Learning biophysical determinants of cell fate with deep neural networks

Deep learning is now a powerful tool in microscopy data analysis, and is routinely used for image processing applications such as segmentation and denoising. However, it has rarely been used to directly learn mechanistic models of a biological system, owing to the complexity of the internal representations. Here, we develop an end-to-end machine learning approach capable of learning an explainable model of a complex biological phenomenon, cell competition, directly from a large corpus of time-lapse microscopy data. Cell competition is a quality control mechanism that eliminates unfit cells from a tissue, during which cell fate is thought to be determined by the local cellular neighbourhood over time. To investigate this, we developed a new approach (τ-VAE) by coupling a probabilistic encoder to a temporal convolution network to predict the fate of each cell in an epithelium. Using the τ-VAE’s latent representation of the local tissue organization and the flow of information in the network, we decode the physical parameters responsible for correct prediction of fate in cell competition. Remarkably, the model autonomously learns that cell density is the single most important factor in predicting cell fate—a conclusion that is in agreement with our current understanding from over a decade of scientific research. Finally, to test the learned internal representation, we challenge the network with experiments performed in the presence of drugs that block signalling pathways involved in competition. We present a novel discriminator network, which using the predictions of the τ-VAE can identify conditions that deviate from the normal behaviour, paving the way for automated, mechanism-aware drug screening. An end-to-end machine learning approach that can learn which mechanisms determine cell fate and competition from a large time-lapse microscopy dataset is developed. The approach makes use of a probabilistic autoencoder to learn an interpretable representation of the organization of cells, and provides cell fate predictions that can be tested in drug screening experiments.