Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs
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Cryo-electron microscopy (cryoEM) is fast becoming the preferred method for protein structure determination. Particle picking is a significant bottleneck in the solving of protein structures from single particle cryoEM. Hand labeling sufficient numbers of particles can take months of effort and current computationally based approaches are often ineffective. Here, we frame particle picking as a positive-unlabeled classification problem in which we seek to learn a convolutional neural network (CNN) to classify micrograph regions as particle or background from a small number of labeled positive examples and many unlabeled examples. However, model fitting with very few labeled data points is a challenging machine learning problem. To address this, we develop a novel objective function, GE-binomial, for learning model parameters in this context. This objective uses a newly-formulated generalized expectation criteria to learn effectively from unlabeled data when using minibatched stochastic gradient descent optimizers. On a high-quality publicly available cryoEM dataset and a difficult unpublished dataset supplied by the Shapiro lab, we show that CNNs trained with this objective classify particles accurately with very few positive training examples and outperform EMAN2's byRef method by a large margin even with fewer labeled training examples. Furthermore, we show that incorporating an autoencoder improves generalization when very few labeled data points are available. We also compare our GE-binomial method with other positive-unlabeled learning methods never before applied to particle picking. We expect our particle picking tool, Topaz, based on CNNs trained with GE-binomial, to be an essential component of single particle cryoEM analysis and our GE-binomial objective function to be widely applicable to positive-unlabeled classification problems.
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