Generative models for graph data are an important research topic in machine learning. Graph data comprise two levels that are typically analyzed separately: node-level properties such as the existence of a link between a pair of nodes, and global aggregate graph-level statistics, such as motif counts. This paper proposes a new multi-level framework that jointly models node-level properties and graph-level statistics, as mutually reinforcing sources of information. We introduce a new micro-macro training objective for graph generation that combines node-level and graph-level losses. We utilize the micro-macro objective to improve graph generation with a GraphVAE, a well-established model based on graph-level latent variables, that provides fast training and generation time for medium-sized graphs. Our experiments show that adding micro-macro modeling to the GraphVAE model improves graph quality scores up to 2 orders of magnitude on five benchmark datasets, while maintaining the GraphVAE generation speed advantage.
We describe a generative network model of the architecture of the enteric nervous system (ENS) in the colon employing data from images of human and mouse tissue samples obtained through confocal microscopy. Our models combine spatial point pattern analysis with graph generation to characterize the spatial and topological properties of the ganglia (clusters of neurons and glial cells), the inter-ganglionic connections, and the neuronal organization within the ganglia. We employ a hybrid hardcore-Strauss process for spatial patterns and a planar random graph generation for constructing the spatially embedded network. We show that our generative model may be helpful in both basic and translational studies, and it is sufficiently expressive to model the ENS architecture of individuals who vary in age and health status. Increased understanding of the ENS connectome will enable the use of neuromodulation strategies in treatment and clarify anatomic diagnostic criteria for people with bowel motility disorders.
Scene graph is structured semantic representation that can be modeled as a form of graph from images and texts. Image-based scene graph generation research has been actively conducted until recently, whereas text-based scene graph generation research has not. In this paper, we focus on the problem of scene graph parsing from textual description of a visual scene. The core idea is to use abstract meaning representation (AMR) instead of the dependency parsing mainly used in previous studies. AMR is a graph-based semantic formalism of natural language which abstracts concepts of words in a sentence contrary to the dependency parsing which considers dependency relationships on all words in a sentence. To this end, we design a simple yet effective two-stage scene graph parsing framework utilizing abstract meaning representation, SGRAM (Scene GRaph parsing via Abstract Meaning representation): 1) transforming a textual description of an image into an AMR graph (Text-to-AMR) and 2) encoding the AMR graph into a Transformer-based language model to generate a scene graph (AMR-to-SG). Experimental results show the scene graphs generated by our framework outperforms the dependency parsing-based model by 11.61\% and the previous state-of-the-art model using a pre-trained Transformer language model by 3.78\%. Furthermore, we apply SGRAM to image retrieval task which is one of downstream tasks for scene graph, and confirm the effectiveness of scene graphs generated by our framework.
Many data-mining applications use dynamic attributed graphs to represent relational information; but due to security and privacy concerns, there is a dearth of available datasets that can be represented as dynamic attributed graphs. Even when such datasets are available, they do not have ground truth that can be used to train deep-learning models. Thus, we present G2A2, an automated graph generator with attributes and anomalies, which encompasses (1) probabilistic models to generate a dynamic bipartite graph, representing time-evolving connections between two independent sets of entities, (2) realistic injection of anomalies using a novel algorithm that captures the general properties of graph anomalies across domains, and (3) a deep generative model to produce realistic attributes, learned from an existing real-world dataset. Using the maximum mean discrepancy (MMD) metric to evaluate the realism of a G2A2-generated graph against three real-world graphs, G2A2 outperforms Kronecker graph generation by reducing the MMD distance by up to six-fold (6x).
