A graph generative model defines a distribution over graphs. One type of generative model is constructed by autoregressive neural networks, which sequentially add nodes and edges to generate a graph. However, the likelihood of a graph under the autoregressive model is intractable, as there are numerous sequences leading to the given graph; this makes maximum likelihood estimation challenging. Instead, in this work we derive the exact joint probability over the graph and the node ordering of the sequential process. From the joint, we approximately marginalize out the node orderings and compute a lower bound on the log-likelihood using variational inference. We train graph generative models by maximizing this bound, without using the ad-hoc node orderings of previous methods. Our experiments show that the log-likelihood bound is significantly tighter than the bound of previous schemes. Moreover, the models fitted with the proposed algorithm can generate high-quality graphs that match the structures of target graphs not seen during training. We have made our code publicly available at \hyperref[https://github.com/tufts-ml/graph-generation-vi]{https://github.com/tufts-ml/graph-generation-vi}.
In this paper, we propose Multiresolution Equivariant Graph Variational Autoencoders (MGVAE), the first hierarchical generative model to learn and generate graphs in a multiresolution and equivariant manner. At each resolution level, MGVAE employs higher order message passing to encode the graph while learning to partition it into mutually exclusive clusters and coarsening into a lower resolution that eventually creates a hierarchy of latent distributions. MGVAE then constructs a hierarchical generative model to variationally decode into a hierarchy of coarsened graphs. Importantly, our proposed framework is end-to-end permutation equivariant with respect to node ordering. MGVAE achieves competitive results with several generative tasks including general graph generation, molecular generation, unsupervised molecular representation learning to predict molecular properties, link prediction on citation graphs, and graph-based image generation.
Prior work in scene graph generation requires categorical supervision at the level of triplets - subjects and objects, and predicates that relate them, either with or without bounding box information. However, scene graph generation is a holistic task: thus holistic, contextual supervision should intuitively improve performance. In this work, we explore how linguistic structures in captions can benefit scene graph generation. Our method captures the information provided in captions about relations between individual triplets, and context for subjects and objects (e.g. visual properties are mentioned). Captions are a weaker type of supervision than triplets since the alignment between the exhaustive list of human-annotated subjects and objects in triplets, and the nouns in captions, is weak. However, given the large and diverse sources of multimodal data on the web (e.g. blog posts with images and captions), linguistic supervision is more scalable than crowdsourced triplets. We show extensive experimental comparisons against prior methods which leverage instance- and image-level supervision, and ablate our method to show the impact of leveraging phrasal and sequential context, and techniques to improve localization of subjects and objects.
Brain graphs (i.e, connectomes) constructed from medical scans such as magnetic resonance imaging (MRI) have become increasingly important tools to characterize the abnormal changes in the human brain. Due to the high acquisition cost and processing time of multimodal MRI, existing deep learning frameworks based on Generative Adversarial Network (GAN) focused on predicting the missing multimodal medical images from a few existing modalities. While brain graphs help better understand how a particular disorder can change the connectional facets of the brain, synthesizing a target brain multigraph (i.e, multiple brain graphs) from a single source brain graph is strikingly lacking. Additionally, existing graph generation works mainly learn one model for each target domain which limits their scalability in jointly predicting multiple target domains. Besides, while they consider the global topological scale of a graph (i.e., graph connectivity structure), they overlook the local topology at the node scale (e.g., how central a node is in the graph). To address these limitations, we introduce topology-aware graph GAN architecture (topoGAN), which jointly predicts multiple brain graphs from a single brain graph while preserving the topological structure of each target graph. Its three key innovations are: (i) designing a novel graph adversarial auto-encoder for predicting multiple brain graphs from a single one, (ii) clustering the encoded source graphs in order to handle the mode collapse issue of GAN and proposing a cluster-specific decoder, (iii) introducing a topological loss to force the prediction of topologically sound target brain graphs. The experimental results using five target domains demonstrated the outperformance of our method in brain multigraph prediction from a single graph in comparison with baseline approaches.
Classical graph modeling approaches such as Erd\H{o}s R\'{e}nyi (ER) random graphs or Barab\'asi-Albert (BA) graphs, here referred to as stylized models, aim to reproduce properties of real-world graphs in an interpretable way. While useful, graph generation with stylized models requires domain knowledge and iterative trial and error simulation. Previous work by Stoehr et al. (2019) addresses these issues by learning the generation process from graph data, using a disentanglement-focused deep autoencoding framework, more specifically, a $\beta$-Variational Autoencoder ($\beta$-VAE). While they successfully recover the generative parameters of ER graphs through the model's latent variables, their model performs badly on sequentially generated graphs such as BA graphs, due to their oversimplified decoder. We focus on recovering the generative parameters of BA graphs by replacing their $\beta$-VAE decoder with a sequential one. We first learn the generative BA parameters in a supervised fashion using a Graph Neural Network (GNN) and a Random Forest Regressor, by minimizing the squared loss between the true generative parameters and the latent variables. Next, we train a $\beta$-VAE model, combining the GNN encoder from the first stage with an LSTM-based decoder with a customized loss.
