Inverse regression for extraction of tumor site from cancer pathology reports

Abhishek K. Dubey; Hong Jun Yoon; Georgia D. Tourassi

doi:10.1109/BHI.2019.8834527

Inverse regression for extraction of tumor site from cancer pathology reports

Abhishek K. Dubey, Hong Jun Yoon, Georgia D. Tourassi

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

2 Scopus citations

Abstract

Pathology reports are the primary source of information for cancer diagnosis of millions of the cancer patients across the United States. Cancer registries label these reports every year. The coded labels incorporate pertinent information such as cancer location, behavior, and histology. This information when combined with clinical information, medical imaging and even genomic information have a great potential to fuel discoveries in cancer research. The coding process is manual and requires many human experts to label the large volume of pathology reports in a timely manner. In this study, we have developed a supervised inverse regression based auto-labeler to automate the task. The experiments were conducted on a set of 942 pathology reports with human expert labels as the ground truth. We observed that the inverse regression based auto-labeler consistently performed better than or comparable to the best performing state-of-The-Art method. These results demonstrate the potential of inverse regression for reliable information extraction from the pathology reports.

Original language	English
Title of host publication	2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings
Publisher	Institute of Electrical and Electronics Engineers Inc.
ISBN (Electronic)	9781728108483
DOIs	https://doi.org/10.1109/BHI.2019.8834527
State	Published - May 2019
Event	2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Chicago, United States Duration: May 19 2019 → May 22 2019

Publication series

Name	2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings

Conference

Conference	2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019
Country/Territory	United States
City	Chicago
Period	05/19/19 → 05/22/19

Funding

This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of the manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). National Laboratory under Contract DE-AC02-06-CH11357

Funders	Funder number
National Laboratory
National Institutes of Health
U.S. Department of Energy
National Cancer Institute
Argonne National Laboratory	DE-AC02-06-CH11357
Lawrence Livermore National Laboratory	DEAC52-07NA27344
Oak Ridge National Laboratory	DE-AC05-00OR22725
Los Alamos National Laboratory	DE-AC5206NA25396

Keywords

Cancer pathology reports
Classification
Localized sliced inverse regression
Supervised subspace learning

UN SDGs

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

Access to Document

10.1109/BHI.2019.8834527

Cite this

Dubey, A. K., Yoon, H. J., & Tourassi, G. D. (2019). Inverse regression for extraction of tumor site from cancer pathology reports. In 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings Article 8834527 (2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BHI.2019.8834527

Dubey, Abhishek K. ; Yoon, Hong Jun ; Tourassi, Georgia D. / Inverse regression for extraction of tumor site from cancer pathology reports. 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 2019. (2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings).

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title = "Inverse regression for extraction of tumor site from cancer pathology reports",

abstract = "Pathology reports are the primary source of information for cancer diagnosis of millions of the cancer patients across the United States. Cancer registries label these reports every year. The coded labels incorporate pertinent information such as cancer location, behavior, and histology. This information when combined with clinical information, medical imaging and even genomic information have a great potential to fuel discoveries in cancer research. The coding process is manual and requires many human experts to label the large volume of pathology reports in a timely manner. In this study, we have developed a supervised inverse regression based auto-labeler to automate the task. The experiments were conducted on a set of 942 pathology reports with human expert labels as the ground truth. We observed that the inverse regression based auto-labeler consistently performed better than or comparable to the best performing state-of-The-Art method. These results demonstrate the potential of inverse regression for reliable information extraction from the pathology reports.",

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doi = "10.1109/BHI.2019.8834527",

language = "English",

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Dubey, AK, Yoon, HJ & Tourassi, GD 2019, Inverse regression for extraction of tumor site from cancer pathology reports. in 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings., 8834527, 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings, Institute of Electrical and Electronics Engineers Inc., 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019, Chicago, United States, 05/19/19. https://doi.org/10.1109/BHI.2019.8834527

Inverse regression for extraction of tumor site from cancer pathology reports. / Dubey, Abhishek K.; Yoon, Hong Jun ; Tourassi, Georgia D.
2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings. Institute of Electrical and Electronics Engineers Inc., 2019. 8834527 (2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings).

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

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AU - Yoon, Hong Jun

AU - Tourassi, Georgia D.

PY - 2019/5

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N2 - Pathology reports are the primary source of information for cancer diagnosis of millions of the cancer patients across the United States. Cancer registries label these reports every year. The coded labels incorporate pertinent information such as cancer location, behavior, and histology. This information when combined with clinical information, medical imaging and even genomic information have a great potential to fuel discoveries in cancer research. The coding process is manual and requires many human experts to label the large volume of pathology reports in a timely manner. In this study, we have developed a supervised inverse regression based auto-labeler to automate the task. The experiments were conducted on a set of 942 pathology reports with human expert labels as the ground truth. We observed that the inverse regression based auto-labeler consistently performed better than or comparable to the best performing state-of-The-Art method. These results demonstrate the potential of inverse regression for reliable information extraction from the pathology reports.

AB - Pathology reports are the primary source of information for cancer diagnosis of millions of the cancer patients across the United States. Cancer registries label these reports every year. The coded labels incorporate pertinent information such as cancer location, behavior, and histology. This information when combined with clinical information, medical imaging and even genomic information have a great potential to fuel discoveries in cancer research. The coding process is manual and requires many human experts to label the large volume of pathology reports in a timely manner. In this study, we have developed a supervised inverse regression based auto-labeler to automate the task. The experiments were conducted on a set of 942 pathology reports with human expert labels as the ground truth. We observed that the inverse regression based auto-labeler consistently performed better than or comparable to the best performing state-of-The-Art method. These results demonstrate the potential of inverse regression for reliable information extraction from the pathology reports.

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Dubey AK, Yoon HJ , Tourassi GD. Inverse regression for extraction of tumor site from cancer pathology reports. In 2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings. Institute of Electrical and Electronics Engineers Inc. 2019. 8834527. (2019 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2019 - Proceedings). doi: 10.1109/BHI.2019.8834527

Inverse regression for extraction of tumor site from cancer pathology reports

Abstract

Publication series

Conference

Funding

Keywords

UN SDGs

Access to Document

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