We introduce SeaDAG, a semi-autoregressive diffusion model for conditional generation of Directed Acyclic Graphs (DAGs). Considering their inherent layer-wise structure, we simulate layer-wise autoregressive generation by designing different denoising speed for different layers. Unlike conventional autoregressive generation that lacks a global graph structure view, our method maintains a complete graph structure at each diffusion step, enabling operations such as property control that require the full graph structure. Leveraging this capability, we evaluate the DAG properties during training by employing a graph property decoder. We explicitly train the model to learn graph conditioning with a condition loss, which enhances the diffusion model's capacity to generate graphs that are both realistic and aligned with specified properties. We evaluate our method on two representative conditional DAG generation tasks: (1) circuit generation from truth tables, where precise DAG structures are crucial for realizing circuit functionality, and (2) molecule generation based on quantum properties. Our approach demonstrates promising results, generating high-quality and realistic DAGs that closely align with given conditions.
Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, including statistical and deep learning methods, often fail to effectively integrate gene interaction knowledge from databases or explicitly learn subtype-specific interactions. To address this mismatch, we propose GeSubNet, which learns a unified representation capable of predicting gene interactions while distinguishing between different disease subtypes. Graphs generated by such representations can be considered subtype-specific networks. GeSubNet is a multi-step representation learning framework with three modules: First, a deep generative model learns distinct disease subtypes from patient gene expression profiles. Second, a graph neural network captures representations of prior gene networks from knowledge databases, ensuring accurate physical gene interactions. Finally, we integrate these two representations using an inference loss that leverages graph generation capabilities, conditioned on the patient separation loss, to refine subtype-specific information in the learned representation. GeSubNet consistently outperforms traditional methods, with average improvements of 30.6%, 21.0%, 20.1%, and 56.6% across four graph evaluation metrics, averaged over four cancer datasets. Particularly, we conduct a biological simulation experiment to assess how the behavior of selected genes from over 11,000 candidates affects subtypes or patient distributions. The results show that the generated network has the potential to identify subtype-specific genes with an 83% likelihood of impacting patient distribution shifts. The GeSubNet resource is available: https://anonymous.4open.science/r/GeSubNet/
Heterogeneous graphs are present in various domains, such as social networks, recommendation systems, and biological networks. Unlike homogeneous graphs, heterogeneous graphs consist of multiple types of nodes and edges, each representing different entities and relationships. Generating realistic heterogeneous graphs that capture the complex interactions among diverse entities is a difficult task due to several reasons. The generator has to model both the node type distribution along with the feature distribution for each node type. In this paper, we look into solving challenges in heterogeneous graph generation, by employing a two phase hierarchical structure, wherein the first phase creates a skeleton graph with node types using a prior diffusion based model and in the second phase, we use an encoder and a sampler structure as generator to assign node type specific features to the nodes. A discriminator is used to guide training of the generator and feature vectors are sampled from a node feature pool. We conduct extensive experiments with subsets of IMDB and DBLP datasets to show the effectiveness of our method and also the need for various architecture components.
Graphs, as a relational data structure, have been widely used for various application scenarios, like molecule design and recommender systems. Recently, large language models (LLMs) are reorganizing in the AI community for their expected reasoning and inference abilities. Making LLMs understand graph-based relational data has great potential, including but not limited to (1) distillate external knowledge base for eliminating hallucination and breaking the context window limit for LLMs' inference during the retrieval augmentation generation process; (2) taking graph data as the input and directly solve the graph-based research tasks like protein design and drug discovery. However, inputting the entire graph data to LLMs is not practical due to its complex topological structure, data size, and the lack of effective and efficient semantic graph representations. A natural question arises: Is there a kind of graph representation that can be described by natural language for LLM's understanding and is also easy to require to serve as the raw input for LLMs? Based on statistical computation, graph laws pre-define a set of parameters (e.g., degree, time, diameter) and identifie their relationships and values by observing the topological distribution of plenty of real-world graph data. We believe this kind of parametric representation of graphs, graph laws, can be a solution for making LLMs understand graph data as the input. In this survey, we first review the previous study of graph laws from multiple perspectives, i.e., macroscope and microscope of graphs, low-order and high-order graphs, static and dynamic graphs, different observation spaces, and newly proposed graph parameters. After we review various real-world applications benefiting from the guidance of graph laws, we conclude the paper with current challenges and future research directions.
