Feature weighted models to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences.

ABSTRACT:

Motivation

Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC), which has a strain- or lineage-based clonal population structure. The evolution of drug-resistance in the MTBC poses a threat to successful treatment and eradication of TB. Machine learning approaches are being increasingly adopted to predict drug-resistance and characterize underlying mutations from whole genome sequences. However, such approaches may not generalize well in clinical practice due to confounding from the population structure of the MTBC.

Results

To investigate how population structure affects machine learning prediction, we compared three different approaches to reduce lineage dependency in random forest (RF) models, including stratification, feature selection,

SUBMITTER: Billows N 

PROVIDER: S-EPMC10351970 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature