Designing new molecules is essential for drug discovery and material science. Recently, deep generative models that aim to model molecule distribution have made promising progress in narrowing down the chemical research space and generating high-fidelity molecules. However, current generative models only focus on modeling either 2D bonding graphs or 3D geometries, which are two complementary descriptors for molecules. The lack of ability to jointly model both limits the improvement of generation quality and further downstream applications. In this paper, we propose a new joint 2D and 3D diffusion model (JODO) that generates complete molecules with atom types, formal charges, bond information, and 3D coordinates. To capture the correlation between molecular graphs and geometries in the diffusion process, we develop a Diffusion Graph Transformer to parameterize the data prediction model that recovers the original data from noisy data. The Diffusion Graph Transformer interacts node and edge representations based on our relational attention mechanism, while simultaneously propagating and updating scalar features and geometric vectors. Our model can also be extended for inverse molecular design targeting single or multiple quantum properties. In our comprehensive evaluation pipeline for unconditional joint generation, the results of the experiment show that JODO remarkably outperforms the baselines on the QM9 and GEOM-Drugs datasets. Furthermore, our model excels in few-step fast sampling, as well as in inverse molecule design and molecular graph generation. Our code is provided in https://github.com/GRAPH-0/JODO.
Effective connectivity can describe the causal patterns among brain regions. These patterns have the potential to reveal the pathological mechanism and promote early diagnosis and effective drug development for cognitive disease. However, the current methods utilize software toolkits to extract empirical features from brain imaging to estimate effective connectivity. These methods heavily rely on manual parameter settings and may result in large errors during effective connectivity estimation. In this paper, a novel brain imaging-to-graph generation (BIGG) framework is proposed to map functional magnetic resonance imaging (fMRI) into effective connectivity for mild cognitive impairment (MCI) analysis. To be specific, the proposed BIGG framework is based on the diffusion denoising probabilistic models (DDPM), where each denoising step is modeled as a generative adversarial network (GAN) to progressively translate the noise and conditional fMRI to effective connectivity. The hierarchical transformers in the generator are designed to estimate the noise at multiple scales. Each scale concentrates on both spatial and temporal information between brain regions, enabling good quality in noise removal and better inference of causal relations. Meanwhile, the transformer-based discriminator constrains the generator to further capture global and local patterns for improving high-quality and diversity generation. By introducing the diffusive factor, the denoising inference with a large sampling step size is more efficient and can maintain high-quality results for effective connectivity generation. Evaluations of the ADNI dataset demonstrate the feasibility and efficacy of the proposed model. The proposed model not only achieves superior prediction performance compared with other competing methods but also predicts MCI-related causal connections that are consistent with clinical studies.
Molecular de novo design is a critical yet challenging task in scientific fields, aiming to design novel molecular structures with desired property profiles. Significant progress has been made by resorting to generative models for graphs. However, limited attention is paid to hierarchical generative models, which can exploit the inherent hierarchical structure (with rich semantic information) of the molecular graphs and generate complex molecules of larger size that we shall demonstrate to be difficult for most existing models. The primary challenge to hierarchical generation is the non-differentiable issue caused by the generation of intermediate discrete coarsened graph structures. To sidestep this issue, we cast the tricky hierarchical generation problem over discrete spaces as the reverse process of hierarchical representation learning and propose MolHF, a new hierarchical flow-based model that generates molecular graphs in a coarse-to-fine manner. Specifically, MolHF first generates bonds through a multi-scale architecture, then generates atoms based on the coarsened graph structure at each scale. We demonstrate that MolHF achieves state-of-the-art performance in random generation and property optimization, implying its high capacity to model data distribution. Furthermore, MolHF is the first flow-based model that can be applied to model larger molecules (polymer) with more than 100 heavy atoms. The code and models are available at https://github.com/violet-sto/MolHF.
