PyGTED: Python Application for Computing Graph Traversal Edit Distance

Journal of computational biology

article

Ali Ebrahimpour Boroojeny¹  Akash Shrestha¹  Ali Sharifi-zarchi²  Suzanne Renick Gallagher¹  Süleyman Cenk Sahinalp³  Hamidreza Chitsaz¹ 

[1] Department of Computer Science, Colorado State University;Department of Computer Engineering, Sharif University of Technology;National Cancer Institute

关键词: clustering genera;    coassembly;    de novo variation detaction;    graph comparison;    graph kernel;    linear programming.;   

DOI  :  10.1089/cmb.2019.0510

来源: Mary Ann Liebert, Inc. Publishers

【 摘 要 】

Graph Traversal Edit Distance (GTED) is a measure of distance (or dissimilarity) between two graphs introduced. This measure is based on the minimum edit distance between two strings formed by the edge labels of respective Eulerian traversals of the two graphs. GTED was motivated by and provides the first mathematical formalism for sequence coassembly and de novo variation detection in bioinformatics. Many problems in applied machine learning deal with graphs (also called networks), including social networks, security, web data mining, protein function prediction, and genome informatics. The kernel paradigm beautifully decouples the learning algorithm from the underlying geometric space, which renders graph kernels important for the aforementioned applications. In this article, we introduce a tool, PyGTED to compute GTED. It implements the algorithm based on the polynomial time algorithm devised for it by the authors. Informally, the GTED is the minimum edit distance between two strings formed by the edge labels of respective Eulerian traversals of the two graphs.

【 授权许可】

Unknown