J Biomed Inform - An ontology-based similarity measure for biomedical data-application to radiology reports.


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


CKGROUND: Determining similarity between two individual concepts or two sets of concepts extracted from a free text document is important for various aspects of biomedicine, for instance, to find prior clinical reports for a patient that are relevant to the current clinical context. Using simple concept matching techniques, such as lexicon based comparisons, is typically not sufficient to determine an accurate measure of similarity.METHODS: In this study, we tested an enhancement to the standard document vector cosine similarity model in which ontological parent-child (is-a) relationships are exploited. For a given concept, we define a semantic vector consisting of all parent concepts and their corresponding weights as determined by the shortest distance between the concept and parent after accounting for all possible paths. Similarity between the two concepts is then determined by taking the cosine angle between the two corresponding vectors. To test the improvement over the non-semantic document vector cosine similarity model, we measured the similarity between groups of reports arising from similar clinical contexts, including anatomy and imaging procedure. We further applied the similarity metrics within a k-nearest-neighbor (k-NN) algorithm to classify reports based on their anatomical and procedure based groups. 2150 production CT radiology reports (952 abdomen reports and 1128 neuro reports) were used in testing with SNOMED CT, restricted to Body structure, Clinical finding and Procedure branches, as the reference ontology.RESULTS: The semantic algorithm preferentially increased the intra-class similarity over the inter-class similarity, with a 0.07 and 0.08 mean increase in the neuro-neuro and abdomen-abdomen pairs versus a 0.04 mean increase in the neuro-abdomen pairs. Using leave-one-out cross-validation in which each document was iteratively used as a test sample while excluding it from the training data, the k-NN based classification accuracy was shown in all cases to be consistently higher with the semantics based measure compared with the non-semantic case. Moreover, the accuracy remained steady even as k value was increased - for the two anatomy related classes accuracy for k=41 was 93.1% with semantics compared to 86.7% without semantics. Similarly, for the eight imaging procedures related classes, accuracy (for k=41) with semantics was 63.8% compared to 60.2% without semantics. At the same k, accuracy improved significantly to 82.8% and 77.4% respectively when procedures were logically grouped together into four classes (such as ignoring contrast information in the imaging procedure description). Similar results were seen at other k-values.CONCLUSIONS: The addition of semantic context into the document vector space model improves the ability of the cosine similarity to differentiate between radiology reports of different anatomical and image procedure-based classes. This effect can be leveraged for document classification tasks, which suggests its potential applicability for biomedical information retrieval.

Resumo Limpo

ckground determin similar two individu concept two set concept extract free text document import various aspect biomedicin instanc find prior clinic report patient relev current clinic context use simpl concept match techniqu lexicon base comparison typic suffici determin accur measur similaritymethod studi test enhanc standard document vector cosin similar model ontolog parentchild isa relationship exploit given concept defin semant vector consist parent concept correspond weight determin shortest distanc concept parent account possibl path similar two concept determin take cosin angl two correspond vector test improv nonsemant document vector cosin similar model measur similar group report aris similar clinic context includ anatomi imag procedur appli similar metric within knearestneighbor knn algorithm classifi report base anatom procedur base group product ct radiolog report abdomen report neuro report use test snome ct restrict bodi structur clinic find procedur branch refer ontologyresult semant algorithm preferenti increas intraclass similar interclass similar mean increas neuroneuro abdomenabdomen pair versus mean increas neuroabdomen pair use leaveoneout