The discovery of new materials has been the essential force which brings a discontinuous improvement to industrial products' performance. However, the extra-vast combinatorial design space of material structures exceeds human experts' capability to explore all, thereby hampering material development. In this paper, we present a material industry-oriented web platform of an AI-driven molecular inverse-design system, which automatically designs brand new molecular structures rapidly and diversely. Different from existing inverse-design solutions, in this system, the combination of substructure-based feature encoding and molecular graph generation algorithms allows a user to gain high-speed, interpretable, and customizable design process. Also, a hierarchical data structure and user-oriented UI provide a flexible and intuitive workflow. The system is deployed on IBM's and our client's cloud servers and has been used by 5 partner companies. To illustrate actual industrial use cases, we exhibit inverse-design of sugar and dye molecules, that were carried out by experimental chemists in those client companies. Compared to general human chemist's standard performance, the molecular design speed was accelerated more than 10 times, and greatly increased variety was observed in the inverse-designed molecules without loss of chemical realism.
The extraction of a scene graph with objects as nodes and mutual relationships as edges is the basis for a deep understanding of image content. Despite recent advances, such as message passing and joint classification, the detection of visual relationships remains a challenging task due to sub-optimal exploration of the mutual interaction among the visual objects. In this work, we propose a novel transformer formulation for scene graph generation and relation prediction. We leverage the encoder-decoder architecture of the transformer for rich feature embedding of nodes and edges. Specifically, we model the node-to-node interaction with the self-attention of the transformer encoder and the edge-to-node interaction with the cross-attention of the transformer decoder. Further, we introduce a novel positional embedding suitable to handle edges in the decoder. Finally, our relation prediction module classifies the directed relation from the learned node and edge embedding. We name this architecture as Relation Transformer Network (RTN). On the Visual Genome and GQA dataset, we have achieved an overall mean of 4.85% and 3.1% point improvement in comparison with state-of-the-art methods. Our experiments show that Relation Transformer can efficiently model context across various datasets with small, medium, and large-scale relation classification.
Previous work on symmetric group equivariant neural networks generally only considered the case where the group acts by permuting the elements of a single vector. In this paper we derive formulae for general permutation equivariant layers, including the case where the layer acts on matrices by permuting their rows and columns simultaneously. This case arises naturally in graph learning and relation learning applications. As a specific case of higher order permutation equivariant networks, we present a second order graph variational encoder, and show that the latent distribution of equivariant generative models must be exchangeable. We demonstrate the efficacy of this architecture on the tasks of link prediction in citation graphs and molecular graph generation.
Scene graph generation (SGG) aims to detect objects in an image along with their pairwise relationships. There are three key properties of scene graph that have been underexplored in recent works: namely, the edge direction information, the difference in priority between nodes, and the long-tailed distribution of relationships. Accordingly, in this paper, we propose a Graph Property Sensing Network (GPS-Net) that fully explores these three properties for SGG. First, we propose a novel message passing module that augments the node feature with node-specific contextual information and encodes the edge direction information via a tri-linear model. Second, we introduce a node priority sensitive loss to reflect the difference in priority between nodes during training. This is achieved by designing a mapping function that adjusts the focusing parameter in the focal loss. Third, since the frequency of relationships is affected by the long-tailed distribution problem, we mitigate this issue by first softening the distribution and then enabling it to be adjusted for each subject-object pair according to their visual appearance. Systematic experiments demonstrate the effectiveness of the proposed techniques. Moreover, GPS-Net achieves state-of-the-art performance on three popular databases: VG, OI, and VRD by significant gains under various settings and metrics. The code and models are available at \url{https://github.com/taksau/GPS-Net}.
