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Shamim Nemati

Title(s)Assistant Professor, Medicine
SchoolHealth Sciences
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    Collapse Biography 
    Collapse Education and Training
    Harvard University, Cambridge, MAPostdoctoral Training12/2014Machine Learning
    Massachusetts Institute of Technology, Cambridge, MAPh.D.12/2012Electrical Engineering & Computer Science
    University of Oklahoma, Norman, OKM.S.05/2007Applied Mathematics & Signal Processing
    University of Oklahoma, Norman, OKB.A.07/2005Mathematics
    Collapse Awards and Honors
    James S. McDonnell Foundation2013  - 2014Postdoctoral Fellowship in Complex Systems

    Collapse Research 
    Collapse Research Activities and Funding
    Multicenter Deployment and Evaluation of DeepAISE-on-FHIR for Early Prediction of Sepsis
    BARDA/ASPR/HHS HHS0100201900015CFeb 1, 2019 - Feb 1, 2020
    Role: Principal Investigator
    Cloud-based Voting System to Improve Labeling of Medical Data
    Gordon and Betty Moore Foundation Dec 1, 2018 - Dec 1, 2019
    Role: Co-Principal Investigator
    Leveraging Heterogeneous Data Across International Borders in a Privacy Preserving Manner for Clinical Deep Learning
    NSF 1822378Mar 15, 2018 - Feb 29, 2020
    Role: Co-Principal Investigator
    DeepFHIR: A Fast Healthcare Interoperability Resources (FHIR)-enabled Deep Learning Platform for Prediction of Decompensation in Critically Ill Patients
    NIH CCREQ- 2016-03-00009Jun 1, 2017 - Feb 1, 2019
    Role: Principal Investigator
    Deep Learning and Streaming Analytics for Prediction of Adverse Events in the ICU
    NIH/NIEHS K01ES025445Sep 30, 2015 - Jul 31, 2020
    Role: Principal Investigator
    Prediction of Adverse Events in the ICU
    NIH/NCATS L30 TR001819Sep 30, 2015 - Jul 31, 2020
    Role: Principal Investigator

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    Collapse Faculty Mentoring
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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Harati S, Crowell A, Huang Y, Mayberg H, Nemati S. Classifying Depression Severity in Recovery from Major Depressive Disorder via Dynamic Facial Features. IEEE J Biomed Health Inform. 2019 Jul 23. PMID: 31352356.
      View in: PubMed
    2. Li Q, Liu C, Li Q, Shashikumar SP, Nemati S, Shen Z, Clifford GD. Ventricular ectopic beat detection using a wavelet transform and a convolutional neural network. Physiol Meas. 2019 Jun 04; 40(5):055002. PMID: 30970338.
      View in: PubMed
    3. Li Q, Li Q, Liu C, Shashikumar SP, Nemati S, Clifford GD. Deep learning in the cross-time frequency domain for sleep staging from a single-lead electrocardiogram. Physiol Meas. 2018 12 21; 39(12):124005. PMID: 30524025.
      View in: PubMed
    4. Reinertsen E, Shashikumar SP, Shah AJ, Nemati S, Clifford GD. Multiscale network dynamics between heart rate and locomotor activity are altered in schizophrenia. Physiol Meas. 2018 10 30; 39(11):115001. PMID: 30222594.
      View in: PubMed
    5. Vest AN, Da Poian G, Li Q, Liu C, Nemati S, Shah AJ, Clifford GD. An open source benchmarked toolbox for cardiovascular waveform and interval analysis. Physiol Meas. 2018 10 11; 39(10):105004. PMID: 30199376.
      View in: PubMed
    6. Liu C, Oster J, Reinertsen E, Li Q, Zhao L, Nemati S, Clifford GD. A comparison of entropy approaches for AF discrimination. Physiol Meas. 2018 07 06; 39(7):074002. PMID: 29897343.
      View in: PubMed
    7. Josef CS, Nemati S. It Is About Time: Extinguishing the Fire of Acute Kidney Injury. Crit Care Med. 2018 Jul; 46(7):1187-1189. PMID: 29912099.
