As the size of accessible compound libraries expands to over 10 billion, the need for more efficient structure-based virtual screening methods is emerging. Different pre-screening methods have been developed for rapid screening, but there is still a lack of structure-based methods applicable to various proteins that perform protein-ligand binding conformation prediction and scoring in an extremely short time. Here, we describe for the first time a deep-learning framework for structure-based pharmacophore modeling to address this challenge. We frame pharmacophore modeling as an instance segmentation problem to determine each protein hotspot and the location of corresponding pharmacophores, and protein-ligand binding pose prediction as a graph-matching problem. PharmacoNet is significantly faster than state-of-the-art structure-based approaches, yet reasonably accurate with a simple scoring function. Furthermore, we show the promising result that PharmacoNet effectively retains hit candidates even under the high pre-screening filtration rates. Overall, our study uncovers the hitherto untapped potential of a pharmacophore modeling approach in deep learning-based drug discovery.
The prevalence of ubiquitous location-aware devices and mobile Internet enables us to collect massive individual-level trajectory dataset from users. Such trajectory big data bring new opportunities to human mobility research but also raise public concerns with regard to location privacy. In this work, we present the Conditional Adversarial Trajectory Synthesis (CATS), a deep-learning-based GeoAI methodological framework for privacy-preserving trajectory data generation and publication. CATS applies K-anonymity to the underlying spatiotemporal distributions of human movements, which provides a distributional-level strong privacy guarantee. By leveraging conditional adversarial training on K-anonymized human mobility matrices, trajectory global context learning using the attention-based mechanism, and recurrent bipartite graph matching of adjacent trajectory points, CATS is able to reconstruct trajectory topology from conditionally sampled locations and generate high-quality individual-level synthetic trajectory data, which can serve as supplements or alternatives to raw data for privacy-preserving trajectory data publication. The experiment results on over 90k GPS trajectories show that our method has a better performance in privacy preservation, spatiotemporal characteristic preservation, and downstream utility compared with baseline methods, which brings new insights into privacy-preserving human mobility research using generative AI techniques and explores data ethics issues in GIScience.
Echocardiogram video segmentation plays an important role in cardiac disease diagnosis. This paper studies the unsupervised domain adaption (UDA) for echocardiogram video segmentation, where the goal is to generalize the model trained on the source domain to other unlabelled target domains. Existing UDA segmentation methods are not suitable for this task because they do not model local information and the cyclical consistency of heartbeat. In this paper, we introduce a newly collected CardiacUDA dataset and a novel GraphEcho method for cardiac structure segmentation. Our GraphEcho comprises two innovative modules, the Spatial-wise Cross-domain Graph Matching (SCGM) and the Temporal Cycle Consistency (TCC) module, which utilize prior knowledge of echocardiogram videos, i.e., consistent cardiac structure across patients and centers and the heartbeat cyclical consistency, respectively. These two modules can better align global and local features from source and target domains, improving UDA segmentation results. Experimental results showed that our GraphEcho outperforms existing state-of-the-art UDA segmentation methods. Our collected dataset and code will be publicly released upon acceptance. This work will lay a new and solid cornerstone for cardiac structure segmentation from echocardiogram videos. Code and dataset are available at: https://github.com/xmed-lab/GraphEcho
Artificial Intelligence makes great advances today and starts to bridge the gap between vision and language. However, we are still far from understanding, explaining and controlling explicitly the visual content from a linguistic perspective, because we still lack a common explainable representation between the two domains. In this work we come to address this limitation and propose the Graph of Events in Space and Time (GEST), by which we can represent, create and explain, both visual and linguistic stories. We provide a theoretical justification of our model and an experimental validation, which proves that GEST can bring a solid complementary value along powerful deep learning models. In particular, GEST can help improve at the content-level the generation of videos from text, by being easily incorporated into our novel video generation engine. Additionally, by using efficient graph matching techniques, the GEST graphs can also improve the comparisons between texts at the semantic level.
