J Am Med Inform Assoc - Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification.

Tópicos

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

Resumo

JECTIVE: This paper describes the approaches the authors developed while participating in the i2b2/VA 2010 challenge to automatically extract medical concepts and annotate assertions on concepts and relations between concepts.DESIGN: The authors'approaches rely on both rule-based and machine-learning methods. Natural language processing is used to extract features from the input texts; these features are then used in the authors' machine-learning approaches. The authors used Conditional Random Fields for concept extraction, and Support Vector Machines for assertion and relation annotation. Depending on the task, the authors tested various combinations of rule-based and machine-learning methods.RESULTS: The authors'assertion annotation system obtained an F-measure of 0.931, ranking fifth out of 21 participants at the i2b2/VA 2010 challenge. The authors' relation annotation system ranked third out of 16 participants with a 0.709 F-measure. The 0.773 F-measure the authors obtained on concept extraction did not make it to the top 10.CONCLUSION: On the one hand, the authors confirm that the use of only machine-learning methods is highly dependent on the annotated training data, and thus obtained better results for well-represented classes. On the other hand, the use of only a rule-based method was not sufficient to deal with new types of data. Finally, the use of hybrid approaches combining machine-learning and rule-based approaches yielded higher scores.

Resumo Limpo

jectiv paper describ approach author develop particip ibva challeng automat extract medic concept annot assert concept relat conceptsdesign authorsapproach reli rulebas machinelearn method natur languag process use extract featur input text featur use author machinelearn approach author use condit random field concept extract support vector machin assert relat annot depend task author test various combin rulebas machinelearn methodsresult authorsassert annot system obtain fmeasur rank fifth particip ibva challeng author relat annot system rank third particip fmeasur fmeasur author obtain concept extract make top conclus one hand author confirm use machinelearn method high depend annot train data thus obtain better result wellrepres class hand use rulebas method suffici deal new type data final use hybrid approach combin machinelearn rulebas approach yield higher score

