higher-order structures, it does not scale well, with a complexity of $O(n^d)$, where $n$ is the number of nodes and $d$ is the order of the structures. In this work, we introduce a novel method that extracts information about higher-order structures in the graph while still using the efficient low-dimensional persistent homology algorithm. On standard benchmark datasets, we show that our method can lead to up to $31\%$ improvements in test accuracy.
Graph neural network(GNN) has been a powerful approach in collaborative filtering(CF) due to its ability to model high-order user-item relationships. Recently, to alleviate the data sparsity and enhance representation learning, many efforts have been conducted to integrate contrastive learning(CL) with GNNs. Despite the promising improvements, the contrastive view generation based on structure and representation perturbations in existing methods potentially disrupts the collaborative information in contrastive views, resulting in limited effectiveness of positive alignment. To overcome this issue, we propose CoGCL, a novel framework that aims to enhance graph contrastive learning by constructing contrastive views with stronger collaborative information via discrete codes. The core idea is to map users and items into discrete codes rich in collaborative information for reliable and informative contrastive view generation. To this end, we initially introduce a multi-level vector quantizer in an end-to-end manner to quantize user and item representations into discrete codes. Based on these discrete codes, we enhance the collaborative information of contrastive views by considering neighborhood structure and semantic relevance respectively. For neighborhood structure, we propose virtual neighbor augmentation by treating discrete codes as virtual neighbors, which expands an observed user-item interaction into multiple edges involving discrete codes. Regarding semantic relevance, we identify similar users/items based on shared discrete codes and interaction targets to generate the semantically relevant view. Through these strategies, we construct contrastive views with stronger collaborative information and develop a triple-view graph contrastive learning approach. Extensive experiments on four public datasets demonstrate the effectiveness of our proposed approach.
Celcomen leverages a mathematical causality framework to disentangle intra- and inter- cellular gene regulation programs in spatial transcriptomics and single-cell data through a generative graph neural network. It can learn gene-gene interactions, as well as generate post-perturbation counterfactual spatial transcriptomics, thereby offering access to experimentally inaccessible samples. We validated its disentanglement, identifiability, and counterfactual prediction capabilities through simulations and in clinically relevant human glioblastoma, human fetal spleen, and mouse lung cancer samples. Celcomen provides the means to model disease and therapy induced changes allowing for new insights into single-cell spatially resolved tissue responses relevant to human health.
Numerical modeling of polycrystal plasticity is computationally intensive. We employ Graph Neural Networks (GNN) to predict stresses on complex geometries for polycrystal plasticity from Finite Element Method (FEM) simulations. We present a novel message-passing GNN that encodes nodal strain and edge distances between FEM mesh cells, and aggregates to obtain embeddings and combines the decoded embeddings with the nodal strains to predict stress tensors on graph nodes. The GNN is trained on subgraphs generated from FEM mesh graphs, in which the mesh cells are converted to nodes and edges are created between adjacent cells. We apply the trained GNN to periodic polycrystals with complex geometries and learn the strain-stress maps based on crystal plasticity theory. The GNN is accurately trained on FEM graphs, in which the $R^2$ for both training and testing sets are larger than 0.99. The proposed GNN approach speeds up more than 150 times compared with FEM on stress predictions. We also apply the trained GNN to unseen simulations for validations and the GNN generalizes well with an overall $R^2$ of 0.992. The GNN accurately predicts the von Mises stress on polycrystals. The proposed model does not overfit and generalizes well beyond the training data, as the error distributions demonstrate. This work outlooks surrogating crystal plasticity simulations using graph data.
In recent years there have been a growing interest in online auditing of information flow over social networks with the goal of monitoring undesirable effects, such as, misinformation and fake news. Most previous work on the subject, focus on the binary classification problem of classifying information as fake or genuine. Nonetheless, in many practical scenarios, the multi-class/label setting is of particular importance. For example, it could be the case that a social media platform may want to distinguish between ``true", ``partly-true", and ``false" information. Accordingly, in this paper, we consider the problem of online multiclass classification of information flow. To that end, driven by empirical studies on information flow over real-world social media networks, we propose a probabilistic information flow model over graphs. Then, the learning task is to detect the label of the information flow, with the goal of minimizing a combination of the classification error and the detection time. For this problem, we propose two detection algorithms; the first is based on the well-known multiple sequential probability ratio test, while the second is a novel graph neural network based sequential decision algorithm. For both algorithms, we prove several strong statistical guarantees. We also construct a data driven algorithm for learning the proposed probabilistic model. Finally, we test our algorithms over two real-world datasets, and show that they outperform other state-of-the-art misinformation detection algorithms, in terms of detection time and classification error.
