Publications
for Discovering
and Applying Knowledge in Clinical Databases (funded by LM006910)
2000
1.
Elkins
JS, Friedman C, Boden-Albala B, Sacco RL, Hripcsak G.
Coding neuroradiology reports for the Northern Manhattan Stroke Study: a
comparison of natural language processing and manual review. Comput Biomed Res 2000;33:110.
2.
Wilcox
A, Hripcsak G, Friedman C. Using knowledge sources to improve classification of
medical text reports. Sixth ACM SIGKDD International Conference on Knowledge
Discovery and Data Mining; 2000 August 20; Boston; 2000:1156.
3.
Wilcox
A, Hripcsak G. Medical text representations for inductive learning. Proc AMIA Symp 2000:9237.
4.
Yu
H, Hripcsak G. Hereditary disease discovery from a clinical data warehouse. Proc AMIA Symp 2000:1161.
5.
Yu
H, Hripcsak G. A large scale, cross-disease family health history data set. Proc AMIA Symp 2000:1162.
6.
Cai J, Hripcsak G, Johnson S. Generic data modeling
for home telemonitoring of chronically ill patients. Proc AMIA Symp 2000:11620.
7.
Liu
H, Friedman C. A method for vocabulary development and visualization based on
medical language processing and XML. Proc AMIA Symp. 2000:5026.
8.
Chuang
J, Hripcsak G, Jenders RA. Considering clustering: a
methodological review of clinical decision support system studies. Proc AMIA Symp 2000:14650.
9.
Wilcox
A. Automated Classification of Medical Text Reports (dissertation). Columbia University,
Department of Medical Informatics, 2000.
2001
10.
Stetson
PD, McKnight LK, Bakken S, Curran CC, Kubose TT,
Cimino JJ. Development of an ontology to model medical
errors, information needs and the clinical communication space. Proc AMIA Symp 2001;6726.
11.
Krauthammer
M, Hripcsak G. A knowledge model for the interpretation and visualization of
NLP-parsed discharge summaries. Proc AMIA Symp 2001: 33943.
12.
Campbell
DA, Johnson SB. Comparing syntactic complexity in medical and non-medical
corpora. Proc AMIA Symp.
2001;904.
13.
Friedman
C, Liu J, Shagina L, Johnson S, Hripcsak G.
Evaluating the UMLS as a source of lexical knowledge for medical language
processing. Proc AMIA Symp
2001:18993.
2002
14.
Hripcsak
G, Heitjan D. Measuring agreement in medical
informatics reliability studies. J Biomed Inform 2002;35:99110.
15.
Hripcsak
G, Austin JHM, Alderson PO, Friedman C. Use of natural language processing to
translate clinical information from a database of 889,921 chest radiographic
reports. Radiology 2002;224:15763.
16.
Hripcsak
G, Wilcox A. Reference standards, judges, comparison subjects: roles for
experts in evaluating system performance. J Am Med Inform Assoc
2002;9:115.
17.
Chuang
JH, Hripcsak G, Heitjan DF. Design and analysis of
controlled trials in naturally clustered environments: implications for medical
informatics. J Am Med Inform Assoc 2002;9:2308.
18.
Yu
H, Hripcsak G, Friedman C. Mapping abbreviations to full forms in biomedical
articles. J Am Med Inform Assoc 2002;9:26272.
19.
Stetson
PD, Johnson SB, Scotch M, Hripcsak G. The sublanguage of cross-coverage. Proc AMIA Symp 2002: 7426.
20.
McKnight
LK, Wilcox A, Hripcsak G. The effect of sample size and disease prevalence on
supervised machine learning of narrative data. Proc
AMIA Symp 2002:51922.
21.
Krauthammer
M, Johnson SB, Hripcsak G, Campbell DA, Friedman C. Representing nested
semantic information in a linear string of text using XML. Proc
AMIA Symp 2002:4059.
22.
Chuang
JH, Friedman C, Hripcsak G. A comparison of the Charlson
comorbidities derived from medical language processing and administrative data.
Proc AMIA Symp 2002: 1604.
23.