      View in: PubMed
    8. Harati S, Crowell A, Mayberg H, Nemati S. Depression Severity Classification from Speech Emotion. Conf Proc IEEE Eng Med Biol Soc. 2018 Jul; 2018:5763-5766. PMID: 30441645.
      View in: PubMed
    9. Lin R, Stanley MD, Ghassemi MM, Nemati S. A Deep Deterministic Policy Gradient Approach to Medication Dosing and Surveillance in the ICU. Conf Proc IEEE Eng Med Biol Soc. 2018 Jul; 2018:4927-4931. PMID: 30441448.
      View in: PubMed
    10. Henry JR, Lynch D, Mals J, Shashikumar SP, Holder A, Sharma A, Nemati S. A FHIR-Enabled Streaming Sepsis Prediction System for ICUs. Conf Proc IEEE Eng Med Biol Soc. 2018 Jul; 2018:4093-4096. PMID: 30441256.
      View in: PubMed
    11. Ghassemi MM, Al-Hanai T, Raffa JD, Mark RG, Nemati S, Chokshi FH. How is the Doctor Feeling? ICU Provider Sentiment is Associated with Diagnostic Imaging Utilization. Conf Proc IEEE Eng Med Biol Soc. 2018 Jul; 2018:4058-4064. PMID: 30441248.
      View in: PubMed
    12. Tabaie A, Chokshi FH, Holder AL, Nemati SN. Doubly-Robust Estimation of Effect of Imaging Resource Utilization on Discharge Decisions in Emergency Departments. Conf Proc IEEE Eng Med Biol Soc. 2018 Jul; 2018:3256-3259. PMID: 30441086.
      View in: PubMed
    13. Nemati S. Looking Into the Seeds of Time to Say Which Fevers Will Grow and Which Will Not. Crit Care Med. 2018 04; 46(4):651-653. PMID: 29538119.
      View in: PubMed
    14. Nemati S, Holder A, Razmi F, Stanley MD, Clifford GD, Buchman TG. An Interpretable Machine Learning Model for Accurate Prediction of Sepsis in the ICU. Crit Care Med. 2018 04; 46(4):547-553. PMID: 29286945.
      View in: PubMed
    15. Holder AL, Overton E, Lyu P, Kempker JA, Nemati S, Razmi F, Martin GS, Buchman TG, Murphy DJ. Serial Daily Organ Failure Assessment Beyond ICU Day 5 Does Not Independently Add Precision to ICU Risk-of-Death Prediction. Crit Care Med. 2017 Dec; 45(12):2014-2022. PMID: 28906286.
      View in: PubMed
    16. Shashikumar SP, Li Q, Clifford GD, Nemati S. Multiscale network representation of physiological time series for early prediction of sepsis. Physiol Meas. 2017 Nov 30; 38(12):2235-2248. PMID: 29091053.
      View in: PubMed
    17. Shashikumar SP, Stanley MD, Sadiq I, Li Q, Holder A, Clifford GD, Nemati S. Early sepsis detection in critical care patients using multiscale blood pressure and heart rate dynamics. J Electrocardiol. 2017 Nov - Dec; 50(6):739-743. PMID: 28916175.
      View in: PubMed
    18. Vest AN, Li Q, Liu C, Nemati S, Shah A, Clifford GD. Benchmarking heart rate variability toolboxes. J Electrocardiol. 2017 Nov - Dec; 50(6):744-747. PMID: 28965961.
      View in: PubMed
    19. Reinertsen E, Nemati S, Vest AN, Vaccarino V, Lampert R, Shah AJ, Clifford GD. Heart rate-based window segmentation improves accuracy of classifying posttraumatic stress disorder using heart rate variability measures. Physiol Meas. 2017 Jun; 38(6):1061-1076. PMID: 28489609.
