Daily Papers

Graph generation has been dominated by autoregressive models due to their simplicity and effectiveness, despite their sensitivity to ordering. Yet diffusion models have garnered increasing attention, as they offer comparable performance while being permutation-invariant. Current graph diffusion models generate graphs in a one-shot fashion, but they require extra features and thousands of denoising steps to achieve optimal performance. We introduce PARD, a Permutation-invariant Auto Regressive Diffusion model that integrates diffusion models with autoregressive methods. PARD harnesses the effectiveness and efficiency of the autoregressive model while maintaining permutation invariance without ordering sensitivity. Specifically, we show that contrary to sets, elements in a graph are not entirely unordered and there is a unique partial order for nodes and edges. With this partial order, PARD generates a graph in a block-by-block, autoregressive fashion, where each block's probability is conditionally modeled by a shared diffusion model with an equivariant network. To ensure efficiency while being expressive, we further propose a higher-order graph transformer, which integrates transformer with PPGN. Like GPT, we extend the higher-order graph transformer to support parallel training of all blocks. Without any extra features, PARD achieves state-of-the-art performance on molecular and non-molecular datasets, and scales to large datasets like MOSES containing 1.9M molecules.

Generation of graphs is a major challenge for real-world tasks that require understanding the complex nature of their non-Euclidean structures. Although diffusion models have achieved notable success in graph generation recently, they are ill-suited for modeling the topological properties of graphs since learning to denoise the noisy samples does not explicitly learn the graph structures to be generated. To tackle this limitation, we propose a generative framework that models the topology of graphs by explicitly learning the final graph structures of the diffusion process. Specifically, we design the generative process as a mixture of endpoint-conditioned diffusion processes which is driven toward the predicted graph that results in rapid convergence. We further introduce a simple parameterization of the mixture process and develop an objective for learning the final graph structure, which enables maximum likelihood training. Through extensive experimental validation on general graph and 2D/3D molecule generation tasks, we show that our method outperforms previous generative models, generating graphs with correct topology with both continuous (e.g. 3D coordinates) and discrete (e.g. atom types) features. Our code is available at https://github.com/harryjo97/GruM.

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.

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.

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements and bonds respectively. Although existing deep learning models perform remarkably well at predicting physicochemical properties and binding affinities, the generation of new molecules with optimized properties remains challenging. Inherently, most GNNs perform poorly in whole-graph representation due to the limitations of the message-passing paradigm. Furthermore, step-by-step graph generation frameworks that use reinforcement learning or other sequential processing can be slow and result in a high proportion of invalid molecules with substantial post-processing needed in order to satisfy the principles of stoichiometry. To address these issues, we propose a representation-first approach to molecular graph generation. We guide the latent representation of an autoencoder by capturing graph structure information with the geometric scattering transform and apply penalties that structure the representation also by molecular properties. We show that this highly structured latent space can be directly used for molecular graph generation by the use of a GAN. We demonstrate that our architecture learns meaningful representations of drug datasets and provides a platform for goal-directed drug synthesis.

Scene graph generation (SGG) aims to predict graph-structured descriptions of input images, in the form of objects and relationships between them. This task is becoming increasingly useful for progress at the interface of vision and language. Here, it is important - yet challenging - to perform well on novel (zero-shot) or rare (few-shot) compositions of objects and relationships. In this paper, we identify two key issues that limit such generalization. Firstly, we show that the standard loss used in this task is unintentionally a function of scene graph density. This leads to the neglect of individual edges in large sparse graphs during training, even though these contain diverse few-shot examples that are important for generalization. Secondly, the frequency of relationships can create a strong bias in this task, such that a blind model predicting the most frequent relationship achieves good performance. Consequently, some state-of-the-art models exploit this bias to improve results. We show that such models can suffer the most in their ability to generalize to rare compositions, evaluating two different models on the Visual Genome dataset and its more recent, improved version, GQA. To address these issues, we introduce a density-normalized edge loss, which provides more than a two-fold improvement in certain generalization metrics. Compared to other works in this direction, our enhancements require only a few lines of code and no added computational cost. We also highlight the difficulty of accurately evaluating models using existing metrics, especially on zero/few shots, and introduce a novel weighted metric.

Scene graph generation (SGG) models have suffered from inherent problems regarding the benchmark datasets such as the long-tailed predicate distribution and missing annotation problems. In this work, we aim to alleviate the long-tailed problem of SGG by utilizing unannotated triplets. To this end, we introduce a Self-Training framework for SGG (ST-SGG) that assigns pseudo-labels for unannotated triplets based on which the SGG models are trained. While there has been significant progress in self-training for image recognition, designing a self-training framework for the SGG task is more challenging due to its inherent nature such as the semantic ambiguity and the long-tailed distribution of predicate classes. Hence, we propose a novel pseudo-labeling technique for SGG, called Class-specific Adaptive Thresholding with Momentum (CATM), which is a model-agnostic framework that can be applied to any existing SGG models. Furthermore, we devise a graph structure learner (GSL) that is beneficial when adopting our proposed self-training framework to the state-of-the-art message-passing neural network (MPNN)-based SGG models. Our extensive experiments verify the effectiveness of ST-SGG on various SGG models, particularly in enhancing the performance on fine-grained predicate classes.

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.

Scene Graph Generation (SGG) converts visual scenes into structured graph representations, providing deeper scene understanding for complex vision tasks. However, existing SGG models often overlook essential spatial relationships and struggle with generalization in open-vocabulary contexts. To address these limitations, we propose LLaVA-SpaceSGG, a multimodal large language model (MLLM) designed for open-vocabulary SGG with enhanced spatial relation modeling. To train it, we collect the SGG instruction-tuning dataset, named SpaceSGG. This dataset is constructed by combining publicly available datasets and synthesizing data using open-source models within our data construction pipeline. It combines object locations, object relations, and depth information, resulting in three data formats: spatial SGG description, question-answering, and conversation. To enhance the transfer of MLLMs' inherent capabilities to the SGG task, we introduce a two-stage training paradigm. Experiments show that LLaVA-SpaceSGG outperforms other open-vocabulary SGG methods, boosting recall by 8.6% and mean recall by 28.4% compared to the baseline. Our codebase, dataset, and trained models are publicly accessible on GitHub at the following URL: https://github.com/Endlinc/LLaVA-SpaceSGG.

Scene Graph Generation (SGG) offers a structured representation critical in many computer vision applications. Traditional SGG approaches, however, are limited by a closed-set assumption, restricting their ability to recognize only predefined object and relation categories. To overcome this, we categorize SGG scenarios into four distinct settings based on the node and edge: Closed-set SGG, Open Vocabulary (object) Detection-based SGG (OvD-SGG), Open Vocabulary Relation-based SGG (OvR-SGG), and Open Vocabulary Detection + Relation-based SGG (OvD+R-SGG). While object-centric open vocabulary SGG has been studied recently, the more challenging problem of relation-involved open-vocabulary SGG remains relatively unexplored. To fill this gap, we propose a unified framework named OvSGTR towards fully open vocabulary SGG from a holistic view. The proposed framework is an end-toend transformer architecture, which learns a visual-concept alignment for both nodes and edges, enabling the model to recognize unseen categories. For the more challenging settings of relation-involved open vocabulary SGG, the proposed approach integrates relation-aware pre-training utilizing image-caption data and retains visual-concept alignment through knowledge distillation. Comprehensive experimental results on the Visual Genome benchmark demonstrate the effectiveness and superiority of the proposed framework.

Scene Graph Generation (SGG) aims to detect all the visual relation triplets <sub, pred, obj> in a given image. With the emergence of various advanced techniques for better utilizing both the intrinsic and extrinsic information in each relation triplet, SGG has achieved great progress over the recent years. However, due to the ubiquitous long-tailed predicate distributions, today's SGG models are still easily biased to the head predicates. Currently, the most prevalent debiasing solutions for SGG are re-balancing methods, e.g., changing the distributions of original training samples. In this paper, we argue that all existing re-balancing strategies fail to increase the diversity of the relation triplet features of each predicate, which is critical for robust SGG. To this end, we propose a novel Compositional Feature Augmentation (CFA) strategy, which is the first unbiased SGG work to mitigate the bias issue from the perspective of increasing the diversity of triplet features. Specifically, we first decompose each relation triplet feature into two components: intrinsic feature and extrinsic feature, which correspond to the intrinsic characteristics and extrinsic contexts of a relation triplet, respectively. Then, we design two different feature augmentation modules to enrich the feature diversity of original relation triplets by replacing or mixing up either their intrinsic or extrinsic features from other samples. Due to its model-agnostic nature, CFA can be seamlessly incorporated into various SGG frameworks. Extensive ablations have shown that CFA achieves a new state-of-the-art performance on the trade-off between different metrics.

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

Scene graph generation (SGG) is a fundamental task aimed at detecting visual relations between objects in an image. The prevailing SGG methods require all object classes to be given in the training set. Such a closed setting limits the practical application of SGG. In this paper, we introduce open-vocabulary scene graph generation, a novel, realistic and challenging setting in which a model is trained on a set of base object classes but is required to infer relations for unseen target object classes. To this end, we propose a two-step method that firstly pre-trains on large amounts of coarse-grained region-caption data and then leverages two prompt-based techniques to finetune the pre-trained model without updating its parameters. Moreover, our method can support inference over completely unseen object classes, which existing methods are incapable of handling. On extensive experiments on three benchmark datasets, Visual Genome, GQA, and Open-Image, our method significantly outperforms recent, strong SGG methods on the setting of Ov-SGG, as well as on the conventional closed SGG.

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

Understanding a visual scene goes beyond recognizing individual objects in isolation. Relationships between objects also constitute rich semantic information about the scene. In this work, we explicitly model the objects and their relationships using scene graphs, a visually-grounded graphical structure of an image. We propose a novel end-to-end model that generates such structured scene representation from an input image. The model solves the scene graph inference problem using standard RNNs and learns to iteratively improves its predictions via message passing. Our joint inference model can take advantage of contextual cues to make better predictions on objects and their relationships. The experiments show that our model significantly outperforms previous methods for generating scene graphs using Visual Genome dataset and inferring support relations with NYU Depth v2 dataset.

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

Panoptic Scene Graph Generation (PSG) aims to segment objects and recognize their relations, enabling the structured understanding of an image. Previous methods focus on predicting predefined object and relation categories, hence limiting their applications in the open world scenarios. With the rapid development of large multimodal models (LMMs), significant progress has been made in open-set object detection and segmentation, yet open-set relation prediction in PSG remains unexplored. In this paper, we focus on the task of open-set relation prediction integrated with a pretrained open-set panoptic segmentation model to achieve true open-set panoptic scene graph generation (OpenPSG). Our OpenPSG leverages LMMs to achieve open-set relation prediction in an autoregressive manner. We introduce a relation query transformer to efficiently extract visual features of object pairs and estimate the existence of relations between them. The latter can enhance the prediction efficiency by filtering irrelevant pairs. Finally, we design the generation and judgement instructions to perform open-set relation prediction in PSG autoregressively. To our knowledge, we are the first to propose the open-set PSG task. Extensive experiments demonstrate that our method achieves state-of-the-art performance in open-set relation prediction and panoptic scene graph generation. Code is available at https://github.com/franciszzj/OpenPSG.

Towards building comprehensive real-world visual perception systems, we propose and study a new problem called panoptic scene graph generation (PVSG). PVSG relates to the existing video scene graph generation (VidSGG) problem, which focuses on temporal interactions between humans and objects grounded with bounding boxes in videos. However, the limitation of bounding boxes in detecting non-rigid objects and backgrounds often causes VidSGG to miss key details crucial for comprehensive video understanding. In contrast, PVSG requires nodes in scene graphs to be grounded by more precise, pixel-level segmentation masks, which facilitate holistic scene understanding. To advance research in this new area, we contribute the PVSG dataset, which consists of 400 videos (289 third-person + 111 egocentric videos) with a total of 150K frames labeled with panoptic segmentation masks as well as fine, temporal scene graphs. We also provide a variety of baseline methods and share useful design practices for future work.