Recent commonsense-reasoning tasks are typically discriminative in nature, where a model answers a multiple-choice question for a certain context. Discriminative tasks are limiting because they fail to adequately evaluate the model's ability to reason and explain predictions with underlying commonsense knowledge. They also allow such models to use reasoning shortcuts and not be "right for the right reasons". In this work, we present ExplaGraphs, a new generative and structured commonsense-reasoning task (and an associated dataset) of explanation graph generation for stance prediction. Specifically, given a belief and an argument, a model has to predict if the argument supports or counters the belief and also generate a commonsense-augmented graph that serves as non-trivial, complete, and unambiguous explanation for the predicted stance. We collect explanation graphs through a novel Create-Verify-And-Refine graph collection framework that improves the graph quality (up to 90%) via multiple rounds of verification and refinement. A significant 79% of our graphs contain external commonsense nodes with diverse structures and reasoning depths. Next, we propose a multi-level evaluation framework, consisting of automatic metrics and human evaluation, that check for the structural and semantic correctness of the generated graphs and their degree of match with ground-truth graphs. Finally, we present several structured, commonsense-augmented, and text generation models as strong starting points for this explanation graph generation task, and observe that there is a large gap with human performance, thereby encouraging future work for this new challenging task. ExplaGraphs will be publicly available at https://explagraphs.github.io.
Scene graph generation is an important visual understanding task with a broad range of vision applications. Despite recent tremendous progress, it remains challenging due to the intrinsic long-tailed class distribution and large intra-class variation. To address these issues, we introduce a novel confidence-aware bipartite graph neural network with adaptive message propagation mechanism for unbiased scene graph generation. In addition, we propose an efficient bi-level data resampling strategy to alleviate the imbalanced data distribution problem in training our graph network. Our approach achieves superior or competitive performance over previous methods on several challenging datasets, including Visual Genome, Open Images V4/V6, demonstrating its effectiveness and generality.
This paper presents a fully convolutional scene graph generation (FCSGG) model that detects objects and relations simultaneously. Most of the scene graph generation frameworks use a pre-trained two-stage object detector, like Faster R-CNN, and build scene graphs using bounding box features. Such pipeline usually has a large number of parameters and low inference speed. Unlike these approaches, FCSGG is a conceptually elegant and efficient bottom-up approach that encodes objects as bounding box center points, and relationships as 2D vector fields which are named as Relation Affinity Fields (RAFs). RAFs encode both semantic and spatial features, and explicitly represent the relationship between a pair of objects by the integral on a sub-region that points from subject to object. FCSGG only utilizes visual features and still generates strong results for scene graph generation. Comprehensive experiments on the Visual Genome dataset demonstrate the efficacy, efficiency, and generalizability of the proposed method. FCSGG achieves highly competitive results on recall and zero-shot recall with significantly reduced inference time.
Scene graph generation aims to identify objects and their relations in images, providing structured image representations that can facilitate numerous applications in computer vision. However, scene graph models usually require supervised learning on large quantities of labeled data with intensive human annotation. In this work, we propose visual distant supervision, a novel paradigm of visual relation learning, which can train scene graph models without any human-labeled data. The intuition is that by aligning commonsense knowledge bases and images, we can automatically create large-scale labeled data to provide distant supervision for visual relation learning. To alleviate the noise in distantly labeled data, we further propose a framework that iteratively estimates the probabilistic relation labels and eliminates the noisy ones. Comprehensive experimental results show that our distantly supervised model outperforms strong weakly supervised and semi-supervised baselines. By further incorporating human-labeled data in a semi-supervised fashion, our model outperforms state-of-the-art fully supervised models by a large margin (e.g., 8.3 micro- and 7.8 macro-recall@50 improvements for predicate classification in Visual Genome evaluation). We make the data and code for this paper publicly available at https://github.com/thunlp/VisualDS.
