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Wang R, Yan J, Yang X. Neural Graph Matching Network: Learning Lawler's Quadratic Assignment Problem With Extension to Hypergraph and Multiple-Graph Matching. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2022; 44:5261-5279. [PMID: 33961550 DOI: 10.1109/tpami.2021.3078053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Graph matching involves combinatorial optimization based on edge-to-edge affinity matrix, which can be generally formulated as Lawler's quadratic assignment problem (QAP). This paper presents a QAP network directly learning with the affinity matrix (equivalently the association graph) whereby the matching problem is translated into a constrained vertex classification task. The association graph is learned by an embedding network for vertex classification, followed by Sinkhorn normalization and a cross-entropy loss for end-to-end learning. We further improve the embedding model on association graph by introducing Sinkhorn based matching-aware constraint, as well as dummy nodes to deal with unequal sizes of graphs. To our best knowledge, this is one of the first network to directly learn with the general Lawler's QAP. In contrast, recent deep matching methods focus on the learning of node/edge features in two graphs respectively. We also show how to extend our network to hypergraph matching, and matching of multiple graphs. Experimental results on both synthetic graphs and real-world images show its effectiveness. For pure QAP tasks on synthetic data and QAPLIB benchmark, our method can perform competitively and even surpass state-of-the-art graph matching and QAP solvers with notable less time cost. We provide a project homepage at http://thinklab.sjtu.edu.cn/project/NGM/index.html.
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Graph matching based point correspondence with alternating direction method of multipliers. Neurocomputing 2021. [DOI: 10.1016/j.neucom.2021.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhu H, Cui C, Deng L, Cheung RCC, Yan H. Elastic Net Constraint-Based Tensor Model for High-Order Graph Matching. IEEE TRANSACTIONS ON CYBERNETICS 2021; 51:4062-4074. [PMID: 31536028 DOI: 10.1109/tcyb.2019.2936176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The procedure of establishing the correspondence between two sets of feature points is important in computer vision applications. In this article, an elastic net constraint-based tensor model is proposed for high-order graph matching. To control the tradeoff between the sparsity and the accuracy of the matching results, an elastic net constraint is introduced into the tensor-based graph matching model. Then, a nonmonotone spectral projected gradient (NSPG) method is derived to solve the proposed matching model. During the optimization of using NSPG, we propose an algorithm to calculate the projection on the feasible convex sets of elastic net constraint. Further, the global convergence of solving the proposed model using the NSPG method was proved. The superiority of the proposed method is verified through experiments on the synthetic data and natural images.
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Supervised learning for parameterized Koopmans–Beckmann’s graph matching. Pattern Recognit Lett 2021. [DOI: 10.1016/j.patrec.2020.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Sussman DL, Park Y, Priebe CE, Lyzinski V. Matched Filters for Noisy Induced Subgraph Detection. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2020; 42:2887-2900. [PMID: 31059426 PMCID: PMC7598933 DOI: 10.1109/tpami.2019.2914651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The problem of finding the vertex correspondence between two noisy graphs with different number of vertices where the smaller graph is still large has many applications in social networks, neuroscience, and computer vision. We propose a solution to this problem via a graph matching matched filter: centering and padding the smaller adjacency matrix and applying graph matching methods to align it to the larger network. The centering and padding schemes can be incorporated into any algorithm that matches using adjacency matrices. Under a statistical model for correlated pairs of graphs, which yields a noisy copy of the small graph within the larger graph, the resulting optimization problem can be guaranteed to recover the true vertex correspondence between the networks. However, there are currently no efficient algorithms for solving this problem. To illustrate the possibilities and challenges of such problems, we use an algorithm that can exploit a partially known correspondence and show via varied simulations and applications to Drosophila and human connectomes that this approach can achieve good performance.
