@inproceedings{d9dcefc8afe444d0acf5115136d571a7,
title = "Algorithms for regular tree grammar network search and their application to mining human-viral infection patterns",
abstract = "Network querying is a powerful approach to mine molecular interaction networks. Most network querying tools support queries in the form of a template sub-network, in case of topology-constrained queries, or a set of colored vertices in case of topology-free queries. A third approach is grammar-based queries, which are more flexible and expressive as they allow the addition of logic rules to the query. Previous grammar-based querying tools defined queries via string grammars and identified paths in graphs. In this paper, we extend the scope of grammar-based queries to regular tree grammar (RTG), and the scope of the identified sub-graphs from paths to trees. We introduce a new problem and propose a novel algorithm to search a given graph for the k highest scoring sub-graphs matching a tree accepted by an RTG. Our algorithm is based on dynamic programming and combines an extension to k-best parsing optimization with color coding. We implement the new algorithm and exemplify its application to mining the human-viral interaction network. Our code is available at http://www.cs.bgu.ac.il/~smolyi/RTGnet/.",
author = "Ilan Smoly and Amir Carmel and Yonat Shemer-Avni and Esti Yeger-Lotem and Michal Ziv-Ukelson",
note = "Funding Information: We thank the anonymous WABI referees for their many helpful comments.The work of Ilan Smoly, Amir Carmel and Michal Ziv-Ukelson was partially supported by the Frankel Center for Computer Science at Ben Gurion University of the Negev and by the Israel Science Foundation (ISF 179/14). Publisher Copyright: {\textcopyright} Springer International Publishing Switzerland 2015.; 15th International Workshop on Algorithms in Bioinformatics, WABI 2015 ; Conference date: 10-09-2015 Through 12-09-2015",
year = "2015",
month = jan,
day = "1",
doi = "https://doi.org/10.1007/978-3-662-48221-6_4",
language = "American English",
isbn = "9783662482209",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer Verlag",
pages = "53--65",
editor = "Mihai Pop and H{\'e}l{\`e}ne Touzet",
booktitle = "Algorithms in Bioinformatics - 15th International Workshop, WABI 2015, Proceedings",
address = "Germany",
}