crossvalid document iter use test sampl exclud train data knn base classif accuraci shown case consist higher semant base measur compar nonsemant case moreov accuraci remain steadi even k valu increas two anatomi relat class accuraci k semant compar without semant similar eight imag procedur relat class accuraci k semant compar without semant k accuraci improv signific respect procedur logic group togeth four class ignor contrast inform imag procedur descript similar result seen kvaluesconclus addit semant context document vector space model improv abil cosin similar differenti radiolog report differ anatom imag procedurebas class effect can leverag document classif task suggest potenti applic biomed inform retriev

Resumos Similares

AMIA Annu Symp Proc - Knowledge-based method for determining the meaning of ambiguous biomedical terms using information content measures of similarity. ( 0,806001535652878 )
J Biomed Inform - Evaluating measures of semantic similarity and relatedness to disambiguate terms in biomedical text. ( 0,786104283842944 )
J Biomed Inform - Evaluating semantic similarity and relatedness over the semantic grouping of clinical term pairs. ( 0,703186026080139 )
Inform Health Soc Care - A model based on multi-features to enhance healthcare and medical document retrieval. ( 0,697097394352076 )
Artif Intell Med - A semantic graph-based approach to biomedical summarisation. ( 0,695482708865624 )
J Biomed Inform - A hybrid knowledge-based and data-driven approach to identifying semantically similar concepts. ( 0,688767576432526 )
AMIA Annu Symp Proc - Extracting semantic lexicons from discharge summaries using machine learning and the C-Value method. ( 0,688304535650972 )
J Biomed Inform - Comparing and combining chunkers of biomedical text. ( 0,669019991853882 )
J Biomed Inform - Enhancing clinical concept extraction with distributional semantics. ( 0,667984594376592 )
J Am Med Inform Assoc - A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. ( 0,651103849788505 )
J Am Med Inform Assoc - Knowledge-based biomedical word sense disambiguation: an evaluation and application to clinical document classification. ( 0,644651213348547 )
J Biomed Inform - Unsupervised biomedical named entity recognition: experiments with clinical and biological texts. ( 0,643458081620444 )
Appl Clin Inform - Automating case definitions using literature-based reasoning. ( 0,643076514899707 )
Artif Intell Med - Improved cosine similarity measures of simplified neutrosophic sets for medical diagnoses. ( 0,638691482035487 )
Artif Intell Med - Approaching the axiomatic enrichment of the Gene Ontology from a lexical perspective. ( 0,635502117309497 )
AMIA Annu Symp Proc - Natural language processing to extract follow-up provider information from hospital discharge summaries. ( 0,626826655341535 )
IEEE Trans Image Process - Label transfer by measuring compactness. ( 0,623990826910194 )
Artif Intell Med - Terminological resources for text mining over biomedical scientific literature. ( 0,61609889915259 )
J Biomed Inform - A controlled greedy supervised approach for co-reference resolution on clinical text. ( 0,615843087781738 )
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. ( 0,612297611501725 )
J Biomed Inform - Lessons learnt from the DDIExtraction-2013 Shared Task. ( 0,609874856618368 )
BMC Med Inform Decis Mak - On the efficacy of per-relation basis performance evaluation for PPI extraction and a high-precision rule-based approach. ( 0,60952657636133 )
J Am Med Inform Assoc - Vaccine adverse event text mining system for extracting features from vaccine safety reports. ( 0,606801215044307 )
J Biomed Inform - Semantic similarity estimation in the biomedical domain: an ontology-based information-theoretic perspective. ( 0,605198545932029 )
J Biomed Inform - A new clustering method for detecting rare senses of abbreviations in clinical notes. ( 0,601636803872127 )
J Biomed Inform - Anaphoric reference in clinical reports: characteristics of an annotated corpus. ( 0,601166393450567 )
J Am Med Inform Assoc - Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text. ( 0,601131216321356 )
AMIA Annu Symp Proc - Using Medical Text Extraction, Reasoning and Mapping System (MTERMS) to process medication information in outpatient clinical notes. ( 0,599629175600395 )
J Biomed Inform - Evaluating the effects of machine pre-annotation and an interactive annotation interface on manual de-identification of clinical text. ( 0,598674334086747 )