Although there exist several libraries for deep learning on graphs, they are aiming at implementing basic operations for graph deep learning. In the research community, implementing and benchmarking various advanced tasks are still painful and time-consuming with existing libraries. To facilitate graph deep learning research, we introduce DIG: Dive into Graphs, a turnkey library that provides a unified testbed for higher level, research-oriented graph deep learning tasks. Currently, we consider graph generation, self-supervised learning on graphs, explainability of graph neural networks, and deep learning on 3D graphs. For each direction, we provide unified implementations of data interfaces, common algorithms, and evaluation metrics. Altogether, DIG is an extensible, open-source, and turnkey library for researchers to develop new methods and effortlessly compare with common baselines using widely used datasets and evaluation metrics. Source code is available at https://github.com/divelab/DIG.
To generate "accurate" scene graphs, almost all existing methods predict pairwise relationships in a deterministic manner. However, we argue that visual relationships are often semantically ambiguous. Specifically, inspired by linguistic knowledge, we classify the ambiguity into three types: Synonymy Ambiguity, Hyponymy Ambiguity, and Multi-view Ambiguity. The ambiguity naturally leads to the issue of \emph{implicit multi-label}, motivating the need for diverse predictions. In this work, we propose a novel plug-and-play Probabilistic Uncertainty Modeling (PUM) module. It models each union region as a Gaussian distribution, whose variance measures the uncertainty of the corresponding visual content. Compared to the conventional deterministic methods, such uncertainty modeling brings stochasticity of feature representation, which naturally enables diverse predictions. As a byproduct, PUM also manages to cover more fine-grained relationships and thus alleviates the issue of bias towards frequent relationships. Extensive experiments on the large-scale Visual Genome benchmark show that combining PUM with newly proposed ResCAGCN can achieve state-of-the-art performances, especially under the mean recall metric. Furthermore, we prove the universal effectiveness of PUM by plugging it into some existing models and provide insightful analysis of its ability to generate diverse yet plausible visual relationships.
Traditional scene graph generation methods are trained using cross-entropy losses that treat objects and relationships as independent entities. Such a formulation, however, ignores the structure in the output space, in an inherently structured prediction problem. In this work, we introduce a novel energy-based learning framework for generating scene graphs. The proposed formulation allows for efficiently incorporating the structure of scene graphs in the output space. This additional constraint in the learning framework acts as an inductive bias and allows models to learn efficiently from a small number of labels. We use the proposed energy-based framework to train existing state-of-the-art models and obtain a significant performance improvement, of up to 21% and 27%, on the Visual Genome and GQA benchmark datasets, respectively. Furthermore, we showcase the learning efficiency of the proposed framework by demonstrating superior performance in the zero- and few-shot settings where data is scarce.
The pre-training on the graph neural network model can learn the general features of large-scale networks or networks of the same type by self-supervised methods, which allows the model to work even when node labels are missing. However, the existing pre-training methods do not take network evolution into consideration. This paper proposes a pre-training method on dynamic graph neural networks (PT-DGNN), which uses dynamic attributed graph generation tasks to simultaneously learn the structure, semantics, and evolution features of the graph. The method includes two steps: 1) dynamic sub-graph sampling, and 2) pre-training with dynamic attributed graph generation task. Comparative experiments on three realistic dynamic network datasets show that the proposed method achieves the best results on the link prediction fine-tuning task.
Graph neural networks have been widely used on modeling graph data, achieving impressive results on node classification and link prediction tasks. Yet, obtaining an accurate representation for a graph further requires a pooling function that maps a set of node representations into a compact form. A simple sum or average over all node representations considers all node features equally without consideration of their task relevance, and any structural dependencies among them. Recently proposed hierarchical graph pooling methods, on the other hand, may yield the same representation for two different graphs that are distinguished by the Weisfeiler-Lehman test, as they suboptimally preserve information from the node features. To tackle these limitations of existing graph pooling methods, we first formulate the graph pooling problem as a multiset encoding problem with auxiliary information about the graph structure, and propose a Graph Multiset Transformer (GMT) which is a multi-head attention based global pooling layer that captures the interaction between nodes according to their structural dependencies. We show that GMT satisfies both injectiveness and permutation invariance, such that it is at most as powerful as the Weisfeiler-Lehman graph isomorphism test. Moreover, our methods can be easily extended to the previous node clustering approaches for hierarchical graph pooling. Our experimental results show that GMT significantly outperforms state-of-the-art graph pooling methods on graph classification benchmarks with high memory and time efficiency, and obtains even larger performance gain on graph reconstruction and generation tasks.
