Subcellular Protein Localisation in the Human Protein Atlas using Ensembles of Diverse Deep Architectures

Automated visual localisation of subcellular proteins can accelerate our understanding of cell function in health and disease. Despite recent advances in machine learning (ML), humans still attain superior accuracy by using diverse clues. We show how this gap can be narrowed by addressing three key aspects: (i) automated improvement of cell annotation quality, (ii) new Convolutional Neural Network (CNN) architectures supporting unbalanced and noisy data, and (iii) informed selection and fusion of multiple & diverse machine learning models. We introduce a new "AI-trains-AI" method for improving the quality of weak labels and propose novel CNN architectures exploiting wavelet filters and Weibull activations. We also explore key factors in the multi-CNN ensembling process by analysing correlations between image-level and cell-level predictions. Finally, in the context of the Human Protein Atlas, we demonstrate that our system achieves state-of-the-art performance in the multi-label single-cell classification of protein localisation patterns. It also significantly improves generalisation ability.