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--- research [2019/08/03 18:00]
shyam [Precision medicine and patient-specific modeling]
+++ research [2019/11/23 19:47]
shyam
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 ~~NOTOC~~
 ===== Research =====
-The Vis Lab is focused on the application of artificial intelligence and machine learning to problems in the Learning Health System (LHS) that include:
+The Vis Lab is focused on the application of artificial intelligence and machine learning to computerized clinical decision support, precision medicine and personalized modeling, causal discovery from genomic and biomedical data, and clinical data warehousing and data harmonization.
-  * Learning electronic medical record (EMR) system and computerized clinical decision support
-  * Precision medicine and personalized modeling
-  * Causal discovery from biomedical data
-  * EMR data warehousing
-  * Automated visual analytics
-The goal of a LHS is to deliver the best care every time, and to learn and improve with each care experience. A LHS has two arms: 1) an afferent (blue) arm that is focused on assembling data from various sources including EMR systems, mobile health (mHealth) applications and research studies into an integrated research data repository, and 2) an efferent (red) arm that is focused on returning results and findings obtained from analyses of the data repository to inform clinical decision support and patient decision support systems.
-{{ wiki:lhs_decic_transparent.png?0x300 }}
-==== Learning electronic medical record (EMR) system and computerized clinical decision support ====
+==== Machine learning for computerized clinical decision support ====
 {{ wiki:lemur_transparent.png?150x0}}
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 This work is funded by a [[https://projectreporter.nih.gov/project_info_description.cfm?aid=9030245|R01 grant from NLM]], NIH.
-Electronic medical records (EMRs) are capturing increasing amounts of patient data that can be leveraged by machine learning methods for computerized clinical decision support. My work focuses on developing a learning EMR system that uses machine learning to provide decision support using the right data, at the right time. In addition, I work with a team of collaborators in developing and implementing machine learning methods for detecting adverse drug events and for identifying anomalies in clinical management of patients. This work is in collaboration with [[http://www.dbmi.pitt.edu/person/gregory-cooper-md-phd|Gregory F. Cooper]], [[http://www.dbmi.pitt.edu/person/harry-hochheiser-phd|Harry Hochheiser]], [[http://people.cs.pitt.edu/~milos/|Milos Hauskrecht]], [[http://www.ccm.pitt.edu/directory/profile/gilles-clermont|Gilles Clermont]], (at the University of Pittsburgh), and [[https://sbmi.uth.edu/faculty-and-staff/dean-sittig.htm|Dean Sittig]] (at the University of Texas Health Science Center at Houston).
+Electronic medical records (EMRs) are capturing increasing amounts of patient data that can be leveraged by machine learning methods for computerized clinical decision support. My work focuses on developing a learning EMR system that uses machine learning to identify and highlight relevant patient data, at the right time, to the right person. In addition, I work with a team of collaborators in developing and implementing machine learning methods for identifying anomalies in clinical management of patients and raising alerts. This work is in collaboration with [[http://www.dbmi.pitt.edu/person/gregory-cooper-md-phd|Gregory F. Cooper]], [[http://www.dbmi.pitt.edu/person/harry-hochheiser-phd|Harry Hochheiser]], [[http://people.cs.pitt.edu/~milos/|Milos Hauskrecht]], [[http://www.ccm.pitt.edu/directory/profile/gilles-clermont|Gilles Clermont]], (at the University of Pittsburgh), and [[https://sbmi.uth.edu/faculty-and-staff/dean-sittig.htm|Dean Sittig]] (at the University of Texas Health Science Center at Houston).
 Publications:
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   * **Visweswaran, S**, Hanbury, P, Saul, M, Cooper, GF. {{papers:2003_detecting_adverse_drug_events_in_discharge_summaries_using_variations_on_the_simple_bayes_model.pdf|Detecting adverse drug events in discharge summaries using variations on the simple Bayes model}}. In: Proceedings of the Fall Symposium of the American Medical Informatics Association. 2003;2003:689-93.
@@ Line 70: / Line 62: @@
   * **Visweswaran, S**. {{papers:2007_dissertation_learning_patient_specific_models_from_clinical_data.pdf|Learning patient-specific models from clinical data}}. Doctoral Dissertation, University of Pittsburgh, Sep 2007.
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   * Strobl, EV, Eack, SM, Swaminathan, V, **Visweswaran, S**. {{papers:2012_predicting_the_risk_of_psychosis_onset_advances_and_prospects.pdf|Predicting the risk of psychosis onset: Advances and prospects. Early Intervention in Psychiatry}}. 2012 Nov;6(4):368-79.
-  * Wei W, **Visweswaran, S**, Cooper, GF. {{papers:2011_the_application_of_naive_bayes_model_averaging_to_predict_alzheimers_disease_from_genome-wide_data.pdf|The application of naive Bayes model averaging to predict Alzheimer's disease from genome-wide data}}. Journal of the American Medical Informatics Association. 2011 Jul-Aug;18(4):370-5.