Deep learning based approaches have been utilized to model and generate graphs subjected to different distributions recently. However, they are typically unsupervised learning based and unconditioned generative models or simply conditioned on the graph-level contexts, which are not associated with rich semantic node-level contexts. Differently, in this paper, we are interested in a novel problem named Time Series Conditioned Graph Generation: given an input multivariate time series, we aim to infer a target relation graph modeling the underlying interrelationships between time series with each node corresponding to each time series. For example, we can study the interrelationships between genes in a gene regulatory network of a certain disease conditioned on their gene expression data recorded as time series. To achieve this, we propose a novel Time Series conditioned Graph Generation-Generative Adversarial Networks (TSGG-GAN) to handle challenges of rich node-level context structures conditioning and measuring similarities directly between graphs and time series. Extensive experiments on synthetic and real-word gene regulatory networks datasets demonstrate the effectiveness and generalizability of the proposed TSGG-GAN.
Learning generative models for graph-structured data is challenging because graphs are discrete, combinatorial, and the underlying data distribution is invariant to the ordering of nodes. However, most of the existing generative models for graphs are not invariant to the chosen ordering, which might lead to an undesirable bias in the learned distribution. To address this difficulty, we propose a permutation invariant approach to modeling graphs, using the recent framework of score-based generative modeling. In particular, we design a permutation equivariant, multi-channel graph neural network to model the gradient of the data distribution at the input graph (a.k.a., the score function). This permutation equivariant model of gradients implicitly defines a permutation invariant distribution for graphs. We train this graph neural network with score matching and sample from it with annealed Langevin dynamics. In our experiments, we first demonstrate the capacity of this new architecture in learning discrete graph algorithms. For graph generation, we find that our learning approach achieves better or comparable results to existing models on benchmark datasets.
Today's scene graph generation (SGG) task is still far from practical, mainly due to the severe training bias, e.g., collapsing diverse "human walk on / sit on / lay on beach" into "human on beach". Given such SGG, the down-stream tasks such as VQA can hardly infer better scene structures than merely a bag of objects. However, debiasing in SGG is not trivial because traditional debiasing methods cannot distinguish between the good and bad bias, e.g., good context prior (e.g., "person read book" rather than "eat") and bad long-tailed bias (e.g., "near" dominating "behind / in front of"). In this paper, we present a novel SGG framework based on causal inference but not the conventional likelihood. We first build a causal graph for SGG, and perform traditional biased training with the graph. Then, we propose to draw the counterfactual causality from the trained graph to infer the effect from the bad bias, which should be removed. In particular, we use Total Direct Effect (TDE) as the proposed final predicate score for unbiased SGG. Note that our framework is agnostic to any SGG model and thus can be widely applied in the community who seeks unbiased predictions. By using the proposed Scene Graph Diagnosis toolkit on the SGG benchmark Visual Genome and several prevailing models, we observed significant improvements over the previous state-of-the-art methods.
Graph generation is an extremely important task, as graphs are found throughout different areas of science and engineering. In this work, we focus on the modern equivalent of the Erdos-Renyi random graph model: the graph variational autoencoder (GVAE). This model assumes edges and nodes are independent in order to generate entire graphs at a time using a multi-layer perceptron decoder. As a result of these assumptions, GVAE has difficulty matching the training distribution and relies on an expensive graph matching procedure. We improve this class of models by building a message passing neural network into GVAE's encoder and decoder. We demonstrate our model on the specific task of generating small organic molecules
Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to smaller molecules. Indeed, as we demonstrate, their performance degrades significantly for larger molecules. In this paper, we propose a new hierarchical graph encoder-decoder that employs significantly larger and more flexible graph motifs as basic building blocks. Our encoder produces a multi-resolution representation for each molecule in a fine-to-coarse fashion, from atoms to connected motifs. Each level integrates the encoding of constituents below with the graph at that level. Our autoregressive coarse-to-fine decoder adds one motif at a time, interleaving the decision of selecting a new motif with the process of resolving its attachments to the emerging molecule. We evaluate our model on multiple molecule generation tasks, including polymers, and show that our model significantly outperforms previous state-of-the-art baselines.
Landmarks are central to how people navigate, but most navigation technologies do not incorporate them into their representations. We propose the landmark graph generation task (creating landmark-based spatial representations from natural language) and introduce a fully end-to-end neural approach to generate these graphs. We evaluate our models on the SAIL route instruction dataset, as well as on a small set of real-world delivery instructions that we collected, and we show that our approach yields high quality results on both our task and the related robotic navigation task.
