Amara Tariq, Omar Kallas, Patricia Balthazar, Scott Jeffery Lee, Terry Desser, Daniel Rubin, Judy Wawira Gichoya, Imon Banerjee
{"title":"Transfer language space with similar domain adaptation: a case study with hepatocellular carcinoma.","authors":"Amara Tariq, Omar Kallas, Patricia Balthazar, Scott Jeffery Lee, Terry Desser, Daniel Rubin, Judy Wawira Gichoya, Imon Banerjee","doi":"10.1186/s13326-022-00262-8","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Method: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusion: </strong>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.</p>","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":" ","pages":"8"},"PeriodicalIF":1.6000,"publicationDate":"2022-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8867666/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Biomedical Semantics","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1186/s13326-022-00262-8","RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
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.
期刊介绍:
Journal of Biomedical Semantics addresses issues of semantic enrichment and semantic processing in the biomedical domain. The scope of the journal covers two main areas:
Infrastructure for biomedical semantics: focusing on semantic resources and repositories, meta-data management and resource description, knowledge representation and semantic frameworks, the Biomedical Semantic Web, and semantic interoperability.
Semantic mining, annotation, and analysis: focusing on approaches and applications of semantic resources; and tools for investigation, reasoning, prediction, and discoveries in biomedicine.