AMIA Annu Symp Proc - An evaluation of the UMLS in representing corpus derived clinical concepts. ( 0,598497418890046 )
J Biomed Inform - An analysis of FMA using structural self-bisimilarity. ( 0,598090574492771 )
Brief. Bioinformatics - A survey on annotation tools for the biomedical literature. ( 0,595998674248268 )
J Am Med Inform Assoc - Towards comprehensive syntactic and semantic annotations of the clinical narrative. ( 0,593044881270741 )
J Biomed Inform - Ontology modularization to improve semantic medical image annotation. ( 0,5927570705383 )
AMIA Annu Symp Proc - Critical finding capture in the impression section of radiology reports. ( 0,591163943609489 )
Comput. Biol. Med. - Similarity measure for quality control of dental CAD/CAM-applications. ( 0,590688466576992 )
J Am Med Inform Assoc - Evaluation of a pictograph enhancement system for patient instruction: a recall study. ( 0,590035816728074 )
AMIA Annu Symp Proc - A cloud-based approach to medical NLP. ( 0,588611518509205 )
J Am Med Inform Assoc - Learning regular expressions for clinical text classification. ( 0,585365796975357 )
J Biomed Inform - Desiderata for ontologies to be used in semantic annotation of biomedical documents. ( 0,584989782960628 )
J Biomed Inform - Ontology-guided feature engineering for clinical text classification. ( 0,584882297406486 )
Appl Clin Inform - Representation of information about family relatives as structured data in electronic health records. ( 0,583702576007027 )
J Am Med Inform Assoc - Anaphoric relations in the clinical narrative: corpus creation. ( 0,581996213459144 )
Neural Comput - A new class of metrics for spike trains. ( 0,581738646449256 )
J Am Med Inform Assoc - Text mining for the Vaccine Adverse Event Reporting System: medical text classification using informative feature selection. ( 0,581737376030165 )
J Biomed Inform - Lexical patterns, features and knowledge resources for coreference resolution in clinical notes. ( 0,575739185253708 )
AMIA Annu Symp Proc - A literature-based assessment of concept pairs as a measure of semantic relatedness. ( 0,574347872039077 )
J Am Med Inform Assoc - Using rule-based natural language processing to improve disease normalization in biomedical text. ( 0,574148639054919 )
J Biomed Inform - UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. ( 0,573612519208545 )
AMIA Annu Symp Proc - Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics. ( 0,573187747920255 )
J Am Med Inform Assoc - Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives. ( 0,572235920757021 )
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. ( 0,571458839990564 )
AMIA Annu Symp Proc - Shortest Path Edit Distance for Enhancing UMLS Integration and Audit. ( 0,571354204912439 )
J Am Med Inform Assoc - Comparing Medline citations using modified N-grams. ( 0,571228072835918 )
AMIA Annu Symp Proc - Word Sense Disambiguation of clinical abbreviations with hyperdimensional computing. ( 0,570816632904468 )
AMIA Annu Symp Proc - Automatic acquisition of sublanguage semantic schema: towards the word sense disambiguation of clinical narratives. ( 0,570109509231472 )
IEEE Trans Image Process - Co-transduction for shape retrieval. ( 0,566418575077381 )
AMIA Annu Symp Proc - Semantic characteristics of NLP-extracted concepts in clinical notes vs. biomedical literature. ( 0,566001195055124 )
J Biomed Inform - Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction. ( 0,565268431756172 )
J Am Med Inform Assoc - Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. ( 0,565185804469121 )
J Am Med Inform Assoc - An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge. ( 0,55941012681614 )
J Am Med Inform Assoc - MITRE system for clinical assertion status classification. ( 0,558221889002367 )
AMIA Annu Symp Proc - A high throughput semantic concept frequency based approach for patient identification: a case study using type 2 diabetes mellitus clinical notes. ( 0,55812717339994 )
IEEE Trans Image Process - View-based discriminative probabilistic modeling for 3D object retrieval and recognition. ( 0,557914577683097 )
J Am Med Inform Assoc - Evaluating temporal relations in clinical text: 2012 i2b2 Challenge. ( 0,557551830653794 )
J Am Med Inform Assoc - A hybrid system for temporal information extraction from clinical text. ( 0,557277171613864 )
