Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper.
Antibiotic resistance is a global public health concern. Bacteria have evolved resistance to most antibiotics, which means that for any given bacterial infection, the bacteria may be resistant to one or several antibiotics. It has been suggested that genomic sequencing and machine learning (ML) coul...
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| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2024-12-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1012579 |
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| _version_ | 1841533219793534976 |
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| author | Faye Orcales Lucy Moctezuma Tan Meris Johnson-Hagler John Matthew Suntay Jameel Ali Kristiene Recto Phelan Glenn Pleuni Pennings |
| author_facet | Faye Orcales Lucy Moctezuma Tan Meris Johnson-Hagler John Matthew Suntay Jameel Ali Kristiene Recto Phelan Glenn Pleuni Pennings |
| author_sort | Faye Orcales |
| collection | DOAJ |
| description | Antibiotic resistance is a global public health concern. Bacteria have evolved resistance to most antibiotics, which means that for any given bacterial infection, the bacteria may be resistant to one or several antibiotics. It has been suggested that genomic sequencing and machine learning (ML) could make resistance testing more accurate and cost-effective. Given that ML is likely to become an ever more important tool in medicine, we believe that it is important for pre-health students and others in the life sciences to learn to use ML tools. This paper provides a step-by-step tutorial to train 4 different ML models (logistic regression, random forests, extreme gradient-boosted trees, and neural networks) to predict drug resistance for Escherichia coli isolates and to evaluate their performance using different metrics and cross-validation techniques. We also guide the user in how to load and prepare the data used for the ML models. The tutorial is accessible to beginners and does not require any software to be installed as it is based on Google Colab notebooks and provides a basic understanding of the different ML models. The tutorial can be used in undergraduate and graduate classes for students in Biology, Public Health, Computer Science, or related fields. |
| format | Article |
| id | doaj-art-297fe424b9ad40c3927e2e0ec4559396 |
| institution | Kabale University |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-297fe424b9ad40c3927e2e0ec45593962025-01-17T05:30:55ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582024-12-012012e101257910.1371/journal.pcbi.1012579Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper.Faye OrcalesLucy Moctezuma TanMeris Johnson-HaglerJohn Matthew SuntayJameel AliKristiene RectoPhelan GlennPleuni PenningsAntibiotic resistance is a global public health concern. Bacteria have evolved resistance to most antibiotics, which means that for any given bacterial infection, the bacteria may be resistant to one or several antibiotics. It has been suggested that genomic sequencing and machine learning (ML) could make resistance testing more accurate and cost-effective. Given that ML is likely to become an ever more important tool in medicine, we believe that it is important for pre-health students and others in the life sciences to learn to use ML tools. This paper provides a step-by-step tutorial to train 4 different ML models (logistic regression, random forests, extreme gradient-boosted trees, and neural networks) to predict drug resistance for Escherichia coli isolates and to evaluate their performance using different metrics and cross-validation techniques. We also guide the user in how to load and prepare the data used for the ML models. The tutorial is accessible to beginners and does not require any software to be installed as it is based on Google Colab notebooks and provides a basic understanding of the different ML models. The tutorial can be used in undergraduate and graduate classes for students in Biology, Public Health, Computer Science, or related fields.https://doi.org/10.1371/journal.pcbi.1012579 |
| spellingShingle | Faye Orcales Lucy Moctezuma Tan Meris Johnson-Hagler John Matthew Suntay Jameel Ali Kristiene Recto Phelan Glenn Pleuni Pennings Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper. PLoS Computational Biology |
| title | Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper. |
| title_full | Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper. |
| title_fullStr | Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper. |
| title_full_unstemmed | Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper. |
| title_short | Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper. |
| title_sort | using genomic data and machine learning to predict antibiotic resistance a tutorial paper |
| url | https://doi.org/10.1371/journal.pcbi.1012579 |
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