Graph generative models are highly important for sharing surrogate data and benchmarking purposes. Real-world complex systems often exhibit dynamic nature, where the interactions among nodes change over time in the form of a temporal network. Most temporal network generation models extend the static graph generation models by incorporating temporality in the generation process. More recently, temporal motifs are used to generate temporal networks with better success. However, existing models are often restricted to a small set of predefined motif patterns due to the high computational cost of counting temporal motifs. In this work, we develop a practical temporal graph generator, Motif Transition Model (MTM), to generate synthetic temporal networks with realistic global and local features. Our key idea is modeling the arrival of new events as temporal motif transition processes. We first calculate the transition properties from the input graph and then simulate the motif transition processes based on the transition probabilities and transition rates. We demonstrate that our model consistently outperforms the baselines with respect to preserving various global and local temporal graph statistics and runtime performance.
Diffusion generative models (DMs) have achieved promising results in image and graph generation. However, real-world graphs, such as social networks, molecular graphs, and traffic graphs, generally share non-Euclidean topologies and hidden hierarchies. For example, the degree distributions of graphs are mostly power-law distributions. The current latent diffusion model embeds the hierarchical data in a Euclidean space, which leads to distortions and interferes with modeling the distribution. Instead, hyperbolic space has been found to be more suitable for capturing complex hierarchical structures due to its exponential growth property. In order to simultaneously utilize the data generation capabilities of diffusion models and the ability of hyperbolic embeddings to extract latent hierarchical distributions, we propose a novel graph generation method called, Hyperbolic Graph Diffusion Model (HGDM), which consists of an auto-encoder to encode nodes into successive hyperbolic embeddings, and a DM that operates in the hyperbolic latent space. HGDM captures the crucial graph structure distributions by constructing a hyperbolic potential node space that incorporates edge information. Extensive experiments show that HGDM achieves better performance in generic graph and molecule generation benchmarks, with a $48\%$ improvement in the quality of graph generation with highly hierarchical structures.
The generation of explanation graphs is a significant task that aims to produce explanation graphs in response to user input, revealing the internal reasoning process. This task is challenging due to the significant discrepancy between unstructured user queries and structured explanation graphs. Current research commonly fine-tunes a text-based pre-trained language model on a small downstream dataset that is annotated with labeled graphs. However, due to the limited scale of available datasets, this approach may prove to be insufficient in bridging the gap between natural language text and structured graphs. In this paper, to alleviate the above limitations, we propose a novel pre-trained framework EG3P(for Explanation Graph Generation via Generative Pre-training over synthetic graphs) for the explanation graph generation task. Specifically, we first propose a text-to-graph generative task to pre-train the model with the goal of bridging the text-graph gap. Additionally, we propose an automatic corpus synthesis strategy for synthesizing a large scale of high-quality corpus, reducing the reliance on costly manual annotation methods. Experimental results on ExplaGraphs show the effectiveness of EG3P that our model surpasses all baseline systems with remarkable margins. Besides, further analysis demonstrates that EG3P is able to generate better explanation graphs on actual reasoning tasks such as CommonsenseQA and OpenbookQA.
Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.
Learning to compose visual relationships from raw images in the form of scene graphs is a highly challenging task due to contextual dependencies, but it is essential in computer vision applications that depend on scene understanding. However, no current approaches in Scene Graph Generation (SGG) aim at providing useful graphs for downstream tasks. Instead, the main focus has primarily been on the task of unbiasing the data distribution for predicting more fine-grained relations. That being said, all fine-grained relations are not equally relevant and at least a part of them are of no use for real-world applications. In this work, we introduce the task of Efficient SGG that prioritizes the generation of relevant relations, facilitating the use of Scene Graphs in downstream tasks such as Image Generation. To support further approaches, we present a new dataset, VG150-curated, based on the annotations of the popular Visual Genome dataset. We show through a set of experiments that this dataset contains more high-quality and diverse annotations than the one usually use in SGG. Finally, we show the efficiency of this dataset in the task of Image Generation from Scene Graphs.
Generating graphs from a target distribution is a significant challenge across many domains, including drug discovery and social network analysis. In this work, we introduce a novel graph generation method leveraging $K^2$-tree representation, originally designed for lossless graph compression. The $K^2$-tree representation {encompasses inherent hierarchy while enabling compact graph generation}. In addition, we make contributions by (1) presenting a sequential $K^2$-treerepresentation that incorporates pruning, flattening, and tokenization processes and (2) introducing a Transformer-based architecture designed to generate the sequence by incorporating a specialized tree positional encoding scheme. Finally, we extensively evaluate our algorithm on four general and two molecular graph datasets to confirm its superiority for graph generation.