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Wang FD, Xue N, Zhang Y, Xia GS, Pelillo M. A Functional Representation for Graph Matching. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2020; 42:2737-2754. [PMID: 31144627 DOI: 10.1109/tpami.2019.2919308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Graph matching is an important and persistent problem in computer vision and pattern recognition for finding node-to-node correspondence between graphs. However, graph matching that incorporates pairwise constraints can be formulated as a quadratic assignment problem (QAP), which is NP-complete and results in intrinsic computational difficulties. This paper presents a functional representation for graph matching (FRGM) that aims to provide more geometric insights on the problem and reduce the space and time complexities. To achieve these goals, we represent each graph by a linear function space equipped with a functional such as inner product or metric, that has an explicit geometric meaning. Consequently, the correspondence matrix between graphs can be represented as a linear representation map. Furthermore, this map can be reformulated as a new parameterization for matching graphs in Euclidean space such that it is consistent with graphs under rigid or nonrigid deformations. This allows us to estimate the correspondence matrix and geometric deformations simultaneously. We use the representation of edge-attributes rather than the affinity matrix to reduce the space complexity and propose an efficient optimization strategy to reduce the time complexity. The experimental results on both synthetic and real-world datasets show that the FRGM can achieve state-of-the-art performance.
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Ma J, Jiang X, Fan A, Jiang J, Yan J. Image Matching from Handcrafted to Deep Features: A Survey. Int J Comput Vis 2020. [DOI: 10.1007/s11263-020-01359-2] [Citation(s) in RCA: 230] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractAs a fundamental and critical task in various visual applications, image matching can identify then correspond the same or similar structure/content from two or more images. Over the past decades, growing amount and diversity of methods have been proposed for image matching, particularly with the development of deep learning techniques over the recent years. However, it may leave several open questions about which method would be a suitable choice for specific applications with respect to different scenarios and task requirements and how to design better image matching methods with superior performance in accuracy, robustness and efficiency. This encourages us to conduct a comprehensive and systematic review and analysis for those classical and latest techniques. Following the feature-based image matching pipeline, we first introduce feature detection, description, and matching techniques from handcrafted methods to trainable ones and provide an analysis of the development of these methods in theory and practice. Secondly, we briefly introduce several typical image matching-based applications for a comprehensive understanding of the significance of image matching. In addition, we also provide a comprehensive and objective comparison of these classical and latest techniques through extensive experiments on representative datasets. Finally, we conclude with the current status of image matching technologies and deliver insightful discussions and prospects for future works. This survey can serve as a reference for (but not limited to) researchers and engineers in image matching and related fields.
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Yang X, Liu ZY, Qiao H. A Continuation Method for Graph Matching Based Feature Correspondence. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2020; 42:1809-1822. [PMID: 30843819 DOI: 10.1109/tpami.2019.2903483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Feature correspondence lays the foundation for many computer vision and image processing tasks, which can be well formulated and solved by graph matching. Because of the high complexity, approximate methods are necessary for graph matching, and the continuous relaxation provides an efficient approximate scheme. But there are still many problems to be settled, such as the highly nonconvex objective function, the ignorance of the combinatorial nature of graph matching in the optimization process, and few attention to the outlier problem. Focusing on these problems, this paper introduces a continuation method directly targeting at the combinatorial optimization problem associated with graph matching. Specifically, first a regularization function incorporating the original objective function and the discrete constraints is proposed. Then a continuation method based on Gaussian smoothing is applied to it, in which the closed forms of relevant functions with respect to the outlier distribution are deduced. Experiments on both synthetic data and real world images validate the effectiveness of the proposed method.