Panoptic Scene Graph Generation (PSG) aims at achieving a comprehensive image understanding by simultaneously segmenting objects and predicting relations among objects. However, the long-tail problem among relations leads to unsatisfactory results in real-world applications. Prior methods predominantly rely on vision information or utilize limited language information, such as object or relation names, thereby overlooking the utility of language information. Leveraging the recent progress in Large Language Models (LLMs), we propose to use language information to assist relation prediction, particularly for rare relations. To this end, we propose the Vision-Language Prompting (VLPrompt) model, which acquires vision information from images and language information from LLMs. Then, through a prompter network based on attention mechanism, it achieves precise relation prediction. Our extensive experiments show that VLPrompt significantly outperforms previous state-of-the-art methods on the PSG dataset, proving the effectiveness of incorporating language information and alleviating the long-tail problem of relations.

Panoptic Scene Graph generation (PSG) is a recently proposed task in image scene understanding that aims to segment the image and extract triplets of subjects, objects and their relations to build a scene graph. This task is particularly challenging for two reasons. First, it suffers from a long-tail problem in its relation categories, making naive biased methods more inclined to high-frequency relations. Existing unbiased methods tackle the long-tail problem by data/loss rebalancing to favor low-frequency relations. Second, a subject-object pair can have two or more semantically overlapping relations. While existing methods favor one over the other, our proposed HiLo framework lets different network branches specialize on low and high frequency relations, enforce their consistency and fuse the results. To the best of our knowledge we are the first to propose an explicitly unbiased PSG method. In extensive experiments we show that our HiLo framework achieves state-of-the-art results on the PSG task. We also apply our method to the Scene Graph Generation task that predicts boxes instead of masks and see improvements over all baseline methods. Code is available at https://github.com/franciszzj/HiLo.

Weakly-Supervised Scene Graph Generation (WSSGG) research has recently emerged as an alternative to the fully-supervised approach that heavily relies on costly annotations. In this regard, studies on WSSGG have utilized image captions to obtain unlocalized triplets while primarily focusing on grounding the unlocalized triplets over image regions. However, they have overlooked the two issues involved in the triplet formation process from the captions: 1) Semantic over-simplification issue arises when extracting triplets from captions, where fine-grained predicates in captions are undesirably converted into coarse-grained predicates, resulting in a long-tailed predicate distribution, and 2) Low-density scene graph issue arises when aligning the triplets in the caption with entity/predicate classes of interest, where many triplets are discarded and not used in training, leading to insufficient supervision. To tackle the two issues, we propose a new approach, i.e., Large Language Model for weakly-supervised SGG (LLM4SGG), where we mitigate the two issues by leveraging the LLM's in-depth understanding of language and reasoning ability during the extraction of triplets from captions and alignment of entity/predicate classes with target data. To further engage the LLM in these processes, we adopt the idea of Chain-of-Thought and the in-context few-shot learning strategy. To validate the effectiveness of LLM4SGG, we conduct extensive experiments on Visual Genome and GQA datasets, showing significant improvements in both Recall@K and mean Recall@K compared to the state-of-the-art WSSGG methods. A further appeal is that LLM4SGG is data-efficient, enabling effective model training with a small amount of training images.

This work introduces DiGress, a discrete denoising diffusion model for generating graphs with categorical node and edge attributes. Our model utilizes a discrete diffusion process that progressively edits graphs with noise, through the process of adding or removing edges and changing the categories. A graph transformer network is trained to revert this process, simplifying the problem of distribution learning over graphs into a sequence of node and edge classification tasks. We further improve sample quality by introducing a Markovian noise model that preserves the marginal distribution of node and edge types during diffusion, and by incorporating auxiliary graph-theoretic features. A procedure for conditioning the generation on graph-level features is also proposed. DiGress achieves state-of-the-art performance on molecular and non-molecular datasets, with up to 3x validity improvement on a planar graph dataset. It is also the first model to scale to the large GuacaMol dataset containing 1.3M drug-like molecules without the use of molecule-specific representations.

The scene graph generation (SGG) task involves detecting objects within an image and predicting predicates that represent the relationships between the objects. However, in SGG benchmark datasets, each subject-object pair is annotated with a single predicate even though a single predicate may exhibit diverse semantics (i.e., semantic diversity), existing SGG models are trained to predict the one and only predicate for each pair. This in turn results in the SGG models to overlook the semantic diversity that may exist in a predicate, thus leading to biased predictions. In this paper, we propose a novel model-agnostic Semantic Diversity-aware Prototype-based Learning (DPL) framework that enables unbiased predictions based on the understanding of the semantic diversity of predicates. Specifically, DPL learns the regions in the semantic space covered by each predicate to distinguish among the various different semantics that a single predicate can represent. Extensive experiments demonstrate that our proposed model-agnostic DPL framework brings significant performance improvement on existing SGG models, and also effectively understands the semantic diversity of predicates.

In panoptic scene graph generation (PSGG), models retrieve interactions between objects in an image which are grounded by panoptic segmentation masks. Previous evaluations on panoptic scene graphs have been subject to an erroneous evaluation protocol where multiple masks for the same object can lead to multiple relation distributions per mask-mask pair. This can be exploited to increase the final score. We correct this flaw and provide a fair ranking over a wide range of existing PSGG models. The observed scores for existing methods increase by up to 7.4 mR@50 for all two-stage methods, while dropping by up to 19.3 mR@50 for all one-stage methods, highlighting the importance of a correct evaluation. Contrary to recent publications, we show that existing two-stage methods are competitive to one-stage methods. Building on this, we introduce the Decoupled SceneFormer (DSFormer), a novel two-stage model that outperforms all existing scene graph models by a large margin of +11 mR@50 and +10 mNgR@50 on the corrected evaluation, thus setting a new SOTA. As a core design principle, DSFormer encodes subject and object masks directly into feature space.

We introduce a new framework for molecular graph generation with 3D molecular generative models. Our Synthetic Coordinate Embedding (SyCo) framework maps molecular graphs to Euclidean point clouds via synthetic conformer coordinates and learns the inverse map using an E(n)-Equivariant Graph Neural Network (EGNN). The induced point cloud-structured latent space is well-suited to apply existing 3D molecular generative models. This approach simplifies the graph generation problem - without relying on molecular fragments nor autoregressive decoding - into a point cloud generation problem followed by node and edge classification tasks. Further, we propose a novel similarity-constrained optimization scheme for 3D diffusion models based on inpainting and guidance. As a concrete implementation of our framework, we develop EDM-SyCo based on the E(3) Equivariant Diffusion Model (EDM). EDM-SyCo achieves state-of-the-art performance in distribution learning of molecular graphs, outperforming the best non-autoregressive methods by more than 30% on ZINC250K and 16% on the large-scale GuacaMol dataset while improving conditional generation by up to 3.9 times.

The scene graph generation (SGG) task is designed to identify the predicates based on the subject-object pairs.However,existing datasets generally include two imbalance cases: one is the class imbalance from the predicted predicates and another is the context imbalance from the given subject-object pairs, which presents significant challenges for SGG. Most existing methods focus on the imbalance of the predicted predicate while ignoring the imbalance of the subject-object pairs, which could not achieve satisfactory results. To address the two imbalance cases, we propose a novel Environment Invariant Curriculum Relation learning (EICR) method, which can be applied in a plug-and-play fashion to existing SGG methods. Concretely, to remove the imbalance of the subject-object pairs, we first construct different distribution environments for the subject-object pairs and learn a model invariant to the environment changes. Then, we construct a class-balanced curriculum learning strategy to balance the different environments to remove the predicate imbalance. Comprehensive experiments conducted on VG and GQA datasets demonstrate that our EICR framework can be taken as a general strategy for various SGG models, and achieve significant improvements.

Knowledge Graph Embedding (KGE) models are used to learn continuous representations of entities and relations. A key task in the literature is predicting missing links between entities. However, Knowledge Graphs are not just sets of links but also have semantics underlying their structure. Semantics is crucial in several downstream tasks, such as query answering or reasoning. We introduce the subgraph inference task, where a model has to generate likely and semantically valid subgraphs. We propose IntelliGraphs, a set of five new Knowledge Graph datasets. The IntelliGraphs datasets contain subgraphs with semantics expressed in logical rules for evaluating subgraph inference. We also present the dataset generator that produced the synthetic datasets. We designed four novel baseline models, which include three models based on traditional KGEs. We evaluate their expressiveness and show that these models cannot capture the semantics. We believe this benchmark will encourage the development of machine learning models that emphasize semantic understanding.

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.

Current Scene Graph Generation (SGG) methods explore contextual information to predict relationships among entity pairs. However, due to the diverse visual appearance of numerous possible subject-object combinations, there is a large intra-class variation within each predicate category, e.g., "man-eating-pizza, giraffe-eating-leaf", and the severe inter-class similarity between different classes, e.g., "man-holding-plate, man-eating-pizza", in model's latent space. The above challenges prevent current SGG methods from acquiring robust features for reliable relation prediction. In this paper, we claim that the predicate's category-inherent semantics can serve as class-wise prototypes in the semantic space for relieving the challenges. To the end, we propose the Prototype-based Embedding Network (PE-Net), which models entities/predicates with prototype-aligned compact and distinctive representations and thereby establishes matching between entity pairs and predicates in a common embedding space for relation recognition. Moreover, Prototype-guided Learning (PL) is introduced to help PE-Net efficiently learn such entitypredicate matching, and Prototype Regularization (PR) is devised to relieve the ambiguous entity-predicate matching caused by the predicate's semantic overlap. Extensive experiments demonstrate that our method gains superior relation recognition capability on SGG, achieving new state-of-the-art performances on both Visual Genome and Open Images datasets.

Existing research addresses scene graph generation (SGG) -- a critical technology for scene understanding in images -- from a detection perspective, i.e., objects are detected using bounding boxes followed by prediction of their pairwise relationships. We argue that such a paradigm causes several problems that impede the progress of the field. For instance, bounding box-based labels in current datasets usually contain redundant classes like hairs, and leave out background information that is crucial to the understanding of context. In this work, we introduce panoptic scene graph generation (PSG), a new problem task that requires the model to generate a more comprehensive scene graph representation based on panoptic segmentations rather than rigid bounding boxes. A high-quality PSG dataset, which contains 49k well-annotated overlapping images from COCO and Visual Genome, is created for the community to keep track of its progress. For benchmarking, we build four two-stage baselines, which are modified from classic methods in SGG, and two one-stage baselines called PSGTR and PSGFormer, which are based on the efficient Transformer-based detector, i.e., DETR. While PSGTR uses a set of queries to directly learn triplets, PSGFormer separately models the objects and relations in the form of queries from two Transformer decoders, followed by a prompting-like relation-object matching mechanism. In the end, we share insights on open challenges and future directions.

As far as Scene Graph Generation (SGG), coarse and fine predicates mix in the dataset due to the crowd-sourced labeling, and the long-tail problem is also pronounced. Given this tricky situation, many existing SGG methods treat the predicates equally and learn the model under the supervision of mixed-granularity predicates in one stage, leading to relatively coarse predictions. In order to alleviate the negative impact of the suboptimum mixed-granularity annotation and long-tail effect problems, this paper proposes a novel Hierarchical Memory Learning (HML) framework to learn the model from simple to complex, which is similar to the human beings' hierarchical memory learning process. After the autonomous partition of coarse and fine predicates, the model is first trained on the coarse predicates and then learns the fine predicates. In order to realize this hierarchical learning pattern, this paper, for the first time, formulates the HML framework using the new Concept Reconstruction (CR) and Model Reconstruction (MR) constraints. It is worth noticing that the HML framework can be taken as one general optimization strategy to improve various SGG models, and significant improvement can be achieved on the SGG benchmark (i.e., Visual Genome).

There is a surge of interest in image scene graph generation (object, attribute and relationship detection) due to the need of building fine-grained image understanding models that go beyond object detection. Due to the lack of a good benchmark, the reported results of different scene graph generation models are not directly comparable, impeding the research progress. We have developed a much-needed scene graph generation benchmark based on the maskrcnn-benchmark and several popular models. This paper presents main features of our benchmark and a comprehensive ablation study of scene graph generation models using the Visual Genome and OpenImages Visual relationship detection datasets. Our codebase is made publicly available at https://github.com/microsoft/scene_graph_benchmark.

Diffusion models have made significant contributions to computer vision, sparking a growing interest in the community recently regarding the application of them to graph generation. Existing discrete graph diffusion models exhibit heightened computational complexity and diminished training efficiency. A preferable and natural way is to directly diffuse the graph within the latent space. However, due to the non-Euclidean structure of graphs is not isotropic in the latent space, the existing latent diffusion models effectively make it difficult to capture and preserve the topological information of graphs. To address the above challenges, we propose a novel geometrically latent diffusion framework HypDiff. Specifically, we first establish a geometrically latent space with interpretability measures based on hyperbolic geometry, to define anisotropic latent diffusion processes for graphs. Then, we propose a geometrically latent diffusion process that is constrained by both radial and angular geometric properties, thereby ensuring the preservation of the original topological properties in the generative graphs. Extensive experimental results demonstrate the superior effectiveness of HypDiff for graph generation with various topologies.

