A review of machine learning in toxicology: current practices and reporting gaps

Abstract

In recent years, machine learning and artificial intelligence approaches have been increasingly applied in the context of toxicological risk assessment. Many published overview, review, and comment papers discuss advantages, disadvantages, success stories, and open challenges for the application of machine learning models in toxicology. Machine learning methods using information from in vitro experiments can help to avoid animal experiments, thus allowing for larger numbers of experiments to be conducted. Drawbacks of machine learning models are the lack of mechanistic interpretability and the need for large amounts of high-quality data. In this work, we present a literature review of papers indexed in PubMed or published in the journal Computational Toxicology in the years 2022 to 2024, to assess the usage of machine learning methods in toxicology as well as the practices in reporting of methods and corresponding results. We do not address the suitability or the performance of methods, which is impossible to assess objectively without reanalysis on raw data, but focus on common practices and gaps in reporting. Major results are that many different machine learning methods are used in toxicology, often with appropriate internal validation. However, in only half of the cases, interpretation methods are used to address the problem that these models often make predictions as a black box. Moreover, there are very frequent gaps in reporting, in particular related to handling of missing values, and availability of data and code. Thus, this review can serve as a starting point for further tailored methodological research and guidance.

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