Evidence map›Paper›PMID 41031083›Full record

ArticleArXiv2023

Ascle: A Python Natural Language Processing Toolkit for Medical Text Generation.

Rui Yang, Qingcheng Zeng, Keen You, Yujie Qiao, Lucas Huang, Chia-Chun Hsieh, Benjamin Rosand, Jeremy Goldwasser, Amisha D Dave, Tiarnan D L Keenan and 6 more

Abstract readPreprint
In one paragraph

Article in ArXiv, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors.

Rui YangCentre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore.
Qingcheng ZengDepartment of Linguistics, Northwestern University, Evanston, IL, USA.
Keen YouDepartment of Computer Science, Yale University, New Haven, CT, USA.
Yujie QiaoYale School of Public Health, Yale University, New Haven, CT, USA.
Lucas HuangDepartment of Computer Science, Yale University, New Haven, CT, USA.
Chia-Chun HsiehDepartment of Computer Science, Yale University, New Haven, CT, USA.
Benjamin RosandDepartment of Computer Science, Yale University, New Haven, CT, USA.
Jeremy GoldwasserDepartment of Computer Science, Yale University, New Haven, CT, USA.
Amisha D DaveYale New Haven Hospital, Yale School of Medicine, Yale University, New Haven, CT, USA.
Tiarnan D L KeenanDivision of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
Emily Y ChewDivision of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
Dragomir RadevDepartment of Computer Science, Yale University, New Haven, CT, USA.
Zhiyong LuNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Hua XuSection of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, CT, USA.
Qingyu ChenNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Irene LiInformation Technology Center, University of Tokyo, Tokyo, Japan.

Funding

Natural language processing and medical imaging analysis for multi-modality computer assisted diagnosis of ophthalmic diseasesK99LM014024 · NLM · YALE UNIVERSITY · PI CHEN, QINGYU · 2023 to 2023
$92k
NLM NIH HHS K99 LM014024
6 · The paper itself

Abstract

Objective: This study introduces Ascle, a pioneering natural language processing (NLP) toolkit designed for medical text generation. Ascle is tailored for biomedical researchers and healthcare professionals with an easy-to-use, all-in-one solution that requires minimal programming expertise. For the first time, Ascle evaluates and provides interfaces for the latest pre-trained language models, encompassing four advanced and challenging generative functions: question-answering, text summarization, text simplification, and machine translation. In addition, Ascle integrates 12 essential NLP functions, along with query and search capabilities for clinical databases. Materials and Methods: We fine-tuned 32 domain-specific language models and evaluated them thoroughly on 24 established benchmarks. Additionally, for the question-answering task, we conducted manual reviews with clinicians, focusing on Readability, Relevancy, Accuracy, and Completeness, to provide users with a more reliable evaluation. Results: The fine-tuned models consistently improved text generation tasks. For instance, it improved the machine translation task by 20.27 in terms of BLEU score. For the answer generation task, manual reviews showed the generated answers had average scores of 4.95 (out of 5), 4.43, 3.9, and 3.31 in Readability, Relevancy, Accuracy, and Completeness, respectively. Conclusions: This study introduces the development and evaluation of Ascle, a user-friendly NLP toolkit designed for medical text generation. Ascle offers an all-in-one solution including four advanced generative functions: question-answering, text summarization, text simplification, and machine translation. The toolkit, its models, and associated data are publicly available via https://github.com/Yale-LILY/Ascle.

Indexed as

generative artificial intelligencehealthcaremachine learningnatural language processing

Identifiers

PMID41031083
PMCPMC12478431

What OpenQuestion holds

Textmetadata
LicenceCC0
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.