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QuateXelero: An Accelerated Exact Network Motif Detection Algorithm

Publication Date: July 18, 2013
Journal: PLOS ONE
Authors: Sahand Khakabimamaghani, Iman Sharafuddin, Norbert Dichter, Ina Koch, et al
Volume: 8
Issue: 7
Pages: e68073
DOI: https://dx.plos.org/10.1371/journal.pone.0068073
Publisher URL: http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0068073
PubMed: http://www.ncbi.nlm.nih.gov/pubmed/23874498
PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715482
Europe PMC: http://europepmc.org/abstract/MED/23874498
Web of Science: 000324146200012
Scopus: 84880408672
Mendeley: http://www.mendeley.com/research/quatexelero-accelerated-exact-network-motif-detection-algorithm

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Mendeley 2401 May 03:20 UTC

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{"title"=>"QuateXelero: An Accelerated Exact Network Motif Detection Algorithm", "type"=>"journal", "authors"=>[{"first_name"=>"Sahand", "last_name"=>"Khakabimamaghani", "scopus_author_id"=>"36470368600"}, {"first_name"=>"Iman", "last_name"=>"Sharafuddin", "scopus_author_id"=>"36523940300"}, {"first_name"=>"Norbert", "last_name"=>"Dichter", "scopus_author_id"=>"55767307100"}, {"first_name"=>"Ina", "last_name"=>"Koch", "scopus_author_id"=>"7006792171"}, {"first_name"=>"Ali", "last_name"=>"Masoudi-Nejad", "scopus_author_id"=>"55911393500"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23874498", "sgr"=>"84880408672", "doi"=>"10.1371/journal.pone.0068073", "scopus"=>"2-s2.0-84880408672", "pui"=>"369379091", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"8cdc743b-940f-3cc1-9755-72955dd8e367", "abstract"=>"Finding motifs in biological, social, technological, and other types of networks has become a widespread method to gain more knowledge about these networks' structure and function. However, this task is very computationally demanding, because it is highly associated with the graph isomorphism which is an NP problem (not known to belong to P or NP-complete subsets yet). Accordingly, this research is endeavoring to decrease the need to call NAUTY isomorphism detection method, which is the most time-consuming step in many existing algorithms. The work provides an extremely fast motif detection algorithm called QuateXelero, which has a Quaternary Tree data structure in the heart. The proposed algorithm is based on the well-known ESU (FANMOD) motif detection algorithm. The results of experiments on some standard model networks approve the overal superiority of the proposed algorithm, namely QuateXelero, compared with two of the fastest existing algorithms, G-Tries and Kavosh. QuateXelero is especially fastest in constructing the central data structure of the algorithm from scratch based on the input network.", "link"=>"http://www.mendeley.com/research/quatexelero-accelerated-exact-network-motif-detection-algorithm", "reader_count"=>22, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>8, "Student > Master"=>4, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>8, "Student > Master"=>4, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Mathematics"=>4, "Agricultural and Biological Sciences"=>5, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>1, "Computer Science"=>6}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Computer Science"=>{"Computer Science"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Mathematics"=>{"Mathematics"=>4}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Turkey"=>1, "Iran"=>1, "United Kingdom"=>1, "Slovenia"=>1}, "group_count"=>2}

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Figshare 23610 May 18:54 UTC

