메뉴 건너뛰기




Volumn 52, Issue , 2014, Pages 199-211

Limestone: High-throughput candidate phenotype generation via tensor factorization

Author keywords

Dimensionality reduction; EHR phenotyping; Nonnegative tensor factorization

Indexed keywords

CLINICAL RESEARCH; DECISION MAKING; DIMENSIONALITY REDUCTION; FACTORIZATION; LIME; LIMESTONE; TENSORS;

EID: 84919839072     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2014.07.001     Document Type: Article
Times cited : (131)

References (80)
  • 3
    • 19844377332 scopus 로고    scopus 로고
    • Data mining applications in healthcare
    • Koh H.C., Tan G. Data mining applications in healthcare. J Healthcare Inform Manage 2005, 19:64-72.
    • (2005) J Healthcare Inform Manage , vol.19 , pp. 64-72
    • Koh, H.C.1    Tan, G.2
  • 5
  • 6
    • 84863901666 scopus 로고    scopus 로고
    • Better medicine through machine learning
    • Savage N. Better medicine through machine learning. Commun ACM 2012, 55:17-19.
    • (2012) Commun ACM , vol.55 , pp. 17-19
    • Savage, N.1
  • 7
    • 84881349035 scopus 로고    scopus 로고
    • Computer-aided diagnosis of pneumonia in patients with chronic obstructive pulmonary disease
    • Morillo D.S., León Jiménez A., Moreno S.A. Computer-aided diagnosis of pneumonia in patients with chronic obstructive pulmonary disease. J Am Med Inform Assoc 2013, 20:e111-e117.
    • (2013) J Am Med Inform Assoc , vol.20 , pp. e111-e117
    • Morillo, D.S.1    León Jiménez, A.2    Moreno, S.A.3
  • 8
    • 33748181096 scopus 로고    scopus 로고
    • Machine learning for detection and diagnosis of disease
    • Sajda P. Machine learning for detection and diagnosis of disease. Annu Rev Biomed Eng 2006, 8:537-565.
    • (2006) Annu Rev Biomed Eng , vol.8 , pp. 537-565
    • Sajda, P.1
  • 9
    • 34247175892 scopus 로고    scopus 로고
    • Implementation of a bundle of quality indicators for the early management of severe sepsis and septic shock is associated with decreased mortality
    • Nguyen H.B., Corbett S.W., Steele R., Banta J., Clark R.T., Hayes S.R., et al. Implementation of a bundle of quality indicators for the early management of severe sepsis and septic shock is associated with decreased mortality. Crit Care Med 2007, 35:1105-1112.
    • (2007) Crit Care Med , vol.35 , pp. 1105-1112
    • Nguyen, H.B.1    Corbett, S.W.2    Steele, R.3    Banta, J.4    Clark, R.T.5    Hayes, S.R.6
  • 10
    • 77956583100 scopus 로고    scopus 로고
    • Integration of early physiological responses predicts later illness severity in preterm infants
    • 48ra65-48ra65
    • Saria S., Rajani A.K., Gould J., Koller D., Penn A.A. Integration of early physiological responses predicts later illness severity in preterm infants. Sci Translat Med 2010, 2. 48ra65-48ra65.
    • (2010) Sci Translat Med , vol.2
    • Saria, S.1    Rajani, A.K.2    Gould, J.3    Koller, D.4    Penn, A.A.5
  • 11
  • 13
    • 66649095072 scopus 로고    scopus 로고
    • Reflections on the use of electronic health record data for clinical research
    • West S.L., Blake C., Liu Z., McKoy J.N., Oertel M.D., Carey T.S. Reflections on the use of electronic health record data for clinical research. Health Inform J 2009, 15:108-121.