The structural properties of naturally arising social graphs are extensively studied to understand their evolution. Prior approaches for modeling network dynamics typically rely on rule-based models, which lack realism and generalizability, or deep learning-based models, which require large-scale training datasets. Social graphs, as abstract graph representations of entity-wise interactions, present an opportunity to explore network evolution mechanisms through realistic simulations of human-item interactions. Leveraging the pre-trained social consensus knowledge embedded in large language models (LLMs), we present GraphAgent-Generator (GAG), a novel simulation-based framework for dynamic, text-attributed social graph generation. GAG simulates the temporal node and edge generation processes for zero-shot social graph generation. The resulting graphs exhibit adherence to seven key macroscopic network properties, achieving an 11% improvement in microscopic graph structure metrics. Through the node classification benchmarking task, we validate GAG effectively captures the intricate text-structure correlations in graph generation. Furthermore, GAG supports generating graphs with up to nearly 100,000 nodes or 10 million edges through large-scale LLM-based agent simulation with parallel acceleration, achieving a minimum speed-up of 90.4%. The source code is available at https://github.com/Ji-Cather/GraphAgent.
In the expanding field of generative artificial intelligence, integrating robust watermarking technologies is essential to protect intellectual property and maintain content authenticity. Traditionally, watermarking techniques have been developed primarily for rich information media such as images and audio. However, these methods have not been adequately adapted for graph-based data, particularly molecular graphs. Latent 3D graph diffusion(LDM-3DG) is an ascendant approach in the molecular graph generation field. This model effectively manages the complexities of molecular structures, preserving essential symmetries and topological features. We adapt the Gaussian Shading, a proven performance lossless watermarking technique, to the latent graph diffusion domain to protect this sophisticated new technology. Our adaptation simplifies the watermark diffusion process through duplication and padding, making it adaptable and suitable for various message types. We conduct several experiments using the LDM-3DG model on publicly available datasets QM9 and Drugs, to assess the robustness and effectiveness of our technique. Our results demonstrate that the watermarked molecules maintain statistical parity in 9 out of 10 performance metrics compared to the original. Moreover, they exhibit a 100% detection rate and a 99% extraction rate in a 2D decoded pipeline, while also showing robustness against post-editing attacks.
This work introduces NetDiff, an expressive graph denoising diffusion probabilistic architecture that generates wireless ad hoc network link topologies. Such networks, with directional antennas, can achieve unmatched performance when the communication links are designed to provide good geometric properties, notably by reducing interference between these links while respecting diverse physical constraints. How to craft such a link assignment algorithm is yet a real problem. Deep graph generation offers multiple advantages compared to traditional approaches: it allows to relieve the network nodes of the communication burden caused by the search of viable links and to avoid resorting to heavy combinatorial methods to find a good link topology. Denoising diffusion also provides a built-in method to update the network over time. Given that graph neural networks sometimes tend to struggle with global, structural properties, we augment the popular graph transformer with cross-attentive modulation tokens in order to improve global control over the predicted topology. We also incorporate simple node and edge features, as well as additional loss terms, to facilitate the compliance with the network topology physical constraints. A network evolution algorithm based on partial diffusion is also proposed to maintain a stable network topology over time when the nodes move. Our results show that the generated links are realistic, present structural properties similar to the dataset graphs', and require only minor corrections and verification steps to be operational.
Reasoning about time and temporal relations is an integral aspect of human cognition, essential for perceiving the world and navigating our experiences. Though large language models (LLMs) have demonstrated impressive performance in many reasoning tasks, temporal reasoning remains challenging due to its intrinsic complexity. In this work, we first study an essential task of temporal reasoning -- temporal graph generation, to unveil LLMs' inherent, global reasoning capabilities. We show that this task presents great challenges even for the most powerful LLMs, such as GPT-3.5/4. We also notice a significant performance gap by small models (<10B) that lag behind LLMs by 50%. Next, we study how to close this gap with a budget constraint, e.g., not using model finetuning. We propose a new prompting technique tailored for temporal reasoning, Narrative-of-Thought (NoT), that first converts the events set to a Python class, then prompts a small model to generate a temporally grounded narrative, guiding the final generation of a temporal graph. Extensive experiments showcase the efficacy of NoT in improving various metrics. Notably, NoT attains the highest F1 on the Schema-11 evaluation set, while securing an overall F1 on par with GPT-3.5. NoT also achieves the best structural similarity across the board, even compared with GPT-3.5/4. Our code is available at https://github.com/launchnlp/NoT.