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Deng C, Yuan X, Deng L, Chen J. Detecting Matching Blunders of Multi-Source Remote Sensing Images via Graph Theory. SENSORS 2020; 20:s20133712. [PMID: 32630824 PMCID: PMC7374350 DOI: 10.3390/s20133712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 11/26/2022]
Abstract
Large radiometric and geometric distortion in multi-source images leads to fewer matching points with high matching blunder ratios, and global geometric relationship models between multi-sensor images are inexplicit. Thus, traditional matching blunder detection methods cannot work effectively. To address this problem, we propose two matching blunder detection methods based on graph theory. The proposed methods can build statistically significant clusters in the case of few matching points with high matching blunder ratios, and use local geometric similarity constraints to detect matching blunders when the global geometric relationship is not explicit. The first method (named the complete graph-based method) uses clusters constructed by matched triangles in complete graphs to encode the local geometric similarity of images, and it can detect matching blunders effectively without considering the global geometric relationship. The second method uses the triangular irregular network (TIN) graph to approximate a complete graph to reduce to computational complexity of the first method. We name this the TIN graph-based method. Experiments show that the two graph-based methods outperform the classical random sample consensus (RANSAC)-based method in recognition rate, false rate, number of remaining matching point pairs, dispersion, positional accuracy in simulated and real data (image pairs from Gaofen1, near infrared ray of Gaofen1, Gaofen2, panchromatic Landsat, Ziyuan3, Jilin1and unmanned aerial vehicle). Notably, in most cases, the mean false rates of RANSAC, the complete graph-based method and the TIN graph-based method in simulated data experiments are 0.50, 0.26 and 0.14, respectively. In addition, the mean positional accuracy (RMSE measured in units of pixels) of the three methods is 2.6, 1.4 and 1.5 in real data experiments, respectively. Furthermore, when matching blunder ratio is no higher than 50%, the computation time of the TIN graph-based method is nearly equal to that of the RANSAC-based method, and roughly 2 to 40 times less than that of the complete graph-based method.
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Moyou M, Rangarajan A, Corring J, Peter AM. A Grassmannian Graph Approach to Affine Invariant Feature Matching. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2019; 29:3374-3387. [PMID: 31880551 DOI: 10.1109/tip.2019.2959722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this work, we present a novel, theoretical approach to address one of the longstanding problems in computer vision: 2D and 3D affine invariant feature matching. Our proposed Grassmannian Graph (GrassGraph) framework employs a two stage procedure that is capable of robustly recovering correspondences between two unorganized, affinely related feature (point) sets. In the ideal case, the first stage maps the feature sets to an affine invariant Grassmannian representation, where the features are mapped into the same subspace. It turns out that coordinate representations extracted from the Grassmannian differ by an arbitrary orthonormal matrix. In the second stage, by approximating the Laplace-Beltrami operator (LBO) on these coordinates, this extra orthonormal factor is nullified, providing true affine invariant coordinates which we then utilize to recover correspondences via simple mutual nearest neighbor relations. Our validation benchmarks use large number of experimental trials performed on 2D and 3D datasets. Experimental results show that the proposed GrassGraph method successfully recovers large affine transformations.
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Jiang B, Tang J, Luo B. Efficient Feature Matching via Nonnegative Orthogonal Relaxation. Int J Comput Vis 2019. [DOI: 10.1007/s11263-019-01185-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Ardeshir S, Borji A. Egocentric Meets Top-View. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2019; 41:1353-1366. [PMID: 29994045 DOI: 10.1109/tpami.2018.2832121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Thanks to the availability and increasing popularity of wearable devices such as GoPro cameras, smart phones, and glasses, we have access to a plethora of videos captured from first person perspective. Surveillance cameras and Unmanned Aerial Vehicles (UAVs) also offer tremendous amounts of video data recorded from top and oblique view points. Egocentric and surveillance vision have been studied extensively but separately in the computer vision community. The relationship between these two domains, however, remains unexplored. In this study, we make the first attempt in this direction by addressing two basic yet challenging questions. First, having a set of egocentric videos and a top-view surveillance video, does the top-view video contain all or some of the egocentric viewers? In other words, have these videos been shot in the same environment at the same time? Second, if so, can we identify the egocentric viewers in the top-view video? These problems can become extremely challenging when videos are not temporally aligned. Each view, egocentric or top, is modeled by a graph and the assignment and time-delays are computed iteratively using the spectral graph matching framework. We evaluate our method in terms of ranking and assigning egocentric viewers to identities present in the top-view video over a dataset of 50 top-view and 188 egocentric videos captured under different conditions. We also evaluate the capability of our proposed approaches in terms of temporal alignment. The experiments and results demonstrate the capability of the proposed approaches in terms of jointly addressing the temporal alignment and assignment tasks.