Resumos Similares

J Am Med Inform Assoc - A flexible framework for recognizing events, temporal expressions, and temporal relations in clinical text. ( 0,860519244655918 )
J Am Med Inform Assoc - Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives. ( 0,826055861759137 )
J Am Med Inform Assoc - Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text. ( 0,820667115824848 )
J Am Med Inform Assoc - Eventual situations for timeline extraction from clinical reports. ( 0,803183288095301 )
J Am Med Inform Assoc - Assisted annotation of medical free text using RapTAT. ( 0,801864829797143 )
J Am Med Inform Assoc - An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge. ( 0,79935308186485 )
J Am Med Inform Assoc - A sense inventory for clinical abbreviations and acronyms created using clinical notes and medical dictionary resources. ( 0,796341012006957 )
J Biomed Inform - MedTime: a temporal information extraction system for clinical narratives. ( 0,795883199170101 )
J Am Med Inform Assoc - Automatic discourse connective detection in biomedical text. ( 0,795841485722804 )
J Am Med Inform Assoc - Knowledge-based biomedical word sense disambiguation: an evaluation and application to clinical document classification. ( 0,792918055616233 )
J Biomed Inform - Enhancing clinical concept extraction with distributional semantics. ( 0,787316892543979 )
J Biomed Inform - A concept-driven biomedical knowledge extraction and visualization framework for conceptualization of text corpora. ( 0,785406100503959 )
Int J Med Inform - Bootstrapping a de-identification system for narrative patient records: cost-performance tradeoffs. ( 0,78527165246298 )
Artif Intell Med - Biomedical events extraction using the hidden vector state model. ( 0,777190819793656 )
J Am Med Inform Assoc - A hybrid system for temporal information extraction from clinical text. ( 0,776722455756043 )
J Am Med Inform Assoc - Evaluating temporal relations in clinical text: 2012 i2b2 Challenge. ( 0,775851727253754 )
AMIA Annu Symp Proc - Qualitative analysis of workflow modifications used to generate the reference standard for the 2010 i2b2/VA challenge. ( 0,774882908979772 )
J Biomed Inform - Development and evaluation of RapTAT: a machine learning system for concept mapping of phrases from medical narratives. ( 0,771721704940372 )
J Biomed Inform - Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction. ( 0,771323582948715 )
Int J Med Inform - Detecting temporal expressions in medical narratives. ( 0,771150392085419 )
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. ( 0,771014920018883 )
Int J Med Inform - Detection of infectious symptoms from VA emergency department and primary care clinical documentation. ( 0,768898240172648 )
J Am Med Inform Assoc - Large-scale evaluation of automated clinical note de-identification and its impact on information extraction. ( 0,768451794033374 )
AMIA Annu Symp Proc - Throw the bath water out, keep the baby: keeping medically-relevant terms for text mining. ( 0,767836303481831 )
J Biomed Inform - Anaphoric reference in clinical reports: characteristics of an annotated corpus. ( 0,765873095314998 )
J Am Med Inform Assoc - Anaphoric relations in the clinical narrative: corpus creation. ( 0,765225381817242 )
AMIA Annu Symp Proc - Natural language processing for lines and devices in portable chest x-rays. ( 0,764650672474573 )
AMIA Annu Symp Proc - Extracting Concepts Related to Homelessness from the Free Text of VA Electronic Medical Records. ( 0,763632911721136 )
J. Med. Internet Res. - Web 2.0-based crowdsourcing for high-quality gold standard development in clinical natural language processing. ( 0,761309965672238 )
J Am Med Inform Assoc - MedXN: an open source medication extraction and normalization tool for clinical text. ( 0,76084164089594 )
Appl Clin Inform - Representation of information about family relatives as structured data in electronic health records. ( 0,759469412286042 )
J Biomed Inform - Towards generating a patient's timeline: extracting temporal relationships from clinical notes. ( 0,75735335701142 )
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. ( 0,756355536318449 )
J Integr Bioinform - Automatic extraction of microorganisms and their habitats from free text using text mining workflows. ( 0,756064167893518 )
J Am Med Inform Assoc - 2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text. ( 0,754932515386567 )
J Biomed Inform - A new clustering method for detecting rare senses of abbreviations in clinical notes. ( 0,753533736733256 )
AMIA Annu Symp Proc - Natural language processing to extract follow-up provider information from hospital discharge summaries. ( 0,751463727891376 )
AMIA Annu Symp Proc - Extracting semantic lexicons from discharge summaries using machine learning and the C-Value method. ( 0,75090922528103 )
AMIA Annu Symp Proc - Mapping annotations with textual evidence using an scLDA model. ( 0,746423614496178 )
BMC Med Inform Decis Mak - Text summarization as a decision support aid. ( 0,744884650487052 )
J Biomed Inform - Identifying non-elliptical entity mentions in a coordinated NP with ellipses. ( 0,743673028856836 )
J Am Med Inform Assoc - MITRE system for clinical assertion status classification. ( 0,743257204330077 )
J Biomed Inform - Evaluating the effects of machine pre-annotation and an interactive annotation interface on manual de-identification of clinical text. ( 0,743102396757959 )
J Biomed Inform - Automatically extracting information needs from complex clinical questions. ( 0,742027206909967 )
J Biomed Inform - Lessons learnt from the DDIExtraction-2013 Shared Task. ( 0,741852729983066 )
J Biomed Inform - Evaluating measures of semantic similarity and relatedness to disambiguate terms in biomedical text. ( 0,739439828096626 )
AMIA Annu Symp Proc - Detecting abbreviations in discharge summaries using machine learning methods. ( 0,738437675551608 )
AMIA Annu Symp Proc - Pharmacovigilance on twitter? Mining tweets for adverse drug reactions. ( 0,737776682416531 )
J Biomed Inform - Extraction of events and temporal expressions from clinical narratives. ( 0,735785452648705 )
J Am Med Inform Assoc - Functional evaluation of out-of-the-box text-mining tools for data-mining tasks. ( 0,735537106510997 )
J Am Med Inform Assoc - A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. ( 0,735056886887709 )
AMIA Annu Symp Proc - Semantic processing to identify adverse drug event information from black box warnings. ( 0,734610824627358 )
