Analysis of the Human Protein Atlas Image Classification competition


Pinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to solve this task. Challenges included training on highly imbalanced classes and predicting multiple labels per image. Over 3 months, 2,172 teams participated. Despite convergence on popular networks and training techniques, there was considerable variety among the solutions. Participants applied strategies for modifying neural networks and loss functions, augmenting data and using pretrained networks. The winning models far outperformed our previous effort at multi-label classification of protein localization patterns by ~20%. These models can be used as classifiers to annotate new images, feature extractors to measure pattern similarity or pretrained networks for a wide range of biological applications.

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Fig. 1: Overview of image dataset and challenge design.
Fig. 2: Competition results.
Fig. 3: Visualization of model spatial attention.
Fig. 4: Visualization of learned features.

Data availability

The dataset used for the HPA competition is available at: The external dataset HPAv18 is publicly available on the HPA: A script is provided for downloading the dataset is available at

Code availability

Source code used to produce the figures has been released under permissive licenses at A HPA classification competition model zoo is being built to offer downloads of the top models generated during the competition. The model zoo can be found at

The source code for the ImJoy plugin HPA-UMAP can be found at

Change history

  • 10 December 2019

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.


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We thank all the participants of the Human Protein Atlas Image Classification competition. We also acknowledge the staff at Kaggle for providing a competition platform that enabled this study and the competition prize sponsors Leica Microsystems and NVIDIA. The staff of the HPA program provided valuable contributions, such as data storage and management, and J. Fall helped with project administrative tasks. Funding was provided by the Knut and Alice Wallenberg Foundation (grant no. 2016.0204) and the Swedish Research Council (grant no. 2017–05327) to E.L.

Author information

E.L. conceived the study. C.F.W., M.H., D.P.S., H.X., C.K. and E.L. designed and implemented the competition together with the Kaggle team. W.O., C.F.W., M.H., L.Å., H.X., A.J.C., C.K. and E.L. performed data analysis and model investigation. S.D. contributed as the Kaggle competition winner and with intermediate analysis for the paper. S.D., Y.W., R.W., X.Z., X.C., K.L.T., D.B., A.K., S.F., D.Panchenko, P.J., C.J., X.Y., H.Z., Z.G., J.X., C.L., Y.G., J.L., R.W., B.T., C.H., K.H., D.Poplavskiy and S.M.G. contributed as participants of the nine selected teams from the Kaggle competition. W.O., A.J.C., C.F.W., M.H. and E.L. wrote the manuscript. W.O., L.Å., M.H., A.J.C. and C.F.W. made the figures. C.K. and S.D. revised the manuscript. E.L. supervised and administered the project and acquired funding. All authors reviewed and approved the final manuscript.

Correspondence to Emma Lundberg.

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The authors declare no competing interests.

Additional information

Peer review information Rita Strack was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–13, Tables 1–9 and Notes 1–9.

Reporting Summary

Supplementary Table 4

Class-wise score for the nine invited teams, Macro F1 score per class for each of the invited teams in the competition.

Supplementary Table 5

Models and ablation study from the nine selected teams, Description of the different models used by the invited teams as well as an analysis of what factors contributed the most to the performance of the models.

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Ouyang, W., Winsnes, C.F., Hjelmare, M. et al. Analysis of the Human Protein Atlas Image Classification competition. Nat Methods 16, 1254–1261 (2019) doi:10.1038/s41592-019-0658-6

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