A systematic review of natural language processing applied to radiology reports

NLP has a significant role in advancing healthcare and has been found to be key in extracting structured information from radiology reports. Understanding recent developments in NLP application to radiology is of significance but recent reviews on this are limited. This study systematically assesses recent literature in NLP applied to radiology reports. Our automated literature search yields 4,799 results using automated filtering, metadata enriching steps and citation search combined with manual review. Our analysis is based on 21 variables including radiology characteristics, NLP methodology, performance, study, and clinical application characteristics. We present a comprehensive analysis of the 164 publications retrieved with each categorised into one of 6 clinical application categories. Deep learning use increases but conventional machine learning approaches are still prevalent. Deep learning remains challenged when data is scarce and there is little evidence of adoption into clinical practice. Despite 17% of studies reporting greater than 0.85 F1 scores, it is hard to comparatively evaluate these approaches given that most of them use different datasets. Only 14 studies made their data and 15 their code available with 10 externally validating results. Automated understanding of clinical narratives of the radiology reports has the potential to enhance the healthcare process but reproducibility and explainability of models are important if the domain is to move applications into clinical use. More could be done to share code enabling validation of methods on different institutional data and to reduce heterogeneity in reporting of study properties allowing inter-study comparisons. Our results have significance for researchers providing a systematic synthesis of existing work to build on, identify gaps, opportunities for collaboration and avoid duplication

The reporting quality of natural language processing studies - systematic review of studies of radiology reports

Abstract Background Automated language analysis of radiology reports using natural language processing (NLP) can provide valuable information on patients’ health and disease. With its rapid development, NLP studies should have transparent methodology to allow comparison of approaches and reproducibility. This systematic review aims to summarise the characteristics and reporting quality of studies applying NLP to radiology reports. Methods We searched Google Scholar for studies published in English that applied NLP to radiology reports of any imaging modality between January 2015 and October 2019. At least two reviewers independently performed screening and completed data extraction. We specified 15 criteria relating to data source, datasets, ground truth, outcomes, and reproducibility for quality assessment. The primary NLP performance measures were precision, recall and F1 score. Results Of the 4,836 records retrieved, we included 164 studies that used NLP on radiology reports. The commonest clinical applications of NLP were disease information or classification (28%) and diagnostic surveillance (27.4%). Most studies used English radiology reports (86%). Reports from mixed imaging modalities were used in 28% of the studies. Oncology (24%) was the most frequent disease area. Most studies had dataset size > 200 (85.4%) but the proportion of studies that described their annotated, training, validation, and test set were 67.1%, 63.4%, 45.7%, and 67.7% respectively. About half of the studies reported precision (48.8%) and recall (53.7%). Few studies reported external validation performed (10.8%), data availability (8.5%) and code availability (9.1%). There was no pattern of performance associated with the overall reporting quality. Conclusions There is a range of potential clinical applications for NLP of radiology reports in health services and research. However, we found suboptimal reporting quality that precludes comparison, reproducibility, and replication. Our results support the need for development of reporting standards specific to clinical NLP studies

Sequencing of 15 622 Gene-bearing BACs Clarifies the Gene-dense Regions of the Barley Genome

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant

A systematic review of natural language processing applied to radiology reports

Background: Natural language processing (NLP) has a significant role in advancing healthcare and has been found to be key in extracting structured information from radiology reports. Understanding recent developments in NLP application to radiology is of significance but recent reviews on this are limited. This study systematically assesses and quantifies recent literature in NLP applied to radiology reports. Methods: We conduct an automated literature search yielding 4836 results using automated filtering, metadata enriching steps and citation search combined with manual review. Our analysis is based on 21 variables including radiology characteristics, NLP methodology, performance, study, and clinical application characteristics. Results: We present a comprehensive analysis of the 164 publications retrieved with publications in 2019 almost triple those in 2015. Each publication is categorised into one of 6 clinical application categories. Deep learning use increases in the period but conventional machine learning approaches are still prevalent. Deep learning remains challenged when data is scarce and there is little evidence of adoption into clinical practice. Despite 17% of studies reporting greater than 0.85 F1 scores, it is hard to comparatively evaluate these approaches given that most of them use different datasets. Only 14 studies made their data and 15 their code available with 10 externally validating results. Conclusions: Automated understanding of clinical narratives of the radiology reports has the potential to enhance the healthcare process and we show that research in this field continues to grow. Reproducibility and explainability of models are important if the domain is to move applications into clinical use. More could be done to share code enabling validation of methods on different institutional data and to reduce heterogeneity in reporting of study properties allowing inter-study comparisons. Our results have significance for researchers in the field providing a systematic synthesis of existing work to build on, identify gaps, opportunities for collaboration and avoid duplication