The recent advances in large language models (LLM) and foundation models with emergent capabilities have been shown to improve the performance of many NLP tasks. LLMs and Knowledge Graphs (KG) can complement each other such that LLMs can be used for KG construction or completion while existing KGs can be used for different tasks such as making LLM outputs explainable or fact-checking in Neuro-Symbolic manner. In this paper, we present Text2KGBench, a benchmark to evaluate the capabilities of language models to generate KGs from natural language text guided by an ontology. Given an input ontology and a set of sentences, the task is to extract facts from the text while complying with the given ontology (concepts, relations, domain/range constraints) and being faithful to the input sentences. We provide two datasets (i) Wikidata-TekGen with 10 ontologies and 13,474 sentences and (ii) DBpedia-WebNLG with 19 ontologies and 4,860 sentences. We define seven evaluation metrics to measure fact extraction performance, ontology conformance, and hallucinations by LLMs. Furthermore, we provide results for two baseline models, Vicuna-13B and Alpaca-LoRA-13B using automatic prompt generation from test cases. The baseline results show that there is room for improvement using both Semantic Web and Natural Language Processing techniques.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

Recent years have seen a growing interest in Scene Graph Generation (SGG), a comprehensive visual scene understanding task that aims to predict entity relationships using a relation encoder-decoder pipeline stacked on top of an object encoder-decoder backbone. Unfortunately, current SGG methods suffer from an information loss regarding the entities local-level cues during the relation encoding process. To mitigate this, we introduce the Vision rElation TransfOrmer (VETO), consisting of a novel local-level entity relation encoder. We further observe that many existing SGG methods claim to be unbiased, but are still biased towards either head or tail classes. To overcome this bias, we introduce a Mutually Exclusive ExperT (MEET) learning strategy that captures important relation features without bias towards head or tail classes. Experimental results on the VG and GQA datasets demonstrate that VETO + MEET boosts the predictive performance by up to 47 percentage over the state of the art while being 10 times smaller.

Recent approaches to empathetic response generation incorporate emotion causalities to enhance comprehension of both the user's feelings and experiences. However, these approaches suffer from two critical issues. First, they only consider causalities between the user's emotion and the user's experiences, and ignore those between the user's experiences. Second, they neglect interdependence among causalities and reason them independently. To solve the above problems, we expect to reason all plausible causalities interdependently and simultaneously, given the user's emotion, dialogue history, and future dialogue content. Then, we infuse these causalities into response generation for empathetic responses. Specifically, we design a new model, i.e., the Conditional Variational Graph Auto-Encoder (CVGAE), for the causality reasoning, and adopt a multi-source attention mechanism in the decoder for the causality infusion. We name the whole framework as CARE, abbreviated for CAusality Reasoning for Empathetic conversation. Experimental results indicate that our method achieves state-of-the-art performance.

In this work, we seek new insights into the underlying challenges of the Scene Graph Generation (SGG) task. Quantitative and qualitative analysis of the Visual Genome dataset implies -- 1) Ambiguity: even if inter-object relationship contains the same object (or predicate), they may not be visually or semantically similar, 2) Asymmetry: despite the nature of the relationship that embodied the direction, it was not well addressed in previous studies, and 3) Higher-order contexts: leveraging the identities of certain graph elements can help to generate accurate scene graphs. Motivated by the analysis, we design a novel SGG framework, Local-to-Global Interaction Networks (LOGIN). Locally, interactions extract the essence between three instances of subject, object, and background, while baking direction awareness into the network by explicitly constraining the input order of subject and object. Globally, interactions encode the contexts between every graph component (i.e., nodes and edges). Finally, Attract & Repel loss is utilized to fine-tune the distribution of predicate embeddings. By design, our framework enables predicting the scene graph in a bottom-up manner, leveraging the possible complementariness. To quantify how much LOGIN is aware of relational direction, a new diagnostic task called Bidirectional Relationship Classification (BRC) is also proposed. Experimental results demonstrate that LOGIN can successfully distinguish relational direction than existing methods (in BRC task), while showing state-of-the-art results on the Visual Genome benchmark (in SGG task).

We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings instead of graphs. Our junction tree variational autoencoder generates molecular graphs in two phases, by first generating a tree-structured scaffold over chemical substructures, and then combining them into a molecule with a graph message passing network. This approach allows us to incrementally expand molecules while maintaining chemical validity at every step. We evaluate our model on multiple tasks ranging from molecular generation to optimization. Across these tasks, our model outperforms previous state-of-the-art baselines by a significant margin.

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating this task. In this paper, we propose MolScribe, a novel image-to-graph generation model that explicitly predicts atoms and bonds, along with their geometric layouts, to construct the molecular structure. Our model flexibly incorporates symbolic chemistry constraints to recognize chirality and expand abbreviated structures. We further develop data augmentation strategies to enhance the model robustness against domain shifts. In experiments on both synthetic and realistic molecular images, MolScribe significantly outperforms previous models, achieving 76-93% accuracy on public benchmarks. Chemists can also easily verify MolScribe's prediction, informed by its confidence estimation and atom-level alignment with the input image. MolScribe is publicly available through Python and web interfaces: https://github.com/thomas0809/MolScribe.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

Inferring objects and their relationships from an image in the form of a scene graph is useful in many applications at the intersection of vision and language. We consider a challenging problem of compositional generalization that emerges in this task due to a long tail data distribution. Current scene graph generation models are trained on a tiny fraction of the distribution corresponding to the most frequent compositions, e.g. <cup, on, table>. However, test images might contain zero- and few-shot compositions of objects and relationships, e.g. <cup, on, surfboard>. Despite each of the object categories and the predicate (e.g. 'on') being frequent in the training data, the models often fail to properly understand such unseen or rare compositions. To improve generalization, it is natural to attempt increasing the diversity of the training distribution. However, in the graph domain this is non-trivial. To that end, we propose a method to synthesize rare yet plausible scene graphs by perturbing real ones. We then propose and empirically study a model based on conditional generative adversarial networks (GANs) that allows us to generate visual features of perturbed scene graphs and learn from them in a joint fashion. When evaluated on the Visual Genome dataset, our approach yields marginal, but consistent improvements in zero- and few-shot metrics. We analyze the limitations of our approach indicating promising directions for future research.

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.

Graph Neural Networks (GNNs) are popular models for graph learning problems. GNNs show strong empirical performance in many practical tasks. However, the theoretical properties have not been completely elucidated. In this paper, we investigate whether GNNs can exploit the graph structure from the perspective of the expressive power of GNNs. In our analysis, we consider graph generation processes that are controlled by hidden (or latent) node features, which contain all information about the graph structure. A typical example of this framework is kNN graphs constructed from the hidden features. In our main results, we show that GNNs can recover the hidden node features from the input graph alone, even when all node features, including the hidden features themselves and any indirect hints, are unavailable. GNNs can further use the recovered node features for downstream tasks. These results show that GNNs can fully exploit the graph structure by themselves, and in effect, GNNs can use both the hidden and explicit node features for downstream tasks. In the experiments, we confirm the validity of our results by showing that GNNs can accurately recover the hidden features using a GNN architecture built based on our theoretical analysis.

Being the most cutting-edge generative methods, diffusion methods have shown great advances in wide generation tasks. Among them, graph generation attracts significant research attention for its broad application in real life. In our survey, we systematically and comprehensively review on diffusion-based graph generative methods. We first make a review on three mainstream paradigms of diffusion methods, which are denoising diffusion probabilistic models, score-based genrative models, and stochastic differential equations. Then we further categorize and introduce the latest applications of diffusion models on graphs. In the end, we point out some limitations of current studies and future directions of future explorations. The summary of existing methods metioned in this survey is in https://github.com/zhejiangzhuque/Diffusion-based-Graph-Generative-Methods.

Current scene graph datasets suffer from strong long-tail distributions of their predicate classes. Due to a very low number of some predicate classes in the test sets, no reliable metrics can be retrieved for the rarest classes. We construct a new panoptic scene graph dataset and a set of metrics that are designed as a benchmark for the predictive performance especially on rare predicate classes. To construct the new dataset, we propose a model-assisted annotation pipeline that efficiently finds rare predicate classes that are hidden in a large set of images like needles in a haystack. Contrary to prior scene graph datasets, Haystack contains explicit negative annotations, i.e. annotations that a given relation does not have a certain predicate class. Negative annotations are helpful especially in the field of scene graph generation and open up a whole new set of possibilities to improve current scene graph generation models. Haystack is 100% compatible with existing panoptic scene graph datasets and can easily be integrated with existing evaluation pipelines. Our dataset and code can be found here: https://lorjul.github.io/haystack/. It includes annotation files and simple to use scripts and utilities, to help with integrating our dataset in existing work.

In this paper, we propose Multiresolution Equivariant Graph Variational Autoencoders (MGVAE), the first hierarchical generative model to learn and generate graphs in a multiresolution and equivariant manner. At each resolution level, MGVAE employs higher order message passing to encode the graph while learning to partition it into mutually exclusive clusters and coarsening into a lower resolution that eventually creates a hierarchy of latent distributions. MGVAE then constructs a hierarchical generative model to variationally decode into a hierarchy of coarsened graphs. Importantly, our proposed framework is end-to-end permutation equivariant with respect to node ordering. MGVAE achieves competitive results with several generative tasks including general graph generation, molecular generation, unsupervised molecular representation learning to predict molecular properties, link prediction on citation graphs, and graph-based image generation.

Graph neural networks (GNNs) have been demonstrated to be powerful in modeling graph-structured data. However, training GNNs usually requires abundant task-specific labeled data, which is often arduously expensive to obtain. One effective way to reduce the labeling effort is to pre-train an expressive GNN model on unlabeled data with self-supervision and then transfer the learned model to downstream tasks with only a few labels. In this paper, we present the GPT-GNN framework to initialize GNNs by generative pre-training. GPT-GNN introduces a self-supervised attributed graph generation task to pre-train a GNN so that it can capture the structural and semantic properties of the graph. We factorize the likelihood of the graph generation into two components: 1) Attribute Generation and 2) Edge Generation. By modeling both components, GPT-GNN captures the inherent dependency between node attributes and graph structure during the generative process. Comprehensive experiments on the billion-scale Open Academic Graph and Amazon recommendation data demonstrate that GPT-GNN significantly outperforms state-of-the-art GNN models without pre-training by up to 9.1% across various downstream tasks.

Recent advances in Graph Neural Networks (GNNs) have revolutionized graph-structured data modeling, yet traditional GNNs struggle with complex heterogeneous structures prevalent in real-world scenarios. Despite progress in handling heterogeneous interactions, two fundamental challenges persist: noisy data significantly compromising embedding quality and learning performance, and existing methods' inability to capture intricate semantic transitions among heterogeneous relations, which impacts downstream predictions. To address these fundamental issues, we present the Heterogeneous Graph Diffusion Model (DiffGraph), a pioneering framework that introduces an innovative cross-view denoising strategy. This advanced approach transforms auxiliary heterogeneous data into target semantic spaces, enabling precise distillation of task-relevant information. At its core, DiffGraph features a sophisticated latent heterogeneous graph diffusion mechanism, implementing a novel forward and backward diffusion process for superior noise management. This methodology achieves simultaneous heterogeneous graph denoising and cross-type transition, while significantly simplifying graph generation through its latent-space diffusion capabilities. Through rigorous experimental validation on both public and industrial datasets, we demonstrate that DiffGraph consistently surpasses existing methods in link prediction and node classification tasks, establishing new benchmarks for robustness and efficiency in heterogeneous graph processing. The model implementation is publicly available at: https://github.com/HKUDS/DiffGraph.

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these structured representations given new sources of information. Although there have been many efforts focusing on improving the performance of the parsers that map text to graphs or parse trees, very few have explored the problem of directly manipulating these representations. In this paper, we explore the novel problem of graph modification, where the systems need to learn how to update an existing scene graph given a new user's command. Our novel models based on graph-based sparse transformer and cross attention information fusion outperform previous systems adapted from the machine translation and graph generation literature. We further contribute our large graph modification datasets to the research community to encourage future research for this new problem.

