J Am Med Inform Assoc - Evaluating the state of the art in disorder recognition and normalization of the clinical narrative.

Tópicos

{ case(1353) use(1143) diagnosi(1136) }
{ extract(1171) text(1153) clinic(932) }
{ learn(2355) train(1041) set(1003) }
{ health(1844) social(1437) communiti(874) }
{ system(1976) rule(880) can(841) }
{ method(2212) result(1239) propos(1039) }
{ imag(1057) registr(996) error(939) }
{ concept(1167) ontolog(924) domain(897) }
{ studi(1410) differ(1259) use(1210) }
{ research(1085) discuss(1038) issu(1018) }
{ state(1844) use(1261) util(961) }
{ decis(3086) make(1611) patient(1517) }
{ featur(3375) classif(2383) classifi(1994) }
{ data(3963) clinic(1234) research(1004) }
{ data(2317) use(1299) case(1017) }
{ group(2977) signific(1463) compar(1072) }
{ use(1733) differ(960) four(931) }
{ implement(1333) system(1263) develop(1122) }
{ motion(1329) object(1292) video(1091) }
{ assess(1506) score(1403) qualiti(1306) }
{ problem(2511) optim(1539) algorithm(950) }
{ search(2224) databas(1162) retriev(909) }
{ model(2341) predict(2261) use(1141) }
{ research(1218) medic(880) student(794) }
{ model(2656) set(1616) predict(1553) }
{ intervent(3218) particip(2042) group(1664) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ measur(2081) correl(1212) valu(896) }
{ bind(1733) structur(1185) ligand(1036) }
{ sequenc(1873) structur(1644) protein(1328) }
{ method(1219) similar(1157) match(930) }
{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ error(1145) method(1030) estim(1020) }
{ chang(1828) time(1643) increas(1301) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ featur(1941) imag(1645) propos(1176) }
{ howev(809) still(633) remain(590) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ patient(2837) hospit(1953) medic(668) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ sampl(1606) size(1419) use(1276) }
{ gene(2352) biolog(1181) express(1162) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ analysi(2126) use(1163) compon(1037) }
{ structur(1116) can(940) graph(676) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

JECTIVE: The ShARe/CLEF eHealth 2013 Evaluation Lab Task 1 was organized to evaluate the state of the art on the clinical text in (i) disorder mention identification/recognition based on Unified Medical Language System (UMLS) definition (Task 1a) and (ii) disorder mention normalization to an ontology (Task 1b). Such a community evaluation has not been previously executed. Task 1a included a total of 22 system submissions, and Task 1b included 17. Most of the systems employed a combination of rules and machine learners.MATERIALS AND METHODS: We used a subset of the Shared Annotated Resources (ShARe) corpus of annotated clinical text--199 clinical notes for training and 99 for testing (roughly 180 K words in total). We provided the community with the annotated gold standard training documents to build systems to identify and normalize disorder mentions. The systems were tested on a held-out gold standard test set to measure their performance.RESULTS: For Task 1a, the best-performing system achieved an F1 score of 0.75 (0.80 precision; 0.71 recall). For Task 1b, another system performed best with an accuracy of 0.59.DISCUSSION: Most of the participating systems used a hybrid approach by supplementing machine-learning algorithms with features generated by rules and gazetteers created from the training data and from external resources.CONCLUSIONS: The task of disorder normalization is more challenging than that of identification. The ShARe corpus is available to the community as a reference standard for future studies.

Resumo Limpo

jectiv shareclef ehealth evalu lab task organ evalu state art clinic text disord mention identificationrecognit base unifi medic languag system uml definit task ii disord mention normal ontolog task b communiti evalu previous execut task includ total system submiss task b includ system employ combin rule machin learnersmateri method use subset share annot resourc share corpus annot clinic text clinic note train test rough k word total provid communiti annot gold standard train document build system identifi normal disord mention system test heldout gold standard test set measur performanceresult task bestperform system achiev f score precis recal task b anoth system perform best accuraci discuss particip system use hybrid approach supplement machinelearn algorithm featur generat rule gazett creat train data extern resourcesconclus task disord normal challeng identif share corpus avail communiti refer standard futur studi