Event skeleton generation, aiming to induce an event schema skeleton graph with abstracted event nodes and their temporal relations from a set of event instance graphs, is a critical step in the temporal complex event schema induction task. Existing methods effectively address this task from a graph generation perspective but suffer from noise-sensitive and error accumulation, e.g., the inability to correct errors while generating schema. We, therefore, propose a novel Diffusion Event Graph Model~(DEGM) to address these issues. Our DEGM is the first workable diffusion model for event skeleton generation, where the embedding and rounding techniques with a custom edge-based loss are introduced to transform a discrete event graph into learnable latent representation. Furthermore, we propose a denoising training process to maintain the model's robustness. Consequently, DEGM derives the final schema, where error correction is guaranteed by iteratively refining the latent representation during the schema generation process. Experimental results on three IED bombing datasets demonstrate that our DEGM achieves better results than other state-of-the-art baselines. Our code and data are available at https://github.com/zhufq00/EventSkeletonGeneration.
Conditional graph generation tasks involve training a model to generate a graph given a set of input conditions. Many previous studies employ autoregressive models to incrementally generate graph components such as nodes and edges. However, as graphs typically lack a natural ordering among their components, converting a graph into a sequence of tokens is not straightforward. While prior works mostly rely on conventional heuristics or graph traversal methods like breadth-first search (BFS) or depth-first search (DFS) to convert graphs to sequences, the impact of ordering on graph generation has largely been unexplored. This paper contributes to this problem by: (1) highlighting the crucial role of ordering in autoregressive graph generation models, (2) proposing a novel theoretical framework that perceives ordering as a dimensionality reduction problem, thereby facilitating a deeper understanding of the relationship between orderings and generated graph accuracy, and (3) introducing "latent sort," a learning-based ordering scheme to perform dimensionality reduction of graph tokens. Our experimental results showcase the effectiveness of latent sort across a wide range of graph generation tasks, encouraging future works to further explore and develop learning-based ordering schemes for autoregressive graph generation.
Large language models (LLMs) have shown great abilities of solving various natural language tasks in different domains. Due to the training objective of LLMs and their pre-training data, LLMs are not very well equipped for tasks involving structured data generation. We propose a framework, Prompting with Iterative Verification (PiVe), to improve graph-based generative capability of LLMs. We show how a small language model could be trained to act as a verifier module for the output of an LLM~(i.e., ChatGPT, GPT-4), and to iteratively improve its performance via fine-grained corrective instructions. We also show how the verifier module could apply iterative corrections offline for a more cost-effective solution to the text-to-graph generation task. Experiments on three graph-based datasets show consistent improvement gained via PiVe. Additionally, we create GenWiki-HIQ and highlight that the verifier module can be used as a data augmentation tool to help improve the quality of automatically generated parallel text-graph datasets.
Designing new molecules is essential for drug discovery and material science. Recently, deep generative models that aim to model molecule distribution have made promising progress in narrowing down the chemical research space and generating high-fidelity molecules. However, current generative models only focus on modeling either 2D bonding graphs or 3D geometries, which are two complementary descriptors for molecules. The lack of ability to jointly model both limits the improvement of generation quality and further downstream applications. In this paper, we propose a new joint 2D and 3D diffusion model (JODO) that generates complete molecules with atom types, formal charges, bond information, and 3D coordinates. To capture the correlation between molecular graphs and geometries in the diffusion process, we develop a Diffusion Graph Transformer to parameterize the data prediction model that recovers the original data from noisy data. The Diffusion Graph Transformer interacts node and edge representations based on our relational attention mechanism, while simultaneously propagating and updating scalar features and geometric vectors. Our model can also be extended for inverse molecular design targeting single or multiple quantum properties. In our comprehensive evaluation pipeline for unconditional joint generation, the results of the experiment show that JODO remarkably outperforms the baselines on the QM9 and GEOM-Drugs datasets. Furthermore, our model excels in few-step fast sampling, as well as in inverse molecule design and molecular graph generation. Our code is provided in https://github.com/GRAPH-0/JODO.
Molecular de novo design is a critical yet challenging task in scientific fields, aiming to design novel molecular structures with desired property profiles. Significant progress has been made by resorting to generative models for graphs. However, limited attention is paid to hierarchical generative models, which can exploit the inherent hierarchical structure (with rich semantic information) of the molecular graphs and generate complex molecules of larger size that we shall demonstrate to be difficult for most existing models. The primary challenge to hierarchical generation is the non-differentiable issue caused by the generation of intermediate discrete coarsened graph structures. To sidestep this issue, we cast the tricky hierarchical generation problem over discrete spaces as the reverse process of hierarchical representation learning and propose MolHF, a new hierarchical flow-based model that generates molecular graphs in a coarse-to-fine manner. Specifically, MolHF first generates bonds through a multi-scale architecture, then generates atoms based on the coarsened graph structure at each scale. We demonstrate that MolHF achieves state-of-the-art performance in random generation and property optimization, implying its high capacity to model data distribution. Furthermore, MolHF is the first flow-based model that can be applied to model larger molecules (polymer) with more than 100 heavy atoms. The code and models are available at https://github.com/violet-sto/MolHF.
