AMIA Annu Symp Proc - Sophia: A Expedient UMLS Concept Extraction Annotator.

Tópicos

{ extract(1171) text(1153) clinic(932) }
{ algorithm(1844) comput(1787) effici(935) }
{ research(1218) medic(880) student(794) }
{ perform(1367) use(1326) method(1137) }
{ implement(1333) system(1263) develop(1122) }
{ studi(2440) review(1878) systemat(933) }
{ perform(999) metric(946) measur(919) }
{ record(1888) medic(1808) patient(1693) }
{ signal(2180) analysi(812) frequenc(800) }
{ can(981) present(881) function(850) }
{ data(1737) use(1416) pattern(1282) }
{ sequenc(1873) structur(1644) protein(1328) }
{ imag(2830) propos(1344) filter(1198) }
{ assess(1506) score(1403) qualiti(1306) }
{ learn(2355) train(1041) set(1003) }
{ data(1714) softwar(1251) tool(1186) }
{ search(2224) databas(1162) retriev(909) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ compound(1573) activ(1297) structur(1058) }
{ health(3367) inform(1360) care(1135) }
{ gene(2352) biolog(1181) express(1162) }
{ high(1669) rate(1365) level(1280) }
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{ network(2748) neural(1063) input(814) }
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{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
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{ concept(1167) ontolog(924) domain(897) }
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{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
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{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
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{ visual(1396) interact(850) tool(830) }
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{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ use(976) code(926) identifi(902) }
{ 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(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

An opportunity exists for meaningful concept extraction and indexing from large corpora of clinical notes in the Veterans Affairs (VA) electronic medical record. Currently available tools such as MetaMap, cTAKES and HITex do not scale up to address this big data need. Sophia, a rapid UMLS concept extraction annotator was developed to fulfill a mandate and address extraction where high throughput is needed while preserving performance. We report on the development, testing and benchmarking of Sophia against MetaMap and cTAKEs. Sophia demonstrated improved performance on recall as compared to cTAKES and MetaMap (0.71 vs 0.66 and 0.38). The overall f-score was similar to cTAKES and an improvement over MetaMap (0.53 vs 0.57 and 0.43). With regard to speed of processing records, we noted Sophia to be several fold faster than cTAKES and the scaled-out MetaMap service. Sophia offers a viable alternative for high-throughput information extraction tasks.

Resumo Limpo

opportun exist meaning concept extract index larg corpora clinic note veteran affair va electron medic record current avail tool metamap ctake hitex scale address big data need sophia rapid uml concept extract annot develop fulfil mandat address extract high throughput need preserv perform report develop test benchmark sophia metamap ctake sophia demonstr improv perform recal compar ctake metamap vs overal fscore similar ctake improv metamap vs regard speed process record note sophia sever fold faster ctake scaledout metamap servic sophia offer viabl altern highthroughput inform extract task

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