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Previously, single classification models were mainly studied to classify human protein cell images, i.e., to identify a certain protein based on a set of different cells. However, a classifier can identify only one protein, in fact, a single cell usually consists of multiple proteins, and the proteins are not completely independent of each other. In this paper, we build a human protein cell classification model by multi-label learning. The logical relationship and distribution characteristics among the labels are analyzed to determine the different proteins contained in a set of different cells (i.e., containing multiple elements in the output space). In this paper, using human protein image data, we conducted comparison experiments on pre-trained Xception and InceptionResnet V2 to optimize the two models in terms of data augmentation, channel settings, and model structure. The results show that the Optimized InceptionResnet V2 model achieves high performance in the classification task. The final accuracy of the Optimized InceptionResnet V2 model we obtained reached 96.1%, which is a 2.82% improvement relative to that before the optimized model. [ABSTRACT FROM AUTHOR]