Motivated by the enumeration of the BPS spectra of certain 3d $\mathcal{N}=2$ supersymmetric quantum field theories, obtained from the compactification of 6d superconformal field theories on three-manifolds, we study the homeomorphism problem for a class of graph-manifolds using Graph Neural Network techniques. Utilizing the JSJ decomposition, a unique representation via a plumbing graph is extracted from a graph-manifold. Homeomorphic graph-manifolds are related via a sequence of von Neumann moves on this graph; the algorithmic application of these moves can determine if two graphs correspond to homeomorphic graph-manifolds in super-polynomial time. However, by employing Graph Neural Networks (GNNs), the same problem can be addressed, at the cost of accuracy, in polynomial time. We build a dataset composed of pairs of plumbing graphs, together with a hidden label encoding whether the pair is homeomorphic. We train and benchmark a variety of network architectures within a supervised learning setting by testing different combinations of two convolutional layers (GEN, GCN, GAT, NNConv), followed by an aggregation layer and a classification layer. We discuss the strengths and weaknesses of the different GNNs for this homeomorphism problem.
The Integrated Process Planning and Scheduling (IPPS) problem combines process route planning and shop scheduling to achieve high efficiency in manufacturing and maximize resource utilization, which is crucial for modern manufacturing systems. Traditional methods using Mixed Integer Linear Programming (MILP) and heuristic algorithms can not well balance solution quality and speed when solving IPPS. In this paper, we propose a novel end-to-end Deep Reinforcement Learning (DRL) method. We model the IPPS problem as a Markov Decision Process (MDP) and employ a Heterogeneous Graph Neural Network (GNN) to capture the complex relationships among operations, machines, and jobs. To optimize the scheduling strategy, we use Proximal Policy Optimization (PPO). Experimental results show that, compared to traditional methods, our approach significantly improves solution efficiency and quality in large-scale IPPS instances, providing superior scheduling strategies for modern intelligent manufacturing systems.
In the rapidly evolving field of cybersecurity, the integration of flow-level and packet-level information for real-time intrusion detection remains a largely untapped area of research. This paper introduces "XG-NID," a novel framework that, to the best of our knowledge, is the first to fuse flow-level and packet-level data within a heterogeneous graph structure, offering a comprehensive analysis of network traffic. Leveraging a heterogeneous graph neural network (GNN) with graph-level classification, XG-NID uniquely enables real-time inference while effectively capturing the intricate relationships between flow and packet payload data. Unlike traditional GNN-based methodologies that predominantly analyze historical data, XG-NID is designed to accommodate the heterogeneous nature of network traffic, providing a robust and real-time defense mechanism. Our framework extends beyond mere classification; it integrates Large Language Models (LLMs) to generate detailed, human-readable explanations and suggest potential remedial actions, ensuring that the insights produced are both actionable and comprehensible. Additionally, we introduce a new set of flow features based on temporal information, further enhancing the contextual and explainable inferences provided by our model. To facilitate practical application and accessibility, we developed "GNN4ID," an open-source tool that enables the extraction and transformation of raw network traffic into the proposed heterogeneous graph structure, seamlessly integrating flow and packet-level data. Our comprehensive quantitative comparative analysis demonstrates that XG-NID achieves an F1 score of 97\% in multi-class classification, outperforming existing baseline and state-of-the-art methods. This sets a new standard in Network Intrusion Detection Systems by combining innovative data fusion with enhanced interpretability and real-time capabilities.
This study presents a novel application of Graph Neural Networks (GNNs) to optimize dealership network planning for a luxury car manufacturer in the U.S. By conducting a comprehensive literature review on dealership location determinants, the study identifies 65 county-level explanatory variables, augmented by two additional measures of regional interconnectedness derived from social and mobility data. An ablation study involving 34 variable combinations and ten state-of-the-art GNN operators reveals key insights into the predictive power of various variables, particularly highlighting the significance of competition, demographic factors, and mobility patterns in influencing dealership location decisions. The analysis pinpoints seven specific counties as promising targets for network expansion. This research not only illustrates the effectiveness of GNNs in solving complex geospatial decision-making problems but also provides actionable recommendations and valuable methodological insights for industry practitioners.
This article introduces PAGE, a parameterized generative interpretive framework. PAGE is capable of providing faithful explanations for any graph neural network without necessitating prior knowledge or internal details. Specifically, we train the auto-encoder to generate explanatory substructures by designing appropriate training strategy. Due to the dimensionality reduction of features in the latent space of the auto-encoder, it becomes easier to extract causal features leading to the model's output, which can be easily employed to generate explanations. To accomplish this, we introduce an additional discriminator to capture the causality between latent causal features and the model's output. By designing appropriate optimization objectives, the well-trained discriminator can be employed to constrain the encoder in generating enhanced causal features. Finally, these features are mapped to substructures of the input graph through the decoder to serve as explanations. Compared to existing methods, PAGE operates at the sample scale rather than nodes or edges, eliminating the need for perturbation or encoding processes as seen in previous methods. Experimental results on both artificially synthesized and real-world datasets demonstrate that our approach not only exhibits the highest faithfulness and accuracy but also significantly outperforms baseline models in terms of efficiency.
