Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design as graph generation problems which provide new opportunities toward the breakthrough of this long-lasting problem. Existing models, however, have many shortcomings, including poor interpretability and controllability toward desired molecular properties. This paper focuses on new methodologies for molecule generation with interpretable and controllable deep generative models, by proposing new monotonically-regularized graph variational autoencoders. The proposed models learn to represent the molecules with latent variables and then learn the correspondence between them and molecule properties parameterized by polynomial functions. To further improve the intepretability and controllability of molecule generation towards desired properties, we derive new objectives which further enforce monotonicity of the relation between some latent variables and target molecule properties such as toxicity and clogP. Extensive experimental evaluation demonstrates the superiority of the proposed framework on accuracy, novelty, disentanglement, and control towards desired molecular properties. The code is open-source at https://anonymous.4open.science/r/MDVAE-FD2C.
Spatiotemporal graph represents a crucial data structure where the nodes and edges are embedded in a geometric space and can evolve dynamically over time. Nowadays, spatiotemporal graph data is becoming increasingly popular and important, ranging from microscale (e.g. protein folding), to middle-scale (e.g. dynamic functional connectivity), to macro-scale (e.g. human mobility network). Although disentangling and understanding the correlations among spatial, temporal, and graph aspects have been a long-standing key topic in network science, they typically rely on network processing hypothesized by human knowledge. This usually fit well towards the graph properties which can be predefined, but cannot do well for the most cases, especially for many key domains where the human has yet very limited knowledge such as protein folding and biological neuronal networks. In this paper, we aim at pushing forward the modeling and understanding of spatiotemporal graphs via new disentangled deep generative models. Specifically, a new Bayesian model is proposed that factorizes spatiotemporal graphs into spatial, temporal, and graph factors as well as the factors that explain the interplay among them. A variational objective function and new mutual information thresholding algorithms driven by information bottleneck theory have been proposed to maximize the disentanglement among the factors with theoretical guarantees. Qualitative and quantitative experiments on both synthetic and real-world datasets demonstrate the superiority of the proposed model over the state-of-the-arts by up to 69.2% for graph generation and 41.5% for interpretability.
Motivated by recent findings from cognitive neural science, we advocate the use of a dual-level model for concept representations: the embodied level consists of concept-oriented feature representations, and the symbolic level consists of concept graphs. Embodied concept representations are modality specific and exist in the form of feature vectors in a feature space. Symbolic concept representations, on the other hand, are amodal and language specific, and exist in the form of word / knowledge-graph embeddings in a concept / knowledge space. The human conceptual system comprises both embodied representations and symbolic representations, which typically interact to drive conceptual processing. As such, we further advocate the use of dual embodied-symbolic concept representations for deep learning. To demonstrate their usage and value, we discuss two important use cases: embodied-symbolic knowledge distillation for few-shot class incremental learning, and embodied-symbolic fused representation for image-text matching. Dual embodied-symbolic concept representations are the foundation for deep learning and symbolic AI integration. We discuss two important examples of such integration: scene graph generation with knowledge graph bridging, and multimodal knowledge graphs.
Human-Robot Interaction (HRI) is an emerging subfield of service robotics. While most existing approaches rely on explicit signals (i.e. voice, gesture) to engage, current literature is lacking solutions to address implicit user needs. In this paper, we present an architecture to (a) detect user implicit need of help and (b) generate a set of assistive actions without prior learning. Task (a) will be performed using state-of-the-art solutions for Scene Graph Generation coupled to the use of commonsense knowledge; whereas, task (b) will be performed using additional commonsense knowledge as well as a sentiment analysis on graph structure. Finally, we propose an evaluation of our solution using established benchmarks (e.g. ActionGenome dataset) along with human experiments. The main motivation of our approach is the embedding of the perception-decision-action loop in a single architecture.
Scene graph generation (SGG) is built on top of detected objects to predict object pairwise visual relations for describing the image content abstraction. Existing works have revealed that if the links between objects are given as prior knowledge, the performance of SGG is significantly improved. Inspired by this observation, in this article, we propose a relation regularized network (R2-Net), which can predict whether there is a relationship between two objects and encode this relation into object feature refinement and better SGG. Specifically, we first construct an affinity matrix among detected objects to represent the probability of a relationship between two objects. Graph convolution networks (GCNs) over this relation affinity matrix are then used as object encoders, producing relation-regularized representations of objects. With these relation-regularized features, our R2-Net can effectively refine object labels and generate scene graphs. Extensive experiments are conducted on the visual genome dataset for three SGG tasks (i.e., predicate classification, scene graph classification, and scene graph detection), demonstrating the effectiveness of our proposed method. Ablation studies also verify the key roles of our proposed components in performance improvement.
