Moving towards more holistic machine learning-based approaches for classification problems in animal studies

Abstract Machine-learning (ML) is revolutionizing field and laboratory studies of animals. However, a challenge when deploying ML for classification tasks is ensuring the models are reliable. Currently, we evaluate models using performance metrics (e.g., precision, recall, F1), but these can overlook the ultimate aim, which is not the outputs themselves (e.g. detected species or individual identities, or behaviour) but their incorporation for hypothesis testing. As improving performance metrics has diminishing returns, particularly when data are inherently noisy (as human-labelled, animal-based data often are), researchers are faced with the conundrum of investing more time in maximising metrics versus doing the actual research. This raises the question: how much noise can we accept in ML models? Here, we start by describing an under-reported factor that can cause metrics to underestimate model performance. Specifically, ambiguity between categories or mistakes in labelling validation data produces hard ceilings that limit performance metrics. This likely widespread issue means that many models could be performing better than their metrics suggest. Next, we argue and show that imperfect models (e.g. low F1 scores) can still be useable. Using a case study on ML-identified behaviour from vulturine guineafowl accelerometer data, we first propose a simulation framework to evaluate robustness of hypothesis testing using models that make classification errors. Second, we show how to determine the utility of a model by supplementing existing performance metrics with ‘biological validations’. This involves applying ML models to unlabelled data and using the models’ outputs to test hypotheses for which we can anticipate the outcome. Together, we show that effects sizes and expected biological patterns can be detected even when performance metrics are relatively low (e.g., F1: 60-70%). In doing so, we provide a roadmap for validation approaches of ML classification models tailored to research in animal behaviour, and other fields with noisy, biological data. Highlights Evaluating machine learning (ML) models must go beyond performance metrics Mislabels in validation data leads to underestimation of model’s performance Underestimated metrics can cause research delays despite models being useful We propose simulations and biological validations to evaluate model performance Models with low standard metrics can still be powerful for hypothesis testing Competing Interest Statement The authors have declared no competing interest. Footnotes ↵+ joint-first authors Revision defines the scope of the paper more clearly (using machine-learning for the classification of raw data to be used in posterior hypothesis testing). Revision entails additional methodological details (Ethical note, Figure S2 to show alignment of accelerometer data with labels).