    • (2009) Health Inform J , vol.15 , pp. 108-121
    • West, S.L.1    Blake, C.2    Liu, Z.3    McKoy, J.N.4    Oertel, M.D.5    Carey, T.S.6
  • 14
    • 84864070998 scopus 로고    scopus 로고
    • Interpretable predictive models for knowledge discovery from home-care electronic health records
    • Westra B.L., Dey S., Fang G., Steinbach M., Kumar V., Oancea C., et al. Interpretable predictive models for knowledge discovery from home-care electronic health records. J Healthcare Eng 2011, 2:55-74.
    • (2011) J Healthcare Eng , vol.2 , pp. 55-74
    • Westra, B.L.1    Dey, S.2    Fang, G.3    Steinbach, M.4    Kumar, V.5    Oancea, C.6
  • 15
    • 84861235431 scopus 로고    scopus 로고
    • Mining electronic health records: towards better research applications and clinical care
    • Jensen P.B., Jensen L.J., Brunak S. Mining electronic health records: towards better research applications and clinical care. Nat Rev: Genet 2012, 13:395-405.
    • (2012) Nat Rev: Genet , vol.13 , pp. 395-405
    • Jensen, P.B.1    Jensen, L.J.2    Brunak, S.3
  • 17
    • 0036756222 scopus 로고    scopus 로고
    • Uniqueness of medical data mining
    • Cios K.J., Moore G.W. Uniqueness of medical data mining. Artif Intell Med 2002, 26:1-24.
    • (2002) Artif Intell Med , vol.26 , pp. 1-24
    • Cios, K.J.1    Moore, G.W.2
  • 18
    • 0032895111 scopus 로고    scopus 로고
    • Selected techniques for data mining in medicine
    • Lavrac N. Selected techniques for data mining in medicine. Artif Intell Med 1999, 16:3-23.
    • (1999) Artif Intell Med , vol.16 , pp. 3-23
    • Lavrac, N.1
  • 19
    • 37849052351 scopus 로고    scopus 로고
    • Exploiting missing clinical data in Bayesian network modeling for predicting medical problems
    • Lin J.-H., Haug P.J. Exploiting missing clinical data in Bayesian network modeling for predicting medical problems. J Biomed Inform 2008, 41:1-14.
    • (2008) J Biomed Inform , vol.41 , pp. 1-14
    • Lin, J.-H.1    Haug, P.J.2
  • 23
    • 77953635924 scopus 로고    scopus 로고
    • Prediction modeling using EHR data: challenges, strategies, and a comparison of machine learning approaches
    • Wu J., Roy J., Stewart W.F. Prediction modeling using EHR data: challenges, strategies, and a comparison of machine learning approaches. Med Care 2010, 48:S106-S113.
    • (2010) Med Care , vol.48 , pp. S106-S113
    • Wu, J.1    Roy, J.2    Stewart, W.F.3
  • 24
    • 84871854103 scopus 로고    scopus 로고
    • Next-generation phenotyping of electronic health records
    • Hripcsak G., Albers D.J. Next-generation phenotyping of electronic health records. J Am Med Inform Assoc 2012, 20:117-121.
    • (2012) J Am Med Inform Assoc , vol.20 , pp. 117-121
    • Hripcsak, G.1    Albers, D.J.2
  • 25
    • 84890473073 scopus 로고    scopus 로고
    • Electronic health records based phenotyping in next-generation clinical trials: a perspective from the NIH Health Care Systems Collaboratory
    • Richesson R.L., Hammond W.E., Nahm M., Wixted D., Simon G.E., Robinson J.G., et al. Electronic health records based phenotyping in next-generation clinical trials: a perspective from the NIH Health Care Systems Collaboratory. J Am Med Inform Assoc 2013, 20:e226-e231. 10.1136/amiajnl-2013-001926.