Graph generation is fundamental in diverse scientific applications, due to its ability to reveal the underlying distribution of complex data, and eventually generate new, realistic data points. Despite the success of diffusion models in this domain, those face limitations in sampling efficiency and flexibility, stemming from the tight coupling between the training and sampling stages. To address this, we propose DeFoG, a novel framework using discrete flow matching for graph generation. DeFoG employs a flow-based approach that features an efficient linear interpolation noising process and a flexible denoising process based on a continuous-time Markov chain formulation. We leverage an expressive graph transformer and ensure desirable node permutation properties to respect graph symmetry. Crucially, our framework enables a disentangled design of the training and sampling stages, enabling more effective and efficient optimization of model performance. We navigate this design space by introducing several algorithmic improvements that boost the model performance, consistently surpassing existing diffusion models. We also theoretically demonstrate that, for general discrete data, discrete flow models can faithfully replicate the ground truth distribution - a result that naturally extends to graph data and reinforces DeFoG's foundations. Extensive experiments show that DeFoG achieves state-of-the-art results on synthetic and molecular datasets, improving both training and sampling efficiency over diffusion models, and excels in conditional generation on a digital pathology dataset.
While large language models (LLMs) have integrated images, adapting them to graphs remains challenging, limiting their applications in materials and drug design. This difficulty stems from the need for coherent autoregressive generation across texts and graphs. To address this, we introduce Llamole, the first multimodal LLM capable of interleaved text and graph generation, enabling molecular inverse design with retrosynthetic planning. Llamole integrates a base LLM with the Graph Diffusion Transformer and Graph Neural Networks for multi-conditional molecular generation and reaction inference within texts, while the LLM, with enhanced molecular understanding, flexibly controls activation among the different graph modules. Additionally, Llamole integrates A* search with LLM-based cost functions for efficient retrosynthetic planning. We create benchmarking datasets and conduct extensive experiments to evaluate Llamole against in-context learning and supervised fine-tuning. Llamole significantly outperforms 14 adapted LLMs across 12 metrics for controllable molecular design and retrosynthetic planning.
Understanding the relationships between geometric structures and semantic concepts is crucial for building accurate models of complex environments. In indoors, certain spatial constraints, such as the relative positioning of planes, remain consistent despite variations in layout. This paper explores how these invariant relationships can be captured in a graph SLAM framework by representing high-level concepts like rooms and walls, linking them to geometric elements like planes through an optimizable factor graph. Several efforts have tackled this issue with add-hoc solutions for each concept generation and with manually-defined factors. This paper proposes a novel method for metric-semantic factor graph generation which includes defining a semantic scene graph, integrating geometric information, and learning the interconnecting factors, all based on Graph Neural Networks (GNNs). An edge classification network (G-GNN) sorts the edges between planes into same room, same wall or none types. The resulting relations are clustered, generating a room or wall for each cluster. A second family of networks (F-GNN) infers the geometrical origin of the new nodes. The definition of the factors employs the same F-GNN used for the metric attribute of the generated nodes. Furthermore, share the new factor graph with the S-Graphs+ algorithm, extending its graph expressiveness and scene representation with the ultimate goal of improving the SLAM performance. The complexity of the environments is increased to N-plane rooms by training the networks on L-shaped rooms. The framework is evaluated in synthetic and simulated scenarios as no real datasets of the required complex layouts are available.
DETR introduces a simplified one-stage framework for scene graph generation (SGG). However, DETR-based SGG models face two challenges: i) Sparse supervision, as each image typically contains fewer than 10 relation annotations, while the models employ over 100 relation queries. This sparsity arises because each ground truth relation is assigned to only one single query during training. ii) False negative samples, since one ground truth relation may have multiple queries with similar matching scores. These suboptimally matched queries are simply treated as negative samples, causing the loss of valuable supervisory signals. As a response, we devise Hydra-SGG, a one-stage SGG method that adopts a new Hybrid Relation Assignment. This assignment combines a One-to-One Relation Assignment with a newly introduced IoU-based One-to-Many Relation Assignment. Specifically, each ground truth is assigned to multiple relation queries with high IoU subject-object boxes. This Hybrid Relation Assignment increases the number of positive training samples, alleviating sparse supervision. Moreover, we, for the first time, empirically show that self-attention over relation queries helps reduce duplicated relation predictions. We, therefore, propose Hydra Branch, a parameter-sharing auxiliary decoder without a self-attention layer. This design promotes One-to-Many Relation Assignment by enabling different queries to predict the same relation. Hydra-SGG achieves state-of-the-art performance with 10.6 mR@20 and 16.0 mR@50 on VG150, while only requiring 12 training epochs. It also sets a new state-of-the-art on Open Images V6 and and GQA.