Malhotra R, Austin JHM, Mujoomdar
A, Powell CA, Pearson GDN, Shiau MC, Raftopoulos H, Hripcsak G. Non-small cell carcinoma of
lung: size of the primary cancer, gender, and age of the patient as predictors
of metastasis to thoracic lymph nodes, lung, bone, liver, and adrenal glands
(abstract). RSNA 2002.
24.
Wilcox
A, Hripcsak G, Knirsch C. Knowledge discovery using
the electronic medical record (poster). Proc AMIA Symp 2002: 1198.
25.
Bu
D, Hripcsak G. Case-based reasoning for medical risk stratification: contrast
associated nephropathy (poster). Proc AMIA Symp 2002: 986.
2003
26.
Hripcsak
G, Bakken S, Stetson PD, Patel VL. Mining complex clinical data for patient
safety research: a framework for event discovery. J Biomed Inform 2003;36:12030.
27.
Cao
H, Stetson P, Hripcsak G. Assessing explicit error reporting in the narrative
electronic medical record using keyword searching. J Biomed Inform 2003;36:99105.
28.
Murff HJ, Patel VL, Hripcsak G, Bates DW. Detecting
adverse events for patient safety research: a review of current methodologies.
J Biomed Inform 2003;36:13143.
29.
Wilcox
AB, Hripcsak G. The role of domain knowledge in automating medical text report
classification. J Am Med Inform Assoc 2003;10:3308.
30.
Cao
H, Stetson P, Hripcsak G. Assessing explicit error reporting in the narrative
electronic medical record using keyword searching (poster). Proc
AMIA Symp 2003:803.
31.
Johnson
SB, Campbell DA, Krauthammer M, Tulipano PK, Medonca EA, Friedman C, Hripcsak G. A native XML database
design for clinical document research (poster). Proc
AMIA Symp 2003:883.
32.
Bates,
D.W., R.S. Evans, H. Murff, P.D. Stetson, L. Pizziferri, and G. Hripcsak, Detecting adverse events using
information technology. J Am Med Inform Assoc, 2003.
10(2): p. 115-28.
2004
33.
Friedman
C, Shagina L, Lussier Y,
Hripcsak G. Automated encoding of clinical documents based on natural language processing . J Am Med Inform Assoc
2004;11:392402.
34.
Hripcsak
G, Stetson PD, Gordon P. Using the FCIM curricular guide and administrative
codes to assess internal medicine resident breadth of experience. Acad Med 2004;79:55763.
35.
Zhou
L, Hripcsak G, Parsons S, Das AK, Johnson SB. Reasoning about time in
electronic discharge summaries using temporal constraint satisfaction
techniques (abstract). Intelligent Data Analysis in Medicine and Pharmacology
Workshop (IDAMAP-2004); 2004 September 6; Stanford, CA; 2004.
36.
Yu
A, Stetson PD, Hripcsak G. Detection of adverse events using conflicts in the
electronic medical record (poster). Medinfo
2004:1923.
37.
Cao
H, Chiang MF, Cimino JJ, Friedman C, Hripcsak G. Automatic summarization of
patient discharge summaries to create problem lists using medical language
processing (poster). Medinfo 2004:1540.
2005
38.
Markatou M, Tian H, Biswas S, Hripcsak G. Analysis of variance of
cross-validation estimators of the generalization error. Journal of Machine
Learning Research, 2005;6:112768..
39.
Melton
GB, Hripcsak G. Automated detection of adverse events using natural language
processing in discharge summaries. J Am Med Inform Assoc
2005;12:44857.
40. Hripcsak G, Rothschild
AS. Agreement, the F-measure, and reliability in information retrieval. J Am
Med Inform Assoc 2005;12:2968.
41.
Hripcsak
G, Zhou L, Parsons S, Das AK, Johnson SB. Modeling electronic discharge
summaries as a simple temporal constraint satisfaction problem. J Am Med Inform
Assoc 2005;12:5563.
42.
Cao
H, Markatou M, Melton GB, Chiang MF, Hripcsak, G.
Mining a clinical data warehouse to discover disease-finding associations using
co-occurrence statistics. Proc AMIA Symp 2005:10610.