Extracting graph representation of visual scenes in image is a challenging task in computer vision. Although there has been encouraging progress of scene graph generation in the past decade, we surprisingly find that the performance of existing approaches is largely limited by the strong biases, which mainly stem from (1) unconsciously assuming relations with certain semantic properties such as symmetric and (2) imbalanced annotations over different relations. To alleviate the negative effects of these biases, we proposed a new and simple architecture named Rich and Fair semantic extraction network (RiFa for short), to not only capture rich semantic properties of the relations, but also fairly predict relations with different scale of annotations. Using pseudo-siamese networks, RiFa embeds the subject and object respectively to distinguish their semantic differences and meanwhile preserve their underlying semantic properties. Then, it further predicts subject-object relations based on both the visual and semantic features of entities under certain contextual area, and fairly ranks the relation predictions for those with a few annotations. Experiments on the popular Visual Genome dataset show that RiFa achieves state-of-the-art performance under several challenging settings of scene graph task. Especially, it performs significantly better on capturing different semantic properties of relations, and obtains the best overall per relation performance.
Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.
Molecular graph generation is a fundamental problem for drug discovery and has been attracting growing attention. The problem is challenging since it requires not only generating chemically valid molecular structures but also optimizing their chemical properties in the meantime. Inspired by the recent progress in deep generative models, in this paper we propose a flow-based autoregressive model for graph generation called GraphAF. GraphAF combines the advantages of both autoregressive and flow-based approaches and enjoys: (1) high model flexibility for data density estimation; (2) efficient parallel computation for training; (3) an iterative sampling process, which allows leveraging chemical domain knowledge for valency checking. Experimental results show that GraphAF is able to generate 68% chemically valid molecules even without chemical knowledge rules and 100% valid molecules with chemical rules. The training process of GraphAF is two times faster than the existing state-of-the-art approach GCPN. After fine-tuning the model for goal-directed property optimization with reinforcement learning, GraphAF achieves state-of-the-art performance on both chemical property optimization and constrained property optimization.
The abundance of interconnected data has fueled the design and implementation of graph generators reproducing real-world linking properties, or gauging the effectiveness of graph algorithms, techniques and applications manipulating these data. We consider graph generation across multiple subfields, such as Semantic Web, graph databases, social networks, and community detection, along with general graphs. Despite the disparate requirements of modern graph generators throughout these communities, we analyze them under a common umbrella, reaching out the functionalities, the practical usage, and their supported operations. We argue that this classification is serving the need of providing scientists, researchers and practitioners with the right data generator at hand for their work. This survey provides a comprehensive overview of the state-of-the-art graph generators by focusing on those that are pertinent and suitable for several data-intensive tasks. Finally, we discuss open challenges and missing requirements of current graph generators along with their future extensions to new emerging fields.
Graph generative models have been extensively studied in the data mining literature. While traditional techniques are based on generating structures that adhere to a pre-decided distribution, recent techniques have shifted towards learning this distribution directly from the data. While learning-based approaches have imparted significant improvement in quality, some limitations remain to be addressed. First, learning graph distributions introduces additional computational overhead, which limits their scalability to large graph databases. Second, many techniques only learn the structure and do not address the need to also learn node and edge labels, which encode important semantic information and influence the structure itself. Third, existing techniques often incorporate domain-specific rules and lack generalizability. Fourth, the experimentation of existing techniques is not comprehensive enough due to either using weak evaluation metrics or focusing primarily on synthetic or small datasets. In this work, we develop a domain-agnostic technique called GraphGen to overcome all of these limitations. GraphGen converts graphs to sequences using minimum DFS codes. Minimum DFS codes are canonical labels and capture the graph structure precisely along with the label information. The complex joint distributions between structure and semantic labels are learned through a novel LSTM architecture. Extensive experiments on million-sized, real graph datasets show GraphGen to be 4 times faster on average than state-of-the-art techniques while being significantly better in quality across a comprehensive set of 11 different metrics. Our code is released at https://github.com/idea-iitd/graphgen.