AMIA Annu Symp Proc - Generalizability and comparison of automatic clinical text de-identification methods and resources. ( 0,556391847706557 )
J Biomed Inform - Identifying non-elliptical entity mentions in a coordinated NP with ellipses. ( 0,555775077235872 )
Comput Math Methods Med - Ranking biomedical annotations with annotator's semantic relevancy. ( 0,554623841649932 )
AMIA Annu Symp Proc - The MiPACQ clinical question answering system. ( 0,554500381404719 )
Int J Med Inform - Detection of infectious symptoms from VA emergency department and primary care clinical documentation. ( 0,553700957119629 )
IEEE J Biomed Health Inform - Identifying Similar Cases in Document Networks using Cross-reference Structures. ( 0,552852411873793 )
IEEE Trans Image Process - Image quality assessment using multi-method fusion. ( 0,552797933010308 )
J Biomed Inform - The need for harmonized structured documentation and chances of secondary use - results of a systematic analysis with automated form comparison for prostate and breast cancer. ( 0,552464883051215 )
J Am Med Inform Assoc - Feature engineering combined with machine learning and rule-based methods for structured information extraction from narrative clinical discharge summaries. ( 0,551847542420607 )
AMIA Annu Symp Proc - Mining Biomedical Literature for Terms related to Epidemiologic Exposures. ( 0,551512753825396 )
J Am Med Inform Assoc - Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification. ( 0,5499952247072 )
Int J Med Inform - Bootstrapping a de-identification system for narrative patient records: cost-performance tradeoffs. ( 0,548652903091651 )
J Biomed Inform - NCBI disease corpus: a resource for disease name recognition and concept normalization. ( 0,548176865434065 )
IEEE Trans Image Process - 3-D object retrieval and recognition with hypergraph analysis. ( 0,547962959174865 )
Med Decis Making - Evaluation of markers and risk prediction models: overview of relationships between NRI and decision-analytic measures. ( 0,547828783984725 )
AMIA Annu Symp Proc - Identifying Granularity Differences between Large Biomedical Ontologies through Rules. ( 0,547201892862638 )
J Am Med Inform Assoc - Automatic discourse connective detection in biomedical text. ( 0,545344232243012 )
J Am Med Inform Assoc - Eventual situations for timeline extraction from clinical reports. ( 0,543950179624181 )
J Am Med Inform Assoc - Automated concept-level information extraction to reduce the need for custom software and rules development. ( 0,543547582968433 )
AMIA Annu Symp Proc - TagLine: Information Extraction for Semi-Structured Text in Medical Progress Notes. ( 0,543087310164088 )
AMIA Annu Symp Proc - A Knowledge Intensive Approach to Mapping Clinical Narrative to LOINC. ( 0,542536225123503 )
J Am Med Inform Assoc - A sense inventory for clinical abbreviations and acronyms created using clinical notes and medical dictionary resources. ( 0,541715676136078 )
J Biomed Inform - Extraction of events and temporal expressions from clinical narratives. ( 0,541246221741641 )
AMIA Annu Symp Proc - Towards a semantic lexicon for clinical natural language processing. ( 0,541240611100341 )
AMIA Annu Symp Proc - Throw the bath water out, keep the baby: keeping medically-relevant terms for text mining. ( 0,540619071025444 )
J Biomed Inform - Towards generating a patient's timeline: extracting temporal relationships from clinical notes. ( 0,53990484325945 )
J Am Med Inform Assoc - A flexible framework for recognizing events, temporal expressions, and temporal relations in clinical text. ( 0,538323955359195 )
IEEE Trans Image Process - Linear time distances between fuzzy sets with applications to pattern matching and classification. ( 0,538013393111862 )
AMIA Annu Symp Proc - Extracting Concepts Related to Homelessness from the Free Text of VA Electronic Medical Records. ( 0,537635243301991 )
BMC Med Inform Decis Mak - Dynamic summarization of bibliographic-based data. ( 0,53763434317317 )
AMIA Annu Symp Proc - U-path: An undirected path-based measure of semantic similarity. ( 0,536775233166146 )
J Am Med Inform Assoc - A comprehensive study of named entity recognition in Chinese clinical text. ( 0,536403439964859 )
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. ( 0,536390761193338 )
J Am Med Inform Assoc - Automated clinical trial eligibility prescreening: increasing the efficiency of patient identification for clinical trials in the emergency department. ( 0,535626607504964 )