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.
Cyber threat and attack intelligence information are available in non-standard format from heterogeneous sources. Comprehending them and utilizing them for threat intelligence extraction requires engaging security experts. Knowledge graphs enable converting this unstructured information from heterogeneous sources into a structured representation of data and factual knowledge for several downstream tasks such as predicting missing information and future threat trends. Existing large-scale knowledge graphs mainly focus on general classes of entities and relationships between them. Open-source knowledge graphs for the security domain do not exist. To fill this gap, we've built \textsf{TINKER} - a knowledge graph for threat intelligence (\textbf{T}hreat \textbf{IN}telligence \textbf{K}nowl\textbf{E}dge g\textbf{R}aph). \textsf{TINKER} is generated using RDF triples describing entities and relations from tokenized unstructured natural language text from 83 threat reports published between 2006-2021. We built \textsf{TINKER} using classes and properties defined by open-source malware ontology and using hand-annotated RDF triples. We also discuss ongoing research and challenges faced while creating \textsf{TINKER}.
In this paper, we propose an effective global relation learning algorithm to recommend an appropriate location of a building unit for in-game customization of residential home complex. Given a construction layout, we propose a visual context-aware graph generation network that learns the implicit global relations among the scene components and infers the location of a new building unit. The proposed network takes as input the scene graph and the corresponding top-view depth image. It provides the location recommendations for a newly-added building units by learning an auto-regressive edge distribution conditioned on existing scenes. We also introduce a global graph-image matching loss to enhance the awareness of essential geometry semantics of the site. Qualitative and quantitative experiments demonstrate that the recommended location well reflects the implicit spatial rules of components in the residential estates, and it is instructive and practical to locate the building units in the 3D scene of the complex construction.
We consider the problem of molecular graph generation using deep models. While graphs are discrete, most existing methods use continuous latent variables, resulting in inaccurate modeling of discrete graph structures. In this work, we propose GraphDF, a novel discrete latent variable model for molecular graph generation based on normalizing flow methods. GraphDF uses invertible modulo shift transforms to map discrete latent variables to graph nodes and edges. We show that the use of discrete latent variables reduces computational costs and eliminates the negative effect of dequantization. Comprehensive experimental results show that GraphDF outperforms prior methods on random generation, property optimization, and constrained optimization 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.
Visual Question Answering (VQA) is of tremendous interest to the research community with important applications such as aiding visually impaired users and image-based search. In this work, we explore the use of scene graphs for solving the VQA task. We conduct experiments on the GQA dataset which presents a challenging set of questions requiring counting, compositionality and advanced reasoning capability, and provides scene graphs for a large number of images. We adopt image + question architectures for use with scene graphs, evaluate various scene graph generation techniques for unseen images, propose a training curriculum to leverage human-annotated and auto-generated scene graphs, and build late fusion architectures to learn from multiple image representations. We present a multi-faceted study into the use of scene graphs for VQA, making this work the first of its kind.
Deep generative models have achieved great success in areas such as image, speech, and natural language processing in the past few years. Thanks to the advances in graph-based deep learning, and in particular graph representation learning, deep graph generation methods have recently emerged with new applications ranging from discovering novel molecular structures to modeling social networks. This paper conducts a comprehensive survey on deep learning-based graph generation approaches and classifies them into five broad categories, namely, autoregressive, autoencoder-based, RL-based, adversarial, and flow-based graph generators, providing the readers a detailed description of the methods in each class. We also present publicly available source codes, commonly used datasets, and the most widely utilized evaluation metrics. Finally, we highlight the existing challenges and discuss future research directions.
To enhance the ability of neural networks to extract local point cloud features and improve their quality, in this paper, we propose a multiscale graph generation method and a self-adaptive graph convolution method. First, we propose a multiscale graph generation method for point clouds. This approach transforms point clouds into a structured multiscale graph form that supports multiscale analysis of point clouds in the scale space and can obtain the dimensional features of point cloud data at different scales, thus making it easier to obtain the best point cloud features. Because traditional convolutional neural networks are not applicable to graph data with irregular vertex neighborhoods, this paper presents an sef-adaptive graph convolution kernel that uses the Chebyshev polynomial to fit an irregular convolution filter based on the theory of optimal approximation. In this paper, we adopt max pooling to synthesize the features of different scale maps and generate the point cloud features. In experiments conducted on three widely used public datasets, the proposed method significantly outperforms other state-of-the-art models, demonstrating its effectiveness and generalizability.
Recent studies have indicated that Graph Convolutional Networks (GCNs) act as a \emph{low pass} filter in spectral domain and encode smoothed node representations. In this paper, we consider their opposite, namely Graph Deconvolutional Networks (GDNs) that reconstruct graph signals from smoothed node representations. We motivate the design of Graph Deconvolutional Networks via a combination of inverse filters in spectral domain and de-noising layers in wavelet domain, as the inverse operation results in a \emph{high pass} filter and may amplify the noise. Based on the proposed GDN, we further propose a graph autoencoder framework that first encodes smoothed graph representations with GCN and then decodes accurate graph signals with GDN. We demonstrate the effectiveness of the proposed method on several tasks including unsupervised graph-level representation , social recommendation and graph generation
Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine learning methods are ideal for the design of large amounts of potential new candidate molecules, which are naturally represented as graphs. Graph generation is being revolutionized by deep learning methods, and molecular generation is one of its most promising applications. In this paper, we introduce a sequential molecular graph generator based on a set of graph neural network modules, which we call MG^2N^2. At each step, a node or a group of nodes is added to the graph, along with its connections. The modular architecture simplifies the training procedure, also allowing an independent retraining of a single module. Sequentiality and modularity make the generation process interpretable. The use of graph neural networks maximizes the information in input at each generative step, which consists of the subgraph produced during the previous steps. Experiments of unconditional generation on the QM9 and Zinc datasets show that our model is capable of generalizing molecular patterns seen during the training phase, without overfitting. The results indicate that our method is competitive, and outperforms challenging baselines for unconditional generation.