Diffusion-based generative graph models have been proven effective in generating high-quality small graphs. However, they need to be more scalable for generating large graphs containing thousands of nodes desiring graph statistics. In this work, we propose EDGE, a new diffusion-based generative graph model that addresses generative tasks with large graphs. To improve computation efficiency, we encourage graph sparsity by using a discrete diffusion process that randomly removes edges at each time step and finally obtains an empty graph. EDGE only focuses on a portion of nodes in the graph at each denoising step. It makes much fewer edge predictions than previous diffusion-based models. Moreover, EDGE admits explicitly modeling the node degrees of the graphs, further improving the model performance. The empirical study shows that EDGE is much more efficient than competing methods and can generate large graphs with thousands of nodes. It also outperforms baseline models in generation quality: graphs generated by our approach have more similar graph statistics to those of the training graphs.
Analysis and extraction of useful information from legal judgments using computational linguistics was one of the earliest problems posed in the domain of information retrieval. Presently, several commercial vendors exist who automate such tasks. However, a crucial bottleneck arises in the form of exorbitant pricing and lack of resources available in analysis of judgements mete out by Hong Kong's Legal System. This paper attempts to bridge this gap by providing several statistical, machine learning, deep learning and zero-shot learning based methods to effectively analyze legal judgments from Hong Kong's Court System. The methods proposed consists of: (1) Citation Network Graph Generation, (2) PageRank Algorithm, (3) Keyword Analysis and Summarization, (4) Sentiment Polarity, and (5) Paragrah Classification, in order to be able to extract key insights from individual as well a group of judgments together. This would make the overall analysis of judgments in Hong Kong less tedious and more automated in order to extract insights quickly using fast inferencing. We also provide an analysis of our results by benchmarking our results using Large Language Models making robust use of the HuggingFace ecosystem.
Graph representation learning models aim to represent the graph structure and its features into low-dimensional vectors in a latent space, which can benefit various downstream tasks, such as node classification and link prediction. Due to its powerful graph data modelling capabilities, various graph embedding models and libraries have been proposed to learn embeddings and help researchers ease conducting experiments. In this paper, we introduce a novel graph representation framework covering various graph embedding models, ranging from shallow to state-of-the-art models, namely Connector. First, we consider graph generation by constructing various types of graphs with different structural relations, including homogeneous, signed, heterogeneous, and knowledge graphs. Second, we introduce various graph representation learning models, ranging from shallow to deep graph embedding models. Finally, we plan to build an efficient open-source framework that can provide deep graph embedding models to represent structural relations in graphs. The framework is available at https://github.com/NSLab-CUK/Connector.
Designing molecules with desirable physiochemical properties and functionalities is a long-standing challenge in chemistry, material science, and drug discovery. Recently, machine learning-based generative models have emerged as promising approaches for \emph{de novo} molecule design. However, further refinement of methodology is highly desired as most existing methods lack unified modeling of 2D topology and 3D geometry information and fail to effectively learn the structure-property relationship for molecule design. Here we present MolCode, a roto-translation equivariant generative framework for \underline{Mol}ecular graph-structure \underline{Co-de}sign. In MolCode, 3D geometric information empowers the molecular 2D graph generation, which in turn helps guide the prediction of molecular 3D structure. Extensive experimental results show that MolCode outperforms previous methods on a series of challenging tasks including \emph{de novo} molecule design, targeted molecule discovery, and structure-based drug design. Particularly, MolCode not only consistently generates valid (99.95$\%$ Validity) and diverse (98.75$\%$ Uniqueness) molecular graphs/structures with desirable properties, but also generate drug-like molecules with high affinity to target proteins (61.8$\%$ high-affinity ratio), which demonstrates MolCode's potential applications in material design and drug discovery. Our extensive investigation reveals that the 2D topology and 3D geometry contain intrinsically complementary information in molecule design, and provide new insights into machine learning-based molecule representation and generation.
We provide a novel approach to construct generative models for graphs. Instead of using the traditional probabilistic models or deep generative models, we propose to instead find an algorithm that generates the data. We achieve this using evolutionary search and a powerful fitness function, implemented by a randomly initialized graph neural network. This brings certain advantages over current deep generative models, for instance, a higher potential for out-of-training-distribution generalization and direct interpretability, as the final graph generative process is expressed as a Python function. We show that this approach can be competitive with deep generative models and under some circumstances can even find the true graph generative process, and as such perfectly generalize.