3D scene graph generation (SGG) has been of high interest in computer vision. Although the accuracy of 3D SGG on coarse classification and single relation label has been gradually improved, the performance of existing works is still far from being perfect for fine-grained and multi-label situations. In this paper, we propose a framework fully exploring contextual information for the 3D SGG task, which attempts to satisfy the requirements of fine-grained entity class, multiple relation labels, and high accuracy simultaneously. Our proposed approach is composed of a Graph Feature Extraction module and a Graph Contextual Reasoning module, achieving appropriate information-redundancy feature extraction, structured organization, and hierarchical inferring. Our approach achieves superior or competitive performance over previous methods on the 3DSSG dataset, especially on the relationship prediction sub-task.
Multivariate time-series forecasting is a critical task for many applications, and graph time-series network is widely studied due to its capability to capture the spatial-temporal correlation simultaneously. However, most existing works focus more on learning with the explicit prior graph structure, while ignoring potential information from the implicit graph structure, yielding incomplete structure modeling. Some recent works attempt to learn the intrinsic or implicit graph structure directly while lacking a way to combine explicit prior structure with implicit structure together. In this paper, we propose Regularized Graph Structure Learning (RGSL) model to incorporate both explicit prior structure and implicit structure together, and learn the forecasting deep networks along with the graph structure. RGSL consists of two innovative modules. First, we derive an implicit dense similarity matrix through node embedding, and learn the sparse graph structure using the Regularized Graph Generation (RGG) based on the Gumbel Softmax trick. Second, we propose a Laplacian Matrix Mixed-up Module (LM3) to fuse the explicit graph and implicit graph together. We conduct experiments on three real-word datasets. Results show that the proposed RGSL model outperforms existing graph forecasting algorithms with a notable margin, while learning meaningful graph structure simultaneously. Our code and models are made publicly available at https://github.com/alipay/RGSL.git.
Learning energy-based models (EBMs) is known to be difficult especially on discrete data where gradient-based learning strategies cannot be applied directly. Although ratio matching is a sound method to learn discrete EBMs, it suffers from expensive computation and excessive memory requirements, thereby resulting in difficulties in learning EBMs on high-dimensional data. Motivated by these limitations, in this study, we propose ratio matching with gradient-guided importance sampling (RMwGGIS). Particularly, we use the gradient of the energy function w.r.t. the discrete data space to approximately construct the provably optimal proposal distribution, which is subsequently used by importance sampling to efficiently estimate the original ratio matching objective. We perform experiments on density modeling over synthetic discrete data, graph generation, and training Ising models to evaluate our proposed method. The experimental results demonstrate that our method can significantly alleviate the limitations of ratio matching, perform more effectively in practice, and scale to high-dimensional problems. Our implementation is available at https://github.com/divelab/RMwGGIS.
Recently there has been increasing interest in developing and deploying deep graph learning algorithms for many tasks, such as fraud detection and recommender systems. Albeit, there is a limited number of publicly available graph-structured datasets, most of which are tiny compared to production-sized applications or are limited in their application domain. This work tackles this shortcoming by proposing a scalable synthetic graph generation tool to scale the datasets to production-size graphs with trillions of edges and billions of nodes. The tool learns a series of parametric models from proprietary datasets that can be released to researchers to study various graph methods on the synthetic data increasing prototype development and novel applications. We demonstrate the generalizability of the framework across a series of datasets, mimicking structural and feature distributions as well as the ability to scale them across varying sizes demonstrating their usefulness for benchmarking and model development. Code can be found on https://github.com/NVIDIA/DeepLearningExamples/tree/master/Tools/DGLPyTorch/SyntheticGraphGeneration.
Scene Graphs are widely applied in computer vision as a graphical representation of relationships between objects shown in images. However, these applications have not yet reached a practical stage of development owing to biased training caused by long-tailed predicate distributions. In recent years, many studies have tackled this problem. In contrast, relatively few works have considered predicate similarities as a unique dataset feature which also leads to the biased prediction. Due to the feature, infrequent predicates (e.g., parked on, covered in) are easily misclassified as closely-related frequent predicates (e.g., on, in). Utilizing predicate similarities, we propose a new classification scheme that branches the process to several fine-grained classifiers for similar predicate groups. The classifiers aim to capture the differences among similar predicates in detail. We also introduce the idea of transfer learning to enhance the features for the predicates which lack sufficient training samples to learn the descriptive representations. The results of extensive experiments on the Visual Genome dataset show that the combination of our method and an existing debiasing approach greatly improves performance on tail predicates in challenging SGCls/SGDet tasks. Nonetheless, the overall performance of the proposed approach does not reach that of the current state of the art, so further analysis remains necessary as future work.
