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Faster Biclique Mining in Near-Bipartite Graphs [article]

Blair D. Sullivan, Andrew van der Poel, Trey Woodlief
2019 arXiv   pre-print
Identifying dense bipartite subgraphs is a common graph data mining task.  ...  whose deletion results in a bipartite graph.  ...  In these "near-bipartite" synthetic graphs, Enum-MIB unsurprisingly is slowest on most instances.  ... 
arXiv:1903.01538v1 fatcat:r3h25ruh5jalxb72k7bjwfvchm

Mining Maximal Induced Bicliques using Odd Cycle Transversals [article]

Kyle Kloster, Blair D. Sullivan, Andrew van der Poel
2019 arXiv   pre-print
When the graph being searched is itself bipartite, Zhang et al. give a faster algorithm where the time per MIB depends on the number of edges in the graph.  ...  In biological applications, the natural model for these dense substructures is often a complete bipartite graph (biclique), and the problem requires enumerating all maximal bicliques (instead of just identifying  ...  Introduction Bicliques (complete bipartite graphs) naturally arise in many data mining applications, including detecting cyber communities [19] , data compression [2] , epidemiology [25] , artificial  ... 
arXiv:1810.11421v2 fatcat:vjvsxeghm5bc7gfy3rlip4trvy

Efficient Exact Algorithms for Maximum Balanced Biclique Search in Bipartite Graphs [article]

Lu Chen, Chengfei Liu, Rui Zhou, Jiajie Xu, Jianxin Li
2020 arXiv   pre-print
This algorithm in fact can find an MBB in near polynomial time for dense bipartite graphs that are common for applications such as VLSI design.  ...  Given a bipartite graph, the maximum balanced biclique (MBB) problem, discovering a mutually connected while equal-sized disjoint sets with the maximum cardinality, plays a significant role for mining  ...  This algorithm in fact can find an MBB in near polynomial time for dense bipartite graphs that are common for applications such as VLSI design.  ... 
arXiv:2007.08836v1 fatcat:dkfq624d6vfb5lzgpqcy5yxgc4

Scalable Large Near-Clique Detection in Large-Scale Networks via Sampling

Michael Mitzenmacher, Jakub Pachocki, Richard Peng, Charalampos Tsourakakis, Shen Chen Xu
2015 Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining - KDD '15  
Extracting dense subgraphs from large graphs is a key primitive in a variety of graph mining applications, ranging from mining social networks and the Web graph to bioinformatics [41] .  ...  We also extend this family of formulations to bipartite graphs by introducing the (p, q)-biclique densest subgraph problem ((p,q)-Biclique-DSP), and devise an exact algorithm that can treat both clique  ...  Acknowledgments Michael Mitzenmacher was supported in part by NSF grants IIS-0964473, CNS-1228598, and CCF-1320231. Jakub Pachocki and Shen Chen Xu were supported in part by NSF grant CCF-1065106.  ... 
doi:10.1145/2783258.2783385 dblp:conf/kdd/MitzenmacherPPT15 fatcat:gmn7sydbezhx3etolrwjameehu

Incremental Maintenance of Maximal Bicliques in a Dynamic Bipartite Graph

Apurba Das, Srikanta Tirthapura
2018 IEEE Transactions on Multi-Scale Computing Systems  
In this work, we present (1)~Near-tight bounds on the magnitude of change in the set of maximal bicliques of a graph, due to a change in the edge set, and an (2)~Incremental algorithm for enumerating the  ...  We consider incremental maintenance of maximal bicliques from a dynamic bipartite graph that changes over time due to the addition of edges.  ...  We present near-tight bounds on the maximum possible change in the set of maximal bicliques, due to a change in the set of edges in the graph.  ... 
doi:10.1109/tmscs.2018.2802920 fatcat:276ms4jthzhzbnbpnaurakng4i

On Finding Dense Subgraphs in Bipartite Graphs: Linear Algorithms [article]

Yikun Ban
2018 arXiv   pre-print
In this paper, we focus on mining dense subgraphs in a bipartite graph.  ...  Detecting dense subgraphs from large graphs is a core component in many applications, ranging from social networks mining, bioinformatics.  ...  In this paper, we focus on mining dense subgraphs in a bipartite graph.  ... 
arXiv:1810.06809v3 fatcat:mbschco44nbfzg7zrec27pwwym

A Change-Sensitive Algorithm for Maintaining Maximal Bicliques in a Dynamic Bipartite Graph [article]

Apurba Das, Srikanta Tirthapura
2017 arXiv   pre-print
In this work, we present (1) near-tight bounds on the magnitude of change in the set of maximal bicliques of a graph, due to a change in the edge set (2) a "change-sensitive" algorithm for enumerating  ...  We consider the maintenance of maximal bicliques from a dynamic bipartite graph that changes over time due to the addition or deletion of edges.  ...  We present near-tight bounds on the maximum possible change in the set of maximal bicliques, due to a change in the set of edges in the graph.  ... 
arXiv:1707.08272v1 fatcat:3ll7sqosbbcevk7mkgdhqxx6aa

Enumerating Maximal Bicliques from a Large Graph using MapReduce [article]

