CHIME leads development of AI-based precision diagnostics using computational pathology. We build large and unique in-house retrospective cohort studies including histopathology whole slide images and clinical information, and develop and validate ML&AI solutions for cancer precision medicine.

CHIME focus on studies in the areas of breast, prostate and colorectal cancer.

Contact

Mattias Rantalainen, PhD (Senior Lecturer, Associate professor)

mattias.rantalainen@ki.se

Group webpage: https://ki.se/en/people/matran

Department of Medical Epidemiology and Biostatistics (MEB)

Karolinska Institute

Stockholm, Sweden

Supported by

The Swedish Cancer Foundation

The Swedish Research Council

VINNOVA

SweLIFE

ERA PerMed

Karolinska Institutet

Data in short:

> 300,000 WSIs

> Population representative cohort studies (breast, colorectal and prostate cancer)

> 600 TB of image data (and growing!)

Papers

Wang Y, Kartasalo K, Weitz P, Acs B, Valkonen M, Larsson C, Ruusuvuori P, Hartman J, Rantalainen M. Predicting molecular phenotypes from histopathology images: A transcriptome-wide expression–morphology analysis in breast cancer. Cancer Research. 2021 Oct 1;81(19):5115-26.

Wang Y, Acs B, Robertson S, Liu B, Solorzano L, Wählby C, Hartman J, Rantalainen M. Improved breast cancer histological grading using deep learning. Annals of Oncology. 2021 Sep 29.

Weitz P, Wang Y, Hartman J, Rantalainen M. An Investigation of Attention Mechanisms in Histopathology Whole-Slide-Image Analysis for Regression Objectives. Proceedings of the IEEE/CVF International Conference on Computer Vision 2021 (pp. 611-619).

Preprints

Wang Y, Kartasalo K, Valkonen M, Larsson C, Ruusuvuori P, Hartman J, Rantalainen M. Predicting molecular phenotypes from histopathology images: a transcriptome-wide expression-morphology analysis in breast cancer. arXiv preprint arXiv:2009.08917. 2020 Sep 18.

Weitz P, Wang Y, Kartasalo K, Egevad L, Lindberg J, Grönberg H, Eklund M, Rantalainen M. Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression based convolutional neural networks. arXiv preprint arXiv:2104.09310. 2021 Apr 19.

Weitz P, Acs B, Hartman J, Rantalainen M. Prediction of Ki67 scores from H&E stained breast cancer sections using convolutional neural networks.

https://openreview.net/forum?id=W9sz0zHk33h

Liu B., Wang Y.,,Weitz P.,,Lindberg J, Egevad L, Grönberg H, Eklund M, Rantalainen M. Using deep learning to detect patients at risk for prostate cancer despite benign biopsies. arXiv preprint

arXiv:2106.14256