Graph Neural Networks (GNNs) have been widely applied to different tasks such as bioinformatics, drug design, and social networks. However, recent studies have shown that GNNs are vulnerable to adversarial attacks which aim to mislead the node or subgraph classification prediction by adding subtle perturbations. Detecting these attacks is challenging due to the small magnitude of perturbation and the discrete nature of graph data. In this paper, we propose a general adversarial edge detection pipeline EDoG without requiring knowledge of the attack strategies based on graph generation. Specifically, we propose a novel graph generation approach combined with link prediction to detect suspicious adversarial edges. To effectively train the graph generative model, we sample several sub-graphs from the given graph data. We show that since the number of adversarial edges is usually low in practice, with low probability the sampled sub-graphs will contain adversarial edges based on the union bound. In addition, considering the strong attacks which perturb a large number of edges, we propose a set of novel features to perform outlier detection as the preprocessing for our detection. Extensive experimental results on three real-world graph datasets including a private transaction rule dataset from a major company and two types of synthetic graphs with controlled properties show that EDoG can achieve above 0.8 AUC against four state-of-the-art unseen attack strategies without requiring any knowledge about the attack type; and around 0.85 with knowledge of the attack type. EDoG significantly outperforms traditional malicious edge detection baselines. We also show that an adaptive attack with full knowledge of our detection pipeline is difficult to bypass it.

Can we model non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The non-Euclidean property have posed a long term challenge in graph modeling. Despite recent GNN and Graphformer efforts encoding graphs as Euclidean vectors, recovering original graph from the vectors remains a challenge. We introduce GraphsGPT, featuring a Graph2Seq encoder that transforms non-Euclidean graphs into learnable graph words in a Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from graph words to ensure information equivalence. We pretrain GraphsGPT on 100M molecules and yield some interesting findings: (1) Pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on 8/9 graph classification and regression tasks. (2) Pretrained GraphGPT serves as a strong graph generator, demonstrated by its ability to perform both unconditional and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known non-Euclidean challenge. (4) Our proposed novel edge-centric GPT pretraining task is effective in graph fields, underscoring its success in both representation and generation.

Evaluating and enhancing the general capabilities of large language models (LLMs) has been an important research topic. Graph is a common data structure in the real world, and understanding graph data is a crucial part for advancing general intelligence. To evaluate and enhance the graph understanding abilities of LLMs, in this paper, we propose a benchmark named GraphInstruct, which comprehensively includes 21 classical graph reasoning tasks, providing diverse graph generation pipelines and detailed reasoning steps. Based on GraphInstruct, we further construct GraphLM through efficient instruction-tuning, which shows prominent graph understanding capability. In order to enhance the LLM with graph reasoning capability as well, we propose a step mask training strategy, and construct a model named GraphLM+. As one of the pioneering efforts to enhance the graph understanding and reasoning abilities of LLMs, extensive experiments have demonstrated the superiority of GraphLM and GraphLM+ over other LLMs. We look forward to more researchers exploring the potential of LLMs in the graph data mining domain through GraphInstruct. Our code for generating GraphInstruct is released publicly at: https://github.com/CGCL-codes/GraphInstruct.

AutoML systems build machine learning models automatically by performing a search over valid data transformations and learners, along with hyper-parameter optimization for each learner. Many AutoML systems use meta-learning to guide search for optimal pipelines. In this work, we present a novel meta-learning system called KGpip which, (1) builds a database of datasets and corresponding pipelines by mining thousands of scripts with program analysis, (2) uses dataset embeddings to find similar datasets in the database based on its content instead of metadata-based features, (3) models AutoML pipeline creation as a graph generation problem, to succinctly characterize the diverse pipelines seen for a single dataset. KGpip's meta-learning is a sub-component for AutoML systems. We demonstrate this by integrating KGpip with two AutoML systems. Our comprehensive evaluation using 126 datasets, including those used by the state-of-the-art systems, shows that KGpip significantly outperforms these systems.

Diffusion models, as a novel generative paradigm, have achieved remarkable success in various image generation tasks such as image inpainting, image-to-text translation, and video generation. Graph generation is a crucial computational task on graphs with numerous real-world applications. It aims to learn the distribution of given graphs and then generate new graphs. Given the great success of diffusion models in image generation, increasing efforts have been made to leverage these techniques to advance graph generation in recent years. In this paper, we first provide a comprehensive overview of generative diffusion models on graphs, In particular, we review representative algorithms for three variants of graph diffusion models, i.e., Score Matching with Langevin Dynamics (SMLD), Denoising Diffusion Probabilistic Model (DDPM), and Score-based Generative Model (SGM). Then, we summarize the major applications of generative diffusion models on graphs with a specific focus on molecule and protein modeling. Finally, we discuss promising directions in generative diffusion models on graph-structured data. For this survey, we also created a GitHub project website by collecting the supporting resources for generative diffusion models on graphs, at the link: https://github.com/ChengyiLIU-cs/Generative-Diffusion-Models-on-Graphs

Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are essential, making prior methods potentially unsuitable in such contexts. Moreover, while trivial adaptations are available, empirical investigations reveal their limited efficacy as they do not properly model the interplay among graph components. To address this, we propose a joint score-based model of nodes and edges for graph generation that considers all graph components. Our approach offers two key novelties: (i) node and edge attributes are combined in an attention module that generates samples based on the two ingredients; and (ii) node, edge and adjacency information are mutually dependent during the graph diffusion process. We evaluate our method on challenging benchmarks involving real-world and synthetic datasets in which edge features are crucial. Additionally, we introduce a new synthetic dataset that incorporates edge values. Furthermore, we propose a novel application that greatly benefits from the method due to its nature: the generation of traffic scenes represented as graphs. Our method outperforms other graph generation methods, demonstrating a significant advantage in edge-related measures.

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.

This work studies a central extremal graph theory problem inspired by a 1975 conjecture of Erdos, which aims to find graphs with a given size (number of nodes) that maximize the number of edges without having 3- or 4-cycles. We formulate this problem as a sequential decision-making problem and compare AlphaZero, a neural network-guided tree search, with tabu search, a heuristic local search method. Using either method, by introducing a curriculum -- jump-starting the search for larger graphs using good graphs found at smaller sizes -- we improve the state-of-the-art lower bounds for several sizes. We also propose a flexible graph-generation environment and a permutation-invariant network architecture for learning to search in the space of graphs.

Visual-textual inconsistency (VTI) evaluation plays a crucial role in cleansing vision-language data. Its main challenges stem from the high variety of image captioning datasets, where differences in content can create a range of inconsistencies (\eg, inconsistencies in scene, entities, entity attributes, entity numbers, entity interactions). Moreover, variations in caption length can introduce inconsistencies at different levels of granularity as well. To tackle these challenges, we design an adaptive evaluation framework, called Hierarchical and Multi-Grained Inconsistency Evaluation (HMGIE), which can provide multi-grained evaluations covering both accuracy and completeness for various image-caption pairs. Specifically, the HMGIE framework is implemented by three consecutive modules. Firstly, the semantic graph generation module converts the image caption to a semantic graph for building a structural representation of all involved semantic items. Then, the hierarchical inconsistency evaluation module provides a progressive evaluation procedure with a dynamic question-answer generation and evaluation strategy guided by the semantic graph, producing a hierarchical inconsistency evaluation graph (HIEG). Finally, the quantitative evaluation module calculates the accuracy and completeness scores based on the HIEG, followed by a natural language explanation about the detection results. Moreover, to verify the efficacy and flexibility of the proposed framework on handling different image captioning datasets, we construct MVTID, an image-caption dataset with diverse types and granularities of inconsistencies. Extensive experiments on MVTID and other benchmark datasets demonstrate the superior performance of the proposed HMGIE to current state-of-the-art methods.

Contextual Text Block Detection (CTBD) is the task of identifying coherent text blocks within the complexity of natural scenes. Previous methodologies have treated CTBD as either a visual relation extraction challenge within computer vision or as a sequence modeling problem from the perspective of natural language processing. We introduce a new framework that frames CTBD as a graph generation problem. This methodology consists of two essential procedures: identifying individual text units as graph nodes and discerning the sequential reading order relationships among these units as graph edges. Leveraging the cutting-edge capabilities of DQ-DETR for node detection, our framework innovates further by integrating a novel mechanism, a Dynamic Relation Transformer (DRFormer), dedicated to edge generation. DRFormer incorporates a dual interactive transformer decoder that deftly manages a dynamic graph structure refinement process. Through this iterative process, the model systematically enhances the graph's fidelity, ultimately resulting in improved precision in detecting contextual text blocks. Comprehensive experimental evaluations conducted on both SCUT-CTW-Context and ReCTS-Context datasets substantiate that our method achieves state-of-the-art results, underscoring the effectiveness and potential of our graph generation framework in advancing the field of CTBD.

In this paper, we present a novel generative task: joint scene graph - image generation. While previous works have explored image generation conditioned on scene graphs or layouts, our task is distinctive and important as it involves generating scene graphs themselves unconditionally from noise, enabling efficient and interpretable control for image generation. Our task is challenging, requiring the generation of plausible scene graphs with heterogeneous attributes for nodes (objects) and edges (relations among objects), including continuous object bounding boxes and discrete object and relation categories. We introduce a novel diffusion model, DiffuseSG, that jointly models the adjacency matrix along with heterogeneous node and edge attributes. We explore various types of encodings for the categorical data, relaxing it into a continuous space. With a graph transformer being the denoiser, DiffuseSG successively denoises the scene graph representation in a continuous space and discretizes the final representation to generate the clean scene graph. Additionally, we introduce an IoU regularization to enhance the empirical performance. Our model significantly outperforms existing methods in scene graph generation on the Visual Genome and COCO-Stuff datasets, both on standard and newly introduced metrics that better capture the problem complexity. Moreover, we demonstrate the additional benefits of our model in two downstream applications: 1) excelling in a series of scene graph completion tasks, and 2) improving scene graph detection models by using extra training samples generated from DiffuseSG.

Relational Language-Image Pre-training (RLIP) aims to align vision representations with relational texts, thereby advancing the capability of relational reasoning in computer vision tasks. However, hindered by the slow convergence of RLIPv1 architecture and the limited availability of existing scene graph data, scaling RLIPv1 is challenging. In this paper, we propose RLIPv2, a fast converging model that enables the scaling of relational pre-training to large-scale pseudo-labelled scene graph data. To enable fast scaling, RLIPv2 introduces Asymmetric Language-Image Fusion (ALIF), a mechanism that facilitates earlier and deeper gated cross-modal fusion with sparsified language encoding layers. ALIF leads to comparable or better performance than RLIPv1 in a fraction of the time for pre-training and fine-tuning. To obtain scene graph data at scale, we extend object detection datasets with free-form relation labels by introducing a captioner (e.g., BLIP) and a designed Relation Tagger. The Relation Tagger assigns BLIP-generated relation texts to region pairs, thus enabling larger-scale relational pre-training. Through extensive experiments conducted on Human-Object Interaction Detection and Scene Graph Generation, RLIPv2 shows state-of-the-art performance on three benchmarks under fully-finetuning, few-shot and zero-shot settings. Notably, the largest RLIPv2 achieves 23.29mAP on HICO-DET without any fine-tuning, yields 32.22mAP with just 1% data and yields 45.09mAP with 100% data. Code and models are publicly available at https://github.com/JacobYuan7/RLIPv2.

This work focuses on training a single visual relationship detector predicting over the union of label spaces from multiple datasets. Merging labels spanning different datasets could be challenging due to inconsistent taxonomies. The issue is exacerbated in visual relationship detection when second-order visual semantics are introduced between pairs of objects. To address this challenge, we propose UniVRD, a novel bottom-up method for Unified Visual Relationship Detection by leveraging vision and language models (VLMs). VLMs provide well-aligned image and text embeddings, where similar relationships are optimized to be close to each other for semantic unification. Our bottom-up design enables the model to enjoy the benefit of training with both object detection and visual relationship datasets. Empirical results on both human-object interaction detection and scene-graph generation demonstrate the competitive performance of our model. UniVRD achieves 38.07 mAP on HICO-DET, outperforming the current best bottom-up HOI detector by 14.26 mAP. More importantly, we show that our unified detector performs as well as dataset-specific models in mAP, and achieves further improvements when we scale up the model. Our code will be made publicly available on GitHub.