This work introduces DiGress, a discrete denoising diffusion model for generating graphs with categorical node and edge attributes. Our model utilizes a discrete diffusion process that progressively edits graphs with noise, through the process of adding or removing edges and changing the categories. A graph transformer network is trained to revert this process, simplifying the problem of distribution learning over graphs into a sequence of node and edge classification tasks. We further improve sample quality by introducing a Markovian noise model that preserves the marginal distribution of node and edge types during diffusion, and by incorporating auxiliary graph-theoretic features. A procedure for conditioning the generation on graph-level features is also proposed. DiGress achieves state-of-the-art performance on molecular and non-molecular datasets, with up to 3x validity improvement on a planar graph dataset. It is also the first model to scale to the large GuacaMol dataset containing 1.3M drug-like molecules without the use of molecule-specific representations.
Retrosynthesis is a major task for drug discovery. It is formulated as a graph-generating problem by many existing approaches. Specifically, these methods firstly identify the reaction center, and break target molecule accordingly to generate synthons. Reactants are generated by either adding atoms sequentially to synthon graphs or directly adding proper leaving groups. However, both two strategies suffer since adding atoms results in a long prediction sequence which increases generation difficulty, while adding leaving groups can only consider the ones in the training set which results in poor generalization. In this paper, we propose a novel end-to-end graph generation model for retrosynthesis prediction, which sequentially identifies the reaction center, generates the synthons, and adds motifs to the synthons to generate reactants. Since chemically meaningful motifs are bigger than atoms and smaller than leaving groups, our method enjoys lower prediction complexity than adding atoms and better generalization than adding leaving groups. Experiments on a benchmark dataset show that the proposed model significantly outperforms previous state-of-the-art algorithms.
Diffusion models have proven effective for various applications such as images, audio and graph generation. Other important applications are image super-resolution and the solution of inverse problems. More recently, some works have used stochastic differential equations (SDEs) to generalize diffusion models to continuous time. In this work, we introduce SDEs to generate super-resolution face images. To the best of our knowledge, this is the first time SDEs have been used for such an application. The proposed method provides an improved peak signal-to-noise ratio (PSNR), structural similarity index measure (SSIM), and consistency than the existing super-resolution methods based on diffusion models. In particular, we also assess the potential application of this method for the face recognition task. A generic facial feature extractor is used to compare the super-resolution images with the ground truth and superior results were obtained compared with other methods. Our code is publicly available at https://github.com/marcelowds/sr-sde
Deep learning-based graph generation approaches have remarkable capacities for graph data modeling, allowing them to solve a wide range of real-world problems. Making these methods able to consider different conditions during the generation procedure even increases their effectiveness by empowering them to generate new graph samples that meet the desired criteria. This paper presents a conditional deep graph generation method called SCGG that considers a particular type of structural conditions. Specifically, our proposed SCGG model takes an initial subgraph and autoregressively generates new nodes and their corresponding edges on top of the given conditioning substructure. The architecture of SCGG consists of a graph representation learning network and an autoregressive generative model, which is trained end-to-end. Using this model, we can address graph completion, a rampant and inherently difficult problem of recovering missing nodes and their associated edges of partially observed graphs. Experimental results on both synthetic and real-world datasets demonstrate the superiority of our method compared with state-of-the-art baselines.