Renal pathology, as the gold standard of kidney disease diagnosis, requires doctors to analyze a series of tissue slices stained by H&E staining and special staining like Masson, PASM, and PAS, respectively. These special staining methods are costly, time-consuming, and hard to standardize for wide use especially in primary hospitals. Advances of supervised learning methods have enabled the virtually conversion of H&E images into special staining images, but achieving pixel-to-pixel alignment for training remains challenging. In contrast, unsupervised learning methods regarding different stains as different style transfer domains can utilize unpaired data, but they ignore the spatial inter-domain correlations and thus decrease the trustworthiness of structural details for diagnosis. In this paper, we propose a novel virtual staining framework AGMDT to translate images into other domains by avoiding pixel-level alignment and meanwhile utilizing the correlations among adjacent tissue slices. We first build a high-quality multi-domain renal histological dataset where each specimen case comprises a series of slices stained in various ways. Based on it, the proposed framework AGMDT discovers patch-level aligned pairs across the serial slices of multi-domains through glomerulus detection and bipartite graph matching, and utilizes such correlations to supervise the end-to-end model for multi-domain staining transformation. Experimental results show that the proposed AGMDT achieves a good balance between the precise pixel-level alignment and unpaired domain transfer by exploiting correlations across multi-domain serial pathological slices, and outperforms the state-of-the-art methods in both quantitative measure and morphological details.
We propose a simple yet effective metric that measures structural similarity between visual instances of architectural floor plans, without the need for learning. Qualitatively, our experiments show that the retrieval results are similar to deeply learned methods. Effectively comparing instances of floor plan data is paramount to the success of machine understanding of floor plan data, including the assessment of floor plan generative models and floor plan recommendation systems. Comparing visual floor plan images goes beyond a sole pixel-wise visual examination and is crucially about similarities and differences in the shapes and relations between subdivisions that compose the layout. Currently, deep metric learning approaches are used to learn a pair-wise vector representation space that closely mimics the structural similarity, in which the models are trained on similarity labels that are obtained by Intersection-over-Union (IoU). To compensate for the lack of structural awareness in IoU, graph-based approaches such as Graph Matching Networks (GMNs) are used, which require pairwise inference for comparing data instances, making GMNs less practical for retrieval applications. In this paper, an effective evaluation metric for judging the structural similarity of floor plans, coined SSIG (Structural Similarity by IoU and GED), is proposed based on both image and graph distances. In addition, an efficient algorithm is developed that uses SSIG to rank a large-scale floor plan database. Code will be openly available.
We present a novel approach for finding multiple noisily embedded template graphs in a very large background graph. Our method builds upon the graph-matching-matched-filter technique proposed in Sussman et al., with the discovery of multiple diverse matchings being achieved by iteratively penalizing a suitable node-pair similarity matrix in the matched filter algorithm. In addition, we propose algorithmic speed-ups that greatly enhance the scalability of our matched-filter approach. We present theoretical justification of our methodology in the setting of correlated Erdos-Renyi graphs, showing its ability to sequentially discover multiple templates under mild model conditions. We additionally demonstrate our method's utility via extensive experiments both using simulated models and real-world dataset, include human brain connectomes and a large transactional knowledge base.
A scientific paper can be divided into two major constructs which are Metadata and Full-body text. Metadata provides a brief overview of the paper while the Full-body text contains key-insights that can be valuable to fellow researchers. To retrieve metadata and key-insights from scientific papers, knowledge acquisition is a central activity. It consists of gathering, analyzing and organizing knowledge embedded in scientific papers in such a way that it can be used and reused whenever needed. Given the wealth of scientific literature, manual knowledge acquisition is a cumbersome task. Thus, computer-assisted and (semi-)automatic strategies are generally adopted. Our purpose in this research was two fold: curate Open Research Knowledge Graph (ORKG) with papers related to ontology learning and define an approach using ORKG as a computer-assisted tool to organize key-insights extracted from research papers. This approach was used to document the "epidemiological surveillance systems design and implementation" research problem and to prepare the related work of this paper. It is currently used to document "food information engineering", "Tabular data to Knowledge Graph Matching" and "Question Answering" research problems and "Neuro-symbolic AI" domain.
Coronary artery disease (CAD) is one of the primary causes leading to death worldwide. Accurate extraction of individual arterial branches on invasive coronary angiograms (ICA) is important for stenosis detection and CAD diagnosis. However, deep learning-based models face challenges in generating semantic segmentation for coronary arteries due to the morphological similarity among different types of coronary arteries. To address this challenge, we propose an innovative approach using the hyper association graph-matching neural network with uncertainty quantification (HAGMN-UQ) for coronary artery semantic labeling on ICAs. The graph-matching procedure maps the arterial branches between two individual graphs, so that the unlabeled arterial segments are classified by the labeled segments, and the coronary artery semantic labeling is achieved. By incorporating the anatomical structural loss and uncertainty, our model achieved an accuracy of 0.9345 for coronary artery semantic labeling with a fast inference speed, leading to an effective and efficient prediction in real-time clinical decision-making scenarios.