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A Review of Point Set Registration: From Pairwise Registration to Groupwise Registration. SENSORS 2019; 19:s19051191. [PMID: 30857205 PMCID: PMC6427196 DOI: 10.3390/s19051191] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/25/2019] [Accepted: 03/05/2019] [Indexed: 01/08/2023]
Abstract
This paper presents a comprehensive literature review on point set registration. The state-of-the-art modeling methods and algorithms for point set registration are discussed and summarized. Special attention is paid to methods for pairwise registration and groupwise registration. Some of the most prominent representative methods are selected to conduct qualitative and quantitative experiments. From the experiments we have conducted on 2D and 3D data, CPD-GL pairwise registration algorithm and JRMPC groupwise registration algorithm seem to outperform their rivals both in accuracy and computational complexity. Furthermore, future research directions and avenues in the area are identified.
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Wang T, Ling H, Lang C, Feng S. Graph Matching with Adaptive and Branching Path Following. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2018; 40:2853-2867. [PMID: 29989966 DOI: 10.1109/tpami.2017.2767591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Graph matching aims at establishing correspondences between graph elements, and is widely used in many computer vision tasks. Among recently proposed graph matching algorithms, those utilizing the path following strategy have attracted special research attentions due to their exhibition of state-of-the-art performances. However, the paths computed in these algorithms often contain singular points, which could hurt the matching performance if not dealt properly. To deal with this issue, we propose a novel path following strategy, named branching path following (BPF), to improve graph matching accuracy. In particular, we first propose a singular point detector by solving a KKT system, and then design a branch switching method to seek for better paths at singular points. Moreover, to reduce the computational burden of the BPF strategy, an adaptive path estimation (APE) strategy is integrated into BPF to accelerate the convergence of searching along each path. A new graph matching algorithm named ABPF-G is developed by applying APE and BPF to a recently proposed path following algorithm named GNCCP (Liu & Qiao 2014). Experimental results reveal how our approach consistently outperforms state-of-the-art algorithms for graph matching on five public benchmark datasets.
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Yang X, Qiao H, Liu ZY. An Algorithm for Finding the Most Similar Given Sized Subgraphs in Two Weighted Graphs. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2018; 29:3295-3300. [PMID: 28692989 DOI: 10.1109/tnnls.2017.2712794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We propose a weighted common subgraph (WCS) matching algorithm to find the most similar subgraphs in two labeled weighted graphs. WCS matching, as a natural generalization of equal-sized graph matching and subgraph matching, has found wide applications in many computer vision and machine learning tasks. In this brief, WCS matching is first formulated as a combinatorial optimization problem over the set of partial permutation matrices. Then, it is approximately solved by a recently proposed combinatorial optimization framework-graduated nonconvexity and concavity procedure. Experimental comparisons on both synthetic graphs and real-world images validate its robustness against noise level, problem size, outlier number, and edge density.
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Hu W, Wu B, Wang P, Yuan C, Li Y, Maybank S. Context-Dependent Random Walk Graph Kernels and Tree Pattern Graph Matching Kernels with Applications to Action Recognition. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2018; 27:5060-5075. [PMID: 29994476 DOI: 10.1109/tip.2018.2849885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Graphs are effective tools for modeling complex data. Setting out from two basic substructures, random walks and trees, we propose a new family of context-dependent random walk graph kernels and a new family of tree pattern graph matching kernels. In our context-dependent graph kernels, context information is incorporated into primary random walk groups. A multiple kernel learning algorithm with a proposed l1,2-norm regularization is applied to combine context-dependent graph kernels of different orders. This improves the similarity measurement between graphs. In our tree-pattern graph matching kernel, a quadratic optimization with a sparse constraint is proposed to select the correctly matched tree-pattern groups. This augments the discriminative power of the tree-pattern graph matching. We apply the proposed kernels to human action recognition, where each action is represented by two graphs which record the spatiotemporal relations between local feature vectors. Experimental comparisons with state-of-the-art algorithms on several benchmark datasets demonstrate the effectiveness of the proposed kernels for recognizing human actions. It is shown that our kernel based on tree-pattern groups, which have more complex structures and exploit more local topologies of graphs than random walks, yields more accurate results but requires more runtime than the context-dependent walk graph kernel.
