A layered, hybrid machine learning analytic workflow for mouse risk assessment behavior

Accurate and efficient quantification of animal behavior facilitates the understanding of the brain. An emerging approach within machine learning (ML) field is to combine multiple ML-based algorithms to quantify animal behavior. These so-called hybrid models have emerged because of limitations associated with supervised (e.g., random forest, RF) and unsupervised (e.g., hidden Markov model, HMM) ML classifiers. For example, RF models lack temporal information across video frames, and HMM latent states are often difficult to interpret. We sought to develop a hybrid model, and did so in the context of a study of mouse risk assessment behavior. We utilized DeepLabCut to estimate the positions of mouse body parts. Positional features were calculated using DeepLabCut outputs and were used to train RF and HMM models with equal number of states, separately. The per-frame predictions from RF and HMM models were then passed to a second HMM model layer ("reHMM"). The outputs of the reHMM layer showed improved interpretability over the initial HMM output. Finally, we combined predictions from RF and HMM models with selected positional features to train a third HMM model ("reHMM+"). This reHMM+ layered hybrid model unveiled distinctive temporal and human-interpretable behavioral patterns. We applied this workflow to investigate risk assessment to trimethylthiazoline and snake feces odor, finding unique behavioral patterns to each that were separable from attractive and neutral stimuli. We conclude that this layered, hybrid machine learning workflow represents a balanced approach for improving the depth and reliability of ML classifiers in chemosensory and other behavioral contexts. Significance StatementIn this study, we integrate two widely-adopted machine learning (ML) classifiers, random forest and hidden Markov model, to develop a layered, hybrid ML-based workflow. Our workflow not only overcomes the intrinsic limitations of each model alone, but also improves the depth and reliability of ML models. Implementing this analytic workflow unveils distinctive and dynamic mouse behavioral patterns to chemosensory cues in the context of mouse risk assessment behavioral experiments. This study provides an efficient and interpretable analytic strategy for the quantification of animal behavior in diverse experimental settings.