计算机科学
结核分枝杆菌
Python(编程语言)
容器(类型理论)
肺结核
互操作性
抗药性
人工智能
机器学习
操作系统
程序设计语言
数据库
医学
微生物学
工程类
生物
机械工程
病理
作者
Julian Libiseller-Egger,Linfeng Wang,Wouter Deelder,Susana Campino,Taane G. Clark,Jody Phelan
标识
DOI:10.1093/bioadv/vbad040
摘要
Machine learning (ML) has shown impressive performance in predicting antimicrobial resistance (AMR) from sequence data, including for Mycobacterium tuberculosis, the causative agent of tuberculosis. However, current ML development and publication practices make it difficult for researchers and clinicians to use, test or reproduce published models.We packaged a number of published and unpublished ML models for predicting AMR of M.tuberculosis into Docker containers. Similarly, the pipelines required for pre-processing genomic data into the formats required by the models were also packaged into separate containers. By following a minimal container I/O standard, we ensured as much interoperability as possible. We also created a command-line application, TB-ML, which can be used to easily combine pre-processing and prediction containers into complete pipelines ready for predicting resistance from novel, raw data with a single command. As long as there is adherence to this minimal standard for the container interface, containers produced by researchers holding new models can likewise be included in these pipelines, making benchmark comparisons of different models simple and facilitating faster uptake in the clinic.TB-ML contains a simple Docker API written in Python and is available at https://github.com/jodyphelan/tb-ml. Example Docker containers for resistance prediction and corresponding data pre-processing as well as a tutorial on how to create new containers for TB-ML are available at https://tb-ml.github.io/tb-ml-containers/.jody.phelan@lshtm.ac.uk.
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