Resumos Similares

J Telemed Telecare - Telecytology for rapid assessment of cytological specimens. ( 0,837333153349513 )
BMC Med Inform Decis Mak - Recognizing clinical entities in hospital discharge summaries using Structural Support Vector Machines with word representation features. ( 0,816632143010515 )
AMIA Annu Symp Proc - A Knowledge Intensive Approach to Mapping Clinical Narrative to LOINC. ( 0,809843755607423 )
Int J Comput Assist Radiol Surg - Structured reporting using a shared indexed multilingual radiology lexicon. ( 0,785173998624543 )
J Am Med Inform Assoc - A rule based solution to co-reference resolution in clinical text. ( 0,775030802544812 )
Int J Comput Assist Radiol Surg - Content-based image-retrieval system in chest computed tomography for a solitary pulmonary nodule: method and preliminary experiments. ( 0,772969792131388 )
AMIA Annu Symp Proc - Building gold standard corpora for medical natural language processing tasks. ( 0,763884302976774 )
J Telemed Telecare - Agreement on diagnoses of mental health problems between an online clinical assignment and a routine clinical assignment. ( 0,75666098426394 )
AMIA Annu Symp Proc - Text Classification towards Detecting Misdiagnosis of an Epilepsy Syndrome in a Pediatric Population. ( 0,734971188824315 )
AMIA Annu Symp Proc - A comparative study of current Clinical Natural Language Processing systems on handling abbreviations in discharge summaries. ( 0,726021600701387 )
J Telemed Telecare - Dynamic telecytopathology for on-site preliminary diagnosis of endoscopic ultrasound-guided fine needle aspiration of pancreatic masses. ( 0,718808597138159 )
AMIA Annu Symp Proc - Application of a temporal reasoning framework tool in analysis of medical device adverse events. ( 0,704050185659599 )
Comput. Biol. Med. - Integration testing through reusing representative unit test cases for high-confidence medical software. ( 0,696223863331616 )
AMIA Annu Symp Proc - Detecting abbreviations in discharge summaries using machine learning methods. ( 0,692116278749935 )
J Am Med Inform Assoc - Capturing patient information at nursing shift changes: methodological evaluation of speech recognition and information extraction. ( 0,690917808104016 )
AMIA Annu Symp Proc - Automated non-alphanumeric symbol resolution in clinical texts. ( 0,687950824959206 )
J Med Syst - Prediction of similarities among rheumatic diseases. ( 0,676947143583225 )
J Telemed Telecare - The accuracy of mobile teleradiology in the evaluation of chest X-rays. ( 0,675967900797692 )
J. Med. Internet Res. - Evaluating a web-based clinical decision support system for language disorders screening in a nursery school. ( 0,67432007678343 )
Telemed J E Health - Help is in your pocket: the potential accuracy of smartphone- and laptop-based remotely guided resuscitative telesonography. ( 0,674182189889222 )
J Telemed Telecare - Telecytology in East Africa: a feasibility study of forty cases using a static imaging system. ( 0,672905207618217 )
Health Informatics J - Tuberculosis-Diagnostic Expert System: an architecture for translating patients information from the web for use in tuberculosis diagnosis. ( 0,671876021951489 )
Artif Intell Med - Biomedical visual data analysis to build an intelligent diagnostic decision support system in medical genetics. ( 0,668977231584245 )
Telemed J E Health - Teledentistry: distant diagnosis of oral disease using e-mails. ( 0,668090147039877 )
Comput Math Methods Med - Deep learning based syndrome diagnosis of chronic gastritis. ( 0,666406888731344 )
J Biomed Inform - Complex epilepsy phenotype extraction from narrative clinical discharge summaries. ( 0,665650631835393 )
J Biomed Inform - Anaphoric reference in clinical reports: characteristics of an annotated corpus. ( 0,662974591657966 )
AMIA Annu Symp Proc - Development and Evaluation of Reference Standards for Image-based Telemedicine Diagnosis and Clinical Research Studies in Ophthalmology. ( 0,662649517826162 )
J Am Med Inform Assoc - Evaluating the impact of pre-annotation on annotation speed and potential bias: natural language processing gold standard development for clinical named entity recognition in clinical trial announcements. ( 0,66105305454278 )
Telemed J E Health - Assessment of static telecytological diagnoses' reproducibility in cervical smears prepared by means of liquid-based cytology. ( 0,65299901111834 )
AMIA Annu Symp Proc - Semantic characteristics of NLP-extracted concepts in clinical notes vs. biomedical literature. ( 0,65208262618108 )
Health Informatics J - University of California, Irvine-Pathology Extraction Pipeline: the pathology extraction pipeline for information extraction from pathology reports. ( 0,645364637552766 )