    • (2013) J Am Med Inform Assoc , vol.20 , pp. e226-e231
    • Richesson, R.L.1    Hammond, W.E.2    Nahm, M.3    Wixted, D.4    Simon, G.E.5    Robinson, J.G.6
  • 26
    • 84983036317 scopus 로고    scopus 로고
    • A high throughput semantic concept frequency based approach for patient identification: a case study using type 2 diabetes mellitus clinical notes
    • Wei W-Q, Tao C, Jiang G, Chute CG. A high throughput semantic concept frequency based approach for patient identification: a case study using type 2 diabetes mellitus clinical notes. In: AMIA annual symposium proceedings 2010; 2010. p. 857-61.
    • (2010) AMIA annual symposium proceedings 2010 , pp. 857-861
    • Wei, W.-Q.1    Tao, C.2    Jiang, G.3    Chute, C.G.4
  • 27
    • 84872022133 scopus 로고    scopus 로고
    • Mining electronic health records in the genomics era
    • e1002823-e1002823
    • Denny J.C. Mining electronic health records in the genomics era. PLoS Comput Biol 2012, 8. e1002823-e1002823.
    • (2012) PLoS Comput Biol , vol.8
    • Denny, J.C.1
  • 29
    • 84881328205 scopus 로고    scopus 로고
    • Validation of electronic medical record-based phenotyping algorithms: results and lessons learned from the eMERGE network
    • Newton K.M., Peissig P.L., Kho A.N., Bielinski S.J., Berg R.L., Choudhary V., et al. Validation of electronic medical record-based phenotyping algorithms: results and lessons learned from the eMERGE network. J Am Med Inform Assoc 2013, 20:e147-54.
    • (2013) J Am Med Inform Assoc , vol.20 , pp. e147-e154
    • Newton, K.M.1    Peissig, P.L.2    Kho, A.N.3    Bielinski, S.J.4    Berg, R.L.5    Choudhary, V.6
  • 30
    • 79959654764 scopus 로고    scopus 로고
    • Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience
    • Pathak J., Wang J., Kashyap S., Basford M., Li R., Masys D.R., et al. Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience. J Am Med Inform Assoc 2011, 18:376-386.
    • (2011) J Am Med Inform Assoc , vol.18 , pp. 376-386
    • Pathak, J.1    Wang, J.2    Kashyap, S.3    Basford, M.4    Li, R.5    Masys, D.R.6
  • 33
    • 84890538875 scopus 로고    scopus 로고
    • A collaborative approach to developing an electronic health record phenotyping algorithm for drug-induced liver injury
    • Overby C.L., Pathak J., Gottesman O., Haerian K., Perotte A., Murphy S., et al. A collaborative approach to developing an electronic health record phenotyping algorithm for drug-induced liver injury. J Am Med Inform Assoc 2013, 20:e243-e252. 10.1136/amiajnl-2013-001930.
    • (2013) J Am Med Inform Assoc , vol.20 , pp. e243-e252
    • Overby, C.L.1    Pathak, J.2    Gottesman, O.3    Haerian, K.4    Perotte, A.5    Murphy, S.6
  • 34
    • 79251581866 scopus 로고    scopus 로고
    • The eMERGE network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies
    • McCarty C.A., Chisholm R.L., Chute C.G., Kullo I.J., Jarvik G.P., Larson E.B., et al. The eMERGE network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies. BMC Med Genom 2011, 4:13.
    • (2011) BMC Med Genom , vol.4 , pp. 13
    • McCarty, C.A.1    Chisholm, R.L.2    Chute, C.G.3    Kullo, I.J.4    Jarvik, G.P.5    Larson, E.B.6
  • 36
  • 37
    • 84888200992 scopus 로고    scopus 로고
    • Applying active learning to high-throughput phenotyping algorithms for electronic health records data
    • Chen Y., Carroll R.J., Hinz E.R.M., Shah A., Eyler A.E., Denny J.C., et al. Applying active learning to high-throughput phenotyping algorithms for electronic health records data. J Am Med Inform Assoc 2013, 20(e2):e253-e259. 10.1136/amiajnl-2013-001945.