Instance-level graph neural network explainers have proven beneficial for explaining such networks on histopathology images. However, there has been few methods that provide model explanations, which are common patterns among samples within the same class. We envision that graph-based histopathological image analysis can benefit significantly from such explanations. On the other hand, current model-level explainers are based on graph generation methods that are not applicable in this domain because of no corresponding image for their generated graphs in real world. Therefore, such explanations are communicable to the experts. To follow this vision, we developed KS-GNNExplainer, the first instance-level graph neural network explainer that leverages current instance-level approaches in an effective manner to provide more informative and reliable explainable outputs, which are crucial for applied AI in the health domain. Our experiments on various datasets, and based on both quantitative and qualitative measures, demonstrate that the proposed explainer is capable of being a global pattern extractor, which is a fundamental limitation of current instance-level approaches in this domain.
Scene graph generation aims to construct a semantic graph structure from an image such that its nodes and edges respectively represent objects and their relationships. One of the major challenges for the task lies in the presence of distracting objects and relationships in images; contextual reasoning is strongly distracted by irrelevant objects or backgrounds and, more importantly, a vast number of irrelevant candidate relations. To tackle the issue, we propose the Selective Quad Attention Network (SQUAT) that learns to select relevant object pairs and disambiguate them via diverse contextual interactions. SQUAT consists of two main components: edge selection and quad attention. The edge selection module selects relevant object pairs, i.e., edges in the scene graph, which helps contextual reasoning, and the quad attention module then updates the edge features using both edge-to-node and edge-to-edge cross-attentions to capture contextual information between objects and object pairs. Experiments demonstrate the strong performance and robustness of SQUAT, achieving the state of the art on the Visual Genome and Open Images v6 benchmarks.
The task of dynamic scene graph generation (SGG) from videos is complicated and challenging due to the inherent dynamics of a scene, temporal fluctuation of model predictions, and the long-tailed distribution of the visual relationships in addition to the already existing challenges in image-based SGG. Existing methods for dynamic SGG have primarily focused on capturing spatio-temporal context using complex architectures without addressing the challenges mentioned above, especially the long-tailed distribution of relationships. This often leads to the generation of biased scene graphs. To address these challenges, we introduce a new framework called TEMPURA: TEmporal consistency and Memory Prototype guided UnceRtainty Attenuation for unbiased dynamic SGG. TEMPURA employs object-level temporal consistencies via transformer-based sequence modeling, learns to synthesize unbiased relationship representations using memory-guided training, and attenuates the predictive uncertainty of visual relations using a Gaussian Mixture Model (GMM). Extensive experiments demonstrate that our method achieves significant (up to 10% in some cases) performance gain over existing methods highlighting its superiority in generating more unbiased scene graphs.
Learning similarity between scene graphs and images aims to estimate a similarity score given a scene graph and an image. There is currently no research dedicated to this task, although it is critical for scene graph generation and downstream applications. Scene graph generation is conventionally evaluated by Recall$@K$ and mean Recall$@K$, which measure the ratio of predicted triplets that appear in the human-labeled triplet set. However, such triplet-oriented metrics fail to demonstrate the overall semantic difference between a scene graph and an image and are sensitive to annotation bias and noise. Using generated scene graphs in the downstream applications is therefore limited. To address this issue, for the first time, we propose a Scene graPh-imAge coNtrastive learning framework, SPAN, that can measure the similarity between scene graphs and images. Our novel framework consists of a graph Transformer and an image Transformer to align scene graphs and their corresponding images in the shared latent space. We introduce a novel graph serialization technique that transforms a scene graph into a sequence with structural encodings. Based on our framework, we propose R-Precision measuring image retrieval accuracy as a new evaluation metric for scene graph generation. We establish new benchmarks on the Visual Genome and Open Images datasets. Extensive experiments are conducted to verify the effectiveness of SPAN, which shows great potential as a scene graph encoder.