Semantic image understanding is a challenging topic in computer vision. It requires to detect all objects in an image, but also to identify all the relations between them. Detected objects, their labels and the discovered relations can be used to construct a scene graph which provides an abstract semantic interpretation of an image. In previous works, relations were identified by solving an assignment problem formulated as Mixed-Integer Linear Programs. In this work, we interpret that formulation as Ordinary Differential Equation (ODE). The proposed architecture performs scene graph inference by solving a neural variant of an ODE by end-to-end learning. It achieves state-of-the-art results on all three benchmark tasks: scene graph generation (SGGen), classification (SGCls) and visual relationship detection (PredCls) on Visual Genome benchmark.
Scene Graph Generation (SGG) aims to extract entities, predicates and their semantic structure from images, enabling deep understanding of visual content, with many applications such as visual reasoning and image retrieval. Nevertheless, existing SGG methods require millions of manually annotated bounding boxes for training, and are computationally inefficient, as they exhaustively process all pairs of object proposals to detect predicates. In this paper, we address those two limitations by first proposing a generalized formulation of SGG, namely Visual Semantic Parsing, which disentangles entity and predicate recognition, and enables sub-quadratic performance. Then we propose the Visual Semantic Parsing Network, VSPNet, based on a dynamic, attention-based, bipartite message passing framework that jointly infers graph nodes and edges through an iterative process. Additionally, we propose the first graph-based weakly supervised learning framework, based on a novel graph alignment algorithm, which enables training without bounding box annotations. Through extensive experiments, we show that VSPNet outperforms weakly supervised baselines significantly and approaches fully supervised performance, while being several times faster. We publicly release the source code of our method.
Scene graphs are powerful representations that parse images into their abstract semantic elements, i.e., objects and their interactions, which facilitates visual comprehension and explainable reasoning. On the other hand, commonsense knowledge graphs are rich repositories that encode how the world is structured, and how general concepts interact. In this paper, we present a unified formulation of these two constructs, where a scene graph is seen as an image-conditioned instantiation of a commonsense knowledge graph. Based on this new perspective, we re-formulate scene graph generation as the inference of a bridge between the scene and commonsense graphs, where each entity or predicate instance in the scene graph has to be linked to its corresponding entity or predicate class in the commonsense graph. To this end, we propose a novel graph-based neural network that iteratively propagates information between the two graphs, as well as within each of them, while gradually refining their bridge in each iteration. Our Graph Bridging Network, GB-Net, successively infers edges and nodes, allowing to simultaneously exploit and refine the rich, heterogeneous structure of the interconnected scene and commonsense graphs. Through extensive experimentation, we showcase the superior accuracy of GB-Net compared to the most recent methods, resulting in a new state of the art. We publicly release the source code of our method.
The (variational) graph auto-encoder and its variants have been popularly used for representation learning on graph-structured data. While the encoder is often a powerful graph convolutional network, the decoder reconstructs the graph structure by only considering two nodes at a time, thus ignoring possible interactions among edges. On the other hand, structured prediction, which considers the whole graph simultaneously, is computationally expensive. In this paper, we utilize the well-known triadic closure property which is exhibited in many real-world networks. We propose the triad decoder, which considers and predicts the three edges involved in a local triad together. The triad decoder can be readily used in any graph-based auto-encoder. In particular, we incorporate this to the (variational) graph auto-encoder. Experiments on link prediction, node clustering and graph generation show that the use of triads leads to more accurate prediction, clustering and better preservation of the graph characteristics.
Generative graph models create instances of graphs that mimic the properties of real-world networks. Generative models are successful at retaining pairwise associations in the underlying networks but often fail to capture higher-order connectivity patterns known as network motifs. Different types of graphs contain different network motifs, an example of which are triangles that often arise in social and biological networks. It is hence vital to capture these higher-order structures to simulate real-world networks accurately. We propose Multi-MotifGAN (MMGAN), a motif-targeted Generative Adversarial Network (GAN) that generalizes the benchmark NetGAN approach. The generalization consists of combining multiple biased random walks, each of which captures a different motif structure. MMGAN outperforms NetGAN at creating new graphs that accurately reflect the network motif statistics of input graphs such as Citeseer, Cora and Facebook.