Abstract
Cryo-electron microscopy single particle analysis requires tens of thousands of particle projections for the structural determination of macromolecules. To free researchers from laborious particle picking work, a number of fully automatic and semi-automatic particle picking approaches have been proposed. However, due to the presence of carbon and different types of high-contrast contaminations, these approaches tend to select a non-negligible number of false-positive particles, which affects the subsequent 3D reconstruction.
In order to overcome this limitation, we present a deep learning-based particle pruning algorithm, PickerOptimizer, to separate erroneously picked particles from the correct ones. PickerOptimizer trained a convolutional neural network based on transfer learning techniques, where the pre-trained model maintains strong generalization ability and can be quickly adapted to the characteristics of the new dataset. Here, we build the first cryo-EM dataset for image classification pre-training which contains particles, carbon regions and high-contrast contaminations from 14 different EMPIAR entries. The PickerOptimizer works by fine-tuning the pre-trained model with only a few manually labeled samples from new datasets. The experiments carried out on several public datasets show that PickerOptimizer is a very efficient approach for particle post-processing, achieving F1 scores above 90%. Moreover, the method is able to identify false-positive particles more accurately than other pruning strategies. A case study further shows that PickerOptimizer can improve conventional particle pickers and complement deep-learning-based ones. The Source code, pre-trained models and datasets are available at https://github.com/LiHongjia-ict/PickerOptimizer/.
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Acknowledgments
The research is supported by the National Key Research and Development Program of China (No. 2017YFA0504702), the NSFC projects grants (61932018, 62072441 and 62072280), and Beijing Municipal Natural Science Foundation Grant (No. L182053).
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Li, H., Chen, G., Gao, S., Li, J., Zhang, F. (2021). PickerOptimizer: A Deep Learning-Based Particle Optimizer for Cryo-Electron Microscopy Particle-Picking Algorithms. In: Wei, Y., Li, M., Skums, P., Cai, Z. (eds) Bioinformatics Research and Applications. ISBRA 2021. Lecture Notes in Computer Science(), vol 13064. Springer, Cham. https://doi.org/10.1007/978-3-030-91415-8_46
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