Diffusion-based generative graph models have been proven effective in generating high-quality small graphs. However, they need to be more scalable for generating large graphs containing thousands of nodes desiring graph statistics. In this work, we propose EDGE, a new diffusion-based generative graph model that addresses generative tasks with large graphs. To improve computation efficiency, we encourage graph sparsity by using a discrete diffusion process that randomly removes edges at each time step and finally obtains an empty graph. EDGE only focuses on a portion of nodes in the graph at each denoising step. It makes much fewer edge predictions than previous diffusion-based models. Moreover, EDGE admits explicitly modeling the node degrees of the graphs, further improving the model performance. The empirical study shows that EDGE is much more efficient than competing methods and can generate large graphs with thousands of nodes. It also outperforms baseline models in generation quality: graphs generated by our approach have more similar graph statistics to those of the training graphs.
Graph representation learning models aim to represent the graph structure and its features into low-dimensional vectors in a latent space, which can benefit various downstream tasks, such as node classification and link prediction. Due to its powerful graph data modelling capabilities, various graph embedding models and libraries have been proposed to learn embeddings and help researchers ease conducting experiments. In this paper, we introduce a novel graph representation framework covering various graph embedding models, ranging from shallow to state-of-the-art models, namely Connector. First, we consider graph generation by constructing various types of graphs with different structural relations, including homogeneous, signed, heterogeneous, and knowledge graphs. Second, we introduce various graph representation learning models, ranging from shallow to deep graph embedding models. Finally, we plan to build an efficient open-source framework that can provide deep graph embedding models to represent structural relations in graphs. The framework is available at https://github.com/NSLab-CUK/Connector.
Designing molecules with desirable physiochemical properties and functionalities is a long-standing challenge in chemistry, material science, and drug discovery. Recently, machine learning-based generative models have emerged as promising approaches for \emph{de novo} molecule design. However, further refinement of methodology is highly desired as most existing methods lack unified modeling of 2D topology and 3D geometry information and fail to effectively learn the structure-property relationship for molecule design. Here we present MolCode, a roto-translation equivariant generative framework for \underline{Mol}ecular graph-structure \underline{Co-de}sign. In MolCode, 3D geometric information empowers the molecular 2D graph generation, which in turn helps guide the prediction of molecular 3D structure. Extensive experimental results show that MolCode outperforms previous methods on a series of challenging tasks including \emph{de novo} molecule design, targeted molecule discovery, and structure-based drug design. Particularly, MolCode not only consistently generates valid (99.95$\%$ Validity) and diverse (98.75$\%$ Uniqueness) molecular graphs/structures with desirable properties, but also generate drug-like molecules with high affinity to target proteins (61.8$\%$ high-affinity ratio), which demonstrates MolCode's potential applications in material design and drug discovery. Our extensive investigation reveals that the 2D topology and 3D geometry contain intrinsically complementary information in molecule design, and provide new insights into machine learning-based molecule representation and generation.
The task of dynamic scene graph generation (SGG) from videos is complicated and challenging due to the inherent dynamics of a scene, temporal fluctuation of model predictions, and the long-tailed distribution of the visual relationships in addition to the already existing challenges in image-based SGG. Existing methods for dynamic SGG have primarily focused on capturing spatio-temporal context using complex architectures without addressing the challenges mentioned above, especially the long-tailed distribution of relationships. This often leads to the generation of biased scene graphs. To address these challenges, we introduce a new framework called TEMPURA: TEmporal consistency and Memory Prototype guided UnceRtainty Attenuation for unbiased dynamic SGG. TEMPURA employs object-level temporal consistencies via transformer-based sequence modeling, learns to synthesize unbiased relationship representations using memory-guided training, and attenuates the predictive uncertainty of visual relations using a Gaussian Mixture Model (GMM). Extensive experiments demonstrate that our method achieves significant (up to 10% in some cases) performance gain over existing methods highlighting its superiority in generating more unbiased scene graphs.