43.
Zhou
L, Friedman C, Parsons S, Hripcsak G. System architecture for temporal
information extraction, representation and reasoning in clinical narrative
reports. Proc AMIA Symp
2005:86973.
44. Stetson PD, Keselman A, Rappaport D, Van Vleck
T, Cooper M, Boyer A, Hripcsak G. Electronic discharge summaries (abstract). Proc AMIA Symp 2005:1121.
2006
45.
Melton
GB, Parsons S, Morrison FP, Rothschild AS, Markatou
M, Hripcsak G. Inter-patient distance metrics using SNOMED CT defining
relationships. J Biomed Inform 2006;39:697705.
46. Zhou L, Melton GB,
Parsons S, Hripcsak G. A temporal constraint structure for extracting temporal
information from clinical narrative. J Biomed Inform 2006;39:42439.
47.
Zhou
L, Parsons S, Hripcsak G. Handling implicit and uncertain temporal information
in medical text (poster). Proc AMIA Symp 2006;1158. PMC1839470
48. Chen ES, Hripcsak G,
Friedman C. Disseminating natural language processed clinical narratives. Proc AMIA Symp 2006:126-30.
PMC1839529
49. Hripcsak G, Bamberger A,
Friedman C. Fever detection in clinic visit notes using a general purpose
processor (abstract). Fifth Annual Syndromic
Surveillance Conference; 2006 September 1920; Baltimore, MD: International
Society for Disease Surveillance, 2006.
50.
Chen
ES, Wajngurt D, Qureshi K,
Hyman S, Hripcsak G. Automated real-time detection and notification of positive
infection cases (poster). Proc AMIA Symp 2006;883. PMC1839567
2007
51.
Cao
H, Hripcsak G, Markatou M. A statistical methodology
for analyzing cooccurrence data from a large sample.
J Biomed Inform 2007;40:343-52. PMC2041889
52.
Hripcsak
G, Knirsch C, Zhou L, Wilcox A, Melton GB. Using
discordance to improve classification in narrative clinical databases: an
application to community-acquired pneumonia. Comput Biol Med 2007;37:296304.
53.
Zhou
L, Hripcsak G. Temporal reasoning with medical dataA review with emphasis on
medical natural language processing. J Biomed Inform 2007;40:
183-202. (republished in the IMIA Yearbook of Medical Informatics)
54.
Xu H, Fan JW, Hripcsak G, Mendonca
EA, Markatou M, Friedman C. Gene symbol
disambiguation using knowledge-based profiles. Bioinformatics 2007;23:101522.
55.
Chen
ES, Stetson PD, Lussier YA, Hripcsak G, Friedman C.
Detection of practice pattern trends through natural language processing of
clinical narratives and biomedical literature. Proc
AMIA Symp 2007.
56.
Hripcsak
G, Kaushal R, Johnson KB, Ash JS, Bates DW, Block R,
Frisse ME, Kern LM, Marchibroda J, Overhage JM,
Wilcox AB. The United Hospital Fund Meeting on Evaluating Health Information
Exchange. J Biomed Inform. 2007 Dec;40(6 Suppl):S310. PMC2140082
57.
Hripcsak
G. Automated public health reporting: a familiar but cantankerous friend.
Advances in Disease Surveillance 2007;3(4):1-2.
58.
Hripcsak
G, Sengupta S, Wilcox A, Green RA. Emergency department access to a
longitudinal medical record. J Am Med Inform Assoc
2007;14:235-8. PMC2213459
2008
59.
Chen
ES, Hripcsak G, Xu H, Markatou
M, Friedman C. Automated acquisition of disease-drug knowledge from biomedical
and clinical documents: an initial study. J Am Med Inform Assoc
2008;15:87-98. PMC2274872
60. Zhou L, Parsons S,
Hripcsak G. The evaluation of a temporal reasoning system in processing
clinical discharge summaries. J Am Med Inform Assoc
2008;15:99106. PMC2274869
61.
Chapman
WW, Dowling JN, Hripcsak G. Evaluation of training with an annotation schema
for manual annotation of clinical conditions from emergency department reports.