      View in: PubMed
    20. Sands SA, Mebrate Y, Edwards BA, Nemati S, Manisty CH, Desai AS, Wellman A, Willson K, Francis DP, Butler JP, Malhotra A. Resonance as the Mechanism of Daytime Periodic Breathing in Patients with Heart Failure. Am J Respir Crit Care Med. 2017 01 15; 195(2):237-246. PMID: 27559818.
      View in: PubMed
    21. Garmire LX, Gliske S, Nguyen QC, Chen JH, Nemati S, VAN Horn JD, Moore JH, Shreffler C, Dunn M. THE TRAINING OF NEXT GENERATION DATA SCIENTISTS IN BIOMEDICINE. Pac Symp Biocomput. 2017; 22:640-645. PMID: 27897014.
      View in: PubMed
    22. Lehman LH, Mark RG, Nemati S. A Model-Based Machine Learning Approach to Probing Autonomic Regulation From Nonstationary Vital-Sign Time Series. IEEE J Biomed Health Inform. 2018 01; 22(1):56-66. PMID: 27959829.
      View in: PubMed
    23. Nemati S, Ghassemi MM, Ambai V, Isakadze N, Levantsevych O, Shah A, Clifford GD. Monitoring and detecting atrial fibrillation using wearable technology. Conf Proc IEEE Eng Med Biol Soc. 2016 08; 2016:3394-3397. PMID: 28269032.
      View in: PubMed
    24. Nemati S, Ghassemi MM, Clifford GD. Optimal medication dosing from suboptimal clinical examples: a deep reinforcement learning approach. Conf Proc IEEE Eng Med Biol Soc. 2016 08; 2016:2978-2981. PMID: 28268938.
      View in: PubMed
    25. Harati S, Crowell A, Mayberg H, Nemati S. Discriminating clinical phases of recovery from major depressive disorder using the dynamics of facial expression. Conf Proc IEEE Eng Med Biol Soc. 2016 08; 2016:2254-2257. PMID: 28268777.
      View in: PubMed
    26. Ghassemi MM, Mark RG, Nemati S. A Visualization of Evolving Clinical Sentiment Using Vector Representations of Clinical Notes. Comput Cardiol (2010). 2015 Sep; 2015:629-632. PMID: 27774487.
      View in: PubMed
    27. Lehman LW, Ghassemi M, Snoek J, Nemati S. Patient Prognosis from Vital Sign Time Series: Combining Convolutional Neural Networks with a Dynamical Systems Approach. Comput Cardiol (2010). 2015; 42:1069-1072. PMID: 27790623.
      View in: PubMed
    28. Lehman LH, Nemati S, Mark RG. Hemodynamic Monitoring Using Switching Autoregressive Dynamics of Multivariate Vital Sign Time Series. Comput Cardiol (2010). 2015; 42:1065-1068. PMID: 27774489.
      View in: PubMed
    29. Johnson AE, Ghassemi MM, Nemati S, Niehaus KE, Clifton DA, Clifford GD. Machine Learning and Decision Support in Critical Care. Proc IEEE Inst Electr Electron Eng. 2016 Feb; 104(2):444-466. PMID: 27765959.
      View in: PubMed
    30. Oster J, Behar J, Sayadi O, Nemati S, Johnson AE, Clifford GD. Semisupervised ECG Ventricular Beat Classification With Novelty Detection Based on Switching Kalman Filters. IEEE Trans Biomed Eng. 2015 Sep; 62(9):2125-34. PMID: 25680203.
      View in: PubMed
    31. Shaw ND, Butler JP, Nemati S, Kangarloo T, Ghassemi M, Malhotra A, Hall JE. Accumulated deep sleep is a powerful predictor of LH pulse onset in pubertal children. J Clin Endocrinol Metab. 2015 Mar; 100(3):1062-70. PMID: 25490277.
      View in: PubMed
    32. Terrill PI, Edwards BA, Nemati S, Butler JP, Owens RL, Eckert DJ, White DP, Malhotra A, Wellman A, Sands SA. Quantifying the ventilatory control contribution to sleep apnoea using polysomnography. Eur Respir J. 2015 Feb; 45(2):408-18. PMID: 25323235; PMCID: PMC4348093.