J. Med. Internet Res. - Web 2.0-based crowdsourcing for high-quality gold standard development in clinical natural language processing. ( 0,645112280848973 )
Int J Med Inform - Artificial intelligence techniques applied to the development of a decision-support system for diagnosing celiac disease. ( 0,643883495130217 )
J Biomed Inform - The EU-ADR corpus: annotated drugs, diseases, targets, and their relationships. ( 0,642465763295105 )
Telemed J E Health - Diagnostic accuracy and image quality using a USB digital eyepiece camera for telecytology-Georgian experience. ( 0,642119270475128 )
AMIA Annu Symp Proc - Active Learning-based corpus annotation--the PathoJen experience. ( 0,639843125153503 )
J Telemed Telecare - A preliminary study of the contribution of telemicroscopy to the diagnosis and management of skin tumours in teledermatology. ( 0,638892186790682 )
Comput. Biol. Med. - Automatic differential diagnosis of pancreatic serous and mucinous cystadenomas based on morphological features. ( 0,635478328715358 )
J Biomed Inform - NCBI disease corpus: a resource for disease name recognition and concept normalization. ( 0,635127628056873 )
J Biomed Inform - Development and evaluation of RapTAT: a machine learning system for concept mapping of phrases from medical narratives. ( 0,633706681687862 )
J Telemed Telecare - Validity and reliability of the assessment and diagnosis of musculoskeletal elbow disorders using telerehabilitation. ( 0,632769120858052 )
Appl Clin Inform - The contribution of the vaccine adverse event text mining system to the classification of possible Guillain-Barr? syndrome reports. ( 0,632197618214172 )
Comput Math Methods Med - Differentiating small (=1cm) focal liver lesions as metastases or cysts by means of computed tomography: a case-study to illustrate a fuzzy logic-based method to assess the impact of diagnostic confidence on radiological diagnosis. ( 0,631177319355537 )
Comput. Biol. Med. - Computational diagnosis and risk evaluation for canine lymphoma. ( 0,631015725138333 )
AMIA Annu Symp Proc - Hedging their mets: the use of uncertainty terms in clinical documents and its potential implications when sharing the documents with patients. ( 0,630575651450822 )
J Am Med Inform Assoc - Knowledge-based biomedical word sense disambiguation: an evaluation and application to clinical document classification. ( 0,628279580663425 )
J Biomed Inform - Disambiguation of ambiguous biomedical terms using examples generated from the UMLS Metathesaurus. ( 0,628120624661922 )
Int J Med Inform - Fuzzy cognitive map in differential diagnosis of alterations in urinary elimination: a nursing approach. ( 0,62669313595631 )
AMIA Annu Symp Proc - Leveraging rich annotations to improve learning of medical concepts from clinical free text. ( 0,626646826553681 )
J Am Med Inform Assoc - Evaluating temporal relations in clinical text: 2012 i2b2 Challenge. ( 0,624053975566925 )
J Biomed Inform - Degree centrality for semantic abstraction summarization of therapeutic studies. ( 0,623576259991448 )
Comput Methods Programs Biomed - Application of clustering analyses to the diagnosis of Huntington disease in mice and other diseases with well-defined group boundaries. ( 0,623468698368473 )
Artif Intell Med - Modern parameterization and explanation techniques in diagnostic decision support system: a case study in diagnostics of coronary artery disease. ( 0,623087790865807 )
J Am Med Inform Assoc - Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives. ( 0,62200027764215 )
J Am Med Inform Assoc - 2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text. ( 0,621532503986506 )
J Med Syst - Decision support algorithm for diagnosis of ADHD using electroencephalograms. ( 0,620615864569386 )
Artif Intell Med - Biomedical events extraction using the hidden vector state model. ( 0,620445415097362 )
J Biomed Inform - Enhancing clinical concept extraction with distributional semantics. ( 0,618094673687636 )
J Biomed Inform - Text summarization in the biomedical domain: a systematic review of recent research. ( 0,616696989548534 )
Comput. Biol. Med. - Fuzzy-based framework for diagnosis of acid-base disorders. ( 0,616110247224224 )
AMIA Annu Symp Proc - Throw the bath water out, keep the baby: keeping medically-relevant terms for text mining. ( 0,615166303358319 )
Int J Med Inform - Automatic identification of heart failure diagnostic criteria, using text analysis of clinical notes from electronic health records. ( 0,614015356953724 )
Appl Clin Inform - Representation of information about family relatives as structured data in electronic health records. ( 0,61255709191378 )
Comput Math Methods Med - Ontology-oriented diagnostic system for traditional Chinese medicine based on relation refinement. ( 0,6120019584094 )