Int J Med Inform 2008;77:10713.
62.
Sengupta
S, Calman NS, Hripcsak G. A model for expanded public
health reporting in the context of HIPAA. J Am Med Inform Assoc
2008;15:569-74.
63.
Cao
H, Melton GB, Markatou M, Hripcsak G. Use of
abstracted patient-specific features to assist an information-theoretic
measurement to assess similarity between medical cases. J Biomed Inform 2008;41:882-8. PMC2584163
64. Lai AM, Parsons S,
Hripcsak G. Fuzzy temporal constraint networks for clinical information. Proc AMIA Symp 2008:374-8.
PMC2655952
65.
Gold
S, Elhadad N, Zhu X, Cimino JJ, Hripcsak G. Extracting structured medication
event information from narrative clinical notes. Proc
AMIA Symp 2008:237-41. PMC2655993
66. Morrison FP, Li L, Lai A, Hripcsak G. Repurposing the clinical record: can an
existing natural language processing system de-identify clinical notes? J Am
Med Inform Assoc 2008;16:37-9.
PMC2605586
2009
67.
Hripcsak
G, Elhadad N, Chen C, Zhou L, Morrison FP. Using empirical semantic correlation
to interpret temporal assertions in clinical texts. J Am Med Inform Assoc 2009;16:220-7. PMC2649319
68. Wang X, Hripcsak G, Markatou M, Friedman C. Active computerized pharmacovigilance using natural language processing,
statistics, and electronic health records: a feasibility study. J Am Med Inform
Assoc 2009;16:328-37.
PMC2732239
69. Sinha A, Hripcsak G, Markatou M. Large data sets in biomedicine: analytical
issues. J Am Med Inform Assoc 2009;16:759-67.
PMC3002128
70.
Hripcsak
G, Soulakis ND, Li L, Morrison FP, Lai AM, Friedman
C, Calman NS, Mostashari F.
Syndromic surveillance using ambulatory electronic
health records. J Am Med Inform Assoc 2009;16:354-61. PMC2732227
71.
Wang
X, Hripcsak G, Friedman C. Characterizing environmental and phenotypic
associations using information theory and electronic health records. BMC
Bioinformatics 2009;10(Suppl
9):S13. PMC2745684
72.
Morrison
FP, Sengupta S, Hripcsak G. Using a pipeline to improve de-identification
performance. Proc AMIA Symp
2009;447-51. PMC2815438
73.
Albers
DJ, Hripcsak G. An information-theoretic approach to the phenome
(abstract). AMIA Summit on Translational Bioinformatics; 2009 March 15-17; San
Francisco, CA; 2009.
74.
Albers
DJ, Hripcsak G. Characterizing EHR laboratory data with information theoretic
predictability (poster). Proc AMIA Symp 2009;759.
75.
Weng
C, Smiley R, Flood P, Cheng B, Friedman C, Hripcsak G. A phenome-wide
association study through secondary uses of clinical and research data
(poster). 2009 AMIA Summit on Translational Bioinformatics.
76.
Zhu
X, Gold S, Lai A, Hripcsak G, Cimino JJ. Using Timeline Displays to Improve
Medication Reconciliation. International Conference on eHealth,
Telemedicine, and Social Medicine (eTELEMED 2009),
2009 February 1-7; Cancun, Mexico, 2009.
2010
77.
Albers
DJ, Hripcsak G. A statistical dynamics approach to the study of human health
data: resolving population scale diurnal variation in laboratory data. Physics
Letters A 2010;374:1159-64. PMC2882798
78.
Khiabanian H, Holmes AB, Kelly BJ, Gururaj M, Hripcsak G, Rabadan R. Signs of the 2009
influenza pandemic in the New York-Presbyterian electronic health records. PLoS ONE 2010;5(9): e12658.
PMC2936568
79.
Botsis T, Anagnostou V, Hartvigsen G, Hripcsak G, Weng C. Developing a
multivariable prognostic model for pancreatic endocrine tumors using the
clinical data warehouse resources of a single institution. Appl
Clin Inform 2010;1:38-49.