-  * Jiang, X, Neapolitan, RE, Barmada, MM, **Visweswaran, S**. {{papers:2011_learning_genetic_epistasis_using_bayesian_network_scoring_criteria.pdf|Learning genetic epistasis using Bayesian network scoring criteria}}. BMC Bioinformatics. 2011 Mar 31;12:89.
-  * Jiang, X, Barmada, MM, **Visweswaran, S**. {{papers:2010_identifying_genetic_interactions_in_genome-wide_data_using_bayesian_networks.pdf|Identifying genetic interactions in genome-wide data using Bayesian networks}}. Genetic Epidemiology. 2010 Sep; 34(6):575-81.
+==== Research data warehousing and data harmonization ====
-==== EMR data warehousing ====
 This work is funded by a [[https://projectreporter.nih.gov/project_info_description.cfm?aid=9260460|UL1 grant from NCATS]], NIH and a [[http://www.pcornet.org/clinical-data-research-networks/cdrn11-university-of-pittsburgh/|CDRN grant from PCORI]].
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 Publications:
+  * **Visweswaran S**, Becich MJ, D’Itri VS, Sendro ER, MacFadden D, Anderson NR, Allen KA, Ranganathan D, Murphy SN, Morrato EH, Pincus HA, Toto R, Firestein GS, Nadler LM, Reis SE. [[https://academic.oup.com/jamiaopen/article/1/2/147/5077449|Accrual to Clinical Trials (ACT): A Clinical and Translational Science Award Consortium network]]. JAMIA Open. 2018 Aug 21.
   * Amin, W, Borromeo, C, Saul, M, Becich, MJ, **Visweswaran, S**. {{papers:2015_informatics_synergies_between_path_and_act_networks.pdf|Informatics synergies between PaTH and ACT networks}}. In: Proceedings of the 2015 Summit on Clinical Research Informatics (Mar 2015).
-  * Visweswaran, S, Tenenbaum, J, Gouripeddi, R. Secondary use of data for research - EHR, omics and environmental data. In: AMIA Joint Summits Translational Science Proceedings (Mar 2016).
@@ Line 131: / Line 121: @@
 Publications:
+  * Bhavnani SK, **Visweswaran S**, Divekar R, Brasier A. [[https://journals.sagepub.com/doi/full/10.1177/0021886318794606|Towards team-centered informatics: Accelerating innovation in multidisciplinary scientific teams through visual analytics]]. The Journal of Applied Behavioral Science. 2019 Mar;55(1):50-72.
+  * Bhavnani SK, Dang B, Kilaru V, Caro M, **Visweswaran S**, Saade G, Smith AK, Menon R. [[http://dx.doi.org/10.1515/jpm-2017-0126|Methylation differences reveal heterogeneity in preterm pathophysiology: Results from bipartite network analyses]]. Journal of Perinatal Medicine. 2018 Jul 26;46(5):509-521.
   * Bhavnani, SK, **Visweswaran, S**, Divekar, R, Bellala, G. {{papers:2015_where_is_the_science_in_big_data_visual_analytics_from_pretty_pictures_to_transformative_biomedical_discoveries.pdf|Where is the science in big data visual analytics? From pretty pictures to transformative biomedical discoveries}}. In: AMIA Joint Summits Translational Science Proceedings. 2015 Mar 23; 2015.
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   * Bhavnani, SK, Dang, B, Caro, M, Bellala, G, **Visweswaran, S**, Asuncion, M, Divekar, R. {{papers:2014_heterogeneity_within_and_across_pediatric_pulmonary_infections_from_bipartite_networks_to_at-risk_subphenotypes.pdf|Heterogeneity within and across pediatric pulmonary infections: From bipartite networks to at-risk subphenotypes}}. In: AMIA Joint Summits Translational Science Proceedings. 2014 Apr 7; 2014:29-34.
-  * Bhavnani, SK, Drake, J, Bellala, G, Dang, B, Peng, B, Oteo, JA, Santibañez-Saenz, P, **Visweswaran, S**, Olano, JP. {{papers:2013_how_cytokines_co-occur_across_rickettsioses_patients_from_bipartite_visual_analytics_to_mechanistic_inferences_of_a_cytokine_storm.pdf|How cytokines co-occur across rickettsioses patients: From bipartite visual analytics to mechanistic inferences of a cytokine storm}}. In: AMIA Joint Summits Translational Science Proceedings. 2013 Mar 18; 2013:15-9.
-  * Bhavnani, SK, Bassler, K, **Visweswaran, S**. [[http://www.google.com/patents/US20130245959|Computer-Implementable Algorithm for Biomarker Discovery Using Bipartite Networks]]. US Patent Application.
-  * Bhavnani, SK, Bellala, G, Victor, S, Bassler, K, **Visweswaran, S**. {{papers:2012_the_role_of_complementary_bipartite_visual_analytical_representations_in_the_analysis_of_snps.pdf|The role of complementary bipartite visual analytical representations in the analysis of SNPs: A case study in ancestral informative markers}}. Journal of the American Medical Informatics Association. 2012 Jun 1; 19(e1):e5-e12.