    • (2013) J Am Med Inform Assoc , vol.20 , Issue.E2 , pp. e253-e259
    • Chen, Y.1    Carroll, R.J.2    Hinz, E.R.M.3    Shah, A.4    Eyler, A.E.5    Denny, J.C.6
  • 38
    • 84880818788 scopus 로고    scopus 로고
    • Modeling and executing electronic health records driven phenotyping algorithms using the NQF quality data model and JBoss® drools engine
    • Li D, Endle CM, Murthy S, Stancl C, Suesse D, Sottara D, et al. Modeling and executing electronic health records driven phenotyping algorithms using the NQF quality data model and JBoss® drools engine. In: AMIA annual symposium proceedings 2012; 2012. p. 532-41.
    • (2012) AMIA annual symposium proceedings 2012 , pp. 532-541
    • Li, D.1    Endle, C.M.2    Murthy, S.3    Stancl, C.4    Suesse, D.5    Sottara, D.6
  • 39
    • 84890520376 scopus 로고    scopus 로고
    • Correlating electronic health record concepts with healthcare process events
    • Hripcsak G., Albers D.J. Correlating electronic health record concepts with healthcare process events. J Am Med Inform Assoc 2013, 20(e2):e311-e318. 10.1136/amiajnl-2013-001922.
    • (2013) J Am Med Inform Assoc , vol.20 , Issue.E2 , pp. e311-e318
    • Hripcsak, G.1    Albers, D.J.2
  • 40
    • 84871551012 scopus 로고    scopus 로고
    • On tensors, sparsity, and nonnegative factorizations
    • Chi E.C., Kolda T.G. On tensors, sparsity, and nonnegative factorizations. SIAM J Matrix Anal Appl 2012, 33:1272-1299.
    • (2012) SIAM J Matrix Anal Appl , vol.33 , pp. 1272-1299
    • Chi, E.C.1    Kolda, T.G.2
  • 43
    • 0033592606 scopus 로고    scopus 로고
    • Learning the parts of objects by non-negative matrix factorization
    • Lee D.D., Seung H.S. Learning the parts of objects by non-negative matrix factorization. Nature 1999, 401:788-791.
    • (1999) Nature , vol.401 , pp. 788-791
    • Lee, D.D.1    Seung, H.S.2
  • 44
    • 84897584251 scopus 로고    scopus 로고
    • Nonnegative matrix factorization: a comprehensive review
    • Wang Y.-X., Zhang Y.-J. Nonnegative matrix factorization: a comprehensive review. IEEE Trans Knowl Data Eng 2013, 25:1336-1353.
    • (2013) IEEE Trans Knowl Data Eng , vol.25 , pp. 1336-1353
    • Wang, Y.-X.1    Zhang, Y.-J.2
  • 47
    • 46649091956 scopus 로고    scopus 로고
    • Reducing microarray data via nonnegative matrix factorization for visualization and clustering analysis
    • Liu W., Yuan K., Ye D. Reducing microarray data via nonnegative matrix factorization for visualization and clustering analysis. J Biomed Inform 2008, 41:602-606.
    • (2008) J Biomed Inform , vol.41 , pp. 602-606
    • Liu, W.1    Yuan, K.2    Ye, D.3
  • 48
    • 68649096448 scopus 로고    scopus 로고
    • Tensor decompositions and applications
    • Kolda T.G., Bader B.W. Tensor decompositions and applications. SIAM Rev 2009, 51:455-500.
    • (2009) SIAM Rev , vol.51 , pp. 455-500
    • Kolda, T.G.1    Bader, B.W.2
  • 49
    • 79960865296 scopus 로고    scopus 로고
    • Applications of tensor (multiway array) factorizations and decompositions in data mining
    • Mørup M. Applications of tensor (multiway array) factorizations and decompositions in data mining. Wiley Interdisc Rev: Data Min Knowl Discov 2011, 1:24-40.
