Extraction, labelling, clustering, and semantic mapping of segments from clinical notes

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00209805%3A_____%2F23%3A00079390" target="_blank" >RIV/00209805:_____/23:00079390 - isvavai.cz</a>

Výsledek na webu

<a href="https://pubmed.ncbi.nlm.nih.gov/37167037/" target="_blank" >https://pubmed.ncbi.nlm.nih.gov/37167037/</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1109/TNB.2023.3275195" target="_blank" >10.1109/TNB.2023.3275195</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Extraction, labelling, clustering, and semantic mapping of segments from clinical notes

Popis výsledku v původním jazyce

This work is motivated by the scarcity of tools for accurate, unsupervised information extraction from unstructured clinical notes in computationally underrepresented languages, such as Czech. We introduce a stepping stone to a broad array of downstream tasks such as summarisation or integration of individual patient records, extraction of structured information for national cancer registry reporting or building of semi-structured semantic patient representations that can be used for computing patient embeddings. More specifically, we present a method for unsupervised extraction of semantically-labelled textual segments from clinical notes and test it out on a dataset of Czech breast cancer patients, provided by Masaryk Memorial Cancer Institute (the largest Czech hospital specialising exclusively in oncology). Our goal was to extract, classify (i.e. label) and cluster segments of the free-text notes that correspond to specific clinical features (e.g., family background, comorbidities or toxicities). Finally, we propose a tool for computer-assisted semantic mapping of segment types to pre-defined ontologies and validate it on a downstream task of category-specific patient similarity. The presented results demonstrate the practical relevance of the proposed approach for building more sophisticated extraction and analytical pipelines deployed on Czech clinical notes.

Název v anglickém jazyce

Extraction, labelling, clustering, and semantic mapping of segments from clinical notes

Popis výsledku anglicky

This work is motivated by the scarcity of tools for accurate, unsupervised information extraction from unstructured clinical notes in computationally underrepresented languages, such as Czech. We introduce a stepping stone to a broad array of downstream tasks such as summarisation or integration of individual patient records, extraction of structured information for national cancer registry reporting or building of semi-structured semantic patient representations that can be used for computing patient embeddings. More specifically, we present a method for unsupervised extraction of semantically-labelled textual segments from clinical notes and test it out on a dataset of Czech breast cancer patients, provided by Masaryk Memorial Cancer Institute (the largest Czech hospital specialising exclusively in oncology). Our goal was to extract, classify (i.e. label) and cluster segments of the free-text notes that correspond to specific clinical features (e.g., family background, comorbidities or toxicities). Finally, we propose a tool for computer-assisted semantic mapping of segment types to pre-defined ontologies and validate it on a downstream task of category-specific patient similarity. The presented results demonstrate the practical relevance of the proposed approach for building more sophisticated extraction and analytical pipelines deployed on Czech clinical notes.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2023

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

IEEE transactions on nanobioscience

ISSN

1536-1241

e-ISSN

1558-2639

Svazek periodika

22

Číslo periodika v rámci svazku

4

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

8

Strana od-do

781-788

Kód UT WoS článku

001082250700011

EID výsledku v databázi Scopus

2-s2.0-85162886349