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Register a new userComHapDet: A Spatial Community Detection Algorithm for Haplotype Assembly
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Added by
Abishek Sankararaman
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individuals susceptibility to hereditary and complex diseases and affect how our bodies respond to therapeutic drugs. Reconstructing haplotypes of an individual from short sequencing reads is an NP-hard problem that becomes even more challenging in the case of polyploids. While increasing lengths of sequencing reads and insert sizes {color{black} helps improve accuracy of reconstruction}, it also exacerbates computational complexity of the haplotype assembly task. This has motivated the pursuit of algorithmic frameworks capable of accurate yet efficient assembly of haplotypes from high-throughput sequencing data. Results: We propose a novel graphical representation of sequencing reads and pose the haplotype assembly problem as an instance of community detection on a spatial random graph. To this end, we construct a graph where each read is a node with an unknown community label associating the read with the haplotype it samples. Haplotype reconstruction can then be thought of as a two-step procedure: first, one recovers the community labels on the nodes (i.e., the reads), and then uses the estimated labels to assemble the haplotypes. Based on this observation, we propose ComHapDet - a novel assembly algorithm for diploid and ployploid haplotypes which allows both bialleleic and multi-allelic variants. Conclusions: Performance of the proposed algorithm is benchmarked on simulated as well as experimental data obtained by sequencing Chromosome $5$ of tetraploid biallelic emph{Solanum-Tuberosum} (Potato). The results demonstrate the efficacy of the proposed method and that it compares favorably with the existing techniques.
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A community reveals the features and connections of its members that are different from those in other communities in a network. Detecting communities is of great significance in network analysis. Despite the classical spectral clustering and statistical inference methods, we notice a significant development of deep learning techniques for community detection in recent years with their advantages in handling high dimensional network data. Hence, a comprehensive overview of community detections latest progress through deep learning is timely to both academics and practitioners. This survey devises and proposes a new taxonomy covering different categories of the state-of-the-art methods, including deep learning-based models upon deep neural networks, deep nonnegative matrix factorization and deep sparse filtering. The main category, i.e., deep neural networks, is further divided into convolutional networks, graph attention networks, generative adversarial networks and autoencoders. The survey also summarizes the popular benchmark data sets, model evaluation metrics, and open-source implementations to address experimentation settings. We then discuss the practical applications of community detection in various domains and point to implementation scenarios. Finally, we outline future directions by suggesting challenging topics in this fast-growing deep learning field.
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Graphs representing real world systems may be studied from their underlying community structure. A community in a network is an intuitive idea for which there is no consensus on its objective mathematical definition. The most used metric in order to detect communities is the modularity, though many disadvantages of this parameter have already been noticed in the literature. In this work, we present a new approach based on a different metric: the surprise. Moreover, the biases of different community detection algorithms and benchmark networks are thoroughly studied, identified and commented about.
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