    • (2011) Wiley Interdisc Rev: Data Min Knowl Discov , vol.1 , pp. 24-40
    • Mørup, M.1
  • 51
    • 79952194000 scopus 로고    scopus 로고
    • A survey of multilinear subspace learning for tensor data
    • Lu H., Plataniotis K.N., Venetsanopoulos A.N. A survey of multilinear subspace learning for tensor data. Pattern Recogn 2011, 44:1540-1551.
    • (2011) Pattern Recogn , vol.44 , pp. 1540-1551
    • Lu, H.1    Plataniotis, K.N.2    Venetsanopoulos, A.N.3
  • 52
    • 84863483091 scopus 로고    scopus 로고
    • Feature selection from high-order tensorial data via sparse decomposition
    • Wang D., Kong S. Feature selection from high-order tensorial data via sparse decomposition. Pattern Recogn Lett 2012, 33:1695-1702.
    • (2012) Pattern Recogn Lett , vol.33 , pp. 1695-1702
    • Wang, D.1    Kong, S.2
  • 53
    • 34250499792 scopus 로고
    • Analysis of individual differences in multidimensional scaling via an N-way generalization of "Eckart-Young" decomposition
    • Carroll J.D., Chang J.-J. Analysis of individual differences in multidimensional scaling via an N-way generalization of "Eckart-Young" decomposition. Psychometrika 1970, 35:283-319.
    • (1970) Psychometrika , vol.35 , pp. 283-319
    • Carroll, J.D.1    Chang, J.-J.2
  • 54
    • 0002740437 scopus 로고
    • Foundations of the PARAFAC procedure: models and conditions for an explanatory multimodal factor analysis
    • Harshman R.A. Foundations of the PARAFAC procedure: models and conditions for an explanatory multimodal factor analysis. UCLA Work Papers Phonet 1970, 16:1-84.
    • (1970) UCLA Work Papers Phonet , vol.16 , pp. 1-84
    • Harshman, R.A.1
  • 55
    • 57049095978 scopus 로고    scopus 로고
    • Unsupervised multiway data analysis: a literature survey
    • Acar E., Yener B. Unsupervised multiway data analysis: a literature survey. IEEE Trans Knowl Data Eng 2009, 21:6-20.
    • (2009) IEEE Trans Knowl Data Eng , vol.21 , pp. 6-20
    • Acar, E.1    Yener, B.2
  • 59
    • 31044456392 scopus 로고    scopus 로고
    • Parallel factor analysis as an exploratory tool for wavelet transformed event-related EEG
    • Mørup M., Hansen L.K., Herrmann C.S., Parnas J., Arnfred S.M. Parallel factor analysis as an exploratory tool for wavelet transformed event-related EEG. NeuroImage 2006, 29. 10-10.
    • (2006) NeuroImage , vol.29 , pp. 10
    • Mørup, M.1    Hansen, L.K.2    Herrmann, C.S.3    Parnas, J.4    Arnfred, S.M.5
  • 60
    • 34547858891 scopus 로고    scopus 로고
    • Nonnegative tensor factorization for continuous EEG classification
    • Lee H., Kim Y.-D., Cichocki A., Choi S. Nonnegative tensor factorization for continuous EEG classification. Int J Neural Syst 2007, 17:305-317.
    • (2007) Int J Neural Syst , vol.17 , pp. 305-317
    • Lee, H.1    Kim, Y.-D.2    Cichocki, A.3    Choi, S.4
  • 66
    • 48249100881 scopus 로고    scopus 로고
    • Algorithms for sparse nonnegative Tucker decompositions
    • Mørup M., Hansen L.K., Arnfred S.M. Algorithms for sparse nonnegative Tucker decompositions. Neural Comput 2008, 20:2112-2131.
    • (2008) Neural Comput , vol.20 , pp. 2112-2131
    • Mørup, M.1    Hansen, L.K.2    Arnfred, S.M.3
  • 67
    • 80052781908 scopus 로고    scopus 로고
    • Sparse non-negative tensor factorization using columnwise coordinate descent
    • Liu J., Liu J., Wonka P., Ye J. Sparse non-negative tensor factorization using columnwise coordinate descent. Pattern Recogn 2012, 45.