Every day, countless surgeries are performed worldwide, each within the distinct settings of operating rooms (ORs) that vary not only in their setups but also in the personnel, tools, and equipment used. This inherent diversity poses a substantial challenge for achieving a holistic understanding of the OR, as it requires models to generalize beyond their initial training datasets. To reduce this gap, we introduce ORacle, an advanced vision-language model designed for holistic OR domain modeling, which incorporates multi-view and temporal capabilities and can leverage external knowledge during inference, enabling it to adapt to previously unseen surgical scenarios. This capability is further enhanced by our novel data augmentation framework, which significantly diversifies the training dataset, ensuring ORacle's proficiency in applying the provided knowledge effectively. In rigorous testing, in scene graph generation, and downstream tasks on the 4D-OR dataset, ORacle not only demonstrates state-of-the-art performance but does so requiring less data than existing models. Furthermore, its adaptability is displayed through its ability to interpret unseen views, actions, and appearances of tools and equipment. This demonstrates ORacle's potential to significantly enhance the scalability and affordability of OR domain modeling and opens a pathway for future advancements in surgical data science. We will release our code and data upon acceptance.

Video-based visual relation detection tasks, such as video scene graph generation, play important roles in fine-grained video understanding. However, current video visual relation detection datasets have two main limitations that hinder the progress of research in this area. First, they do not explore complex human-human interactions in multi-person scenarios. Second, the relation types of existing datasets have relatively low-level semantics and can be often recognized by appearance or simple prior information, without the need for detailed spatio-temporal context reasoning. Nevertheless, comprehending high-level interactions between humans is crucial for understanding complex multi-person videos, such as sports and surveillance videos. To address this issue, we propose a new video visual relation detection task: video human-human interaction detection, and build a dataset named SportsHHI for it. SportsHHI contains 34 high-level interaction classes from basketball and volleyball sports. 118,075 human bounding boxes and 50,649 interaction instances are annotated on 11,398 keyframes. To benchmark this, we propose a two-stage baseline method and conduct extensive experiments to reveal the key factors for a successful human-human interaction detector. We hope that SportsHHI can stimulate research on human interaction understanding in videos and promote the development of spatio-temporal context modeling techniques in video visual relation detection.

The rise of large language models (LLMs) and instruction tuning has led to the current trend of instruction-tuned large language and vision models (LLVMs). This trend involves either meticulously curating numerous instruction tuning datasets tailored to specific objectives or enlarging LLVMs to manage vast amounts of vision language (VL) data. However, current LLVMs have disregarded the detailed and comprehensive real-world scene understanding available from specialized computer vision (CV) models in visual perception tasks such as segmentation, detection, scene graph generation (SGG), and optical character recognition (OCR). Instead, the existing LLVMs rely mainly on the large capacity and emergent capabilities of their LLM backbones. Therefore, we present a new LLVM, Mixture of All Intelligence (MoAI), which leverages auxiliary visual information obtained from the outputs of external segmentation, detection, SGG, and OCR models. MoAI operates through two newly introduced modules: MoAI-Compressor and MoAI-Mixer. After verbalizing the outputs of the external CV models, the MoAI-Compressor aligns and condenses them to efficiently use relevant auxiliary visual information for VL tasks. MoAI-Mixer then blends three types of intelligence (1) visual features, (2) auxiliary features from the external CV models, and (3) language features by utilizing the concept of Mixture of Experts. Through this integration, MoAI significantly outperforms both open-source and closed-source LLVMs in numerous zero-shot VL tasks, particularly those related to real-world scene understanding such as object existence, positions, relations, and OCR without enlarging the model size or curating extra visual instruction tuning datasets.

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.

With the rise of multimodal applications, instruction data has become critical for training multimodal language models capable of understanding complex image-based queries. Existing practices rely on powerful but costly large language models (LLMs) or multimodal language models (MLMs) to produce instruction data. These are often prone to hallucinations, licensing issues and the generation process is often hard to scale and interpret. In this work, we present a programmatic approach that employs scene graphs as symbolic representations of images and human-written programs to systematically synthesize vision-centric instruction data. Our approach ensures the interpretability and controllability of the data generation process and scales efficiently while maintaining factual accuracy. By implementing a suite of 24 single-image, 14 multi-image instruction generators, and a scene graph generation pipeline, we build a scalable, cost-effective system: ProVision which produces diverse question-answer pairs concerning objects, attributes, relations, depth, etc., for any given image. Applied to Visual Genome and DataComp datasets, we generate over 10 million instruction data points, ProVision-10M, and leverage them in both pretraining and instruction tuning stages of MLMs. When adopted in the instruction tuning stage, our single-image instruction data yields up to a 7% improvement on the 2D split and 8% on the 3D split of CVBench, along with a 3% increase in performance on QBench2, RealWorldQA, and MMMU. Our multi-image instruction data leads to an 8% improvement on Mantis-Eval. Incorporation of our data in both pre-training and fine-tuning stages of xGen-MM-4B leads to an averaged improvement of 1.6% across 11 benchmarks.

Recently, Retrieval-Augmented Generation (RAG) has achieved remarkable success in addressing the challenges of Large Language Models (LLMs) without necessitating retraining. By referencing an external knowledge base, RAG refines LLM outputs, effectively mitigating issues such as ``hallucination'', lack of domain-specific knowledge, and outdated information. However, the complex structure of relationships among different entities in databases presents challenges for RAG systems. In response, GraphRAG leverages structural information across entities to enable more precise and comprehensive retrieval, capturing relational knowledge and facilitating more accurate, context-aware responses. Given the novelty and potential of GraphRAG, a systematic review of current technologies is imperative. This paper provides the first comprehensive overview of GraphRAG methodologies. We formalize the GraphRAG workflow, encompassing Graph-Based Indexing, Graph-Guided Retrieval, and Graph-Enhanced Generation. We then outline the core technologies and training methods at each stage. Additionally, we examine downstream tasks, application domains, evaluation methodologies, and industrial use cases of GraphRAG. Finally, we explore future research directions to inspire further inquiries and advance progress in the field.

Deep generative models (DGMs) have been widely developed for graph data. However, much less investigation has been carried out on understanding the latent space of such pretrained graph DGMs. These understandings possess the potential to provide constructive guidelines for crucial tasks, such as graph controllable generation. Thus in this work, we are interested in studying this problem and propose GraphCG, a method for the unsupervised discovery of steerable factors in the latent space of pretrained graph DGMs. We first examine the representation space of three pretrained graph DGMs with six disentanglement metrics, and we observe that the pretrained representation space is entangled. Motivated by this observation, GraphCG learns the steerable factors via maximizing the mutual information between semantic-rich directions, where the controlled graph moving along the same direction will share the same steerable factors. We quantitatively verify that GraphCG outperforms four competitive baselines on two graph DGMs pretrained on two molecule datasets. Additionally, we qualitatively illustrate seven steerable factors learned by GraphCG on five pretrained DGMs over five graph datasets, including two for molecules and three for point clouds.

Learning to converse using only a few examples is a great challenge in conversational AI. The current best conversational models, which are either good chit-chatters (e.g., BlenderBot) or goal-oriented systems (e.g., MinTL), are language models (LMs) fine-tuned on large conversational datasets. Training these models is expensive, both in terms of computational resources and time, and it is hard to keep them up to date with new conversational skills. A simple yet unexplored solution is prompt-based few-shot learning (Brown et al. 2020) which does not require gradient-based fine-tuning but instead uses a few examples in the LM context as the only source of learning. In this paper, we explore prompt-based few-shot learning in dialogue tasks. We benchmark LMs of different sizes in nine response generation tasks, which include four knowledge-grounded tasks, a task-oriented generations task, three open-chat tasks, and controlled stylistic generation, and five conversational parsing tasks, which include dialogue state tracking, graph path generation, persona information extraction, document retrieval, and internet query generation. The current largest released LM (GPT-J-6B) using prompt-based few-shot learning, and thus requiring no training, achieves competitive performance to fully trained state-of-the-art models. Moreover, we propose a novel prompt-based few-shot classifier, that also does not require any fine-tuning, to select the most appropriate prompt given a dialogue history. Finally, by combining the power of prompt-based few-shot learning and a Skill Selector, we create an end-to-end chatbot named the Few-Shot Bot (FSB), which automatically selects the most appropriate conversational skill, queries different knowledge bases or the internet, and uses the retrieved knowledge to generate a human-like response, all using only few dialogue examples per skill.

3D vision-language grounding, which focuses on aligning language with the 3D physical environment, stands as a cornerstone in the development of embodied agents. In comparison to recent advancements in the 2D domain, grounding language in 3D scenes faces several significant challenges: (i) the inherent complexity of 3D scenes due to the diverse object configurations, their rich attributes, and intricate relationships; (ii) the scarcity of paired 3D vision-language data to support grounded learning; and (iii) the absence of a unified learning framework to distill knowledge from grounded 3D data. In this work, we aim to address these three major challenges in 3D vision-language by examining the potential of systematically upscaling 3D vision-language learning in indoor environments. We introduce the first million-scale 3D vision-language dataset, SceneVerse, encompassing about 68K 3D indoor scenes and comprising 2.5M vision-language pairs derived from both human annotations and our scalable scene-graph-based generation approach. We demonstrate that this scaling allows for a unified pre-training framework, Grounded Pre-training for Scenes (GPS), for 3D vision-language learning. Through extensive experiments, we showcase the effectiveness of GPS by achieving state-of-the-art performance on all existing 3D visual grounding benchmarks. The vast potential of SceneVerse and GPS is unveiled through zero-shot transfer experiments in the challenging 3D vision-language tasks. Project website: https://scene-verse.github.io .

Temporal reasoning is a crucial NLP task, providing a nuanced understanding of time-sensitive contexts within textual data. Although recent advancements in LLMs have demonstrated their potential in temporal reasoning, the predominant focus has been on tasks such as temporal expression and temporal relation extraction. These tasks are primarily designed for the extraction of direct and past temporal cues and to engage in simple reasoning processes. A significant gap remains when considering complex reasoning tasks such as event forecasting, which requires multi-step temporal reasoning on events and prediction on the future timestamp. Another notable limitation of existing methods is their incapability to provide an illustration of their reasoning process, hindering explainability. In this paper, we introduce the first task of explainable temporal reasoning, to predict an event's occurrence at a future timestamp based on context which requires multiple reasoning over multiple events, and subsequently provide a clear explanation for their prediction. Our task offers a comprehensive evaluation of both the LLMs' complex temporal reasoning ability, the future event prediction ability, and explainability-a critical attribute for AI applications. To support this task, we present the first multi-source instruction-tuning dataset of explainable temporal reasoning (ExpTime) with 26k derived from the temporal knowledge graph datasets and their temporal reasoning paths, using a novel knowledge-graph-instructed-generation strategy. Based on the dataset, we propose the first open-source LLM series TimeLlaMA based on the foundation LlaMA2, with the ability of instruction following for explainable temporal reasoning. We compare the performance of our method and a variety of LLMs, where our method achieves the state-of-the-art performance of temporal prediction and explanation.

Graph-to-text generation has benefited from pre-trained language models (PLMs) in achieving better performance than structured graph encoders. However, they fail to fully utilize the structure information of the input graph. In this paper, we aim to further improve the performance of the pre-trained language model by proposing a structured graph-to-text model with a two-step fine-tuning mechanism which first fine-tunes the model on Wikipedia before adapting to the graph-to-text generation. In addition to using the traditional token and position embeddings to encode the knowledge graph (KG), we propose a novel tree-level embedding method to capture the inter-dependency structures of the input graph. This new approach has significantly improved the performance of all text generation metrics for the English WebNLG 2017 dataset.

Large language models (LLMs) have demonstrated remarkable capabilities in a wide range of tasks, yet their application to specialized domains remains challenging due to the need for deep expertise. Retrieval-augmented generation (RAG) has emerged as a promising solution to customize LLMs for professional fields by seamlessly integrating external knowledge bases, enabling real-time access to domain-specific expertise during inference. Despite its potential, traditional RAG systems, based on flat text retrieval, face three critical challenges: (i) complex query understanding in professional contexts, (ii) difficulties in knowledge integration across distributed sources, and (iii) system efficiency bottlenecks at scale. This survey presents a systematic analysis of Graph-based Retrieval-Augmented Generation (GraphRAG), a new paradigm that revolutionizes domain-specific LLM applications. GraphRAG addresses traditional RAG limitations through three key innovations: (i) graph-structured knowledge representation that explicitly captures entity relationships and domain hierarchies, (ii) efficient graph-based retrieval techniques that enable context-preserving knowledge retrieval with multihop reasoning ability, and (iii) structure-aware knowledge integration algorithms that leverage retrieved knowledge for accurate and logical coherent generation of LLMs. In this survey, we systematically analyze the technical foundations of GraphRAG and examine current implementations across various professional domains, identifying key technical challenges and promising research directions. All the related resources of GraphRAG, including research papers, open-source data, and projects, are collected for the community in blue{https://github.com/DEEP-PolyU/Awesome-GraphRAG}.