Arko Provo Mukherjee, Srikanta Tirthapura
2014 arXiv   pre-print
We consider the enumeration of maximal bipartite cliques (bicliques) from a large graph, a task central to many practical data mining problems in social network analysis and bioinformatics.  ...  To our knowledge, this is the first work on maximal biclique enumeration for graphs of this scale.  ...  this approach perform on even larger clusters, and consequently, larger input graphs? What are the bottlenecks here? and (2) Are there further improvements in search space pruning, and load balancing?  ... 
arXiv:1404.4910v1 fatcat:qhbiyx6orfbqbk4c2dmeuxajiq

Enumerating Maximal Bicliques from a Large Graph Using MapReduce

Arko Provo Mukherjee, Srikanta Tirthapura
2017 IEEE Transactions on Services Computing  
We consider the enumeration of maximal bipartite cliques (bicliques) from a large graph, a task central to many data mining problems arising in social network analysis and bioinformatics.  ...  To our knowledge, this is the first work on maximal biclique enumeration for graphs of this scale.  ...  bipartite cliques (bicliques) from a large graph, a task central to many data mining problems arising in social network analysis and bioinformatics.  ... 
doi:10.1109/tsc.2016.2523997 fatcat:kivpaowf3faf7pi5zhvl45btdm

Enumerating Maximal Bicliques from a Large Graph Using MapReduce

Arko Provo Mukherjee, Srikanta Tirthapura
2014 2014 IEEE International Congress on Big Data  
We consider the enumeration of maximal bipartite cliques (bicliques) from a large graph, a task central to many data mining problems arising in social network analysis and bioinformatics.  ...  To our knowledge, this is the first work on maximal biclique enumeration for graphs of this scale.  ...  bipartite cliques (bicliques) from a large graph, a task central to many data mining problems arising in social network analysis and bioinformatics.  ... 
doi:10.1109/bigdata.congress.2014.105 dblp:conf/bigdata/MukherjeeT14 fatcat:q5upqincsjarxdb3adoj4w2vaa

FCA in a Logical Programming Setting for Visualization-Oriented Graph Compression [chapter]

Lucas Bourneuf, Jacques Nicolas
2017 Lecture Notes in Computer Science  
Royer et al. introduced in 2008 Power graph analysis, a dedicated program using classes of nodes with similar properties and classes of edges linking node classes to achieve a lossless graph compression  ...  Most layout techniques (edge and nodes spatial organization) prove insufficient in this case.  ...  Théret (Inserm) for providing us the networks used in the results section. We would also like to express our gratitude to the reviewers for their feedbacks.  ... 
doi:10.1007/978-3-319-59271-8_6 fatcat:j7dhxcnpnjc63apn3fqeahi66e

A Survey of Algorithms for Dense Subgraph Discovery [chapter]

Victor E. Lee, Ning Ruan, Ruoming Jin, Charu Aggarwal
2010 Managing and Mining Graph Data  
The problem of dense subgraph discovery may wither be defined over single or multiple graphs. We explore both cases.  ...  In this chapter, we present a survey of algorithms for dense subgraph discovery.  ...  Anderson [3] develops a local search algorithm to find a dense bipartite subgraph near a specified starting vertex in a bipartite graph.  ... 
doi:10.1007/978-1-4419-6045-0_10 dblp:series/ads/LeeRJA10 fatcat:u5vzetjlovetpdcxdwjqihdjnq

Compressed representations for web and social graphs

Cecilia Hernández, Gonzalo Navarro
2013 Knowledge and Information Systems  
Compressed representations have become effective to store and access large Web and social graphs, in order to support various graph querying and mining tasks.  ...  On those representations, we support out-neighbor and out/in-neighbor queries, as well as mining queries based on the dense subgraphs.  ...  This representation supports not only out/in-neighbor navigation, but also various graph mining queries based on the dense subgraphs discovered, such as listing cliques and bicliques, retrieving density  ... 
doi:10.1007/s10115-013-0648-4 fatcat:zt4zdfp42bdrdgmcwws3cr6qsy

Un-complicating protein complex prediction [article]

Konstantinos Koutroumpas, François Képès
2015 bioRxiv   pre-print
In most cases several parameters are introduced that have to be trained before application. But how do we select the parameter values when there are no training data available?  ...  Advances in experimental techniques have enabled the construction of large-scale protein-protein interaction networks, and computational methods have been developed to analyze high-throughput data.  ...  CODEC [15] uses an unweighted bipartite graph to model AP-MS purifications. The method starts by mining the graph for bicliques.  ... 
doi:10.1101/017376 fatcat:srevgrjvlvfnzbq4x56bdhyhry

Heuristic algorithms for the bipartite unconstrained 0-1 quadratic programming problem [article]

Daniel Karapetyan, Abraham P. Punnen
2013 arXiv   pre-print
maximum weight biclique, bipartite maximum weight cut, maximum weight induced subgraph of a bipartite graph, etc.  ...  In particular, we establish complexity of all neighborhood search algorithms and establish tight worst-case performance ratio for the greedy algorithm.  ...  The Max Biclique instances model the problem of finding a biclique of the maximum weight in a bipartite graph.  ... 
arXiv:1210.3684v2 fatcat:5dse62coknhpze37mqq3a473xi
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