Dataset Information

Incorporating User Interaction and Topological Constraints within Contour Completion via Discrete Calculus.

ABSTRACT: We study the problem of interactive segmentation and contour completion for multiple objects. The form of constraints our model incorporates are those coming from user scribbles (interior or exterior constraints) as well as information regarding the topology of the 2-D space after partitioning (number of closed contours desired). We discuss how concepts from discrete calculus and a simple identity using the Euler characteristic of a planar graph can be utilized to derive a practical algorithm for this problem. We also present specialized branch and bound methods for the case of single contour completion under such constraints. On an extensive dataset of ~ 1000 images, our experiments suggest that a small amount of side knowledge can give strong improvements over fully unsupervised contour completion methods. We show that by interpreting user indications topologically, user effort is substantially reduced.

SUBMITTER: Xu J

PROVIDER: S-EPMC8118905 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

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Publications

Incorporating User Interaction and Topological Constraints within Contour Completion via Discrete Calculus.

Xu Jia J Collins Maxwell D MD Singh Vikas V

Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition 20130601

We study the problem of interactive segmentation and contour completion for multiple objects. The form of constraints our model incorporates are those coming from user scribbles (interior or exterior constraints) as well as information regarding the topology of the 2-D space after partitioning (number of closed contours desired). We discuss how concepts from discrete calculus and a simple identity using the Euler characteristic of a planar graph can be utilized to derive a practical algorithm fo ...[more]

PMID: 33994765

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Project description:BackgroundDiscovering robust markers for cancer prognosis based on gene expression data is an important yet challenging problem in translational bioinformatics. By integrating additional information in biological pathways or a protein-protein interaction (PPI) network, we can find better biomarkers that lead to more accurate and reproducible prognostic predictions. In fact, recent studies have shown that, "modular markers," that integrate multiple genes with potential interactions can improve disease classification and also provide better understanding of the disease mechanisms.ResultsIn this work, we propose a novel algorithm for finding robust and effective subnetwork markers that can accurately predict cancer prognosis. To simultaneously discover multiple synergistic subnetwork markers in a human PPI network, we build on our previous work that uses affinity propagation, an efficient clustering algorithm based on a message-passing scheme. Using affinity propagation, we identify potential subnetwork markers that consist of discriminative genes that display coherent expression patterns and whose protein products are closely located on the PPI network. Furthermore, we incorporate the topological information from the PPI network to evaluate the potential of a given set of proteins to be involved in a functional module. Primarily, we adopt widely made assumptions that densely connected subnetworks may likely be potential functional modules and that proteins that are not directly connected but interact with similar sets of other proteins may share similar functionalities.ConclusionsIncorporating topological attributes based on these assumptions can enhance the prediction of potential subnetwork markers. We evaluate the performance of the proposed subnetwork marker identification method by performing classification experiments using multiple independent breast cancer gene expression datasets and PPI networks. We show that our method leads to the discovery of robust subnetwork markers that can improve cancer classification.

Dataset Information

Incorporating User Interaction and Topological Constraints within Contour Completion via Discrete Calculus.

Publications

Incorporating User Interaction and Topological Constraints within Contour Completion via Discrete Calculus.

Similar Datasets

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