A unified framework for tumor proliferation score prediction in breast histopathology

Kyunghyun Paeng; Sangheum Hwang; Sunggyun Park; Minsoo Kim

doi:10.1007/978-3-319-67558-9_27

A unified framework for tumor proliferation score prediction in breast histopathology

Kyunghyun Paeng
, Sangheum Hwang
, Sunggyun Park
, Minsoo Kim

Dept. of Industrial Engineering

Lunit, Inc.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

52 Scopus citations

Abstract

We present a unified framework to predict tumor proliferation scores from breast histopathology whole slide images. Our system offers a fully automated solution to predicting both a molecular data-based, and a mitosis counting-based tumor proliferation score. The framework integrates three modules, each fine-tuned to maximize the overall performance: An image processing component for handling whole slide images, a deep learning based mitosis detection network, and a proliferation scores prediction module. We have achieved 0.567 quadratic weighted Cohen’s kappa in mitosis counting-based score prediction and 0.652 F1-score in mitosis detection. On Spearman’s correlation coefficient, which evaluates predictive accuracy on the molecular data based score, the system obtained 0.6171. Our approach won first place in all of the three tasks in Tumor Proliferation Assessment Challenge 2016 which is MICCAI grand challenge.

Original language	English
Title of host publication	Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - 3rd International Workshop, DLMIA 2017 and 7th International Workshop, ML-CDS 2017 Held in Conjunction with MICCAI 2017, Proceedings
Editors	Tal Arbel, M. Jorge Cardoso
Publisher	Springer Verlag
Pages	231-239
Number of pages	9
ISBN (Print)	9783319675572
DOIs	https://doi.org/10.1007/978-3-319-67558-9_27
State	Published - 2017
Event	3rd International Workshop on Deep Learning in Medical Image Analysis, DLMIA 2017 and 7th International Workshop on Multimodal Learning for Clinical Decision Support, ML-CDS 2017 held in Conjunction with 20th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2017 - Quebec City, Canada Duration: 14 Sep 2017 → 14 Sep 2017

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	10553 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	3rd International Workshop on Deep Learning in Medical Image Analysis, DLMIA 2017 and 7th International Workshop on Multimodal Learning for Clinical Decision Support, ML-CDS 2017 held in Conjunction with 20th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2017
Country/Territory	Canada
City	Quebec City
Period	14/09/17 → 14/09/17

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Breast histopathology
Convolutional neural networks
Mitosis detection
Tumor proliferation

Access to Document

10.1007/978-3-319-67558-9_27

Cite this

Paeng, K., Hwang, S., Park, S., & Kim, M. (2017). A unified framework for tumor proliferation score prediction in breast histopathology. In T. Arbel, & M. J. Cardoso (Eds.), Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - 3rd International Workshop, DLMIA 2017 and 7th International Workshop, ML-CDS 2017 Held in Conjunction with MICCAI 2017, Proceedings (pp. 231-239). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 10553 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-67558-9_27

Paeng, Kyunghyun ; Hwang, Sangheum ; Park, Sunggyun et al. / A unified framework for tumor proliferation score prediction in breast histopathology. Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - 3rd International Workshop, DLMIA 2017 and 7th International Workshop, ML-CDS 2017 Held in Conjunction with MICCAI 2017, Proceedings. editor / Tal Arbel ; M. Jorge Cardoso. Springer Verlag, 2017. pp. 231-239 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

@inproceedings{432ded6277924b19b49362d1703b1465,

title = "A unified framework for tumor proliferation score prediction in breast histopathology",

abstract = "We present a unified framework to predict tumor proliferation scores from breast histopathology whole slide images. Our system offers a fully automated solution to predicting both a molecular data-based, and a mitosis counting-based tumor proliferation score. The framework integrates three modules, each fine-tuned to maximize the overall performance: An image processing component for handling whole slide images, a deep learning based mitosis detection network, and a proliferation scores prediction module. We have achieved 0.567 quadratic weighted Cohen{\textquoteright}s kappa in mitosis counting-based score prediction and 0.652 F1-score in mitosis detection. On Spearman{\textquoteright}s correlation coefficient, which evaluates predictive accuracy on the molecular data based score, the system obtained 0.6171. Our approach won first place in all of the three tasks in Tumor Proliferation Assessment Challenge 2016 which is MICCAI grand challenge.",

keywords = "Breast histopathology, Convolutional neural networks, Mitosis detection, Tumor proliferation",

author = "Kyunghyun Paeng and Sangheum Hwang and Sunggyun Park and Minsoo Kim",

note = "Publisher Copyright: {\textcopyright} Springer International Publishing AG 2017.; 3rd International Workshop on Deep Learning in Medical Image Analysis, DLMIA 2017 and 7th International Workshop on Multimodal Learning for Clinical Decision Support, ML-CDS 2017 held in Conjunction with 20th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2017 ; Conference date: 14-09-2017 Through 14-09-2017",

year = "2017",

doi = "10.1007/978-3-319-67558-9\_27",

language = "English",

isbn = "9783319675572",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer Verlag",

pages = "231--239",

editor = "Tal Arbel and Cardoso, \{M. Jorge\}",

booktitle = "Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - 3rd International Workshop, DLMIA 2017 and 7th International Workshop, ML-CDS 2017 Held in Conjunction with MICCAI 2017, Proceedings",