Community detection is a classic network problem with extensive applications in various fields. Its most common method is using modularity maximization heuristics which rarely return an optimal partition or anything similar. Partitions with globally optimal modularity are difficult to compute, and therefore have been underexplored. Using structurally diverse networks, we compare 30 community detection methods including our proposed algorithm that offers optimality and approximation guarantees: the Bayan algorithm. Unlike existing methods, Bayan globally maximizes modularity or approximates it within a factor. Our results show the distinctive accuracy and stability of maximum-modularity partitions in retrieving planted partitions at rates higher than most alternatives for a wide range of parameter settings in two standard benchmarks. Compared to the partitions from 29 other algorithms, maximum-modularity partitions have the best medians for description length, coverage, performance, average conductance, and well clusteredness. These advantages come at the cost of additional computations which Bayan makes possible for small networks (networks that have up to 3000 edges in their largest connected component). Bayan is several times faster than using open-source and commercial solvers for modularity maximization, making it capable of finding optimal partitions for instances that cannot be optimized by any other existing method. Our results point to a few well performing algorithms, among which Bayan stands out as the most reliable method for small networks. A Python implementation of the Bayan algorithm (bayanpy) is publicly available through the package installer for Python.
Several techniques have recently aimed to improve the performance of deep learning models for Scene Graph Generation (SGG) by incorporating background knowledge. State-of-the-art techniques can be divided into two families: one where the background knowledge is incorporated into the model in a subsymbolic fashion, and another in which the background knowledge is maintained in symbolic form. Despite promising results, both families of techniques face several shortcomings: the first one requires ad-hoc, more complex neural architectures increasing the training or inference cost; the second one suffers from limited scalability w.r.t. the size of the background knowledge. Our work introduces a regularization technique for injecting symbolic background knowledge into neural SGG models that overcomes the limitations of prior art. Our technique is model-agnostic, does not incur any cost at inference time, and scales to previously unmanageable background knowledge sizes. We demonstrate that our technique can improve the accuracy of state-of-the-art SGG models, by up to 33%.
A social network (SN) is a social structure consisting of a group representing the interaction between them. SNs have recently been widely used and, subsequently, have become suitable and popular platforms for product promotion and information diffusion. People in an SN directly influence each other's interests and behavior. One of the most important problems in SNs is to find people who can have the maximum influence on other nodes in the network in a cascade manner if they are chosen as the seed nodes of a network diffusion scenario. Influential diffusers are people who, if they are chosen as the seed set in a publishing issue in the network, that network will have the most people who have learned about that diffused entity. This is a well-known problem in literature known as influence maximization (IM) problem. Although it has been proven that this is an NP-complete problem and does not have a solution in polynomial time, it has been argued that it has the properties of sub modular functions and, therefore, can be solved using a greedy algorithm. Most of the methods proposed to improve this complexity are based on the assumption that the entire graph is visible. However, this assumption does not hold for many real-world graphs. This study is conducted to extend current maximization methods with link prediction techniques to pseudo-visibility graphs. To this end, a graph generation method called the exponential random graph model (ERGM) is used for link prediction. The proposed method is tested using the data from the Snap dataset of Stanford University. According to the experimental tests, the proposed method is efficient on real-world graphs.
Scene graph generation (SGG) is a fundamental task aimed at detecting visual relations between objects in an image. The prevailing SGG methods require all object classes to be given in the training set. Such a closed setting limits the practical application of SGG. In this paper, we introduce open-vocabulary scene graph generation, a novel, realistic and challenging setting in which a model is trained on a set of base object classes but is required to infer relations for unseen target object classes. To this end, we propose a two-step method that firstly pre-trains on large amounts of coarse-grained region-caption data and then leverages two prompt-based techniques to finetune the pre-trained model without updating its parameters. Moreover, our method can support inference over completely unseen object classes, which existing methods are incapable of handling. On extensive experiments on three benchmark datasets, Visual Genome, GQA, and Open-Image, our method significantly outperforms recent, strong SGG methods on the setting of Ov-SGG, as well as on the conventional closed SGG.