Finding similar patients is a common objective in precision medicine, facilitating treatment outcome assessment and clinical decision support. Choosing widely-available patient features and appropriate mathematical methods for similarity calculations is crucial. International Statistical Classification of Diseases and Related Health Problems (ICD) codes are used worldwide to encode diseases and are available for nearly all patients. Aggregated as sets consisting of primary and secondary diagnoses they can display a degree of comorbidity and reveal comorbidity patterns. It is possible to compute the similarity of patients based on their ICD codes by using semantic similarity algorithms. These algorithms have been traditionally evaluated using a single-term expert rated data set. However, real-word patient data often display varying degrees of documented comorbidities that might impair algorithm performance. To account for this, we present a scale term that considers documented comorbidity-variance. In this work, we compared the performance of 80 combinations of established algorithms in terms of semantic similarity based on ICD-code sets. The sets have been extracted from patients with a C25.X (pancreatic cancer) primary diagnosis and provide a variety of different combinations of ICD-codes. Using our scale term we yielded the best results with a combination of level-based information content, Leacock & Chodorow concept similarity and bipartite graph matching for the set similarities reaching a correlation of 0.75 with our expert's ground truth. Our results highlight the importance of accounting for comorbidity variance while demonstrating how well current semantic similarity algorithms perform.
This paper focuses on the statistical analysis of shapes of data objects called shape graphs, a set of nodes connected by articulated curves with arbitrary shapes. A critical need here is a constrained registration of points (nodes to nodes, edges to edges) across objects. This, in turn, requires optimization over the permutation group, made challenging by differences in nodes (in terms of numbers, locations) and edges (in terms of shapes, placements, and sizes) across objects. This paper tackles this registration problem using a novel neural-network architecture and involves an unsupervised loss function developed using the elastic shape metric for curves. This architecture results in (1) state-of-the-art matching performance and (2) an order of magnitude reduction in the computational cost relative to baseline approaches. We demonstrate the effectiveness of the proposed approach using both simulated data and real-world 2D and 3D shape graphs. Code and data will be made publicly available after review to foster research.
Current point cloud registration methods are mainly based on local geometric information and usually ignore the semantic information contained in the scenes. In this paper, we treat the point cloud registration problem as a semantic instance matching and registration task, and propose a deep semantic graph matching method (DeepSGM) for large-scale outdoor point cloud registration. Firstly, the semantic categorical labels of 3D points are obtained using a semantic segmentation network. The adjacent points with the same category labels are then clustered together using the Euclidean clustering algorithm to obtain the semantic instances, which are represented by three kinds of attributes including spatial location information, semantic categorical information, and global geometric shape information. Secondly, the semantic adjacency graph is constructed based on the spatial adjacency relations of semantic instances. To fully explore the topological structures between semantic instances in the same scene and across different scenes, the spatial distribution features and the semantic categorical features are learned with graph convolutional networks, and the global geometric shape features are learned with a PointNet-like network. These three kinds of features are further enhanced with the self-attention and cross-attention mechanisms. Thirdly, the semantic instance matching is formulated as an optimal transport problem, and solved through an optimal matching layer. Finally, the geometric transformation matrix between two point clouds is first estimated by the SVD algorithm and then refined by the ICP algorithm. Experimental results conducted on the KITTI Odometry dataset demonstrate that the proposed method improves the registration performance and outperforms various state-of-the-art methods.
Graph Neural Networks (GNNs) have proven to be effective in processing and learning from graph-structured data. However, previous works mainly focused on understanding single graph inputs while many real-world applications require pair-wise analysis for graph-structured data (e.g., scene graph matching, code searching, and drug-drug interaction prediction). To this end, recent works have shifted their focus to learning the interaction between pairs of graphs. Despite their improved performance, these works were still limited in that the interactions were considered at the node-level, resulting in high computational costs and suboptimal performance. To address this issue, we propose a novel and efficient graph-level approach for extracting interaction representations using co-attention in graph pooling. Our method, Co-Attention Graph Pooling (CAGPool), exhibits competitive performance relative to existing methods in both classification and regression tasks using real-world datasets, while maintaining lower computational complexity.
Occlusion is a common problem with biometric recognition in the wild. The generalization ability of CNNs greatly decreases due to the adverse effects of various occlusions. To this end, we propose a novel unified framework integrating the merits of both CNNs and graph models to overcome occlusion problems in biometric recognition, called multiscale dynamic graph representation (MS-DGR). More specifically, a group of deep features reflected on certain subregions is recrafted into a feature graph (FG). Each node inside the FG is deemed to characterize a specific local region of the input sample, and the edges imply the co-occurrence of non-occluded regions. By analyzing the similarities of the node representations and measuring the topological structures stored in the adjacent matrix, the proposed framework leverages dynamic graph matching to judiciously discard the nodes corresponding to the occluded parts. The multiscale strategy is further incorporated to attain more diverse nodes representing regions of various sizes. Furthermore, the proposed framework exhibits a more illustrative and reasonable inference by showing the paired nodes. Extensive experiments demonstrate the superiority of the proposed framework, which boosts the accuracy in both natural and occlusion-simulated cases by a large margin compared with that of baseline methods.