J Am Med Inform Assoc - A comprehensive study of named entity recognition in Chinese clinical text. ( 0,734508667814025 )
Comput Math Methods Med - Ranking biomedical annotations with annotator's semantic relevancy. ( 0,734169469038221 )
AMIA Annu Symp Proc - Automatically pairing measured findings across narrative abdomen CT reports. ( 0,734126218401878 )
J Med Syst - Redactable signatures for signed CDA Documents. ( 0,731179605493185 )
AMIA Annu Symp Proc - A cloud-based approach to medical NLP. ( 0,730159851200557 )
Perspect Health Inf Manag - A comparison of two approaches to text processing: facilitating chart reviews of radiology reports in electronic medical records. ( 0,728671705425098 )
AMIA Annu Symp Proc - TagLine: Information Extraction for Semi-Structured Text in Medical Progress Notes. ( 0,727417778137784 )
AMIA Annu Symp Proc - Critical finding capture in the impression section of radiology reports. ( 0,726692979088364 )
AMIA Annu Symp Proc - Towards a semantic lexicon for clinical natural language processing. ( 0,725872392644252 )
J Am Med Inform Assoc - Text mining for the Vaccine Adverse Event Reporting System: medical text classification using informative feature selection. ( 0,725705914871782 )
J Biomed Inform - Lexical patterns, features and knowledge resources for coreference resolution in clinical notes. ( 0,724772622580919 )
J Am Med Inform Assoc - Using rule-based natural language processing to improve disease normalization in biomedical text. ( 0,724121978845194 )
Appl Clin Inform - Comparing the effectiveness of computerized adverse drug event monitoring systems to enhance clinical decision support for hospitalized patients. ( 0,722885607472559 )
Int J Med Inform - A methodology to enhance spatial understanding of disease outbreak events reported in news articles. ( 0,720693876129088 )
AMIA Annu Symp Proc - Developing a section labeler for clinical documents. ( 0,720083422146757 )
J Am Med Inform Assoc - A la Recherche du Temps Perdu: extracting temporal relations from medical text in the 2012 i2b2 NLP challenge. ( 0,718615916346424 )
J Biomed Inform - NCBI disease corpus: a resource for disease name recognition and concept normalization. ( 0,71788035038675 )
Comput Methods Programs Biomed - BioAnnote: a software platform for annotating biomedical documents with application in medical learning environments. ( 0,716707709049719 )
AMIA Annu Symp Proc - Discovering peripheral arterial disease cases from radiology notes using natural language processing. ( 0,715187490428506 )
J Biomed Inform - Automatic recognition of disorders, findings, pharmaceuticals and body structures from clinical text: an annotation and machine learning study. ( 0,71309835180755 )
AMIA Annu Symp Proc - Combining corpus-derived sense profiles with estimated frequency information to disambiguate clinical abbreviations. ( 0,711860682689071 )
J Biomed Inform - Desiderata for ontologies to be used in semantic annotation of biomedical documents. ( 0,71091364976378 )
AMIA Annu Symp Proc - Building gold standard corpora for medical natural language processing tasks. ( 0,710633217948295 )
Brief. Bioinformatics - A survey on annotation tools for the biomedical literature. ( 0,707951405597443 )
AMIA Annu Symp Proc - EpiDEA: extracting structured epilepsy and seizure information from patient discharge summaries for cohort identification. ( 0,707441189708995 )
AMIA Annu Symp Proc - Voice-dictated versus typed-in clinician notes: linguistic properties and the potential implications on natural language processing. ( 0,706978984703715 )
J Biomed Inform - UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. ( 0,706826525714127 )
J Am Med Inform Assoc - Machine-learned solutions for three stages of clinical information extraction: the state of the art at i2b2 2010. ( 0,706673394754638 )
J Am Med Inform Assoc - Extracting drug indication information from structured product labels using natural language processing. ( 0,706181054734021 )
BMC Med Inform Decis Mak - Detecting causality from online psychiatric texts using inter-sentential language patterns. ( 0,705683491722341 )
J Biomed Inform - The DDI corpus: an annotated corpus with pharmacological substances and drug-drug interactions. ( 0,70426764923196 )
J Am Med Inform Assoc - Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. ( 0,70181571624804 )
J Biomed Inform - Using an ensemble system to improve concept extraction from clinical records. ( 0,701144398353921 )
J Biomed Inform - Text summarization in the biomedical domain: a systematic review of recent research. ( 0,699490997652155 )
AMIA Annu Symp Proc - Generalizability and comparison of automatic clinical text de-identification methods and resources. ( 0,699188963612375 )
J Biomed Inform - Common data model for natural language processing based on two existing standard information models: CDA+GrAF. ( 0,698734190464739 )
J Am Med Inform Assoc - Towards comprehensive syntactic and semantic annotations of the clinical narrative. ( 0,698472166250623 )
J Am Med Inform Assoc - A supervised framework for resolving coreference in clinical records. ( 0,698196583798054 )
J Biomed Inform - Text de-identification for privacy protection: a study of its impact on clinical text information content. ( 0,696877949423698 )
Sci Data - Building the graph of medicine from millions of clinical narratives. ( 0,696346191238717 )
AMIA Annu Symp Proc - Word Sense Disambiguation of clinical abbreviations with hyperdimensional computing. ( 0,695570677959462 )
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. ( 0,69542803469112 )
J Am Med Inform Assoc - Using machine learning for concept extraction on clinical documents from multiple data sources. ( 0,694835367044818 )
AMIA Annu Symp Proc - A comparative study of current Clinical Natural Language Processing systems on handling abbreviations in discharge summaries. ( 0,694301101755962 )
J Biomed Inform - Degree centrality for semantic abstraction summarization of therapeutic studies. ( 0,693755023534485 )
J Am Med Inform Assoc - Comparison of a semi-automatic annotation tool and a natural language processing application for the generation of clinical statement entries. ( 0,692477659188198 )
AMIA Annu Symp Proc - Identifying discourse connectives in biomedical text. ( 0,692109591563154 )
J Am Med Inform Assoc - Automated extraction of clinical traits of multiple sclerosis in electronic medical records. ( 0,691018617427782 )