This paper presents a simple method for a posteriori (historical) multi-variate multi-stage optimal trading under transaction costs and a diversification constraint. Starting from a given amount of money in some currency, we analyze the stage-wise optimal allocation over a time horizon with potential investments in multiple currencies and various assets. Three variants are discussed, including unconstrained trading frequency, a fixed number of total admissable trades, and the waiting of a specific time-period after every executed trade until the next trade. The developed methods are based on efficient graph generation and consequent graph search, and are evaluated quantitatively on real-world data. The fundamental motivation of this work is preparatory labeling of financial time-series data for supervised machine learning.
Synthetic data is emerging as a promising solution to the scalability issue of supervised deep learning, especially when real data are difficult to acquire or hard to annotate. Synthetic data generation, however, can itself be prohibitively expensive when domain experts have to manually and painstakingly oversee the process. Moreover, neural networks trained on synthetic data often do not perform well on real data because of the domain gap. To solve these challenges, we propose Sim2SG, a self-supervised automatic scene generation technique for matching the distribution of real data. Importantly, Sim2SG does not require supervision from the real-world dataset, thus making it applicable in situations for which such annotations are difficult to obtain. Sim2SG is designed to bridge both the content and appearance gaps, by matching the content of real data, and by matching the features in the source and target domains. We select scene graph (SG) generation as the downstream task, due to the limited availability of labeled datasets. Experiments demonstrate significant improvements over leading baselines in reducing the domain gap both qualitatively and quantitatively, on several synthetic datasets as well as the real-world KITTI dataset.
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.
Significant progress has been made in scene understanding which seeks to build 3D, metric and object-oriented representations of the world. Concurrently, reinforcement learning has made impressive strides largely enabled by advances in simulation. Comparatively, there has been less focus in simulation for perception algorithms. Simulation is becoming increasingly vital as sophisticated perception approaches such as metric-semantic mapping or 3D dynamic scene graph generation require precise 3D, 2D, and inertial information in an interactive environment. To that end, we present TESSE (Task Execution with Semantic Segmentation Environments), an open source simulator for developing scene understanding and task execution algorithms. TESSE has been used to develop state-of-the-art solutions for metric-semantic mapping and 3D dynamic scene graph generation. Additionally, TESSE served as the platform for the GOSEEK Challenge at the International Conference of Robotics and Automation (ICRA) 2020, an object search competition with an emphasis on reinforcement learning. Code for TESSE is available at https://github.com/MIT-TESSE.
The study of adverse childhood experiences and their consequences has emerged over the past 20 years. In this study, we aimed to leverage explainable artificial intelligence, and propose a proof-of-concept prototype for a knowledge-driven evidence-based recommendation system to improve surveillance of adverse childhood experiences. We used concepts from an ontology that we have developed to build and train a question-answering agent using the Google DialogFlow engine. In addition to the question-answering agent, the initial prototype includes knowledge graph generation and recommendation components that leverage third-party graph technology. To showcase the framework functionalities, we here present a prototype design and demonstrate the main features through four use case scenarios motivated by an initiative currently implemented at a children hospital in Memphis, Tennessee. Ongoing development of the prototype requires implementing an optimization algorithm of the recommendations, incorporating a privacy layer through a personal health library, and conducting a clinical trial to assess both usability and usefulness of the implementation. This semantic-driven explainable artificial intelligence prototype can enhance health care practitioners ability to provide explanations for the decisions they make.
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.
Visual scene graph generation is a challenging task. Previous works have achieved great progress, but most of them do not explicitly consider the class imbalance issue in scene graph generation. Models learned without considering the class imbalance tend to predict the majority classes, which leads to a good performance on trivial frequent predicates, but poor performance on informative infrequent predicates. However, predicates of minority classes often carry more semantic and precise information~(\textit{e.g.}, \emph{`on'} v.s \emph{`parked on'}). % which leads to a good score of recall, but a poor score of mean recall. To alleviate the influence of the class imbalance, we propose a novel model, dubbed \textit{dual ResGCN}, which consists of an object residual graph convolutional network and a relation residual graph convolutional network. The two networks are complementary to each other. The former captures object-level context information, \textit{i.e.,} the connections among objects. We propose a novel ResGCN that enhances object features in a cross attention manner. Besides, we stack multiple contextual coefficients to alleviate the imbalance issue and enrich the prediction diversity. The latter is carefully designed to explicitly capture relation-level context information \textit{i.e.,} the connections among relations. We propose to incorporate the prior about the co-occurrence of relation pairs into the graph to further help alleviate the class imbalance issue. Extensive evaluations of three tasks are performed on the large-scale database VG to demonstrate the superiority of the proposed method.
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.