There have been tremendous efforts over the past decades dedicated to the generation of realistic graphs in a variety of domains, ranging from social networks to computer networks, from gene regulatory networks to online transaction networks. Despite the remarkable success, the vast majority of these works are unsupervised in nature and are typically trained to minimize the expected graph reconstruction loss, which would result in the representation disparity issue in the generated graphs, i.e., the protected groups (often minorities) contribute less to the objective and thus suffer from systematically higher errors. In this paper, we aim to tailor graph generation to downstream mining tasks by leveraging label information and user-preferred parity constraints. In particular, we start from the investigation of representation disparity in the context of graph generative models. To mitigate the disparity, we propose a fairness-aware graph generative model named FairGen. Our model jointly trains a label-informed graph generation module and a fair representation learning module by progressively learning the behaviors of the protected and unprotected groups, from the `easy' concepts to the `hard' ones. In addition, we propose a generic context sampling strategy for graph generative models, which is proven to be capable of fairly capturing the contextual information of each group with a high probability. Experimental results on seven real-world data sets, including web-based graphs, demonstrate that FairGen (1) obtains performance on par with state-of-the-art graph generative models across nine network properties, (2) mitigates the representation disparity issues in the generated graphs, and (3) substantially boosts the model performance by up to 17% in downstream tasks via data augmentation.
Scene Graph Generation (SGG) aims to extract <subject, predicate, object> relationships in images for vision understanding. Although recent works have made steady progress on SGG, they still suffer long-tail distribution issues that tail-predicates are more costly to train and hard to distinguish due to a small amount of annotated data compared to frequent predicates. Existing re-balancing strategies try to handle it via prior rules but are still confined to pre-defined conditions, which are not scalable for various models and datasets. In this paper, we propose a Cross-modal prediCate boosting (CaCao) framework, where a visually-prompted language model is learned to generate diverse fine-grained predicates in a low-resource way. The proposed CaCao can be applied in a plug-and-play fashion and automatically strengthen existing SGG to tackle the long-tailed problem. Based on that, we further introduce a novel Entangled cross-modal prompt approach for open-world predicate scene graph generation (Epic), where models can generalize to unseen predicates in a zero-shot manner. Comprehensive experiments on three benchmark datasets show that CaCao consistently boosts the performance of multiple scene graph generation models in a model-agnostic way. Moreover, our Epic achieves competitive performance on open-world predicate prediction. The data and code for this paper are publicly available.
Current video-based scene graph generation (VidSGG) methods have been found to perform poorly on predicting predicates that are less represented due to the inherent biased distribution in the training data. In this paper, we take a closer look at the predicates and identify that most visual relations (e.g. sit_above) involve both actional pattern (sit) and spatial pattern (above), while the distribution bias is much less severe at the pattern level. Based on this insight, we propose a decoupled label learning (DLL) paradigm to address the intractable visual relation prediction from the pattern-level perspective. Specifically, DLL decouples the predicate labels and adopts separate classifiers to learn actional and spatial patterns respectively. The patterns are then combined and mapped back to the predicate. Moreover, we propose a knowledge-level label decoupling method to transfer non-target knowledge from head predicates to tail predicates within the same pattern to calibrate the distribution of tail classes. We validate the effectiveness of DLL on the commonly used VidSGG benchmark, i.e. VidVRD. Extensive experiments demonstrate that the DLL offers a remarkably simple but highly effective solution to the long-tailed problem, achieving the state-of-the-art VidSGG performance.
