Cargando…

Deep learning generates synthetic cancer histology for explainability and education

Artificial intelligence methods including deep neural networks (DNN) can provide rapid molecular classification of tumors from routine histology with accuracy that matches or exceeds human pathologists. Discerning how neural networks make their predictions remains a significant challenge, but explai...

Descripción completa

Detalles Bibliográficos
Autores principales: Dolezal, James M., Wolk, Rachelle, Hieromnimon, Hanna M., Howard, Frederick M., Srisuwananukorn, Andrew, Karpeyev, Dmitry, Ramesh, Siddhi, Kochanny, Sara, Kwon, Jung Woo, Agni, Meghana, Simon, Richard C., Desai, Chandni, Kherallah, Raghad, Nguyen, Tung D., Schulte, Jefree J., Cole, Kimberly, Khramtsova, Galina, Garassino, Marina Chiara, Husain, Aliya N., Li, Huihua, Grossman, Robert, Cipriani, Nicole A., Pearson, Alexander T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10227067/
https://www.ncbi.nlm.nih.gov/pubmed/37248379
http://dx.doi.org/10.1038/s41698-023-00399-4
_version_ 1785050690155970560
author Dolezal, James M.
Wolk, Rachelle
Hieromnimon, Hanna M.
Howard, Frederick M.
Srisuwananukorn, Andrew
Karpeyev, Dmitry
Ramesh, Siddhi
Kochanny, Sara
Kwon, Jung Woo
Agni, Meghana
Simon, Richard C.
Desai, Chandni
Kherallah, Raghad
Nguyen, Tung D.
Schulte, Jefree J.
Cole, Kimberly
Khramtsova, Galina
Garassino, Marina Chiara
Husain, Aliya N.
Li, Huihua
Grossman, Robert
Cipriani, Nicole A.
Pearson, Alexander T.
author_facet Dolezal, James M.
Wolk, Rachelle
Hieromnimon, Hanna M.
Howard, Frederick M.
Srisuwananukorn, Andrew
Karpeyev, Dmitry
Ramesh, Siddhi
Kochanny, Sara
Kwon, Jung Woo
Agni, Meghana
Simon, Richard C.
Desai, Chandni
Kherallah, Raghad
Nguyen, Tung D.
Schulte, Jefree J.
Cole, Kimberly
Khramtsova, Galina
Garassino, Marina Chiara
Husain, Aliya N.
Li, Huihua
Grossman, Robert
Cipriani, Nicole A.
Pearson, Alexander T.
author_sort Dolezal, James M.
collection PubMed
description Artificial intelligence methods including deep neural networks (DNN) can provide rapid molecular classification of tumors from routine histology with accuracy that matches or exceeds human pathologists. Discerning how neural networks make their predictions remains a significant challenge, but explainability tools help provide insights into what models have learned when corresponding histologic features are poorly defined. Here, we present a method for improving explainability of DNN models using synthetic histology generated by a conditional generative adversarial network (cGAN). We show that cGANs generate high-quality synthetic histology images that can be leveraged for explaining DNN models trained to classify molecularly-subtyped tumors, exposing histologic features associated with molecular state. Fine-tuning synthetic histology through class and layer blending illustrates nuanced morphologic differences between tumor subtypes. Finally, we demonstrate the use of synthetic histology for augmenting pathologist-in-training education, showing that these intuitive visualizations can reinforce and improve understanding of histologic manifestations of tumor biology.
format Online
Article
Text
id pubmed-10227067
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-102270672023-05-31 Deep learning generates synthetic cancer histology for explainability and education Dolezal, James M. Wolk, Rachelle Hieromnimon, Hanna M. Howard, Frederick M. Srisuwananukorn, Andrew Karpeyev, Dmitry Ramesh, Siddhi Kochanny, Sara Kwon, Jung Woo Agni, Meghana Simon, Richard C. Desai, Chandni Kherallah, Raghad Nguyen, Tung D. Schulte, Jefree J. Cole, Kimberly Khramtsova, Galina Garassino, Marina Chiara Husain, Aliya N. Li, Huihua Grossman, Robert Cipriani, Nicole A. Pearson, Alexander T. NPJ Precis Oncol Article Artificial intelligence methods including deep neural networks (DNN) can provide rapid molecular classification of tumors from routine histology with accuracy that matches or exceeds human pathologists. Discerning how neural networks make their predictions remains a significant challenge, but explainability tools help provide insights into what models have learned when corresponding histologic features are poorly defined. Here, we present a method for improving explainability of DNN models using synthetic histology generated by a conditional generative adversarial network (cGAN). We show that cGANs generate high-quality synthetic histology images that can be leveraged for explaining DNN models trained to classify molecularly-subtyped tumors, exposing histologic features associated with molecular state. Fine-tuning synthetic histology through class and layer blending illustrates nuanced morphologic differences between tumor subtypes. Finally, we demonstrate the use of synthetic histology for augmenting pathologist-in-training education, showing that these intuitive visualizations can reinforce and improve understanding of histologic manifestations of tumor biology. Nature Publishing Group UK 2023-05-29 /pmc/articles/PMC10227067/ /pubmed/37248379 http://dx.doi.org/10.1038/s41698-023-00399-4 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Dolezal, James M.
Wolk, Rachelle
Hieromnimon, Hanna M.
Howard, Frederick M.
Srisuwananukorn, Andrew
Karpeyev, Dmitry
Ramesh, Siddhi
Kochanny, Sara
Kwon, Jung Woo
Agni, Meghana
Simon, Richard C.
Desai, Chandni
Kherallah, Raghad
Nguyen, Tung D.
Schulte, Jefree J.
Cole, Kimberly
Khramtsova, Galina
Garassino, Marina Chiara
Husain, Aliya N.
Li, Huihua
Grossman, Robert
Cipriani, Nicole A.
Pearson, Alexander T.
Deep learning generates synthetic cancer histology for explainability and education
title Deep learning generates synthetic cancer histology for explainability and education
title_full Deep learning generates synthetic cancer histology for explainability and education
title_fullStr Deep learning generates synthetic cancer histology for explainability and education
title_full_unstemmed Deep learning generates synthetic cancer histology for explainability and education
title_short Deep learning generates synthetic cancer histology for explainability and education
title_sort deep learning generates synthetic cancer histology for explainability and education
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10227067/
https://www.ncbi.nlm.nih.gov/pubmed/37248379
http://dx.doi.org/10.1038/s41698-023-00399-4
work_keys_str_mv AT dolezaljamesm deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT wolkrachelle deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT hieromnimonhannam deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT howardfrederickm deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT srisuwananukornandrew deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT karpeyevdmitry deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT rameshsiddhi deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT kochannysara deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT kwonjungwoo deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT agnimeghana deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT simonrichardc deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT desaichandni deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT kherallahraghad deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT nguyentungd deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT schultejefreej deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT colekimberly deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT khramtsovagalina deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT garassinomarinachiara deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT husainaliyan deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT lihuihua deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT grossmanrobert deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT ciprianinicolea deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation
AT pearsonalexandert deeplearninggeneratessyntheticcancerhistologyforexplainabilityandeducation