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Abstract
Establishing correspondence between point sets lays the foundation for many computer vision and pattern recognition tasks. It can be well defined and solved by graph matching. However, outliers may significantly deteriorate its performance, especially when outliers exist in both point sets and meanwhile the inlier number is unknown. In this paper, we propose an adaptive graph matching algorithm to tackle this problem. Specifically, a novel formulation is proposed to make the graph matching model adaptively determine the number of inliers and match them, then by relaxing the discrete domain to its convex hull the discrete optimization problem is relaxed to be a continuous one, and finally a graduated projection scheme is used to get a discrete matching solution. Consequently, the proposed algorithm could realize inlier number estimation, inlier selection, and inlier matching in one optimization framework. Experiments on both synthetic data and real world images witness the effectiveness of the proposed algorithm.
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Yang X, Liu ZY, Qiao H, Song YB, Ren SN, Ji DX, Zheng SW. Underwater image matching by incorporating structural constraints. INT J ADV ROBOT SYST 2017. [DOI: 10.1177/1729881417738100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Xu Yang
- State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Zhi-Yong Liu
- State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Hong Qiao
- State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yong-Bo Song
- State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Shu-Nan Ren
- State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Da-Xiong Ji
- Ocean College, Zhejiang University, Zhoushan, Peoples’s Republic of China
| | - Sui-Wu Zheng
- State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Huizhou Advanced Manufacturing Technology Research Center Co., Ltd, Huizhou, People’s Republic of China
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Yang X, Liu ZY, Qiao H, Su JH. Probabilistic hypergraph matching based on affinity tensor updating. Neurocomputing 2017. [DOI: 10.1016/j.neucom.2016.12.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
The recent proliferation in mobile touch-based devices paves the way for increasingly efficient, easy to use natural user interfaces (NUI). Unfortunately, touch-based NUIs might prove difficult, or even impossible to operate, in certain conditions e.g. when suffering from motor dysfunction such as Parkinson’s Disease (PD). Yet, the prevalence of such devices makes them particularly suitable for acquiring motor function data, and enabling the early detection of PD symptoms and other conditions. In this work we acquired a unique database of more than 12,500 annotated NUI multi-touch gestures, collected from PD patients and healthy volunteers, that were analyzed by applying advanced shape analysis and statistical inference schemes. The proposed analysis leads to a novel detection scheme for early stages of PD. Moreover, our computational analysis revealed that young subjects may be using a ‘slang’ form of gesture-making to reduce effort and attention cost while maintaining meaning, whereas older subjects put an emphasis on content and precise performance.
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Kazemi E, Hassani H, Grossglauser M, Pezeshgi Modarres H. PROPER: global protein interaction network alignment through percolation matching. BMC Bioinformatics 2016; 17:527. [PMID: 27955623 PMCID: PMC5153870 DOI: 10.1186/s12859-016-1395-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 11/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PPI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging. RESULTS In this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria. CONCLUSIONS We highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch .
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Affiliation(s)
- Ehsan Kazemi
- School of Computer and Communication Sciences, EPFL, Lausanne, Switzerland.
| | - Hamed Hassani
- Department of Computer Science, ETHZ, Zurich, Switzerland
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Heimowitz A, Keller Y. Image Segmentation via Probabilistic Graph Matching. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2016; 25:4743-4752. [PMID: 27416599 DOI: 10.1109/tip.2016.2590832] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This paper presents an unsupervised and semi-automatic image segmentation approach where we formulate the segmentation as an inference problem based on unary and pairwise assignment probabilities computed using low-level image cues. The inference is solved via a probabilistic graph matching scheme, which allows rigorous incorporation of low-level image cues and automatic tuning of parameters. The proposed scheme is experimentally shown to compare favorably with contemporary semi-supervised and unsupervised image segmentation schemes, when applied to contemporary state-of-the-art image sets.
