Titlebook: Analysis and Enumeration; Algorithms for Biolo Andrea Marino Book 2015 Atlantis Press and the authors 2015 Bubbles.Cycles and Paths.Enumera

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Enumeration Algorithmsir complexity. Among these, we will discuss brute force approaches and basic paradigms, like backtracking, binary partition, and reverse search. Moreover, amortized analysis will be introduced by discussing basic amortization, amortization by children, and push out amortization.

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Telling Stories: Enumerating Maximal Directed Acyclic Graphs with Constrained Set of Sources and Tarrute force approach. The problem is a constrained version of the problem of enumerating all maximal directed acyclic subgraphs (DAG) of a graph .. In this version, we enumerate maximal DAGs whose sources and targets belong to a predefined subset of the vertices. We call such DAGs .. Given a Metaboli

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Enumerating Bubbles: Listing Pairs of Vertex Disjoint Pathserns have been called mouths, or bubbles in the literature. They correspond to two vertex-disjoint directed paths between a source . and a target .. Due to the high number of such bubbles that may be present in real data, their enumeration is a major issue concerning the efficiency of dedicated algo

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Book 2015to efficiently deal with some biological problems modelled by using biological networks: enumerating central and peripheral nodes of a network, enumerating stories, enumerating paths or cycles, and enumerating bubbles. Notice that the corresponding computational problems we define are of more genera

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2212-8557 ture on enumeration algorithms in general and on biological In this work we plan to revise the main techniques for enumeration algorithms and to show four examples of enumeration algorithms that can be applied to efficiently deal with some biological problems modelled by using biological networks: e

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https://doi.org/10.1007/978-1-4939-1127-1ue to the high number of such bubbles that may be present in real data, their enumeration is a major issue concerning the efficiency of dedicated algorithms. We propose the first linear delay algorithm to enumerate all bubbles with a given source, by properly transforming the graph in input and enumerating special cycles.

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Ming-Hsu Wang,Bi-Hui Chen,Wen-Ko Chiouthm, we show that in practice it runs often in . time. This study implies the analysis of the diameter and radius of a network so that we will evaluate the effectiveness of our algorithms in finding such measures.