While Retrieval-Augmented Generation (RAG) enhances the accuracy and relevance of responses by generative language models, it falls short in graph-based contexts where both textual and topological information are important. Naive RAG approaches inherently neglect the structural intricacies of textual graphs, resulting in a critical gap in the generation process. To address this challenge, we introduce Graph Retrieval-Augmented Generation (GRAG), which significantly enhances both the retrieval and generation processes by emphasizing the importance of subgraph structures. Unlike RAG approaches that focus solely on text-based entity retrieval, GRAG maintains an acute awareness of graph topology, which is crucial for generating contextually and factually coherent responses. Our GRAG approach consists of four main stages: indexing of k-hop ego-graphs, graph retrieval, soft pruning to mitigate the impact of irrelevant entities, and generation with pruned textual subgraphs. GRAG's core workflow-retrieving textual subgraphs followed by soft pruning-efficiently identifies relevant subgraph structures while avoiding the computational infeasibility typical of exhaustive subgraph searches, which are NP-hard. Moreover, we propose a novel prompting strategy that achieves lossless conversion from textual subgraphs to hierarchical text descriptions. Extensive experiments on graph multi-hop reasoning benchmarks demonstrate that in scenarios requiring multi-hop reasoning on textual graphs, our GRAG approach significantly outperforms current state-of-the-art RAG methods while effectively mitigating hallucinations.

Knowledge Graph-to-Text (G2T) generation involves verbalizing structured knowledge graphs into natural language text. Recent advancements in Pretrained Language Models (PLMs) have improved G2T performance, but their effectiveness depends on datasets with precise graph-text alignment. However, the scarcity of high-quality, general-domain G2T generation datasets restricts progress in the general-domain G2T generation research. To address this issue, we introduce Wikipedia Ontology-Free Graph-text dataset (WikiOFGraph), a new large-scale G2T dataset generated using a novel method that leverages Large Language Model (LLM) and Data-QuestEval. Our new dataset, which contains 5.85M general-domain graph-text pairs, offers high graph-text consistency without relying on external ontologies. Experimental results demonstrate that PLM fine-tuned on WikiOFGraph outperforms those trained on other datasets across various evaluation metrics. Our method proves to be a scalable and effective solution for generating high-quality G2T data, significantly advancing the field of G2T generation.

Generating images from scene graphs is a challenging task that attracted substantial interest recently. Prior works have approached this task by generating an intermediate layout description of the target image. However, the representation of each object in the layout was generated independently, which resulted in high overlap, low coverage, and an overall blurry layout. We propose a novel method that alleviates these issues by generating the entire layout description gradually to improve inter-object dependency. We empirically show on the COCO-STUFF dataset that our approach improves the quality of both the intermediate layout and the final image. Our approach improves the layout coverage by almost 20 points and drops object overlap to negligible amounts.

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called MedGraphRAG, aimed at enhancing Large Language Model (LLM) capabilities and generating evidence-based results, thereby improving safety and reliability when handling private medical data. Our comprehensive pipeline begins with a hybrid static-semantic approach to document chunking, significantly improving context capture over traditional methods. Extracted entities are used to create a three-tier hierarchical graph structure, linking entities to foundational medical knowledge sourced from medical papers and dictionaries. These entities are then interconnected to form meta-graphs, which are merged based on semantic similarities to develop a comprehensive global graph. This structure supports precise information retrieval and response generation. The retrieval process employs a U-retrieve method to balance global awareness and indexing efficiency of the LLM. Our approach is validated through a comprehensive ablation study comparing various methods for document chunking, graph construction, and information retrieval. The results not only demonstrate that our hierarchical graph construction method consistently outperforms state-of-the-art models on multiple medical Q\&A benchmarks, but also confirms that the responses generated include source documentation, significantly enhancing the reliability of medical LLMs in practical applications. Code will be at: https://github.com/MedicineToken/Medical-Graph-RAG/tree/main

Large Language Models (LLMs) are being adopted at an unprecedented rate, yet still face challenges in knowledge-intensive domains like biomedicine. Solutions such as pre-training and domain-specific fine-tuning add substantial computational overhead, requiring further domain expertise. Here, we introduce a token-optimized and robust Knowledge Graph-based Retrieval Augmented Generation (KG-RAG) framework by leveraging a massive biomedical KG (SPOKE) with LLMs such as Llama-2-13b, GPT-3.5-Turbo and GPT-4, to generate meaningful biomedical text rooted in established knowledge. Compared to the existing RAG technique for Knowledge Graphs, the proposed method utilizes minimal graph schema for context extraction and uses embedding methods for context pruning. This optimization in context extraction results in more than 50% reduction in token consumption without compromising the accuracy, making a cost-effective and robust RAG implementation on proprietary LLMs. KG-RAG consistently enhanced the performance of LLMs across diverse biomedical prompts by generating responses rooted in established knowledge, accompanied by accurate provenance and statistical evidence (if available) to substantiate the claims. Further benchmarking on human curated datasets, such as biomedical true/false and multiple-choice questions (MCQ), showed a remarkable 71% boost in the performance of the Llama-2 model on the challenging MCQ dataset, demonstrating the framework's capacity to empower open-source models with fewer parameters for domain specific questions. Furthermore, KG-RAG enhanced the performance of proprietary GPT models, such as GPT-3.5 and GPT-4. In summary, the proposed framework combines explicit and implicit knowledge of KG and LLM in a token optimized fashion, thus enhancing the adaptability of general-purpose LLMs to tackle domain-specific questions in a cost-effective fashion.

Open-ended text generation with autoregressive language models (LMs) is one of the core tasks in natural language processing. However, maximization-based decoding methods (e.g., greedy/beam search) often lead to the degeneration problem, i.e., the generated text is unnatural and contains undesirable repetitions. Existing solutions to this problem either introduce randomness prone to incoherence or require a look-ahead mechanism that demands extra computational overhead. In this study, we formulate open-ended text generation from a new perspective, i.e., we view it as an exploration process within a directed graph. Thereby, we understand the phenomenon of degeneration as circular loops within the directed graph. Based on our formulation, we propose a novel decoding method -- momentum decoding -- which encourages the LM to greedily explore new nodes outside the current graph. Meanwhile, it also allows the LM to return to the existing nodes with a momentum downgraded by a pre-defined resistance function. We extensively test our approach on three benchmarks from different domains through automatic and human evaluations. The results show that momentum decoding performs comparably with the current state of the art while enjoying notably improved inference speed and computation FLOPs. Furthermore, we conduct a detailed analysis to reveal the merits and inner workings of our approach. Our codes and other related resources are publicly available at https://github.com/gmftbyGMFTBY/MomentumDecoding.

Recent improvements in KG-to-text generation are due to additional auxiliary pre-training tasks designed to give the fine-tune task a boost in performance. These tasks require extensive computational resources while only suggesting marginal improvements. Here, we demonstrate that by fusing graph-aware elements into existing pre-trained language models, we are able to outperform state-of-the-art models and close the gap imposed by additional pre-training tasks. We do so by proposing a mask structure to capture neighborhood information and a novel type encoder that adds a bias to the graph-attention weights depending on the connection type. Experiments on two KG-to-text benchmark datasets show our models are competitive while involving fewer parameters and no additional pre-training tasks. By formulating the problem as a framework, we can interchange the various proposed components and begin interpreting KG-to-text generative models based on the topological and type information found in a graph.

In the continuously advancing AI landscape, crafting context-rich and meaningful responses via Large Language Models (LLMs) is essential. Researchers are becoming more aware of the challenges that LLMs with fewer parameters encounter when trying to provide suitable answers to open-ended questions. To address these hurdles, the integration of cutting-edge strategies, augmentation of rich external domain knowledge to LLMs, offers significant improvements. This paper introduces a novel framework that combines graph-driven context retrieval in conjunction to knowledge graphs based enhancement, honing the proficiency of LLMs, especially in domain specific community question answering platforms like AskUbuntu, Unix, and ServerFault. We conduct experiments on various LLMs with different parameter sizes to evaluate their ability to ground knowledge and determine factual accuracy in answers to open-ended questions. Our methodology GraphContextGen consistently outperforms dominant text-based retrieval systems, demonstrating its robustness and adaptability to a larger number of use cases. This advancement highlights the importance of pairing context rich data retrieval with LLMs, offering a renewed approach to knowledge sourcing and generation in AI systems. We also show that, due to rich contextual data retrieval, the crucial entities, along with the generated answer, remain factually coherent with the gold answer.

Advancements in generative models have sparked significant interest in generating images while adhering to specific structural guidelines. Scene graph to image generation is one such task of generating images which are consistent with the given scene graph. However, the complexity of visual scenes poses a challenge in accurately aligning objects based on specified relations within the scene graph. Existing methods approach this task by first predicting a scene layout and generating images from these layouts using adversarial training. In this work, we introduce a novel approach to generate images from scene graphs which eliminates the need of predicting intermediate layouts. We leverage pre-trained text-to-image diffusion models and CLIP guidance to translate graph knowledge into images. Towards this, we first pre-train our graph encoder to align graph features with CLIP features of corresponding images using a GAN based training. Further, we fuse the graph features with CLIP embedding of object labels present in the given scene graph to create a graph consistent CLIP guided conditioning signal. In the conditioning input, object embeddings provide coarse structure of the image and graph features provide structural alignment based on relationships among objects. Finally, we fine tune a pre-trained diffusion model with the graph consistent conditioning signal with reconstruction and CLIP alignment loss. Elaborate experiments reveal that our method outperforms existing methods on standard benchmarks of COCO-stuff and Visual Genome dataset.

The paper presents a novel approach for vector-floorplan generation via a diffusion model, which denoises 2D coordinates of room/door corners with two inference objectives: 1) a single-step noise as the continuous quantity to precisely invert the continuous forward process; and 2) the final 2D coordinate as the discrete quantity to establish geometric incident relationships such as parallelism, orthogonality, and corner-sharing. Our task is graph-conditioned floorplan generation, a common workflow in floorplan design. We represent a floorplan as 1D polygonal loops, each of which corresponds to a room or a door. Our diffusion model employs a Transformer architecture at the core, which controls the attention masks based on the input graph-constraint and directly generates vector-graphics floorplans via a discrete and continuous denoising process. We have evaluated our approach on RPLAN dataset. The proposed approach makes significant improvements in all the metrics against the state-of-the-art with significant margins, while being capable of generating non-Manhattan structures and controlling the exact number of corners per room. A project website with supplementary video and document is here https://aminshabani.github.io/housediffusion.

Despite advancements in Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) systems, their effectiveness is often hindered by a lack of integration with entity relationships and community structures, limiting their ability to provide contextually rich and accurate information retrieval for fact-checking. We introduce CommunityKG-RAG (Community Knowledge Graph-Retrieval Augmented Generation), a novel zero-shot framework that integrates community structures within Knowledge Graphs (KGs) with RAG systems to enhance the fact-checking process. Capable of adapting to new domains and queries without additional training, CommunityKG-RAG utilizes the multi-hop nature of community structures within KGs to significantly improve the accuracy and relevance of information retrieval. Our experimental results demonstrate that CommunityKG-RAG outperforms traditional methods, representing a significant advancement in fact-checking by offering a robust, scalable, and efficient solution.

Modeling and designing urban building layouts is of significant interest in computer vision, computer graphics, and urban applications. A building layout consists of a set of buildings in city blocks defined by a network of roads. We observe that building layouts are discrete structures, consisting of multiple rows of buildings of various shapes, and are amenable to skeletonization for mapping arbitrary city block shapes to a canonical form. Hence, we propose a fully automatic approach to building layout generation using graph attention networks. Our method generates realistic urban layouts given arbitrary road networks, and enables conditional generation based on learned priors. Our results, including user study, demonstrate superior performance as compared to prior layout generation networks, support arbitrary city block and varying building shapes as demonstrated by generating layouts for 28 large cities.