Learning similarity between scene graphs and images aims to estimate a similarity score given a scene graph and an image. There is currently no research dedicated to this task, although it is critical for scene graph generation and downstream applications. Scene graph generation is conventionally evaluated by Recall$@K$ and mean Recall$@K$, which measure the ratio of predicted triplets that appear in the human-labeled triplet set. However, such triplet-oriented metrics fail to demonstrate the overall semantic difference between a scene graph and an image and are sensitive to annotation bias and noise. Using generated scene graphs in the downstream applications is therefore limited. To address this issue, for the first time, we propose a Scene graPh-imAge coNtrastive learning framework, SPAN, that can measure the similarity between scene graphs and images. Our novel framework consists of a graph Transformer and an image Transformer to align scene graphs and their corresponding images in the shared latent space. We introduce a novel graph serialization technique that transforms a scene graph into a sequence with structural encodings. Based on our framework, we propose R-Precision measuring image retrieval accuracy as a new evaluation metric for scene graph generation. We establish new benchmarks on the Visual Genome and Open Images datasets. Extensive experiments are conducted to verify the effectiveness of SPAN, which shows great potential as a scene graph encoder.
Scene Graph Generation (SGG) aims to extract <subject, predicate, object> relationships in images for vision understanding. Although recent works have made steady progress on SGG, they still suffer long-tail distribution issues that tail-predicates are more costly to train and hard to distinguish due to a small amount of annotated data compared to frequent predicates. Existing re-balancing strategies try to handle it via prior rules but are still confined to pre-defined conditions, which are not scalable for various models and datasets. In this paper, we propose a Cross-modal prediCate boosting (CaCao) framework, where a visually-prompted language model is learned to generate diverse fine-grained predicates in a low-resource way. The proposed CaCao can be applied in a plug-and-play fashion and automatically strengthen existing SGG to tackle the long-tailed problem. Based on that, we further introduce a novel Entangled cross-modal prompt approach for open-world predicate scene graph generation (Epic), where models can generalize to unseen predicates in a zero-shot manner. Comprehensive experiments on three benchmark datasets show that CaCao consistently boosts the performance of multiple scene graph generation models in a model-agnostic way. Moreover, our Epic achieves competitive performance on open-world predicate prediction. The data and code for this paper are publicly available.
Current video-based scene graph generation (VidSGG) methods have been found to perform poorly on predicting predicates that are less represented due to the inherent biased distribution in the training data. In this paper, we take a closer look at the predicates and identify that most visual relations (e.g. sit_above) involve both actional pattern (sit) and spatial pattern (above), while the distribution bias is much less severe at the pattern level. Based on this insight, we propose a decoupled label learning (DLL) paradigm to address the intractable visual relation prediction from the pattern-level perspective. Specifically, DLL decouples the predicate labels and adopts separate classifiers to learn actional and spatial patterns respectively. The patterns are then combined and mapped back to the predicate. Moreover, we propose a knowledge-level label decoupling method to transfer non-target knowledge from head predicates to tail predicates within the same pattern to calibrate the distribution of tail classes. We validate the effectiveness of DLL on the commonly used VidSGG benchmark, i.e. VidVRD. Extensive experiments demonstrate that the DLL offers a remarkably simple but highly effective solution to the long-tailed problem, achieving the state-of-the-art VidSGG performance.
In this paper, we propose a novel model called SGFormer, Semantic Graph TransFormer for point cloud-based 3D scene graph generation. The task aims to parse a point cloud-based scene into a semantic structural graph, with the core challenge of modeling the complex global structure. Existing methods based on graph convolutional networks (GCNs) suffer from the over-smoothing dilemma and can only propagate information from limited neighboring nodes. In contrast, SGFormer uses Transformer layers as the base building block to allow global information passing, with two types of newly-designed layers tailored for the 3D scene graph generation task. Specifically, we introduce the graph embedding layer to best utilize the global information in graph edges while maintaining comparable computation costs. Furthermore, we propose the semantic injection layer to leverage linguistic knowledge from large-scale language model (i.e., ChatGPT), to enhance objects' visual features. We benchmark our SGFormer on the established 3DSSG dataset and achieve a 40.94% absolute improvement in relationship prediction's R@50 and an 88.36% boost on the subset with complex scenes over the state-of-the-art. Our analyses further show SGFormer's superiority in the long-tail and zero-shot scenarios. Our source code is available at https://github.com/Andy20178/SGFormer.
Scene Graph Generation (SGG) is a visual understanding task, aiming to describe a scene as a graph of entities and their relationships with each other. Existing works rely on location labels in form of bounding boxes or segmentation masks, increasing annotation costs and limiting dataset expansion. Recognizing that many applications do not require location data, we break this dependency and introduce location-free scene graph generation (LF-SGG). This new task aims at predicting instances of entities, as well as their relationships, without the explicit calculation of their spatial localization. To objectively evaluate the task, the predicted and ground truth scene graphs need to be compared. We solve this NP-hard problem through an efficient branching algorithm. Additionally, we design the first LF-SGG method, Pix2SG, using autoregressive sequence modeling. We demonstrate the effectiveness of our method on three scene graph generation datasets as well as two downstream tasks, image retrieval and visual question answering, and show that our approach is competitive to existing methods while not relying on location cues.