PMC3087306
80. Albers DJ, Hripcsak G.
EHR dynamics and stratification (abstract). AMIA Summit on Translational
Bioinformatics; 2010 March 10-12; San Francisco, CA; 2010.
81.
Albers
DJ, Hripcsak G. Aggregating EHR subpopulations to leverage EHR population size
for calculating temporal information theoretic quantities (abstract). Proc AMIA Symp 2010.
82.
Wang
X, Chase H, Markatou M, Hripcsak G, Friedman C.
Selecting information in electronic health records for knowledge acquisition. J
Biomed Inform 2010;43:595-601. PMC2902678
83.
Perotte
A, Hripcsak G. Using the entropy of ICD9 documentation across patients to
characterize disease chronicity (abstract). Proc AMIA
Symp 2010.
2011
84. Hripcsak G, Albers DJ,
Perotte A. Exploiting time in electronic health record correlations. J Am Med
Inform Assoc 2011;18:Suppl 1
i109-i115. Published Online First 2011 Nov 23. doi:10.1136/amiajnl-2011-000463.
85.
Hripcsak
G, Knirsch C, Zhou L, Wilcox A, Melton GB. Bias
associated with mining electronic health records. J Biomed Discov
Collab 2011;6:48-52. PMC3149555
86. Kleinberg S, Hripcsak G.
A review of causal inference for biomedical informatics. J Biomed Inform 2011;44:1102-12.
87.
Wilcox
AB, Chen YH, Hripcsak G. Minimizing electronic health record patient-note
mismatches. J Am Med Inform Assoc 2011;18(4):511-4. PMC3128397
88. Hripcsak G, Vawdrey DK,
Fred MR, Bostwick SB. Use of
electronic clinical documentation: time spent and team interactions. J Am Med
Inform Assoc 2011;18:112-7.
PMC3116265
89. Harpaz R, Perez H, Chase HS,
Rabadan R, Hripcsak G, Friedman C. Biclustering of
adverse drug events in FDAs spontaneous reporting system. Clin
Pharmacol Ther 2011;89:243-50. PMC3282185
90. Albers DJ, Schmidt M,
Hripcsak G. Population physiology: conjoining EHR dynamics with physiological
modeling (abstract). In: AMIA Summit on Translational Bioinformatics; 2011
March 7-9; San Francisco, CA; 2011.
91.
Kleinberg
S, Hripcsak G. Understanding variable representation for causal inference in
EHRs (poster). AMIA Summit on Translational Bioinformatics; 2011 March 7-9; San
Francisco, CA; 2011.
92.
Perotte
A, Hripcsak G. Using Density Estimates to Aggregate Patients and Summarize
Disease Evolution (poster). AMIA Summit on Translational Bioinformatics; 2011
March 7-9; San Francisco, CA; 2011;138.
93.
Hripcsak
G, Albers DJ. Electronic health record (EHR) dynamics: an introduction
(abstract). Society for Industrial and Applied Mathematics Conference on
Applications of Dynamical Systems; 2011 May 22-26; Snowbird, UT; 2011.
94. Hripcsak G, Albers DJ,
Perotte A. Using lagged linear correlation to find relationships between
laboratory values and clinician concepts (abstract). AMIA Summit on
Translational Bioinformatics; 2011 March 7-9; San Francisco, CA; 2011.
95.
Albers
DJ, Hripcsak G. Macroscopic physiology (abstract). Society for Industrial and
Applied Mathematics Conference on Applications of Dynamical Systems; 2011 May
22-26; Snowbird, UT; 2011.
2012
96. Hripcsak G, Albers DJ.
Next-generation phenotyping of electronic health
records. J Am Med Inform Assoc 2012;20:117-21.
97.
Vawdrey
D, Hripcsak G. Publication bias in clinical trials of electronic health
records. J Biomed Inform 2012;46:139-41.
98. Mamykina L, Vawdrey D, Stetson
P, Zheng K, Hripcsak G. Clinical Documentation:
Composition Or Synthesis? J Am Med Inform Assoc 2012;19:1025-31.