We contribute to the sparsely populated area of unsupervised deep graph matching with application to keypoint matching in images. Contrary to the standard \emph{supervised} approach, our method does not require ground truth correspondences between keypoint pairs. Instead, it is self-supervised by enforcing consistency of matchings between images of the same object category. As the matching and the consistency loss are discrete, their derivatives cannot be straightforwardly used for learning. We address this issue in a principled way by building our method upon the recent results on black-box differentiation of combinatorial solvers. This makes our method exceptionally flexible, as it is compatible with arbitrary network architectures and combinatorial solvers. Our experimental evaluation suggests that our technique sets a new state-of-the-art for unsupervised graph matching.
Classical graph matching aims to find a node correspondence between two unlabeled graphs of known topologies. This problem has a wide range of applications, from matching identities in social networks to identifying similar biological network functions across species. However, when the underlying graphs are unknown, the use of conventional graph matching methods requires inferring the graph topologies first, a process that is highly sensitive to observation errors. In this paper, we tackle the blind graph matching problem with unknown underlying graphs directly using observations of graph signals, which are generated from graph filters applied to graph signal excitations. We propose to construct sample covariance matrices from the observed signals and match the nodes based on the selected sample eigenvectors. Our analysis shows that the blind matching outcome converges to the result obtained with known graph topologies when the signal sampling size is large and the signal noise is small. Numerical results showcase the performance improvement of the proposed algorithm compared to matching two estimated underlying graphs learned from the graph signals.
Deep generative models for Natural Language data offer a new angle on the problem of graph synthesis: by optimizing differentiable models that directly generate graphs, it is possible to side-step expensive search procedures in the discrete and vast space of possible graphs. We introduce LIC-GAN, an implicit, likelihood-free generative model for small graphs that circumvents the need for expensive graph matching procedures. Our method takes as input a natural language query and using a combination of language modelling and Generative Adversarial Networks (GANs) and returns a graph that closely matches the description of the query. We combine our approach with a reward network to further enhance the graph generation with desired properties. Our experiments, show that LIC-GAN does well on metrics such as PropMatch and Closeness getting scores of 0.36 and 0.48. We also show that LIC-GAN performs as good as ChatGPT, with ChatGPT getting scores of 0.40 and 0.42. We also conduct a few experiments to demonstrate the robustness of our method, while also highlighting a few interesting caveats of the model.
Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates some central challenges from multiple tasks, including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding and elicits continuous differential attention that encapsulates and evolves with latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.
We propose an efficient algorithm for matching two correlated Erd\H{o}s--R\'enyi graphs with $n$ vertices whose edges are correlated through a latent vertex correspondence. When the edge density $q= n^{- \alpha+o(1)}$ for a constant $\alpha \in [0,1)$, we show that our algorithm has polynomial running time and succeeds to recover the latent matching as long as the edge correlation is non-vanishing. This is closely related to our previous work on a polynomial-time algorithm that matches two Gaussian Wigner matrices with non-vanishing correlation, and provides the first polynomial-time random graph matching algorithm (regardless of the regime of $q$) when the edge correlation is below the square root of the Otter's constant (which is $\approx 0.338$).
We consider the problem of graph matching, or learning vertex correspondence, between two correlated stochastic block models (SBMs). The graph matching problem arises in various fields, including computer vision, natural language processing and bioinformatics, and in particular, matching graphs with inherent community structure has significance related to de-anonymization of correlated social networks. Compared to the correlated Erdos-Renyi (ER) model, where various efficient algorithms have been developed, among which a few algorithms have been proven to achieve the exact matching with constant edge correlation, no low-order polynomial algorithm has been known to achieve exact matching for the correlated SBMs with constant correlation. In this work, we propose an efficient algorithm for matching graphs with community structure, based on the comparison between partition trees rooted from each vertex, by extending the idea of Mao et al. (2021) to graphs with communities. The partition tree divides the large neighborhoods of each vertex into disjoint subsets using their edge statistics to different communities. Our algorithm is the first low-order polynomial-time algorithm achieving exact matching between two correlated SBMs with high probability in dense graphs.