AMYPred-FRL is a novel approach for accurate prediction of amyloid proteins by using feature representation learning.
Authors
Charoenkwan, Phasit
Ahmed, Saeed
Nantasenamat, Chanin
Quinn, Julian MW
Moni, Mohammad Ali
Lio', Pietro
Shoombuatong, Watshara
Publication Date
2022-05-11Journal Title
Sci Rep
ISSN
2045-2322
Publisher
Springer Science and Business Media LLC
Volume
12
Issue
1
Language
en
Type
Article
This Version
VoR
Metadata
Show full item recordCitation
Charoenkwan, P., Ahmed, S., Nantasenamat, C., Quinn, J. M., Moni, M. A., Lio', P., & Shoombuatong, W. (2022). AMYPred-FRL is a novel approach for accurate prediction of amyloid proteins by using feature representation learning.. Sci Rep, 12 (1) https://doi.org/10.1038/s41598-022-11897-z
Description
Funder: Mahidol University
Funder: Chiang Mai University
Funder: College of Arts, Media and Technology, Chiang Mai University
Funder: Information Technology Service Center (ITSC) of Chiang Mai University
Abstract
Amyloid proteins have the ability to form insoluble fibril aggregates that have important pathogenic effects in many tissues. Such amyloidoses are prominently associated with common diseases such as type 2 diabetes, Alzheimer's disease, and Parkinson's disease. There are many types of amyloid proteins, and some proteins that form amyloid aggregates when in a misfolded state. It is difficult to identify such amyloid proteins and their pathogenic properties, but a new and effective approach is by developing effective bioinformatics tools. While several machine learning (ML)-based models for in silico identification of amyloid proteins have been proposed, their predictive performance is limited. In this study, we present AMYPred-FRL, a novel meta-predictor that uses a feature representation learning approach to achieve more accurate amyloid protein identification. AMYPred-FRL combined six well-known ML algorithms (extremely randomized tree, extreme gradient boosting, k-nearest neighbor, logistic regression, random forest, and support vector machine) with ten different sequence-based feature descriptors to generate 60 probabilistic features (PFs), as opposed to state-of-the-art methods developed by a single feature-based approach. A logistic regression recursive feature elimination (LR-RFE) method was used to find the optimal m number of 60 PFs in order to improve the predictive performance. Finally, using the meta-predictor approach, the 20 selected PFs were fed into a logistic regression method to create the final hybrid model (AMYPred-FRL). Both cross-validation and independent tests showed that AMYPred-FRL achieved superior predictive performance than its constituent baseline models. In an extensive independent test, AMYPred-FRL outperformed the existing methods by 5.5% and 16.1%, respectively, with accuracy and MCC of 0.873 and 0.710. To expedite high-throughput prediction, a user-friendly web server of AMYPred-FRL is freely available at http://pmlabstack.pythonanywhere.com/AMYPred-FRL . It is anticipated that AMYPred-FRL will be a useful tool in helping researchers to identify new amyloid proteins.
Keywords
Article, /631/114, /631/114/2397, /631/114/1305, article
Identifiers
s41598-022-11897-z, 11897
External DOI: https://doi.org/10.1038/s41598-022-11897-z
This record's URL: https://www.repository.cam.ac.uk/handle/1810/337022
Rights
Licence:
http://creativecommons.org/licenses/by/4.0/
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