Current open-vocabulary scene graph generation algorithms highly rely on both 3D scene point cloud data and posed RGB-D images and thus have limited applications in scenarios where RGB-D images or camera poses are not readily available. To solve this problem, we propose Point2Graph, a novel end-to-end point cloud-based 3D open-vocabulary scene graph generation framework in which the requirement of posed RGB-D image series is eliminated. This hierarchical framework contains room and object detection/segmentation and open-vocabulary classification. For the room layer, we leverage the advantage of merging the geometry-based border detection algorithm with the learning-based region detection to segment rooms and create a "Snap-Lookup" framework for open-vocabulary room classification. In addition, we create an end-to-end pipeline for the object layer to detect and classify 3D objects based solely on 3D point cloud data. Our evaluation results show that our framework can outperform the current state-of-the-art (SOTA) open-vocabulary object and room segmentation and classification algorithm on widely used real-scene datasets.
Training-free guidance methods for continuous data have seen an explosion of interest due to the fact that they enable foundation diffusion models to be paired with interchangable guidance models. Currently, equivalent guidance methods for discrete diffusion models are unknown. We present a framework for applying training-free guidance to discrete data and demonstrate its utility on molecular graph generation tasks using the discrete diffusion model architecture of DiGress. We pair this model with guidance functions that return the proportion of heavy atoms that are a specific atom type and the molecular weight of the heavy atoms and demonstrate our method's ability to guide the data generation.
RGB-D cameras supply rich and dense visual and spatial information for various robotics tasks such as scene understanding, map reconstruction, and localization. Integrating depth and visual information can aid robots in localization and element mapping, advancing applications like 3D scene graph generation and Visual Simultaneous Localization and Mapping (VSLAM). While point cloud data containing such information is primarily used for enhanced scene understanding, exploiting their potential to capture and represent rich semantic information has yet to be adequately targeted. This paper presents a real-time pipeline for localizing building components, including wall and ground surfaces, by integrating geometric calculations for pure 3D plane detection followed by validating their semantic category using point cloud data from RGB-D cameras. It has a parallel multi-thread architecture to precisely estimate poses and equations of all the planes detected in the environment, filters the ones forming the map structure using a panoptic segmentation validation, and keeps only the validated building components. Incorporating the proposed method into a VSLAM framework confirmed that constraining the map with the detected environment-driven semantic elements can improve scene understanding and map reconstruction accuracy. It can also ensure (re-)association of these detected components into a unified 3D scene graph, bridging the gap between geometric accuracy and semantic understanding. Additionally, the pipeline allows for the detection of potential higher-level structural entities, such as rooms, by identifying the relationships between building components based on their layout.
Interacting with real-world cluttered scenes pose several challenges to robotic agents that need to understand complex spatial dependencies among the observed objects to determine optimal pick sequences or efficient object retrieval strategies. Existing solutions typically manage simplified scenarios and focus on predicting pairwise object relationships following an initial object detection phase, but often overlook the global context or struggle with handling redundant and missing object relations. In this work, we present a modern take on visual relational reasoning for grasp planning. We introduce D3GD, a novel testbed that includes bin picking scenes with up to 35 objects from 97 distinct categories. Additionally, we propose D3G, a new end-to-end transformer-based dependency graph generation model that simultaneously detects objects and produces an adjacency matrix representing their spatial relationships. Recognizing the limitations of standard metrics, we employ the Average Precision of Relationships for the first time to evaluate model performance, conducting an extensive experimental benchmark. The obtained results establish our approach as the new state-of-the-art for this task, laying the foundation for future research in robotic manipulation. We publicly release the code and dataset at https://paolotron.github.io/d3g.github.io.