Language technologies for a multilingual Europe

This volume of the series “Translation and Multilingual Natural Language Processing” includes most of the papers presented at the Workshop “Language Technology for a Multilingual Europe”, held at the University of Hamburg on September 27, 2011 in the framework of the conference GSCL 2011 with the topic “Multilingual Resources and Multilingual Applications”, along with several additional contributions. In addition to an overview article on Machine Translation and two contributions on the European initiatives META-NET and Multilingual Web, the volume includes six full research articles. Our intention with this workshop was to bring together various groups concerned with the umbrella topics of multilingualism and language technology, especially multilingual technologies. This encompassed, on the one hand, representatives from research and development in the field of language technologies, and, on the other hand, users from diverse areas such as, among others, industry, administration and funding agencies. The Workshop “Language Technology for a Multilingual Europe” was co-organised by the two GSCL working groups “Text Technology” and “Machine Translation” (http://gscl.info) as well as by META-NET (http://www.meta-net.eu)

Language technologies for a multilingual Europe

This volume of the series “Translation and Multilingual Natural Language Processing” includes most of the papers presented at the Workshop “Language Technology for a Multilingual Europe”, held at the University of Hamburg on September 27, 2011 in the framework of the conference GSCL 2011 with the topic “Multilingual Resources and Multilingual Applications”, along with several additional contributions. In addition to an overview article on Machine Translation and two contributions on the European initiatives META-NET and Multilingual Web, the volume includes six full research articles. Our intention with this workshop was to bring together various groups concerned with the umbrella topics of multilingualism and language technology, especially multilingual technologies. This encompassed, on the one hand, representatives from research and development in the field of language technologies, and, on the other hand, users from diverse areas such as, among others, industry, administration and funding agencies. The Workshop “Language Technology for a Multilingual Europe” was co-organised by the two GSCL working groups “Text Technology” and “Machine Translation” (http://gscl.info) as well as by META-NET (http://www.meta-net.eu)

Language technologies for a multilingual Europe

This volume of the series “Translation and Multilingual Natural Language Processing” includes most of the papers presented at the Workshop “Language Technology for a Multilingual Europe”, held at the University of Hamburg on September 27, 2011 in the framework of the conference GSCL 2011 with the topic “Multilingual Resources and Multilingual Applications”, along with several additional contributions. In addition to an overview article on Machine Translation and two contributions on the European initiatives META-NET and Multilingual Web, the volume includes six full research articles. Our intention with this workshop was to bring together various groups concerned with the umbrella topics of multilingualism and language technology, especially multilingual technologies. This encompassed, on the one hand, representatives from research and development in the field of language technologies, and, on the other hand, users from diverse areas such as, among others, industry, administration and funding agencies. The Workshop “Language Technology for a Multilingual Europe” was co-organised by the two GSCL working groups “Text Technology” and “Machine Translation” (http://gscl.info) as well as by META-NET (http://www.meta-net.eu)

Language technologies for a multilingual Europe

This volume of the series “Translation and Multilingual Natural Language Processing” includes most of the papers presented at the Workshop “Language Technology for a Multilingual Europe”, held at the University of Hamburg on September 27, 2011 in the framework of the conference GSCL 2011 with the topic “Multilingual Resources and Multilingual Applications”, along with several additional contributions. In addition to an overview article on Machine Translation and two contributions on the European initiatives META-NET and Multilingual Web, the volume includes six full research articles. Our intention with this workshop was to bring together various groups concerned with the umbrella topics of multilingualism and language technology, especially multilingual technologies. This encompassed, on the one hand, representatives from research and development in the field of language technologies, and, on the other hand, users from diverse areas such as, among others, industry, administration and funding agencies. The Workshop “Language Technology for a Multilingual Europe” was co-organised by the two GSCL working groups “Text Technology” and “Machine Translation” (http://gscl.info) as well as by META-NET (http://www.meta-net.eu)

Language technologies for a multilingual Europe

This volume of the series “Translation and Multilingual Natural Language Processing” includes most of the papers presented at the Workshop “Language Technology for a Multilingual Europe”, held at the University of Hamburg on September 27, 2011 in the framework of the conference GSCL 2011 with the topic “Multilingual Resources and Multilingual Applications”, along with several additional contributions. In addition to an overview article on Machine Translation and two contributions on the European initiatives META-NET and Multilingual Web, the volume includes six full research articles. Our intention with this workshop was to bring together various groups concerned with the umbrella topics of multilingualism and language technology, especially multilingual technologies. This encompassed, on the one hand, representatives from research and development in the field of language technologies, and, on the other hand, users from diverse areas such as, among others, industry, administration and funding agencies. The Workshop “Language Technology for a Multilingual Europe” was co-organised by the two GSCL working groups “Text Technology” and “Machine Translation” (http://gscl.info) as well as by META-NET (http://www.meta-net.eu)