Research question answering requires accurate retrieval and contextual understanding of scientific literature. However, current Retrieval-Augmented Generation (RAG) methods often struggle to balance complex document relationships with precise information retrieval. In this paper, we introduce Contextualized Graph Retrieval-Augmented Generation (CG-RAG), a novel framework that integrates sparse and dense retrieval signals within graph structures to enhance retrieval efficiency and subsequently improve generation quality for research question answering. First, we propose a contextual graph representation for citation graphs, effectively capturing both explicit and implicit connections within and across documents. Next, we introduce Lexical-Semantic Graph Retrieval (LeSeGR), which seamlessly integrates sparse and dense retrieval signals with graph encoding. It bridges the gap between lexical precision and semantic understanding in citation graph retrieval, demonstrating generalizability to existing graph retrieval and hybrid retrieval methods. Finally, we present a context-aware generation strategy that utilizes the retrieved graph-structured information to generate precise and contextually enriched responses using large language models (LLMs). Extensive experiments on research question answering benchmarks across multiple domains demonstrate that our CG-RAG framework significantly outperforms RAG methods combined with various state-of-the-art retrieval approaches, delivering superior retrieval accuracy and generation quality.

We introduce a novel approach to enhance the capabilities of text-to-image models by incorporating a graph-based RAG. Our system dynamically retrieves detailed character information and relational data from the knowledge graph, enabling the generation of visually accurate and contextually rich images. This capability significantly improves upon the limitations of existing T2I models, which often struggle with the accurate depiction of complex or culturally specific subjects due to dataset constraints. Furthermore, we propose a novel self-correcting mechanism for text-to-image models to ensure consistency and fidelity in visual outputs, leveraging the rich context from the graph to guide corrections. Our qualitative and quantitative experiments demonstrate that Context Canvas significantly enhances the capabilities of popular models such as Flux, Stable Diffusion, and DALL-E, and improves the functionality of ControlNet for fine-grained image editing tasks. To our knowledge, Context Canvas represents the first application of graph-based RAG in enhancing T2I models, representing a significant advancement for producing high-fidelity, context-aware multi-faceted images.

Ensuring factual accuracy while maintaining the creative capabilities of Large Language Model Agents (LMAs) poses significant challenges in the development of intelligent agent systems. LMAs face prevalent issues such as information hallucinations, catastrophic forgetting, and limitations in processing long contexts when dealing with knowledge-intensive tasks. This paper introduces a KG-RAG (Knowledge Graph-Retrieval Augmented Generation) pipeline, a novel framework designed to enhance the knowledge capabilities of LMAs by integrating structured Knowledge Graphs (KGs) with the functionalities of LLMs, thereby significantly reducing the reliance on the latent knowledge of LLMs. The KG-RAG pipeline constructs a KG from unstructured text and then performs information retrieval over the newly created graph to perform KGQA (Knowledge Graph Question Answering). The retrieval methodology leverages a novel algorithm called Chain of Explorations (CoE) which benefits from LLMs reasoning to explore nodes and relationships within the KG sequentially. Preliminary experiments on the ComplexWebQuestions dataset demonstrate notable improvements in the reduction of hallucinated content and suggest a promising path toward developing intelligent systems adept at handling knowledge-intensive tasks.

Retrieval-Augmented Generation (RAG) offers a cost-effective approach to injecting real-time knowledge into large language models (LLMs). Nevertheless, constructing and validating high-quality knowledge repositories require considerable effort. We propose a pre-retrieval framework named Pseudo-Graph Retrieval-Augmented Generation (PG-RAG), which conceptualizes LLMs as students by providing them with abundant raw reading materials and encouraging them to engage in autonomous reading to record factual information in their own words. The resulting concise, well-organized mental indices are interconnected through common topics or complementary facts to form a pseudo-graph database. During the retrieval phase, PG-RAG mimics the human behavior in flipping through notes, identifying fact paths and subsequently exploring the related contexts. Adhering to the principle of the path taken by many is the best, it integrates highly corroborated fact paths to provide a structured and refined sub-graph assisting LLMs. We validated PG-RAG on three specialized question-answering datasets. In single-document tasks, PG-RAG significantly outperformed the current best baseline, KGP-LLaMA, across all key evaluation metrics, with an average overall performance improvement of 11.6%. Specifically, its BLEU score increased by approximately 14.3%, and the QE-F1 metric improved by 23.7%. In multi-document scenarios, the average metrics of PG-RAG were at least 2.35% higher than the best baseline. Notably, the BLEU score and QE-F1 metric showed stable improvements of around 7.55% and 12.75%, respectively. Our code: https://github.com/IAAR-Shanghai/PGRAG.

Most graph neural network models learn embeddings of nodes in static attributed graphs for predictive analysis. Recent attempts have been made to learn temporal proximity of the nodes. We find that real dynamic attributed graphs exhibit complex co-evolution of node attributes and graph structure. Learning node embeddings for forecasting change of node attributes and birth and death of links over time remains an open problem. In this work, we present a novel framework called CoEvoGNN for modeling dynamic attributed graph sequence. It preserves the impact of earlier graphs on the current graph by embedding generation through the sequence. It has a temporal self-attention mechanism to model long-range dependencies in the evolution. Moreover, CoEvoGNN optimizes model parameters jointly on two dynamic tasks, attribute inference and link prediction over time. So the model can capture the co-evolutionary patterns of attribute change and link formation. This framework can adapt to any graph neural algorithms so we implemented and investigated three methods based on it: CoEvoGCN, CoEvoGAT, and CoEvoSAGE. Experiments demonstrate the framework (and its methods) outperform strong baselines on predicting an entire unseen graph snapshot of personal attributes and interpersonal links in dynamic social graphs and financial graphs.

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both human and protein languages: (i) taking a protein sequence as input to predict its textual function description and (ii) using natural language to prompt protein sequence generation. To achieve this, we first pre-train an LLM on both protein and natural language corpora, enabling it to comprehend individual languages. Then supervised instruction tuning is employed to facilitate the alignment of these two distinct languages. Herein, we introduce a knowledge graph-based instruction generation framework to construct a high-quality instruction dataset, addressing annotation imbalance and instruction deficits in existing protein-text corpus. In particular, the instructions inherit the structural relations between proteins and function annotations in knowledge graphs, which empowers our model to engage in the causal modeling of protein functions, akin to the chain-of-thought processes in natural languages. Extensive experiments on bidirectional protein-text generation tasks show that InstructProtein outperforms state-of-the-art LLMs by large margins. Moreover, InstructProtein serves as a pioneering step towards text-based protein function prediction and sequence design, effectively bridging the gap between protein and human language understanding.

Graph neural networks have recently achieved remarkable success in representing graph-structured data, with rapid progress in both the node embedding and graph pooling methods. Yet, they mostly focus on capturing information from the nodes considering their connectivity, and not much work has been done in representing the edges, which are essential components of a graph. However, for tasks such as graph reconstruction and generation, as well as graph classification tasks for which the edges are important for discrimination, accurately representing edges of a given graph is crucial to the success of the graph representation learning. To this end, we propose a novel edge representation learning framework based on Dual Hypergraph Transformation (DHT), which transforms the edges of a graph into the nodes of a hypergraph. This dual hypergraph construction allows us to apply message-passing techniques for node representations to edges. After obtaining edge representations from the hypergraphs, we then cluster or drop edges to obtain holistic graph-level edge representations. We validate our edge representation learning method with hypergraphs on diverse graph datasets for graph representation and generation performance, on which our method largely outperforms existing graph representation learning methods. Moreover, our edge representation learning and pooling method also largely outperforms state-of-the-art graph pooling methods on graph classification, not only because of its accurate edge representation learning, but also due to its lossless compression of the nodes and removal of irrelevant edges for effective message-passing.

Large language models (LLMs), such as ChatGPT and GPT4, are making new waves in the field of natural language processing and artificial intelligence, due to their emergent ability and generalizability. However, LLMs are black-box models, which often fall short of capturing and accessing factual knowledge. In contrast, Knowledge Graphs (KGs), Wikipedia and Huapu for example, are structured knowledge models that explicitly store rich factual knowledge. KGs can enhance LLMs by providing external knowledge for inference and interpretability. Meanwhile, KGs are difficult to construct and evolving by nature, which challenges the existing methods in KGs to generate new facts and represent unseen knowledge. Therefore, it is complementary to unify LLMs and KGs together and simultaneously leverage their advantages. In this article, we present a forward-looking roadmap for the unification of LLMs and KGs. Our roadmap consists of three general frameworks, namely, 1) KG-enhanced LLMs, which incorporate KGs during the pre-training and inference phases of LLMs, or for the purpose of enhancing understanding of the knowledge learned by LLMs; 2) LLM-augmented KGs, that leverage LLMs for different KG tasks such as embedding, completion, construction, graph-to-text generation, and question answering; and 3) Synergized LLMs + KGs, in which LLMs and KGs play equal roles and work in a mutually beneficial way to enhance both LLMs and KGs for bidirectional reasoning driven by both data and knowledge. We review and summarize existing efforts within these three frameworks in our roadmap and pinpoint their future research directions.

Retrieval-augmented generation (RAG) has revitalized Large Language Models (LLMs) by injecting non-parametric factual knowledge. Compared with long-context LLMs, RAG is considered an effective summarization tool in a more concise and lightweight manner, which can interact with LLMs multiple times using diverse queries to get comprehensive responses. However, the LLM-generated historical responses, which contain potentially insightful information, are largely neglected and discarded by existing approaches, leading to suboptimal results. In this paper, we propose graph of records (GoR), which leverages historical responses generated by LLMs to enhance RAG for long-context global summarization. Inspired by the retrieve-then-generate paradigm of RAG, we construct a graph by establishing an edge between the retrieved text chunks and the corresponding LLM-generated response. To further uncover the intricate correlations between them, GoR further features a graph neural network and an elaborately designed BERTScore-based objective for self-supervised model training, enabling seamless supervision signal backpropagation between reference summaries and node embeddings. We comprehensively compare GoR with 12 baselines across four long-context summarization datasets, and the results indicate that our proposed method reaches the best performance e.g., 15\%, 8\%, and 19\% improvement over retrievers w.r.t. Rouge-L, Rouge-1, and Rouge-2 on the WCEP dataset). Extensive experiments further demonstrate the effectiveness of GoR. Code is available at https://github.com/ulab-uiuc/GoR

Natural language explanations (NLEs) are commonly used to provide plausible free-text explanations of a model's reasoning about its predictions. However, recent work has questioned the faithfulness of NLEs, as they may not accurately reflect the model's internal reasoning process regarding its predicted answer. In contrast, highlight explanations -- input fragments identified as critical for the model's predictions -- exhibit measurable faithfulness, which has been incrementally improved through existing research. Building on this foundation, we propose G-Tex, a Graph-Guided Textual Explanation Generation framework designed to enhance the faithfulness of NLEs by leveraging highlight explanations. Specifically, highlight explanations are extracted as highly faithful cues representing the model's reasoning and are subsequently encoded through a graph neural network layer, which explicitly guides the NLE generation process. This alignment ensures that the generated explanations closely reflect the model's underlying reasoning. Experiments on T5 and BART using three reasoning datasets show that G-Tex improves NLE faithfulness by up to 17.59% compared to baseline methods. Additionally, G-Tex generates NLEs with greater semantic and lexical similarity to human-written ones. Human evaluations show that G-Tex can decrease redundant content and enhance the overall quality of NLEs. As our work introduces a novel method for explicitly guiding NLE generation to improve faithfulness, we hope it will serve as a stepping stone for addressing additional criteria for NLE and generated text overall.

Inverse molecular design with diffusion models holds great potential for advancements in material and drug discovery. Despite success in unconditional molecular generation, integrating multiple properties such as synthetic score and gas permeability as condition constraints into diffusion models remains unexplored. We present the Graph Diffusion Transformer (Graph DiT) for multi-conditional molecular generation. Graph DiT integrates an encoder to learn numerical and categorical property representations with the Transformer-based denoiser. Unlike previous graph diffusion models that add noise separately on the atoms and bonds in the forward diffusion process, Graph DiT is trained with a novel graph-dependent noise model for accurate estimation of graph-related noise in molecules. We extensively validate Graph DiT for multi-conditional polymer and small molecule generation. Results demonstrate the superiority of Graph DiT across nine metrics from distribution learning to condition control for molecular properties. A polymer inverse design task for gas separation with feedback from domain experts further demonstrates its practical utility.

