Cargando…

Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma

BACKGROUND: Transfer learning is a common practice in image classification with deep learning where the available data is often limited for training a complex model with millions of parameters. However, transferring language models requires special attention since cross-domain vocabularies (e.g. bet...

Descripción completa

Detalles Bibliográficos
Autores principales: Tariq, Amara, Kallas, Omar, Balthazar, Patricia, Lee, Scott Jeffery, Desser, Terry, Rubin, Daniel, Gichoya, Judy Wawira, Banerjee, Imon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8867666/
https://www.ncbi.nlm.nih.gov/pubmed/35197110
http://dx.doi.org/10.1186/s13326-022-00262-8
_version_ 1784656099513729024
author Tariq, Amara
Kallas, Omar
Balthazar, Patricia
Lee, Scott Jeffery
Desser, Terry
Rubin, Daniel
Gichoya, Judy Wawira
Banerjee, Imon
author_facet Tariq, Amara
Kallas, Omar
Balthazar, Patricia
Lee, Scott Jeffery
Desser, Terry
Rubin, Daniel
Gichoya, Judy Wawira
Banerjee, Imon
author_sort Tariq, Amara
collection PubMed
description BACKGROUND: Transfer learning is a common practice in image classification with deep learning where the available data is often limited for training a complex model with millions of parameters. However, transferring language models requires special attention since cross-domain vocabularies (e.g. between two different modalities MR and US) do not always overlap as the pixel intensity range overlaps mostly for images. METHOD: We present a concept of similar domain adaptation where we transfer inter-institutional language models (context-dependent and context-independent) between two different modalities (ultrasound and MRI) to capture liver abnormalities. RESULTS: We use MR and US screening exam reports for hepatocellular carcinoma as the use-case and apply the transfer language space strategy to automatically label imaging exams with and without structured template with > 0.9 average f1-score. CONCLUSION: We conclude that transfer learning along with fine-tuning the discriminative model is often more effective for performing shared targeted tasks than the training for a language space from scratch.
format Online
Article
Text
id pubmed-8867666
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-88676662022-02-28 Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma Tariq, Amara Kallas, Omar Balthazar, Patricia Lee, Scott Jeffery Desser, Terry Rubin, Daniel Gichoya, Judy Wawira Banerjee, Imon J Biomed Semantics Research BACKGROUND: Transfer learning is a common practice in image classification with deep learning where the available data is often limited for training a complex model with millions of parameters. However, transferring language models requires special attention since cross-domain vocabularies (e.g. between two different modalities MR and US) do not always overlap as the pixel intensity range overlaps mostly for images. METHOD: We present a concept of similar domain adaptation where we transfer inter-institutional language models (context-dependent and context-independent) between two different modalities (ultrasound and MRI) to capture liver abnormalities. RESULTS: We use MR and US screening exam reports for hepatocellular carcinoma as the use-case and apply the transfer language space strategy to automatically label imaging exams with and without structured template with > 0.9 average f1-score. CONCLUSION: We conclude that transfer learning along with fine-tuning the discriminative model is often more effective for performing shared targeted tasks than the training for a language space from scratch. BioMed Central 2022-02-23 /pmc/articles/PMC8867666/ /pubmed/35197110 http://dx.doi.org/10.1186/s13326-022-00262-8 Text en © The Author(s) 2022 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Tariq, Amara
Kallas, Omar
Balthazar, Patricia
Lee, Scott Jeffery
Desser, Terry
Rubin, Daniel
Gichoya, Judy Wawira
Banerjee, Imon
Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma
title Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma
title_full Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma
title_fullStr Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma
title_full_unstemmed Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma
title_short Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma
title_sort transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8867666/
https://www.ncbi.nlm.nih.gov/pubmed/35197110
http://dx.doi.org/10.1186/s13326-022-00262-8
work_keys_str_mv AT tariqamara transferlanguagespacewithsimilardomainadaptationacasestudywithhepatocellularcarcinoma
AT kallasomar transferlanguagespacewithsimilardomainadaptationacasestudywithhepatocellularcarcinoma
AT balthazarpatricia transferlanguagespacewithsimilardomainadaptationacasestudywithhepatocellularcarcinoma
AT leescottjeffery transferlanguagespacewithsimilardomainadaptationacasestudywithhepatocellularcarcinoma
AT desserterry transferlanguagespacewithsimilardomainadaptationacasestudywithhepatocellularcarcinoma
AT rubindaniel transferlanguagespacewithsimilardomainadaptationacasestudywithhepatocellularcarcinoma
AT gichoyajudywawira transferlanguagespacewithsimilardomainadaptationacasestudywithhepatocellularcarcinoma
AT banerjeeimon transferlanguagespacewithsimilardomainadaptationacasestudywithhepatocellularcarcinoma