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Zhou F, de la Torre F. Factorized Graph Matching. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2016; 38:1774-1789. [PMID: 26595909 DOI: 10.1109/tpami.2015.2501802] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Graph matching (GM) is a fundamental problem in computer science, and it plays a central role to solve correspondence problems in computer vision. GM problems that incorporate pairwise constraints can be formulated as a quadratic assignment problem (QAP). Although widely used, solving the correspondence problem through GM has two main limitations: (1) the QAP is NP-hard and difficult to approximate; (2) GM algorithms do not incorporate geometric constraints between nodes that are natural in computer vision problems. To address aforementioned problems, this paper proposes factorized graph matching (FGM). FGM factorizes the large pairwise affinity matrix into smaller matrices that encode the local structure of each graph and the pairwise affinity between edges. Four are the benefits that follow from this factorization: (1) There is no need to compute the costly (in space and time) pairwise affinity matrix; (2) The factorization allows the use of a path-following optimization algorithm, that leads to improved optimization strategies and matching performance; (3) Given the factorization, it becomes straight-forward to incorporate geometric transformations (rigid and non-rigid) to the GM problem. (4) Using a matrix formulation for the GM problem and the factorization, it is easy to reveal commonalities and differences between different GM methods. The factorization also provides a clean connection with other matching algorithms such as iterative closest point; Experimental results on synthetic and real databases illustrate how FGM outperforms state-of-the-art algorithms for GM. The code is available at http://humansensing.cs.cmu.edu/fgm.
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Yan J, Cho M, Zha H, Yang X, Chu SM. Multi-Graph Matching via Affinity Optimization with Graduated Consistency Regularization. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2016; 38:1228-1242. [PMID: 26372208 DOI: 10.1109/tpami.2015.2477832] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This paper addresses the problem of matching common node correspondences among multiple graphs referring to an identical or related structure. This multi-graph matching problem involves two correlated components: i) the local pairwise matching affinity across pairs of graphs; ii) the global matching consistency that measures the uniqueness of the pairwise matchings by different composition orders. Previous studies typically either enforce the matching consistency constraints in the beginning of an iterative optimization, which may propagate matching error both over iterations and across graph pairs; or separate affinity optimization and consistency enforcement into two steps. This paper is motivated by the observation that matching consistency can serve as a regularizer in the affinity objective function especially when the function is biased due to noises or inappropriate modeling. We propose composition-based multi-graph matching methods to incorporate the two aspects by optimizing the affinity score, meanwhile gradually infusing the consistency. We also propose two mechanisms to elicit the common inliers against outliers. Compelling results on synthetic and real images show the competency of our algorithms.
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Yan J, Wang J, Zha H, Yang X, Chu S. Consistency-driven alternating optimization for multigraph matching: a unified approach. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2015; 24:994-1009. [PMID: 25576568 DOI: 10.1109/tip.2014.2387386] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The problem of graph matching (GM) in general is nondeterministic polynomial-complete and many approximate pairwise matching techniques have been proposed. For a general setting in real applications, it typically requires to find the consistent matching across a batch of graphs. Sequentially performing pairwise matching is prone to error propagation along the pairwise matching sequence, and the sequences generated in different pairwise matching orders can lead to contradictory solutions. Motivated by devising a robust and consistent multiple-GM model, we propose a unified alternating optimization framework for multi-GM. In addition, we define and use two metrics related to graphwise and pairwise consistencies. The former is used to find an appropriate reference graph, which induces a set of basis variables and launches the iteration procedure. The latter defines the order in which the considered graphs in the iterations are manipulated. We show two embodiments under the proposed framework that can cope with the nonfactorized and factorized affinity matrix, respectively. Our multi-GM model has two major characters: 1) the affinity information across multiple graphs are explored in each iteration by fixing part of the matching variables via a consistency-driven mechanism and 2) the framework is flexible to incorporate various existing pairwise GM solvers in an out-of-box fashion, and also can proceed with the output of other multi-GM methods. The experimental results on both synthetic data and real images empirically show that the proposed framework performs competitively with the state-of-the-art.