Scene graph generation (SGG) has gained tremendous progress in recent years. However, its underlying long-tailed distribution of predicate classes is a challenging problem. For extremely unbalanced predicate distributions, existing approaches usually construct complicated context encoders to extract the intrinsic relevance of scene context to predicates and complex networks to improve the learning ability of network models for highly imbalanced predicate distributions. To address the unbiased SGG problem, we introduce a simple yet effective method dubbed Context-Aware Mixture-of-Experts (CAME) to improve model diversity and mitigate biased SGG without complicated design. Specifically, we propose to integrate the mixture of experts with a divide and ensemble strategy to remedy the severely long-tailed distribution of predicate classes, which is applicable to the majority of unbiased scene graph generators. The biased SGG is thereby reduced, and the model tends to anticipate more evenly distributed predicate predictions. To differentiate between various predicate distribution levels, experts with the same weights are not sufficiently diverse. In order to enable the network dynamically exploit the rich scene context and further boost the diversity of model, we simply use the built-in module to create a context encoder. The importance of each expert to scene context and each predicate to each expert is dynamically associated with expert weighting (EW) and predicate weighting (PW) strategy. We have conducted extensive experiments on three tasks using the Visual Genome dataset, showing that CAME outperforms recent methods and achieves state-of-the-art performance. Our code will be available publicly.
This study sought to (1) expand our existing Urban Population Health Observatory (UPHO) system by incorporating a semantics layer; (2) cohesively employ machine learning and semantic/logical inference to provide measurable evidence and detect pathways leading to undesirable health outcomes; (3) provide clinical use case scenarios and design case studies to identify socioenvironmental determinants of health associated with the prevalence of obesity, and (4) design a dashboard that demonstrates the use of UPHO in the context of obesity surveillance using the provided scenarios. The system design includes a knowledge graph generation component that provides contextual knowledge from relevant domains of interest. This system leverages semantics using concepts, properties, and axioms from existing ontologies. In addition, we used the publicly available US Centers for Disease Control and Prevention 500 Cities data set to perform multivariate analysis. A cohesive approach that employs machine learning and semantic/logical inference reveals pathways leading to diseases. In this study, we present 2 clinical case scenarios and a proof-of-concept prototype design of a dashboard that provides warnings, recommendations, and explanations and demonstrates the use of UPHO in the context of obesity surveillance, treatment, and prevention. While exploring the case scenarios using a support vector regression machine learning model, we found that poverty, lack of physical activity, education, and unemployment were the most important predictive variables that contribute to obesity in Memphis, TN. The application of UPHO could help reduce health disparities and improve urban population health. The expanded UPHO feature incorporates an additional level of interpretable knowledge to enhance physicians, researchers, and health officials' informed decision-making at both patient and community levels.
The Scene Graph Generation (SGG) task aims to detect all the objects and their pairwise visual relationships in a given image. Although SGG has achieved remarkable progress over the last few years, almost all existing SGG models follow the same training paradigm: they treat both object and predicate classification in SGG as a single-label classification problem, and the ground-truths are one-hot target labels. However, this prevalent training paradigm has overlooked two characteristics of current SGG datasets: 1) For positive samples, some specific subject-object instances may have multiple reasonable predicates. 2) For negative samples, there are numerous missing annotations. Regardless of the two characteristics, SGG models are easy to be confused and make wrong predictions. To this end, we propose a novel model-agnostic Label Semantic Knowledge Distillation (LS-KD) for unbiased SGG. Specifically, LS-KD dynamically generates a soft label for each subject-object instance by fusing a predicted Label Semantic Distribution (LSD) with its original one-hot target label. LSD reflects the correlations between this instance and multiple predicate categories. Meanwhile, we propose two different strategies to predict LSD: iterative self-KD and synchronous self-KD. Extensive ablations and results on three SGG tasks have attested to the superiority and generality of our proposed LS-KD, which can consistently achieve decent trade-off performance between different predicate categories.