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Morphological and molecular breast cancer profiling through explainable machine learning

A preprint version of the article is available at arXiv.


Recent advances in cancer research and diagnostics largely rely on new developments in microscopic or molecular profiling techniques, offering high levels of detail with respect to either spatial or molecular features, but usually not both. Here, we present an explainable machine-learning approach for the integrated profiling of morphological, molecular and clinical features from breast cancer histology. First, our approach allows for the robust detection of cancer cells and tumour-infiltrating lymphocytes in histological images, providing precise heatmap visualizations explaining the classifier decisions. Second, molecular features, including DNA methylation, gene expression, copy number variations, somatic mutations and proteins are predicted from histology. Molecular predictions reach balanced accuracies up to 78%, whereas accuracies of over 95% can be achieved for subgroups of patients. Finally, our explainable AI approach allows assessment of the link between morphological and molecular cancer properties. The resulting computational multiplex-histology analysis can help promote basic cancer research and precision medicine through an integrated diagnostic scoring of histological, clinical and molecular features.

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Fig. 1: Workflow of machine-learning-based morphological and molecular feature prediction and heatmapping.
Fig. 2: Spatial heatmapping results showing detection and localization of carcinoma cells and TiLs in breast cancer.
Fig. 3: Explainable machine learning avoids black-box limitation of conventional machine learning.
Fig. 4: Positive tail accuracies for molecular property prediction from histology.
Fig. 5: Computationally generated ‘fluorescence microscopy’ visualizing correlation of spatiomorphological and molecular features.
Fig. 6: Validation of computational morphomolecular predictions.

Data availability

The data used for the main analyses presented here are available for non-commercial use at

Code availability

The code used for the machine-learning analyses has been deposited at


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This work was funded by the Charité Institute of Pathology, Berlin, the Technical University of Berlin, the Human Frontier Science Program (HFSP) Young Investigator Grant (M.I. and F.K.) and the Einstein Foundation Berlin (F.K.) and partly by the German Research Foundation to A.H. (DFG SFB-TR84, B6, Z1a) and the German Consortium for Translational Cancer Research (DKTK). F.K. was also supported by the German Ministry for Education and Research (BMBF) within the Berlin Institute for the Foundations of Learning and Data (BIFOLD; grant no. 01IS18025D and 01IS18037E), the clinical mass spectrometry centre MSTARS (grant no. 031L0220A) and CompLS Patho234 (grant no. 031L0207B) and the European Research Council under Horizon 2020 of the EU Framework Programme for Research and Innovation (647257). A.B. acknowledges support by the Ministry of Education AcRF Tier 2 grant MOE2016-T2-2-154, and expresses gratitude to SUTD for the SGPAIRS1811 grant. M.B. was supported in part by the University Medical Center Hamburg-Eppendorf. K.R.M. was supported in part by the Institute of Information and Communications Technology Planning and Evaluation (IITP) grant funded by the Korean government (no. 2017-0-00451, Development of BCI based Brain and Cognitive Computing Technology for Recognizing User’s Intentions using Deep Learning and no. 2019-0-00079, Artificial Intelligence Graduate School Program, Korea University), and by the German Ministry for Education and Research (BMBF) under grants 01IS14013A-E, 01GQ1115, 01GQ0850, 01IS18025A, 031L0207D and 01IS18037A; the German Research Foundation (DFG) under grant Math+, EXC 2046/1, project ID 390685689.

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Authors and Affiliations



A.B., M.B., M.H., K.-R.M. and F.K. conceptualized the project. A.B., M.B., K.H., M.H., S.W., D.H., K.-R.M. and F.K. were responsible for the methodology. A.B., M.B., M.H., S.W., D.H., K.-R.M. and F.K. developed the software. A.B., M.B., M.H., K.-R.M. and F.K. were responsible for validation. A.B., M.B., M.H. and F.K. conducted the formal analysis. A.B., M.B., M.H., C.D., K.-R.M. and F.K. performed investigation. A.B., M.I., C.D., K.-R.M. and F.K. were responsible for resources. Data curation was completed by A.B., M.B., D.H. and F.K.; A.B., M.B., K.-R.M. and F.K. wrote the first draft, which was reviewed and edited by A.B., M.B., M.H., S.W., D.H., K.H., D.T., M.I., A.S., A.H., C.D., K.-R.M. and F.K. Visualization was performed by A.B., M.B., M.H. and F.K.; K.-R.M. and F.K. supervised the project. Funding was secured by A.B., M.I., K.-R.M. and F.K.

Corresponding authors

Correspondence to Klaus-Robert Müller or Frederick Klauschen.

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The authors declare no competing interests.

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Peer review information Nature Machine Intelligence thanks Carsten Marr and the other, anonymous, reviewers for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Methods, Figs. 1–17, Tables 1–13.

Supplementary Data 1

Balanced accuracies and significance of molecular predictions.

Supplementary Data 2

Area under the curve of molecular prediction.

Supplementary Data 3

Number of predictable cases after tail probability analysis for different tails.

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Binder, A., Bockmayr, M., Hägele, M. et al. Morphological and molecular breast cancer profiling through explainable machine learning. Nat Mach Intell 3, 355–366 (2021).

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