As a structured representation of the image content, the visual scene graph (visual relationship) acts as a bridge between computer vision and natural language processing. Existing models on the scene graph generation task notoriously require tens or hundreds of labeled samples. By contrast, human beings can learn visual relationships from a few or even one example. Inspired by this, we design a task named One-Shot Scene Graph Generation, where each relationship triplet (e.g., "dog-has-head") comes from only one labeled example. The key insight is that rather than learning from scratch, one can utilize rich prior knowledge. In this paper, we propose Multiple Structured Knowledge (Relational Knowledge and Commonsense Knowledge) for the one-shot scene graph generation task. Specifically, the Relational Knowledge represents the prior knowledge of relationships between entities extracted from the visual content, e.g., the visual relationships "standing in", "sitting in", and "lying in" may exist between "dog" and "yard", while the Commonsense Knowledge encodes "sense-making" knowledge like "dog can guard yard". By organizing these two kinds of knowledge in a graph structure, Graph Convolution Networks (GCNs) are used to extract knowledge-embedded semantic features of the entities. Besides, instead of extracting isolated visual features from each entity generated by Faster R-CNN, we utilize an Instance Relation Transformer encoder to fully explore their context information. Based on a constructed one-shot dataset, the experimental results show that our method significantly outperforms existing state-of-the-art methods by a large margin. Ablation studies also verify the effectiveness of the Instance Relation Transformer encoder and the Multiple Structured Knowledge.
Scene graph generation from images is a task of great interest to applications such as robotics, because graphs are the main way to represent knowledge about the world and regulate human-robot interactions in tasks such as Visual Question Answering (VQA). Unfortunately, its corresponding area of machine learning is still relatively in its infancy, and the solutions currently offered do not specialize well in concrete usage scenarios. Specifically, they do not take existing "expert" knowledge about the domain world into account; and that might indeed be necessary in order to provide the level of reliability demanded by the use case scenarios. In this paper, we propose an initial approximation to a framework called Ontology-Guided Scene Graph Generation (OG-SGG), that can improve the performance of an existing machine learning based scene graph generator using prior knowledge supplied in the form of an ontology (specifically, using the axioms defined within); and we present results evaluated on a specific scenario founded in telepresence robotics. These results show quantitative and qualitative improvements in the generated scene graphs.
Generating informative scene graphs from images requires integrating and reasoning from various graph components, i.e., objects and relationships. However, current scene graph generation (SGG) methods, including the unbiased SGG methods, still struggle to predict informative relationships due to the lack of 1) high-level inference such as transitive inference between relationships and 2) efficient mechanisms that can incorporate all interactions of graph components. To address the issues mentioned above, we devise a hyper-relationship learning network, termed HLN, for SGG. Specifically, the proposed HLN stems from hypergraphs and two graph attention networks (GATs) are designed to infer relationships: 1) the object-relationship GAT or OR-GAT to explore interactions between objects and relationships, and 2) the hyper-relationship GAT or HR-GAT to integrate transitive inference of hyper-relationships, i.e., the sequential relationships between three objects for transitive reasoning. As a result, HLN significantly improves the performance of scene graph generation by integrating and reasoning from object interactions, relationship interactions, and transitive inference of hyper-relationships. We evaluate HLN on the most popular SGG dataset, i.e., the Visual Genome dataset, and the experimental results demonstrate its great superiority over recent state-of-the-art methods. For example, the proposed HLN improves the recall per relationship from 11.3\% to 13.1\%, and maintains the recall per image from 19.8\% to 34.9\%. We will release the source code and pretrained models on GitHub.
The growing importance of understanding and addressing algorithmic bias in artificial intelligence (AI) has led to a surge in research on AI fairness, which often assumes that the underlying data is independent and identically distributed (IID). However, real-world data frequently exists in non-IID graph structures that capture connections among individual units. To effectively mitigate bias in AI systems, it is essential to bridge the gap between traditional fairness literature, designed for IID data, and the prevalence of non-IID graph data. This survey reviews recent advancements in fairness amidst non-IID graph data, including the newly introduced fair graph generation and the commonly studied fair graph classification. In addition, available datasets and evaluation metrics for future research are identified, the limitations of existing work are highlighted, and promising future directions are proposed.
Generating molecules with desired biological activities has attracted growing attention in drug discovery. Previous molecular generation models are designed as chemocentric methods that hardly consider the drug-target interaction, limiting their practical applications. In this paper, we aim to generate molecular drugs in a target-aware manner that bridges biological activity and molecular design. To solve this problem, we compile a benchmark dataset from several publicly available datasets and build baselines in a unified framework. Building on the recent advantages of flow-based molecular generation models, we propose SiamFlow, which forces the flow to fit the distribution of target sequence embeddings in latent space. Specifically, we employ an alignment loss and a uniform loss to bring target sequence embeddings and drug graph embeddings into agreements while avoiding collapse. Furthermore, we formulate the alignment into a one-to-many problem by learning spaces of target sequence embeddings. Experiments quantitatively show that our proposed method learns meaningful representations in the latent space toward the target-aware molecular graph generation and provides an alternative approach to bridge biology and chemistry in drug discovery.
Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or cannot sufficiently model the complex dependency between nodes and edges, which is crucial for generating real-world graphs such as molecules. To overcome such limitations, we propose a novel score-based generative model for graphs with a continuous-time framework. Specifically, we propose a new graph diffusion process that models the joint distribution of the nodes and edges through a system of stochastic differential equations (SDEs). Then, we derive novel score matching objectives tailored for the proposed diffusion process to estimate the gradient of the joint log-density with respect to each component, and introduce a new solver for the system of SDEs to efficiently sample from the reverse diffusion process. We validate our graph generation method on diverse datasets, on which it either achieves significantly superior or competitive performance to the baselines. Further analysis shows that our method is able to generate molecules that lie close to the training distribution yet do not violate the chemical valency rule, demonstrating the effectiveness of the system of SDEs in modeling the node-edge relationships. Our code is available at https://github.com/harryjo97/GDSS.
We propose a framework using normalizing-flow based models, SELF-Referencing Embedded Strings, and multi-objective optimization that efficiently generates small molecules. With an initial training set of only 100 small molecules, FastFlows generates thousands of chemically valid molecules in seconds. Because of the efficient sampling, substructure filters can be applied as desired to eliminate compounds with unreasonable moieties. Using easily computable and learned metrics for druglikeness, synthetic accessibility, and synthetic complexity, we perform a multi-objective optimization to demonstrate how FastFlows functions in a high-throughput virtual screening context. Our model is significantly simpler and easier to train than autoregressive molecular generative models, and enables fast generation and identification of druglike, synthesizable molecules.
Generative models for graphs have been actively studied for decades, and they have a wide range of applications. Recently, learning-based graph generation that reproduces real-world graphs has been attracting the attention of many researchers. Although several generative models that utilize modern machine learning technologies have been proposed, conditional generation of general graphs has been less explored in the field. In this paper, we propose a generative model that allows us to tune the value of a global-level structural feature as a condition. Our model, called GraphTune, makes it possible to tune the value of any structural feature of generated graphs using Long Short Term Memory (LSTM) and a Conditional Variational AutoEncoder (CVAE). We performed comparative evaluations of GraphTune and conventional models on a real graph dataset. The evaluations show that GraphTune makes it possible to more clearly tune the value of a global-level structural feature better than conventional models.
Different objects in the same scene are more or less related to each other, but only a limited number of these relationships are noteworthy. Inspired by DETR, which excels in object detection, we view scene graph generation as a set prediction problem and propose an end-to-end scene graph generation model RelTR which has an encoder-decoder architecture. The encoder reasons about the visual feature context while the decoder infers a fixed-size set of triplets subject-predicate-object using different types of attention mechanisms with coupled subject and object queries. We design a set prediction loss performing the matching between the ground truth and predicted triplets for the end-to-end training. In contrast to most existing scene graph generation methods, RelTR is a one-stage method that predicts a set of relationships directly only using visual appearance without combining entities and labeling all possible predicates. Extensive experiments on the Visual Genome and Open Images V6 datasets demonstrate the superior performance and fast inference of our model.
As a structured prediction task, scene graph generation aims to build a visually-grounded scene graph to explicitly model objects and their relationships in an input image. Currently, the mean field variational Bayesian framework is the de facto methodology used by the existing methods, in which the unconstrained inference step is often implemented by a message passing neural network. However, such formulation fails to explore other inference strategies, and largely ignores the more general constrained optimization models. In this paper, we present a constrained structure learning method, for which an explicit constrained variational inference objective is proposed. Instead of applying the ubiquitous message-passing strategy, a generic constrained optimization method - entropic mirror descent - is utilized to solve the constrained variational inference step. We validate the proposed generic model on various popular scene graph generation benchmarks and show that it outperforms the state-of-the-art methods.
Accurate forecasting of multivariate time series is an extensively studied subject in finance, transportation, and computer science. Fully mining the correlation and causation between the variables in a multivariate time series exhibits noticeable results in improving the performance of a time series model. Recently, some models have explored the dependencies between variables through end-to-end graph structure learning without the need for predefined graphs. However, current models do not incorporate the trade-off between efficiency and flexibility and lack the guidance of domain knowledge in the design of graph structure learning algorithms. This paper alleviates the above issues by proposing Balanced Graph Structure Learning for Forecasting (BGSLF), a novel deep learning model that joins graph structure learning and forecasting. Technically, BGSLF leverages the spatial information into convolutional operations and extracts temporal dynamics using the diffusion convolutional recurrent network. The proposed framework balance the trade-off between efficiency and flexibility by introducing Multi-Graph Generation Network (MGN) and Graph Selection Module. In addition, a method named Smooth Sparse Unit (SSU) is designed to sparse the learned graph structures, which conforms to the sparse spatial correlations in the real world. Extensive experiments on four real-world datasets demonstrate that our model achieves state-of-the-art performances with minor trainable parameters. Code will be made publicly available.