We note that most existing approaches for molecular graph generation fail to guarantee the intrinsic property of permutation invariance, resulting in unexpected bias in generative models. In this work, we propose GraphEBM to generate molecular graphs using energy-based models. In particular, we parameterize the energy function in a permutation invariant manner, thus making GraphEBM permutation invariant. We apply Langevin dynamics to train the energy function by approximately maximizing likelihood and generate samples with low energies. Furthermore, to generate molecules with a desirable property, we propose a simple yet effective strategy, which pushes down energies with flexible degrees according to the properties of corresponding molecules. Finally, we explore the use of GraphEBM for generating molecules with multiple objectives in a compositional manner. Comprehensive experimental results on random, goal-directed, and compositional generation tasks demonstrate the effectiveness of our proposed method.
We propose ways to speed up the initial pose-graph generation for global Structure-from-Motion algorithms. To avoid forming tentative point correspondences by FLANN and geometric verification by RANSAC, which are the most time-consuming steps of the pose-graph creation, we propose two new methods - built on the fact that image pairs usually are matched consecutively. Thus, candidate relative poses can be recovered from paths in the partly-built pose-graph. We propose a heuristic for the A* traversal, considering global similarity of images and the quality of the pose-graph edges. Given a relative pose from a path, descriptor-based feature matching is made "light-weight" by exploiting the known epipolar geometry. To speed up PROSAC-based sampling when RANSAC is applied, we propose a third method to order the correspondences by their inlier probabilities from previous estimations. The algorithms are tested on 402130 image pairs from the 1DSfM dataset and they speed up the feature matching 17 times and pose estimation 5 times.
A major challenge in the pharmaceutical industry is to design novel molecules with specific desired properties, especially when the property evaluation is costly. Here, we propose MNCE-RL, a graph convolutional policy network for molecular optimization with molecular neighborhood-controlled embedding grammars through reinforcement learning. We extend the original neighborhood-controlled embedding grammars to make them applicable to molecular graph generation and design an efficient algorithm to infer grammatical production rules from given molecules. The use of grammars guarantees the validity of the generated molecular structures. By transforming molecular graphs to parse trees with the inferred grammars, the molecular structure generation task is modeled as a Markov decision process where a policy gradient strategy is utilized. In a series of experiments, we demonstrate that our approach achieves state-of-the-art performance in a diverse range of molecular optimization tasks and exhibits significant superiority in optimizing molecular properties with a limited number of property evaluations.
From object segmentation to word vector representations, Scene Graph Generation (SGG) became a complex task built upon numerous research results. In this paper, we focus on the last module of this model: the fusion function. The role of this latter is to combine three hidden states. We perform an ablation test in order to compare different implementations. First, we reproduce the state-of-the-art results using SUM, and GATE functions. Then we expand the original solution by adding more model-agnostic functions: an adapted version of DIST and a mixture between MFB and GATE. On the basis of the state-of-the-art configuration, DIST performed the best Recall @ K, which makes it now part of the state-of-the-art.
This paper presents the first study on using large-scale pre-trained language models for automated generation of an event-level temporal graph for a document. Despite the huge success of neural pre-training methods in NLP tasks, its potential for temporal reasoning over event graphs has not been sufficiently explored. Part of the reason is the difficulty in obtaining large training corpora with human-annotated events and temporal links. We address this challenge by using existing IE/NLP tools to automatically generate a large quantity (89,000) of system-produced document-graph pairs, and propose a novel formulation of the contextualized graph generation problem as a sequence-to-sequence mapping task. These strategies enable us to leverage and fine-tune pre-trained language models on the system-induced training data for the graph generation task. Our experiments show that our approach is highly effective in generating structurally and semantically valid graphs. Further, evaluation on a challenging hand-labeled, out-domain corpus shows that our method outperforms the closest existing method by a large margin on several metrics. Code and pre-trained models are available at https://github.com/madaan/temporal-graph-gen.
Deep generative models for graphs have exhibited promising performance in ever-increasing domains such as design of molecules (i.e, graph of atoms) and structure prediction of proteins (i.e., graph of amino acids). Existing work typically focuses on static rather than dynamic graphs, which are actually very important in the applications such as protein folding, molecule reactions, and human mobility. Extending existing deep generative models from static to dynamic graphs is a challenging task, which requires to handle the factorization of static and dynamic characteristics as well as mutual interactions among node and edge patterns. Here, this paper proposes a novel framework of factorized deep generative models to achieve interpretable dynamic graph generation. Various generative models are proposed to characterize conditional independence among node, edge, static, and dynamic factors. Then, variational optimization strategies as well as dynamic graph decoders are proposed based on newly designed factorized variational autoencoders and recurrent graph deconvolutions. Extensive experiments on multiple datasets demonstrate the effectiveness of the proposed models.