99. Albers DJ, Hripcsak G, Schmidt M. Population physiology: leveraging electronic
health record data to understand human endocrine dynamics. PLoS
ONE 2012;7(12):e48058.
doi:10.1371/journal.pone.0048058.
100. Albers DJ, Hripcsak G.
Using time-delayed mutual information to discover and interpret temporal
correlation structure in complex populations. Chaos 24 January 2012;22:013111; doi:10.1063/1.3675621.
101. Albers DJ, Hripcsak G.
Estimation of time-delayed mutual information and bias for irregularly and
sparsely sampled time-series. Chaos, Solitons &
Fractals 2012;45:853-60.
102. Hripcsak G. Visualizing
the Operating Range of a Classification System. J Am Med Inform Assoc 2012;19:529-32.
103. Hripcsak G, Albers D.
Interpreting lagged linear correlation and using range to prioritize
(abstract). AMIA Summit on Translational Bioinformatics; 2012 March 19-21; San
Francisco, CA; 2012.
104. Albers D, Claassen
J, Perotte A, Kleinberg S, Hripcsak G.
Using NICU data to understand physiology and identify damage in patients with
acute brain injury (poster). AMIA Summit on Translational Bioinformatics; 2012
March 19-21; San Francisco, CA; 2012.
105. Kleinberg S, Hripcsak G.
Automated temporal causal inference from EHR data (abstract). AMIA Summit on
Translational Bioinformatics; 2012 March 19-21; San Francisco, CA; 2012.
106. Maurer MS, Albers D,
Perotte A, Chen C, Hripcsak G. Hemoconcentration is
associated with lower mortality post hospitalization for heart failure
(poster). American College of Cardiology 61st Annual Scientific Session and
ACC-i2 with TCT; 2012 March 24-27; Chicago, IL; 2012.
107. Sedigh-Sarvestan M, Albers DJ, Gluckman BJ. Data assimilation of glucose dynamics for use
in the intensive care unit. 34th Annual International Conference of the
Engineering in Medicine and Biology Society; 2012 Aug 28 Sep 1; San Diego,
CA; 2012.
108. Maurer MS, Albers D,
Perotte A, Chen C, Hripcsak G. Hemoconcentration is
associated with lower mortality post hospitalization for heart failure
(poster). American College of Cardiology 61st Annual Scientific Session and
ACC-i2 with TCT; 2012 March 24-27; Chicago, IL; 2012.
2013
109. Albers DJ, Claassen J,
Schmidt M, Hripcsak G. A methodology for detecting and exploring non-convulsive
seizures in patients with SAH. 2013 International Symposium on Nonlinear Theory
and its Applications (NOLTA2013); 2013 September 8-12; Santa Fe, CA; 2013.
110. Overby CL, Weng C, Haerian K, Perotte A, Friedman C, Hripcsak G. Evaluation
considerations for EHR-based phenotyping algorithms:
a case study for drug-induced liver injury. AMIA Summit on Translational
Bioinformatics; 2013 March 18-20; San Francisco, CA; 2013.
In press
111. Perotte A, Hripcsak G.
Temporal properties of diagnosis code time series in aggregate. IEEE
Transactions on Information Technology in Biomedicine, in press.
112. Collins SA, Cato K,
Albers D, Scott K, Stetson PD, Bakken S, Vawdrey DK. Relationship between
nursing documentation and mortality. J Am Med Inform Assoc,
accepted for publication.
113. Boland MR, Hripcsak G,
Albers DJ, Wei Y, Wilcox AB, Wei J, Li J, Lin S, Breene
M, Myers R, Zimmerman J, Weng C. Discovering medical conditions associated with
periodontitis using linked electronic health records. Journal of Clinical Peridontology, in press.
114. Claassen J, Perotte A,
Albers D, Kleinberg S, Schmidt JM, Tu B, Badjatia N, Lantigua H, Hirsch
LJ, Mayer SA, Connoly ES, Hripcsak G. Nonconvulsive seizures after subarachnoid hemorrhage:
multimodality detection and outcomes. Annals of Neurology, in press.