Scene Graph Generation (SGG) aims to build a structured representation of a scene using objects and pairwise relationships, which benefits downstream tasks. However, current SGG methods usually suffer from sub-optimal scene graph generation because of the long-tailed distribution of training data. To address this problem, we propose Resistance Training using Prior Bias (RTPB) for the scene graph generation. Specifically, RTPB uses a distributed-based prior bias to improve models' detecting ability on less frequent relationships during training, thus improving the model generalizability on tail categories. In addition, to further explore the contextual information of objects and relationships, we design a contextual encoding backbone network, termed as Dual Transformer (DTrans). We perform extensive experiments on a very popular benchmark, VG150, to demonstrate the effectiveness of our method for the unbiased scene graph generation. In specific, our RTPB achieves an improvement of over 10% under the mean recall when applied to current SGG methods. Furthermore, DTrans with RTPB outperforms nearly all state-of-the-art methods with a large margin.
Deep learning techniques have led to remarkable breakthroughs in the field of generic object detection and have spawned a lot of scene-understanding tasks in recent years. Scene graph has been the focus of research because of its powerful semantic representation and applications to scene understanding. Scene Graph Generation (SGG) refers to the task of automatically mapping an image into a semantic structural scene graph, which requires the correct labeling of detected objects and their relationships. Although this is a challenging task, the community has proposed a lot of SGG approaches and achieved good results. In this paper, we provide a comprehensive survey of recent achievements in this field brought about by deep learning techniques. We review 138 representative works that cover different input modalities, and systematically summarize existing methods of image-based SGG from the perspective of feature extraction and fusion. We attempt to connect and systematize the existing visual relationship detection methods, to summarize, and interpret the mechanisms and the strategies of SGG in a comprehensive way. Finally, we finish this survey with deep discussions about current existing problems and future research directions. This survey will help readers to develop a better understanding of the current research status and ideas.
Scene Graph Generation (SGG) remains a challenging visual understanding task due to its compositional property. Most previous works adopt a bottom-up two-stage or a point-based one-stage approach, which often suffers from high time complexity or sub-optimal designs. In this work, we propose a novel SGG method to address the aforementioned issues, formulating the task as a bipartite graph construction problem. To solve the problem, we develop a transformer-based end-to-end framework that first generates the entity and predicate proposal set, followed by inferring directed edges to form the relation triplets. In particular, we develop a new entity-aware predicate representation based on a structural predicate generator that leverages the compositional property of relationships. Moreover, we design a graph assembling module to infer the connectivity of the bipartite scene graph based on our entity-aware structure, enabling us to generate the scene graph in an end-to-end manner. Extensive experimental results show that our design is able to achieve the state-of-the-art or comparable performance on two challenging benchmarks, surpassing most of the existing approaches and enjoying higher efficiency in inference. We hope our model can serve as a strong baseline for the Transformer-based scene graph generation. Code is available: https://github.com/Scarecrow0/SGTR
Unsupervised graph-level representation learning plays a crucial role in a variety of tasks such as molecular property prediction and community analysis, especially when data annotation is expensive. Currently, most of the best-performing graph embedding methods are based on Infomax principle. The performance of these methods highly depends on the selection of negative samples and hurt the performance, if the samples were not carefully selected. Inter-graph similarity-based methods also suffer if the selected set of graphs for similarity matching is low in quality. To address this, we focus only on utilizing the current input graph for embedding learning. We are motivated by an observation from real-world graph generation processes where the graphs are formed based on one or more global factors which are common to all elements of the graph (e.g., topic of a discussion thread, solubility level of a molecule). We hypothesize extracting these common factors could be highly beneficial. Hence, this work proposes a new principle for unsupervised graph representation learning: Graph-wise Common latent Factor EXtraction (GCFX). We further propose a deep model for GCFX, deepGCFX, based on the idea of reversing the above-mentioned graph generation process which could explicitly extract common latent factors from an input graph and achieve improved results on downstream tasks to the current state-of-the-art. Through extensive experiments and analysis, we demonstrate that, while extracting common latent factors is beneficial for graph-level tasks to alleviate distractions caused by local variations of individual nodes or local neighbourhoods, it also benefits node-level tasks by enabling long-range node dependencies, especially for disassortative graphs.