Sublinear Graph Augmentation for Fast Query Implementation

ABSTRACTGraph-based genome reference representations have seen significant development, motivated by the inadequacy of the current human genome reference for capturing the diverse genetic information from different human populations and its inability to maintain the same level of accuracy for non-European ancestries. While there have been many efforts to develop computationally efficient graph-based bioinformatics toolkits, how to curate genomic variants and subsequently construct genome graphs remains an understudied problem that inevitably determines the effectiveness of the end-to-end bioinformatics pipeline. In this study, we discuss major obstacles encountered during graph construction and propose methods for sample selection based on population diversity, graph augmentation with structural variants and resolution of graph reference ambiguity caused by information overload. Moreover, we present the case for iteratively augmenting tailored genome graphs for targeted populations and test the proposed approach on the whole-genome samples of African ancestry. Our results show that, as more representative alternatives to linear or generic graph references, population-specific graphs can achieve significantly lower read mapping errors, increased variant calling sensitivity and provide the improvements of joint variant calling without the need of computationally intensive post-processing steps.

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Approximation algorithms for graph augmentation

Automata, Languages and Programming - Lecture Notes in Computer Science ◽

10.1007/3-540-55719-9_85 ◽

1992 ◽

pp. 330-341 ◽

Cited By ~ 7

Author(s):

Samir Khuller ◽

Ramakrishna Thurimella

Keyword(s):

Approximation Algorithms ◽

Graph Augmentation

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Plane Geometric Graph Augmentation: A Generic Perspective

Thirty Essays on Geometric Graph Theory ◽

10.1007/978-1-4614-0110-0_17 ◽

2012 ◽

pp. 327-354 ◽

Cited By ~ 9

Author(s):

Ferran Hurtado ◽

Csaba D. Tóth

Keyword(s):

Geometric Graph ◽

Graph Augmentation

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Adding Edges for Maximizing Weighted Reachability

Algorithms ◽

10.3390/a13030068 ◽

2020 ◽

Vol 13 (3) ◽

pp. 68 ◽

Cited By ~ 1

Author(s):

Federico Corò ◽

Gianlorenzo D'Angelo ◽

Cristina M. Pinotti

Keyword(s):

Polynomial Time ◽

Greedy Algorithms ◽

Dynamic Programming Algorithm ◽

Directed Acyclic Graphs ◽

Constant Factor ◽

Programming Algorithm ◽

Single Source ◽

Graph Augmentation ◽

Set Size ◽

Acyclic Graphs

In this paper, we consider the problem of improving the reachability of a graph. We approach the problem from a graph augmentation perspective, in which a limited set size of edges is added to the graph to increase the overall number of reachable nodes. We call this new problem the Maximum Connectivity Improvement (MCI) problem. We first show that, for the purpose of solve solving MCI, we can focus on Directed Acyclic Graphs (DAG) only. We show that approximating the MCI problem on DAG to within any constant factor greater than 1 − 1 / e is NP -hard even if we restrict to graphs with a single source or a single sink, and the problem remains NP -complete if we further restrict to unitary weights. Finally, this paper presents a dynamic programming algorithm for the MCI problem on trees with a single source that produces optimal solutions in polynomial time. Then, we propose two polynomial-time greedy algorithms that guarantee ( 1 − 1 / e ) -approximation ratio on DAGs with a single source, a single sink or two sources.

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Societal context-dependent multi-modal transportation network augmentation in Johannesburg, South Africa

PLoS ONE ◽

10.1371/journal.pone.0249014 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0249014

Author(s):

Thembani Moyo ◽

Alain Y. Kibangou ◽

Walter Musakwa

Keyword(s):

South African ◽

Transportation Network ◽

Routing Algorithm ◽

Minimum Cost ◽

Weighted Graphs ◽

Graph Augmentation ◽

Transportation Services ◽

Societal Context ◽

African Context ◽

The City

In most developing countries, formal and informal transportation schemes coexist without effective and smart integration. In this paper, the authors show how to leverage opportunities offered by formal and informal transportation schemes to build an integrated multi-modal network. Precisely, the authors consider integration of rickshaws to a bus-train network, by taking into account accessibility and societal constraints. By modelling the respective networks with weighted graphs, a graph augmentation problem is solved with respect to a composite cost taking into account constraints on the use of rickshaws. The solution, is based on finding a minimum cost spanning tree of a merged graph. The method is applied in the South African context, in the city of Johannesburg where rickshaws are not yet a significant part of the transportation system. The implications of the study reveal that using non-motorised transportation services is a viable option of improving mobility in the city. The composite cost introduced herein could be used for new routing algorithm including societal, environmental, architectural contexts and commuter experiences through rating.

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