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Paeng, K, Hwang, S, Park, S & Kim, M 2017, A unified framework for tumor proliferation score prediction in breast histopathology. in T Arbel & MJ Cardoso (eds), Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - 3rd International Workshop, DLMIA 2017 and 7th International Workshop, ML-CDS 2017 Held in Conjunction with MICCAI 2017, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 10553 LNCS, Springer Verlag, pp. 231-239, 3rd International Workshop on Deep Learning in Medical Image Analysis, DLMIA 2017 and 7th International Workshop on Multimodal Learning for Clinical Decision Support, ML-CDS 2017 held in Conjunction with 20th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2017, Quebec City, Canada, 14/09/17. https://doi.org/10.1007/978-3-319-67558-9_27

A unified framework for tumor proliferation score prediction in breast histopathology. / Paeng, Kyunghyun; Hwang, Sangheum; Park, Sunggyun et al.
Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - 3rd International Workshop, DLMIA 2017 and 7th International Workshop, ML-CDS 2017 Held in Conjunction with MICCAI 2017, Proceedings. ed. / Tal Arbel; M. Jorge Cardoso. Springer Verlag, 2017. p. 231-239 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 10553 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - A unified framework for tumor proliferation score prediction in breast histopathology

AU - Paeng, Kyunghyun

AU - Hwang, Sangheum

AU - Park, Sunggyun

AU - Kim, Minsoo

N1 - Publisher Copyright: © Springer International Publishing AG 2017.

PY - 2017

Y1 - 2017

N2 - We present a unified framework to predict tumor proliferation scores from breast histopathology whole slide images. Our system offers a fully automated solution to predicting both a molecular data-based, and a mitosis counting-based tumor proliferation score. The framework integrates three modules, each fine-tuned to maximize the overall performance: An image processing component for handling whole slide images, a deep learning based mitosis detection network, and a proliferation scores prediction module. We have achieved 0.567 quadratic weighted Cohen’s kappa in mitosis counting-based score prediction and 0.652 F1-score in mitosis detection. On Spearman’s correlation coefficient, which evaluates predictive accuracy on the molecular data based score, the system obtained 0.6171. Our approach won first place in all of the three tasks in Tumor Proliferation Assessment Challenge 2016 which is MICCAI grand challenge.

AB - We present a unified framework to predict tumor proliferation scores from breast histopathology whole slide images. Our system offers a fully automated solution to predicting both a molecular data-based, and a mitosis counting-based tumor proliferation score. The framework integrates three modules, each fine-tuned to maximize the overall performance: An image processing component for handling whole slide images, a deep learning based mitosis detection network, and a proliferation scores prediction module. We have achieved 0.567 quadratic weighted Cohen’s kappa in mitosis counting-based score prediction and 0.652 F1-score in mitosis detection. On Spearman’s correlation coefficient, which evaluates predictive accuracy on the molecular data based score, the system obtained 0.6171. Our approach won first place in all of the three tasks in Tumor Proliferation Assessment Challenge 2016 which is MICCAI grand challenge.

KW - Breast histopathology

KW - Convolutional neural networks

KW - Mitosis detection

KW - Tumor proliferation

UR - https://www.scopus.com/pages/publications/85029818605

U2 - 10.1007/978-3-319-67558-9_27

DO - 10.1007/978-3-319-67558-9_27

M3 - Conference contribution

AN - SCOPUS:85029818605

SN - 9783319675572

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 231

EP - 239

BT - Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - 3rd International Workshop, DLMIA 2017 and 7th International Workshop, ML-CDS 2017 Held in Conjunction with MICCAI 2017, Proceedings

A2 - Arbel, Tal

A2 - Cardoso, M. Jorge

PB - Springer Verlag

T2 - 3rd International Workshop on Deep Learning in Medical Image Analysis, DLMIA 2017 and 7th International Workshop on Multimodal Learning for Clinical Decision Support, ML-CDS 2017 held in Conjunction with 20th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2017

Y2 - 14 September 2017 through 14 September 2017

ER -

Paeng K, Hwang S, Park S, Kim M. A unified framework for tumor proliferation score prediction in breast histopathology. In Arbel T, Cardoso MJ, editors, Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support - 3rd International Workshop, DLMIA 2017 and 7th International Workshop, ML-CDS 2017 Held in Conjunction with MICCAI 2017, Proceedings. Springer Verlag. 2017. p. 231-239. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-67558-9_27

A unified framework for tumor proliferation score prediction in breast histopathology

Abstract

Publication series

Conference

UN SDGs

Keywords

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