A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high computational efficiency. With the rapid expansion of synthetically accessible chemical space, traditional look-up table approaches face significant challenges. In this study, we address this issue using a modern data-driven approach, developing ByteFF, an Amber-compatible force field for drug-like molecules. To create ByteFF, we generated an expansive and highly diverse molecular dataset at the B3LYP-D3(BJ)/DZVP level of theory. This dataset includes 2.4 million optimized molecular fragment geometries with analytical Hessian matrices, along with 3.2 million torsion profiles. We then trained an edge-augmented, symmetry-preserving molecular graph neural network (GNN) on this dataset, employing a carefully optimized training strategy. Our model predicts all bonded and non-bonded MM force field parameters for drug-like molecules simultaneously across a broad chemical space. ByteFF demonstrates state-of-the-art performance on various benchmark datasets, excelling in predicting relaxed geometries, torsional energy profiles, and conformational energies and forces. Its exceptional accuracy and expansive chemical space coverage make ByteFF a valuable tool for multiple stages of computational drug discovery.
Evolving networks are complex data structures that emerge in a wide range of systems in science and engineering. Learning expressive representations for such networks that encode their structural connectivity and temporal evolution is essential for downstream data analytics and machine learning applications. In this study, we introduce a self-supervised method for learning representations of temporal networks and employ these representations in the dynamic link prediction task. While temporal networks are typically characterized as a sequence of interactions over the continuous time domain, our study focuses on their discrete-time versions. This enables us to balance the trade-off between computational complexity and precise modeling of the interactions. We propose a recurrent message-passing neural network architecture for modeling the information flow over time-respecting paths of temporal networks. The key feature of our method is the contrastive training objective of the model, which is a combination of three loss functions: link prediction, graph reconstruction, and contrastive predictive coding losses. The contrastive predictive coding objective is implemented using infoNCE losses at both local and global scales of the input graphs. We empirically show that the additional self-supervised losses enhance the training and improve the model's performance in the dynamic link prediction task. The proposed method is tested on Enron, COLAB, and Facebook datasets and exhibits superior results compared to existing models.
Multi-behavior recommendation systems enhance effectiveness by leveraging auxiliary behaviors (such as page views and favorites) to address the limitations of traditional models that depend solely on sparse target behaviors like purchases. Existing approaches to multi-behavior recommendations typically follow one of two strategies: some derive initial node representations from individual behavior subgraphs before integrating them for a comprehensive profile, while others interpret multi-behavior data as a heterogeneous graph, applying graph neural networks to achieve a unified node representation. However, these methods do not adequately explore the intricate patterns of behavior among users and items. To bridge this gap, we introduce a novel algorithm called Behavior Pattern mining-based Multi-behavior Recommendation (BPMR). Our method extensively investigates the diverse interaction patterns between users and items, utilizing these patterns as features for making recommendations. We employ a Bayesian approach to streamline the recommendation process, effectively circumventing the challenges posed by graph neural network algorithms, such as the inability to accurately capture user preferences due to over-smoothing. Our experimental evaluation on three real-world datasets demonstrates that BPMR significantly outperforms existing state-of-the-art algorithms, showing an average improvement of 268.29% in Recall@10 and 248.02% in NDCG@10 metrics. The code of our BPMR is openly accessible for use and further research at https://github.com/rookitkitlee/BPMR.
Persistent homology, a fundamental technique within Topological Data Analysis (TDA), captures structural and shape characteristics of graphs, yet encounters computational difficulties when applied to dynamic directed graphs. This paper introduces the Dynamic Neural Dowker Network (DNDN), a novel framework specifically designed to approximate the results of dynamic Dowker filtration, aiming to capture the high-order topological features of dynamic directed graphs. Our approach creatively uses line graph transformations to produce both source and sink line graphs, highlighting the shared neighbor structures that Dowker complexes focus on. The DNDN incorporates a Source-Sink Line Graph Neural Network (SSLGNN) layer to effectively capture the neighborhood relationships among dynamic edges. Additionally, we introduce an innovative duality edge fusion mechanism, ensuring that the results for both the sink and source line graphs adhere to the duality principle intrinsic to Dowker complexes. Our approach is validated through comprehensive experiments on real-world datasets, demonstrating DNDN's capability not only to effectively approximate dynamic Dowker filtration results but also to perform exceptionally in dynamic graph classification tasks.
The medical community believes binary medical event outcomes in EHR data contain sufficient information for making a sensible recommendation. However, there are two challenges to effectively utilizing such data: (1) modeling the relationship between massive 0,1 event outcomes is difficult, even with expert knowledge; (2) in practice, learning can be stalled by the binary values since the equally important 0 entries propagate no learning signals. Currently, there is a large gap between the assumed sufficient information and the reality that no promising results have been shown by utilizing solely the binary data: visiting or secondary information is often necessary to reach acceptable performance. In this paper, we attempt to build the first successful binary EHR data-oriented drug recommendation system by tackling the two difficulties, making sensible drug recommendations solely using the binary EHR medical records. To this end, we take a statistical perspective to view the EHR data as a sample from its cohorts and transform them into continuous Bernoulli probabilities. The transformed entries not only model a deterministic binary event with a distribution but also allow reflecting \emph{event-event} relationship by conditional probability. A graph neural network is learned on top of the transformation. It captures event-event correlations while emphasizing \emph{event-to-patient} features. Extensive results demonstrate that the proposed method achieves state-of-the-art performance on large-scale databases, outperforming baseline methods that use secondary information by a large margin. The source code is available at \url{https://github.com/chenzRG/BEHRMecom}