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{"files"=>["https://ndownloader.figshare.com/files/1121664"], "description"=>"Experimental Limitations.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks"], "article_id"=>747716, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.t008", "stats"=>{"downloads"=>4, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Experimental_Limitations_/747716", "title"=>"Experimental Limitations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121646"], "description"=>"The root node and internal nodes have at most four children.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks", "quaternary"], "article_id"=>747699, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.g001", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_quaternary_tree_of_depth_3_/747699", "title"=>"An example quaternary tree of depth 3.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121647"], "description"=>"Searching starts at the root of the tree. After respectively visiting children 3 and 2 throughout the path, the search finishes in a newly added leaf, corresponding to number 1.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks", "quaternary"], "article_id"=>747700, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.g002", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Searching_a_sample_quaternary_tree_for_input_string_8220_321_8221_/747700", "title"=>"Searching a sample quaternary tree for input string “321”.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121649"], "description"=>"In this figure, −1 indicates one way connection from the existing vertex to added vertex, 0 indicates no connection between them, 1 stands for a one way connection in the reverse direction, and 2 shows a two way connection. The order of numbers in the input string is the same order as the corresponding vertices are added during expanding the subgraph (that is 1, 2, 3, and then 4 in this example).", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks", "taken", "quaternary", "expanding"], "article_id"=>747702, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Steps_taken_to_search_the_quaternary_tree_during_expanding_enumerating_a_sample_subgraph_/747702", "title"=>"Steps taken to search the quaternary tree during expanding (enumerating) a sample subgraph.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121650"], "description"=>"1) The quaternary tree is searched and the new leaf is added 2) Because the leaf is new and its pointers is not set, NAUTY is executed for the subgraph being enumerated 3) After finding the canonical label for the subgraph, the binary tree is searched using that label and the corresponding leaf in the binary tree is identified 4) The subgraph counter of that leaf (which indicates the number of subgraph of that class found so far in the network) is increase one unit 5) The pointer of the leaf of quaternary tree is set to the identified leaf of the Binary Tree.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks", "taken", "classifying", "quaternary"], "article_id"=>747703, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.g004", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Steps_taken_during_classifying_a_subgraph_in_which_a_new_leaf_is_added_to_the_quaternary_tree_/747703", "title"=>"Steps taken during classifying a subgraph, in which a new leaf is added to the quaternary tree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121651"], "description"=>"1) The quaternary tree is searched and the corresponding leaf is identified 2) Using the identified leaf’s pointer to the corresponding leaf from binary tree, the latter’s counter is augmented.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks", "taken", "classifying", "subgraph", "reached", "quaternary"], "article_id"=>747704, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.g005", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Steps_taken_during_classifying_a_subgraph_which_has_reached_a_previously_existing_leaf_in_the_quaternary_tree_/747704", "title"=>"Steps taken during classifying a subgraph which has reached a previously existing leaf in the quaternary tree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121652"], "description"=>"In the charts, the horizontal axis indicates the size of motif and the vertical axis is the log of running time. The bases of logarithms are set to integer numbers close to the average running time growth rates shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068073#pone-0068073-t005\" target=\"_blank\">Table 5</a> for each network. The growing gaps are more visible in the charts for Yeast, Electronic, and E.coli networks.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks", "times", "kavosh"], "article_id"=>747705, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.g006", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Growing_gap_between_the_running_times_of_Kavosh_and_QuateXelero_/747705", "title"=>"Growing gap between the running times of Kavosh and QuateXelero.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121653"], "description"=>"Positive and negative equality points are illustrated respectively in the left and the right charts. The vertical axis t indicates the total time of algorithms and the horizontal axis r shows the number of random networks used for motif detection.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks"], "article_id"=>747706, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.g007", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_concept_of_Equality_Point_/747706", "title"=>"The concept of Equality Point.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121655"], "description"=>"Numbers in the parenthesis show the size of the motif for which the experiments are conducted (the results can be generalized to other motif sizes). The vertical axis indicates the ratio (in percentage) of run time to the run time for 20 random networks. Except Yeast, the other networks exhibit a decline in the random network census time for the successive random networks.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks", "networks", "census"], "article_id"=>747707, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.g008", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_number_of_random_networks_on_average_time_of_census_on_a_single_random_network_/747707", "title"=>"Effect of number of random networks on average time of census on a single random network.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121656"], "description"=>"The ratio in the left chart indicates the ratio of average time spent by QuateXelero for census on random networks to the same time required for G-Tries.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks", "census", "undirected"], "article_id"=>747708, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.g009", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trends_of_random_network_census_time_ratio_left_and_Equality_Point_right_for_undirected_networks_/747708", "title"=>"Trends of random network census time ratio (left) and Equality Point (right) for undirected networks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121657"], "description"=>"Experimental Results for QuateXelero vs. Kavosh.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks", "quatexelero"], "article_id"=>747709, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.t004", "stats"=>{"downloads"=>6, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Experimental_Results_for_QuateXelero_vs_Kavosh_/747709", "title"=>"Experimental Results for QuateXelero vs. Kavosh.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121658"], "description"=>"10, 100, 100, and 100 random networks were used respectively for Yeast, Social, E.coli, and Electronic networks.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks", "g-tries", "smaller"], "article_id"=>747710, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.t005", "stats"=>{"downloads"=>5, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_QuateXelero_QX_vs_G_Tries_in_smaller_motifs_/747710", "title"=>"QuateXelero (QX) vs. G-Tries in smaller motifs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-18 01:40:29"}
{"files"=>["https://ndownloader.figshare.com/files/1121659"], "description"=>"5 random networks were used in all experiments. Bolded italic values for Yeast network are estimated with respect to the results in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068073#pone-0068073-t005\" target=\"_blank\">Table 5</a>.", "links"=>[], "tags"=>["Computational biology", "Metabolic networks", "Model organisms", "Prokaryotic models", "Escherichia coli", "Yeast and fungal models", "Saccharomyces cerevisiae", "Computer applications", "Computer-aided design", "Computer modeling", "Computing methods", "Programming languages", "Applied mathematics", "algorithms", "Sociology", "social networks", "g-tries", "larger"], "article_id"=>747711, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Sociology"], "users"=>["Sahand Khakabimamaghani", "Iman Sharafuddin", "Norbert Dichter", "Ina Koch", "Ali Masoudi-Nejad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0068073.t006", "stats"=>{"downloads"=>7, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_QuateXelero_QX_vs_G_Tries_in_larger_motifs_/747711", "title"=>"QuateXelero (QX) vs. G-Tries in larger motifs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-18 01:40:29"}

PMC Usage Stats 45317 Feb 19:28 UTC

PMC Usage Stats | Further Information

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Relative Metric 8935910 May 16:54 UTC

Relative Metric

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F1000Prime24 Feb 12:37 UTC

F1000Prime

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