Relabeling metabolic pathway data with groups to improve prediction outcomes

Author:

Basher Abdur Rahman M. A.ORCID,Hallam Steven J.ORCID

Abstract

AbstractMetabolic pathway inference from genomic sequence information is an integral scientific problem with wide ranging applications in the life sciences. As sequencing throughput increases, scalable and performative methods for pathway prediction at different levels of genome complexity and completion become compulsory. In this paper, we present reMap (relabeling metabolic pathway data with groups) a simple, and yet, generic framework, that performs relabeling examples to a different set of labels, characterized as groups. A pathway group is comprised of a subset of statistically correlated pathways that can be further distributed between multiple pathway groups. This has important implications for pathway prediction, where a learning algorithm can revisit a pathway multiple times across groups to improve sensitivity. The relabeling process in reMap is achieved through an alternating feedback process. In the first feed-forward phase, a minimal subset of pathway groups is picked to label each example. In the second feed-backward phase, reMap’s internal parameters are updated to increase the accuracy of mapping examples to pathway groups. The resulting pathway group dataset is then be used to train a multi-label learning algorithm. reMap’s effectiveness was evaluated on metabolic pathway prediction where resulting performance metrics equaled or exceeded other prediction methods on organismal genomes with improved predictive performance.

Publisher

Cold Spring Harbor Laboratory

Reference53 articles.

1. Biocyc: Online resource for genome and metabolic pathway analysis;The FASEB Journal,2016

2. Chang, H.S. , Learned-Miller, E. , McCallum, A. : Active bias: Training more accurate neural networks by emphasizing high variance samples. In: Advances in Neural Information Processing Systems. pp. 1002–1012 (2017)

3. Detection of gene pathways with predictive power for breast cancer prognosis

4. The information science of microbial ecology

5. A network-based approach to identify substrate classes of bacterial glycosyltransferases

Cited by 1 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

1. Relabeling Metabolic Pathway Data with Groups to Improve Prediction Outcomes;Computational Advances in Bio and Medical Sciences;2022

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