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<italic>Objective</italic>: Gait analysis of animal disease models can provide valuable insights into in vivo compound effects and thus help in preclinical drug development. The purpose of this paper is to establish a computational gait analysis approach for the Noldus Catwalk system, in which footprints are automatically captured and stored. <italic>Methods</italic>: We present a - to our knowledge - first machine learning based approach for the Catwalk system, which comprises a step decomposition, definition and extraction of meaningful features, multivariate step sequence alignment, feature selection, and training of different classifiers (gradient boosting machine, random forest, and elastic net). <italic>Results</italic>: Using animal-wise leave-one-out cross validation we demonstrate that with our method we can reliable separate movement patterns of a putative Parkinson&#x0027;s disease animal model and several control groups. Furthermore, we show that we can predict the time point after and the type of different brain lesions and can even forecast the brain region, where the intervention was applied. We provide an in-depth analysis of the features involved into our classifiers via statistical techniques for model interpretation. <italic> Conclusion</italic>: A machine learning method for automated analysis of data from the Noldus Catwalk system was established. <italic>Significance:</italic> Our works shows the ability of machine learning to discriminate pharmacologically relevant animal groups based on their walking behavior in a multivariate manner. Further interesting aspects of the approach include the ability to learn from past experiments, improve with more data arriving and to make predictions for single animals in future studies.

A Machine Learning Approach to Automated Gait Analysis for the Noldus Catwalk System