In this paper, we propose a novel model called SGFormer, Semantic Graph TransFormer for point cloud-based 3D scene graph generation. The task aims to parse a point cloud-based scene into a semantic structural graph, with the core challenge of modeling the complex global structure. Existing methods based on graph convolutional networks (GCNs) suffer from the over-smoothing dilemma and can only propagate information from limited neighboring nodes. In contrast, SGFormer uses Transformer layers as the base building block to allow global information passing, with two types of newly-designed layers tailored for the 3D scene graph generation task. Specifically, we introduce the graph embedding layer to best utilize the global information in graph edges while maintaining comparable computation costs. Furthermore, we propose the semantic injection layer to leverage linguistic knowledge from large-scale language model (i.e., ChatGPT), to enhance objects' visual features. We benchmark our SGFormer on the established 3DSSG dataset and achieve a 40.94% absolute improvement in relationship prediction's R@50 and an 88.36% boost on the subset with complex scenes over the state-of-the-art. Our analyses further show SGFormer's superiority in the long-tail and zero-shot scenarios. Our source code is available at https://github.com/Andy20178/SGFormer.
Scene Graph Generation (SGG) is a visual understanding task, aiming to describe a scene as a graph of entities and their relationships with each other. Existing works rely on location labels in form of bounding boxes or segmentation masks, increasing annotation costs and limiting dataset expansion. Recognizing that many applications do not require location data, we break this dependency and introduce location-free scene graph generation (LF-SGG). This new task aims at predicting instances of entities, as well as their relationships, without the explicit calculation of their spatial localization. To objectively evaluate the task, the predicted and ground truth scene graphs need to be compared. We solve this NP-hard problem through an efficient branching algorithm. Additionally, we design the first LF-SGG method, Pix2SG, using autoregressive sequence modeling. We demonstrate the effectiveness of our method on three scene graph generation datasets as well as two downstream tasks, image retrieval and visual question answering, and show that our approach is competitive to existing methods while not relying on location cues.
Today's scene graph generation (SGG) models typically require abundant manual annotations to learn new predicate types. Therefore, it is difficult to apply them to real-world applications with massive uncommon predicate categories whose annotations are hard to collect. In this paper, we focus on Few-Shot SGG (FSSGG), which encourages SGG models to be able to quickly transfer previous knowledge and recognize unseen predicates well with only a few examples. However, current methods for FSSGG are hindered by the high intra-class variance of predicate categories in SGG: On one hand, each predicate category commonly has multiple semantic meanings under different contexts. On the other hand, the visual appearance of relation triplets with the same predicate differs greatly under different subject-object compositions. Such great variance of inputs makes it hard to learn generalizable representation for each predicate category with current few-shot learning (FSL) methods. However, we found that this intra-class variance of predicates is highly related to the composed subjects and objects. To model the intra-class variance of predicates with subject-object context, we propose a novel Decomposed Prototype Learning (DPL) model for FSSGG. Specifically, we first construct a decomposable prototype space to capture diverse semantics and visual patterns of subjects and objects for predicates by decomposing them into multiple prototypes. Afterwards, we integrate these prototypes with different weights to generate query-adaptive predicate representation with more reliable semantics for each query sample. We conduct extensive experiments and compare with various baseline methods to show the effectiveness of our method.
Automatic radiology report summarization is a crucial clinical task, whose key challenge is to maintain factual accuracy between produced summaries and ground truth radiology findings. Existing research adopts reinforcement learning to directly optimize factual consistency metrics such as CheXBert or RadGraph score. However, their decoding method using greedy search or beam search considers no factual consistency when picking the optimal candidate, leading to limited factual consistency improvement. To address it, we propose a novel second-stage summarizing approach FactReranker, the first attempt that learns to choose the best summary from all candidates based on their estimated factual consistency score. We propose to extract medical facts of the input medical report, its gold summary, and candidate summaries based on the RadGraph schema and design the fact-guided reranker to efficiently incorporate the extracted medical facts for selecting the optimal summary. We decompose the fact-guided reranker into the factual knowledge graph generation and the factual scorer, which allows the reranker to model the mapping between the medical facts of the input text and its gold summary, thus can select the optimal summary even the gold summary can't be observed during inference. We also present a fact-based ranking metric (RadMRR) for measuring the ability of the reranker on selecting factual consistent candidates. Experimental results on two benchmark datasets demonstrate the superiority of our method in generating summaries with higher factual consistency scores when compared with existing methods.
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.