Graphs can be leveraged to model polyphonic multitrack symbolic music, where notes, chords and entire sections may be linked at different levels of the musical hierarchy by tonal and rhythmic relationships. Nonetheless, there is a lack of works that consider graph representations in the context of deep learning systems for music generation. This paper bridges this gap by introducing a novel graph representation for music and a deep Variational Autoencoder that generates the structure and the content of musical graphs separately, one after the other, with a hierarchical architecture that matches the structural priors of music. By separating the structure and content of musical graphs, it is possible to condition generation by specifying which instruments are played at certain times. This opens the door to a new form of human-computer interaction in the context of music co-creation. After training the model on existing MIDI datasets, the experiments show that the model is able to generate appealing short and long musical sequences and to realistically interpolate between them, producing music that is tonally and rhythmically consistent. Finally, the visualization of the embeddings shows that the model is able to organize its latent space in accordance with known musical concepts.

Retrieval-augmented generation (RAG) has proven effective in integrating knowledge into large language models (LLMs). However, conventional RAGs struggle to capture complex relationships between pieces of knowledge, limiting their performance in intricate reasoning that requires integrating knowledge from multiple sources. Recently, graph-enhanced retrieval augmented generation (GraphRAG) builds graph structure to explicitly model these relationships, enabling more effective and efficient retrievers. Nevertheless, its performance is still hindered by the noise and incompleteness within the graph structure. To address this, we introduce GFM-RAG, a novel graph foundation model (GFM) for retrieval augmented generation. GFM-RAG is powered by an innovative graph neural network that reasons over graph structure to capture complex query-knowledge relationships. The GFM with 8M parameters undergoes a two-stage training process on large-scale datasets, comprising 60 knowledge graphs with over 14M triples and 700k documents. This results in impressive performance and generalizability for GFM-RAG, making it the first graph foundation model applicable to unseen datasets for retrieval without any fine-tuning required. Extensive experiments on three multi-hop QA datasets and seven domain-specific RAG datasets demonstrate that GFM-RAG achieves state-of-the-art performance while maintaining efficiency and alignment with neural scaling laws, highlighting its potential for further improvement.

Retrieval-augmented generation (RAG) improves the response quality of large language models (LLMs) by retrieving knowledge from external databases. Typical RAG approaches split the text database into chunks, organizing them in a flat structure for efficient searches. To better capture the inherent dependencies and structured relationships across the text database, researchers propose to organize textual information into an indexing graph, known asgraph-based RAG. However, we argue that the limitation of current graph-based RAG methods lies in the redundancy of the retrieved information, rather than its insufficiency. Moreover, previous methods use a flat structure to organize retrieved information within the prompts, leading to suboptimal performance. To overcome these limitations, we propose PathRAG, which retrieves key relational paths from the indexing graph, and converts these paths into textual form for prompting LLMs. Specifically, PathRAG effectively reduces redundant information with flow-based pruning, while guiding LLMs to generate more logical and coherent responses with path-based prompting. Experimental results show that PathRAG consistently outperforms state-of-the-art baselines across six datasets and five evaluation dimensions. The code is available at the following link: https://github.com/BUPT-GAMMA/PathRAG

Failure mode and effects analysis (FMEA) is a critical tool for mitigating potential failures, particular during ramp-up phases of new products. However, its effectiveness is often limited by the missing reasoning capabilities of the FMEA tools, which are usually tabular structured. Meanwhile, large language models (LLMs) offer novel prospects for fine-tuning on custom datasets for reasoning within FMEA contexts. However, LLMs face challenges in tasks that require factual knowledge, a gap that retrieval-augmented generation (RAG) approaches aim to fill. RAG retrieves information from a non-parametric data store and uses a language model to generate responses. Building on this idea, we propose to advance the non-parametric data store with a knowledge graph (KG). By enhancing the RAG framework with a KG, our objective is to leverage analytical and semantic question-answering capabilities on FMEA data. This paper contributes by presenting a new ontology for FMEA observations, an algorithm for creating vector embeddings from the FMEA KG, and a KG enhanced RAG framework. Our approach is validated through a human study and we measure the performance of the context retrieval recall and precision.

Abstract meaning representation (AMR) highlights the core semantic information of text in a graph structure. Recently, pre-trained language models (PLMs) have advanced tasks of AMR parsing and AMR-to-text generation, respectively. However, PLMs are typically pre-trained on textual data, thus are sub-optimal for modeling structural knowledge. To this end, we investigate graph self-supervised training to improve the structure awareness of PLMs over AMR graphs. In particular, we introduce two graph auto-encoding strategies for graph-to-graph pre-training and four tasks to integrate text and graph information during pre-training. We further design a unified framework to bridge the gap between pre-training and fine-tuning tasks. Experiments on both AMR parsing and AMR-to-text generation show the superiority of our model. To our knowledge, we are the first to consider pre-training on semantic graphs.

Prior work on Data-To-Text Generation, the task of converting knowledge graph (KG) triples into natural text, focused on domain-specific benchmark datasets. In this paper, however, we verbalize the entire English Wikidata KG, and discuss the unique challenges associated with a broad, open-domain, large-scale verbalization. We further show that verbalizing a comprehensive, encyclopedic KG like Wikidata can be used to integrate structured KGs and natural language corpora. In contrast to the many architectures that have been developed to integrate these two sources, our approach converts the KG into natural text, allowing it to be seamlessly integrated into existing language models. It carries the further advantages of improved factual accuracy and reduced toxicity in the resulting language model. We evaluate this approach by augmenting the retrieval corpus in a retrieval language model and showing significant improvements on the knowledge intensive tasks of open domain QA and the LAMA knowledge probe.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}

In this paper, we propose the first framework that enables solving graph learning tasks of all levels (node, edge and graph) and all types (generation, regression and classification) with one model. We first propose Latent Graph Diffusion (LGD), a generative model that can generate node, edge, and graph-level features of all categories simultaneously. We achieve this goal by embedding the graph structures and features into a latent space leveraging a powerful encoder which can also be decoded, then training a diffusion model in the latent space. LGD is also capable of conditional generation through a specifically designed cross-attention mechanism. Then we formulate prediction tasks including regression and classification as (conditional) generation, which enables our LGD to solve tasks of all levels and all types with provable guarantees. We verify the effectiveness of our framework with extensive experiments, where our models achieve state-of-the-art or highly competitive results across generation and regression tasks.

Controllable 3D scene generation has extensive applications in virtual reality and interior design, where the generated scenes should exhibit high levels of realism and controllability in terms of geometry. Scene graphs provide a suitable data representation that facilitates these applications. However, current graph-based methods for scene generation are constrained to text-based inputs and exhibit insufficient adaptability to flexible user inputs, hindering the ability to precisely control object geometry. To address this issue, we propose MMGDreamer, a dual-branch diffusion model for scene generation that incorporates a novel Mixed-Modality Graph, visual enhancement module, and relation predictor. The mixed-modality graph allows object nodes to integrate textual and visual modalities, with optional relationships between nodes. It enhances adaptability to flexible user inputs and enables meticulous control over the geometry of objects in the generated scenes. The visual enhancement module enriches the visual fidelity of text-only nodes by constructing visual representations using text embeddings. Furthermore, our relation predictor leverages node representations to infer absent relationships between nodes, resulting in more coherent scene layouts. Extensive experimental results demonstrate that MMGDreamer exhibits superior control of object geometry, achieving state-of-the-art scene generation performance. Project page: https://yangzhifeio.github.io/project/MMGDreamer.

Many real-world user queries (e.g. "How do to make egg fried rice?") could benefit from systems capable of generating responses with both textual steps with accompanying images, similar to a cookbook. Models designed to generate interleaved text and images face challenges in ensuring consistency within and across these modalities. To address these challenges, we present ISG, a comprehensive evaluation framework for interleaved text-and-image generation. ISG leverages a scene graph structure to capture relationships between text and image blocks, evaluating responses on four levels of granularity: holistic, structural, block-level, and image-specific. This multi-tiered evaluation allows for a nuanced assessment of consistency, coherence, and accuracy, and provides interpretable question-answer feedback. In conjunction with ISG, we introduce a benchmark, ISG-Bench, encompassing 1,150 samples across 8 categories and 21 subcategories. This benchmark dataset includes complex language-vision dependencies and golden answers to evaluate models effectively on vision-centric tasks such as style transfer, a challenging area for current models. Using ISG-Bench, we demonstrate that recent unified vision-language models perform poorly on generating interleaved content. While compositional approaches that combine separate language and image models show a 111% improvement over unified models at the holistic level, their performance remains suboptimal at both block and image levels. To facilitate future work, we develop ISG-Agent, a baseline agent employing a "plan-execute-refine" pipeline to invoke tools, achieving a 122% performance improvement.

GraphRAG addresses significant challenges in Retrieval-Augmented Generation (RAG) by leveraging graphs with embedded knowledge to enhance the reasoning capabilities of Large Language Models (LLMs). Despite its promising potential, the GraphRAG community currently lacks a unified framework for fine-grained decomposition of the graph-based knowledge retrieval process. Furthermore, there is no systematic categorization or evaluation of existing solutions within the retrieval process. In this paper, we present LEGO-GraphRAG, a modular framework that decomposes the retrieval process of GraphRAG into three interconnected modules: subgraph-extraction, path-filtering, and path-refinement. We systematically summarize and classify the algorithms and neural network (NN) models relevant to each module, providing a clearer understanding of the design space for GraphRAG instances. Additionally, we identify key design factors, such as Graph Coupling and Computational Cost, that influence the effectiveness of GraphRAG implementations. Through extensive empirical studies, we construct high-quality GraphRAG instances using a representative selection of solutions and analyze their impact on retrieval and reasoning performance. Our findings offer critical insights into optimizing GraphRAG instance design, ultimately contributing to the advancement of more accurate and contextually relevant LLM applications.

Generative commonsense reasoning (GCR) in natural language is to reason about the commonsense while generating coherent text. Recent years have seen a surge of interest in improving the generation quality of commonsense reasoning tasks. Nevertheless, these approaches have seldom investigated diversity in the GCR tasks, which aims to generate alternative explanations for a real-world situation or predict all possible outcomes. Diversifying GCR is challenging as it expects to generate multiple outputs that are not only semantically different but also grounded in commonsense knowledge. In this paper, we propose MoKGE, a novel method that diversifies the generative reasoning by a mixture of expert (MoE) strategy on commonsense knowledge graphs (KG). A set of knowledge experts seek diverse reasoning on KG to encourage various generation outputs. Empirical experiments demonstrated that MoKGE can significantly improve the diversity while achieving on par performance on accuracy on two GCR benchmarks, based on both automatic and human evaluations.

To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.

We present EchoScene, an interactive and controllable generative model that generates 3D indoor scenes on scene graphs. EchoScene leverages a dual-branch diffusion model that dynamically adapts to scene graphs. Existing methods struggle to handle scene graphs due to varying numbers of nodes, multiple edge combinations, and manipulator-induced node-edge operations. EchoScene overcomes this by associating each node with a denoising process and enables collaborative information exchange, enhancing controllable and consistent generation aware of global constraints. This is achieved through an information echo scheme in both shape and layout branches. At every denoising step, all processes share their denoising data with an information exchange unit that combines these updates using graph convolution. The scheme ensures that the denoising processes are influenced by a holistic understanding of the scene graph, facilitating the generation of globally coherent scenes. The resulting scenes can be manipulated during inference by editing the input scene graph and sampling the noise in the diffusion model. Extensive experiments validate our approach, which maintains scene controllability and surpasses previous methods in generation fidelity. Moreover, the generated scenes are of high quality and thus directly compatible with off-the-shelf texture generation. Code and trained models are open-sourced.

Previous works on knowledge-to-text generation take as input a few RDF triples or key-value pairs conveying the knowledge of some entities to generate a natural language description. Existing datasets, such as WIKIBIO, WebNLG, and E2E, basically have a good alignment between an input triple/pair set and its output text. However, in practice, the input knowledge could be more than enough, since the output description may only cover the most significant knowledge. In this paper, we introduce a large-scale and challenging dataset to facilitate the study of such a practical scenario in KG-to-text. Our dataset involves retrieving abundant knowledge of various types of main entities from a large knowledge graph (KG), which makes the current graph-to-sequence models severely suffer from the problems of information loss and parameter explosion while generating the descriptions. We address these challenges by proposing a multi-graph structure that is able to represent the original graph information more comprehensively. Furthermore, we also incorporate aggregation methods that learn to extract the rich graph information. Extensive experiments demonstrate the effectiveness of our model architecture.