    • (2012) Pattern Recogn , vol.45
    • Liu, J.1    Liu, J.2    Wonka, P.3    Ye, J.4
  • 70
    • 79952444246 scopus 로고    scopus 로고
    • American heart association advocacy coordinating committee, stroke council, council on cardiovascular radiology and intervention, council on clinical cardiology, council on epidemiology and prevention, council on arteriosclerosis, thrombosis and vascular biology, council on cardiopulmonary, critical care, perioperative and resuscitation, council on cardiovascular nursing, council on the kidney in
    • Heidenreich P.A., Trogdon J.G., Khavjou O.A., Butler J., Dracup K., Ezekowitz M.D., et al. American heart association advocacy coordinating committee, stroke council, council on cardiovascular radiology and intervention, council on clinical cardiology, council on epidemiology and prevention, council on arteriosclerosis, thrombosis and vascular biology, council on cardiopulmonary, critical care, perioperative and resuscitation, council on cardiovascular nursing, council on the kidney in cardiovascular disease, council on cardiovascular surgery and anesthesia, and interdisciplinary council on quality of care and outcomes research, forecasting the future of cardiovascular disease in the United States: a policy statement from the American heart association. Circulation 2011, 123:933-944.
    • (2011) Circulation , vol.123 , pp. 933-944
    • Heidenreich, P.A.1    Trogdon, J.G.2    Khavjou, O.A.3    Butler, J.4    Dracup, K.5    Ezekowitz, M.D.6
  • 71
    • 84855353573 scopus 로고    scopus 로고
    • American heart association statistics committee and stroke statistics subcommittee, heart disease and stroke statistics-2012 update: a report from the American heart association
    • Roger V.L., Go A.S., Lloyd-Jones D.M., Benjamin E.J., Berry J.D., Borden W.B., et al. American heart association statistics committee and stroke statistics subcommittee, heart disease and stroke statistics-2012 update: a report from the American heart association. Circulation 2012, 125:e2-e220.
    • (2012) Circulation , vol.125 , pp. e2-e220
    • Roger, V.L.1    Go, A.S.2    Lloyd-Jones, D.M.3    Benjamin, E.J.4    Berry, J.D.5    Borden, W.B.6
  • 72
    • 84884308321 scopus 로고    scopus 로고
    • Readmissions to U.S. hospitals by diagnosis
    • 2010. Healthcare cost and utilization project (HCUP) statistical briefs, agency for healthcare research and quality
    • Elixhauser A, Steiner C. Readmissions to U.S. hospitals by diagnosis, 2010. Healthcare cost and utilization project (HCUP) statistical briefs, agency for healthcare research and quality; 2012.
    • (2012)
    • Elixhauser, A.1    Steiner, C.2
  • 75
    • 33645392238 scopus 로고    scopus 로고
    • Predicting readmissions and cardiovascular events in heart failure patients
    • Mejhert M., Kahan T., Persson H., Edner M. Predicting readmissions and cardiovascular events in heart failure patients. Int J Cardiol 2006, 109:108-113.
    • (2006) Int J Cardiol , vol.109 , pp. 108-113
    • Mejhert, M.1    Kahan, T.2    Persson, H.3    Edner, M.4
  • 80
    • 77952822074 scopus 로고    scopus 로고
    • PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations
    • Denny J.C., Ritchie M.D., Basford M.A., Pulley J.M., Bastarache L., Brown-Gentry K., et al. PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinformatics 2010, 26:1205-1210.
    • (2010) Bioinformatics , vol.26 , pp. 1205-1210
    • Denny, J.C.1    Ritchie, M.D.2    Basford, M.A.3    Pulley, J.M.4    Bastarache, L.5    Brown-Gentry, K.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.