Int J Med Inform - Application of a model based on fuzzy logic for evaluating nursing diagnostic accuracy of students. ( 0,608935505889883 )
AMIA Annu Symp Proc - Semantic processing to identify adverse drug event information from black box warnings. ( 0,608875942690345 )
J Biomed Inform - Automatic detection of patients with invasive fungal disease from free-text computed tomography (CT) scans. ( 0,608273502956906 )
J Am Med Inform Assoc - An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge. ( 0,60706738150489 )
AMIA Annu Symp Proc - Inter-annotator reliability of medical events, coreferences and temporal relations in clinical narratives by annotators with varying levels of clinical expertise. ( 0,606925902345128 )
J Biomed Inform - Classifying obstructive sleep apnea using smartphones. ( 0,60637401421567 )
J Telemed Telecare - Feasibility and diagnostic accuracy of Internet-based dynamic telepathology between Uganda and Germany. ( 0,605530070819498 )
AMIA Annu Symp Proc - Automatically pairing measured findings across narrative abdomen CT reports. ( 0,605477167153384 )
Int J Med Inform - Variations in faculty assessment of NICU flowsheet data: implications for electronic data display. ( 0,604619513623187 )
Perspect Health Inf Manag - A comparison of two approaches to text processing: facilitating chart reviews of radiology reports in electronic medical records. ( 0,603888803198188 )
J Am Med Inform Assoc - Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. ( 0,602463312001476 )
Artif Intell Med - Fuzzy logic-based diagnostic algorithm for implantable cardioverter defibrillators. ( 0,601176114319238 )
J Am Med Inform Assoc - MITRE system for clinical assertion status classification. ( 0,599864921662148 )
Artif Intell Med - A preclustering-based ensemble learning technique for acute appendicitis diagnoses. ( 0,59972445716893 )
Comput. Biol. Med. - A Bayesian network decision model for supporting the diagnosis of dementia, Alzheimers disease and mild cognitive impairment. ( 0,598546868468934 )
J Am Med Inform Assoc - Automatic discourse connective detection in biomedical text. ( 0,594464409465375 )
J Biomed Inform - The DDI corpus: an annotated corpus with pharmacological substances and drug-drug interactions. ( 0,594280051911687 )
AMIA Annu Symp Proc - Natural language processing for lines and devices in portable chest x-rays. ( 0,591724507684983 )
J Telemed Telecare - A prospective study of mobile phones for dermatology in a clinical setting. ( 0,591204725625435 )
AMIA Annu Symp Proc - The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies. ( 0,590248209296124 )
Med Decis Making - Automatically annotating topics in transcripts of patient-provider interactions via machine learning. ( 0,590192426047818 )
J Am Med Inform Assoc - A hybrid system for temporal information extraction from clinical text. ( 0,589184499413604 )
AMIA Annu Symp Proc - Towards a semantic lexicon for clinical natural language processing. ( 0,588379836800926 )
AMIA Annu Symp Proc - Extracting patient demographics and personal medical information from online health forums. ( 0,58714391505864 )
J Am Med Inform Assoc - A flexible framework for recognizing events, temporal expressions, and temporal relations in clinical text. ( 0,586569841213292 )
J Am Med Inform Assoc - Eventual situations for timeline extraction from clinical reports. ( 0,586544883435957 )
Comput Methods Programs Biomed - A web-based system for clinical decision support and knowledge maintenance for deterioration monitoring of hemato-oncological patients. ( 0,586302082233724 )
AMIA Annu Symp Proc - Pharmacovigilance on twitter? Mining tweets for adverse drug reactions. ( 0,586114128356539 )
J Am Med Inform Assoc - Functional evaluation of out-of-the-box text-mining tools for data-mining tasks. ( 0,58524749314193 )
J Biomed Inform - MedTime: a temporal information extraction system for clinical narratives. ( 0,585192565261639 )
AMIA Annu Symp Proc - Natural language processing to extract follow-up provider information from hospital discharge summaries. ( 0,585039570845106 )
Comput. Biol. Med. - Randomized pilot study and qualitative evaluation of a clinical decision support system for brain tumour diagnosis based on SV ?H MRS: evaluation as an additional information procedure for novice radiologists. ( 0,583961205894948 )
J Biomed Inform - Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction. ( 0,583937388967887 )
J Biomed Inform - Evaluating the effects of machine pre-annotation and an interactive annotation interface on manual de-identification of clinical text. ( 0,582228220574838 )
BMC Med Inform Decis Mak - The freetext matching algorithm: a computer program to extract diagnoses and causes of death from unstructured text in electronic health records. ( 0,581279485765539 )