Automating architectural floorplan design is vital for housing and interior design, offering a faster, cost-effective alternative to manual sketches by architects. However, existing methods, including rule-based and learning-based approaches, face challenges in design complexity and constrained generation with extensive post-processing, and tend to obvious geometric inconsistencies such as misalignment, overlap, and gaps. In this work, we propose a novel generative framework for vector floorplan design via structural graph generation, called GSDiff, focusing on wall junction generation and wall segment prediction to capture both geometric and semantic aspects of structural graphs. To improve the geometric rationality of generated structural graphs, we propose two innovative geometry enhancement methods. In wall junction generation, we propose a novel alignment loss function to improve geometric consistency. In wall segment prediction, we propose a random self-supervision method to enhance the model's perception of the overall geometric structure, thereby promoting the generation of reasonable geometric structures. Employing the diffusion model and the Transformer model, as well as the geometry enhancement strategies, our framework can generate wall junctions, wall segments and room polygons with structural and semantic information, resulting in structural graphs that accurately represent floorplans. Extensive experiments show that the proposed method surpasses existing techniques, enabling free generation and constrained generation, marking a shift towards structure generation in architectural design. Code and data are available at https://github.com/SizheHu/GSDiff.
Hypergraphs are powerful mathematical structures that can model complex, high-order relationships in various domains, including social networks, bioinformatics, and recommender systems. However, generating realistic and diverse hypergraphs remains challenging due to their inherent complexity and lack of effective generative models. In this paper, we introduce a diffusion-based Hypergraph Generation (HYGENE) method that addresses these challenges through a progressive local expansion approach. HYGENE works on the bipartite representation of hypergraphs, starting with a single pair of connected nodes and iteratively expanding it to form the target hypergraph. At each step, nodes and hyperedges are added in a localized manner using a denoising diffusion process, which allows for the construction of the global structure before refining local details. Our experiments demonstrated the effectiveness of HYGENE, proving its ability to closely mimic a variety of properties in hypergraphs. To the best of our knowledge, this is the first attempt to employ deep learning models for hypergraph generation, and our work aims to lay the groundwork for future research in this area.
Heterogeneous Graph Neural Networks (HGNNs) have expanded graph representation learning to heterogeneous graph fields. Recent studies have demonstrated their superior performance across various applications, including medical analysis and recommendation systems, often surpassing existing methods. However, GPUs often experience inefficiencies when executing HGNNs due to their unique and complex execution patterns. Compared to traditional Graph Neural Networks, these patterns further exacerbate irregularities in memory access. To tackle these challenges, recent studies have focused on developing domain-specific accelerators for HGNNs. Nonetheless, most of these efforts have concentrated on optimizing the datapath or scheduling data accesses, while largely overlooking the potential benefits that could be gained from leveraging the inherent properties of the semantic graph, such as its topology, layout, and generation. In this work, we focus on leveraging the properties of semantic graphs to enhance HGNN performance. First, we analyze the Semantic Graph Build (SGB) stage and identify significant opportunities for data reuse during semantic graph generation. Next, we uncover the phenomenon of buffer thrashing during the Graph Feature Processing (GFP) stage, revealing potential optimization opportunities in semantic graph layout. Furthermore, we propose a lightweight hardware accelerator frontend for HGNNs, called SiHGNN. This accelerator frontend incorporates a tree-based Semantic Graph Builder for efficient semantic graph generation and features a novel Graph Restructurer for optimizing semantic graph layouts. Experimental results show that SiHGNN enables the state-of-the-art HGNN accelerator to achieve an average performance improvement of 2.95$\times$.
Scene Graph Generation (SGG) aims to generate a comprehensive graphical representation that accurately captures the semantic information of a given scenario. However, the SGG model's performance in predicting more fine-grained predicates is hindered by a significant predicate bias. According to existing works, the long-tail distribution of predicates in training data results in the biased scene graph. However, the semantic overlap between predicate categories makes predicate prediction difficult, and there is a significant difference in the sample size of semantically similar predicates, making the predicate prediction more difficult. Therefore, higher requirements are placed on the discriminative ability of the model. In order to address this problem, this paper proposes Ensemble Predicate Decoding (EPD), which employs multiple decoders to attain unbiased scene graph generation. Two auxiliary decoders trained on lower-frequency predicates are used to improve the discriminative ability of the model. Extensive experiments are conducted on the VG, and the experiment results show that EPD enhances the model's representation capability for predicates. In addition, we find that our approach ensures a relatively superior predictive capability for more frequent predicates compared to previous unbiased SGG methods.