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Cai Z, Wen L, Lei Z, Vasconcelos N, Li SZ. Robust deformable and occluded object tracking with dynamic graph. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2014; 23:5497-5509. [PMID: 25350927 DOI: 10.1109/tip.2014.2364919] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
While some efforts have been paid to handle deformation and occlusion in visual tracking, they are still great challenges. In this paper, a dynamic graph-based tracker (DGT) is proposed to address these two challenges in a unified framework. In the dynamic target graph, nodes are the target local parts encoding appearance information, and edges are the interactions between nodes encoding inner geometric structure information. This graph representation provides much more information for tracking in the presence of deformation and occlusion. The target tracking is then formulated as tracking this dynamic undirected graph, which is also a matching problem between the target graph and the candidate graph. The local parts within the candidate graph are separated from the background with Markov random field, and spectral clustering is used to solve the graph matching. The final target state is determined through a weighted voting procedure according to the reliability of part correspondence, and refined with recourse to a foreground/background segmentation. An effective online updating mechanism is proposed to update the model, allowing DGT to robustly adapt to variations of target structure. Experimental results show improved performance over several state-of-the-art trackers, in various challenging scenarios.
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Liu F, Yang G, Yin Y, Wang S. Singular value decomposition based minutiae matching method for finger vein recognition. Neurocomputing 2014. [DOI: 10.1016/j.neucom.2014.05.069] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Liu ZY, Qiao H. GNCCP-Graduated NonConvexityand Concavity Procedure. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2014; 36:1258-1267. [PMID: 26353285 DOI: 10.1109/tpami.2013.223] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this paper we propose the graduated nonconvexity and concavity procedure (GNCCP) as a general optimization framework to approximately solve the combinatorial optimization problems defined on the set of partial permutation matrices. GNCCP comprises two sub-procedures, graduated nonconvexity which realizes a convex relaxation and graduated concavity which realizes a concave relaxation. It is proved that GNCCP realizes exactly a type of convex-concave relaxation procedure (CCRP), but with a much simpler formulation without needing convex or concave relaxation in an explicit way. Actually, GNCCP involves only the gradient of the objective function and is therefore very easy to use in practical applications. Two typical related NP-hard problems, partial graph matching and quadratic assignment problem (QAP), are employed to demonstrate its simplicity and state-of-the-art performance.
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Feldman-Haber S, Keller Y. A probabilistic graph-based framework for plug-and-play multi-cue visual tracking. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2014; 23:2291-2301. [PMID: 24818248 DOI: 10.1109/tip.2014.2312286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this paper, we propose a novel approach for integrating multiple tracking cues within a unified probabilistic graph-based Markov random fields (MRFs) representation. We show how to integrate temporal and spatial cues encoded by unary and pairwise probabilistic potentials. As the inference of such high-order MRF models is known to be NP-hard, we propose an efficient spectral relaxation-based inference scheme. The proposed scheme is exemplified by applying it to a mixture of five tracking cues, and is shown to be applicable to wider sets of cues. This paves the way for a modular plug-and-play tracking framework that can be easily adapted to diverse tracking scenarios. The proposed scheme is experimentally shown to compare favorably with contemporary state-of-the-art schemes, and provides accurate tracking results.
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Liu ZY, Qiao H, Yang X, Hoi SCH. Graph Matching by Simplified Convex-Concave Relaxation Procedure. Int J Comput Vis 2014. [DOI: 10.1007/s11263-014-0707-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Chertok M, Keller Y. Efficient high order matching. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2010; 32:2205-2215. [PMID: 20975118 DOI: 10.1109/tpami.2010.51] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present a computational approach to high-order matching of data sets in IR(d). Those are matchings based on data affinity measures that score the matching of more than two pairs of points at a time. High-order affinities are represented by tensors and the matching is then given by a rank-one approximation of the affinity tensor and a corresponding discretization. Our approach is rigorously justified by extending Zass and Shashua's hypergraph matching to high-order spectral matching. This paves the way for a computationally efficient dual-marginalization spectral matching scheme. We also show that, based on the spectral properties of random matrices, affinity tensors can be randomly sparsified while retaining the matching accuracy. Our contributions are experimentally validated by applying them to synthetic as well as real data sets.
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Affiliation(s)
- Michael Chertok
- School of Engineering, Bar-Ilan University, Ramat Gan, Israel.
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