      View in: PubMed, PubMed Central
    33. Gederi E, Nemati S, Edwards BA, Clifford GD, Malhotra A, Wellman A. Model-based estimation of loop gain using spontaneous breathing: a validation study. Respir Physiol Neurobiol. 2014 Sep 15; 201:84-92. PMID: 25038522.
      View in: PubMed
    34. Lehman LW, Adams RP, Mayaud L, Moody GB, Malhotra A, Mark RG, Nemati S. A physiological time series dynamics-based approach to patient monitoring and outcome prediction. IEEE J Biomed Health Inform. 2015 May; 19(3):1068-76. PMID: 25014976; PMCID: PMC4346516.
      View in: PubMed, PubMed Central
    35. Nemati S, Edwards BA, Lee J, Pittman-Polletta B, Butler JP, Malhotra A. Respiration and heart rate complexity: effects of age and gender assessed by band-limited transfer entropy. Respir Physiol Neurobiol. 2013 Oct 01; 189(1):27-33. PMID: 23811194; PMCID: PMC3821922.
      View in: PubMed, PubMed Central
    36. Wellman A, Edwards BA, Sands SA, Owens RL, Nemati S, Butler J, Passaglia CL, Jackson AC, Malhotra A, White DP. A simplified method for determining phenotypic traits in patients with obstructive sleep apnea. J Appl Physiol (1985). 2013 Apr; 114(7):911-22. PMID: 23349453.
      View in: PubMed
    37. Lehman LW, Nemati S, Adams RP, Moody G, Malhotra A, Mark RG. Tracking progression of patient state of health in critical care using inferred shared dynamics in physiological time series. Conf Proc IEEE Eng Med Biol Soc. 2013; 2013:7072-5. PMID: 24111374.
      View in: PubMed
    38. Nemati S, Lehman LW, Adams RP. Learning outcome-discriminative dynamics in multivariate physiological cohort time series. Conf Proc IEEE Eng Med Biol Soc. 2013; 2013:7104-7. PMID: 24111382.
      View in: PubMed
    39. Lee J, Nemati S, Silva I, Edwards BA, Butler JP, Malhotra A. Transfer entropy estimation and directional coupling change detection in biomedical time series. Biomed Eng Online. 2012 Apr 13; 11:19. PMID: 22500692; PMCID: PMC3403001.
      View in: PubMed, PubMed Central
    40. Nemati S, Lehman LW, Adams RP, Malhotra A. Discovering shared cardiovascular dynamics within a patient cohort. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:6526-9. PMID: 23367424.
      View in: PubMed
    41. Lehman LW, Nemati S, Adams RP, Mark RG. Discovering shared dynamics in physiological signals: application to patient monitoring in ICU. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:5939-42. PMID: 23367281.
      View in: PubMed
    42. Nemati S, Edwards BA, Sands SA, Berger PJ, Wellman A, Verghese GC, Malhotra A, Butler JP. Model-based characterization of ventilatory stability using spontaneous breathing. J Appl Physiol (1985). 2011 Jul; 111(1):55-67. PMID: 21474696; PMCID: PMC3137535.
      View in: PubMed, PubMed Central
    43. Nemati S, Malhotra A, Clifford GD. T-wave alternans patterns during sleep in healthy, cardiac disease, and sleep apnea patients. J Electrocardiol. 2011 Mar-Apr; 44(2):126-30. PMID: 21163493; PMCID: PMC3062089.
      View in: PubMed, PubMed Central
    44. Nemati S, Abdala O, Monasterio V, Yim-Yeh S, Malhotra A, Clifford GD. A nonparametric surrogate-based test of significance for T-wave alternans detection. IEEE Trans Biomed Eng. 2011 May; 58(5):1356-64. PMID: 20409986.
      View in: PubMed
    45. Clifford GD, Nemati S, Sameni R. An artificial vector model for generating abnormal electrocardiographic rhythms. Physiol Meas. 2010 May; 31(5):595-609. PMID: 20308774.
      View in: PubMed
    46. Nemati S, Malhotra A, Clifford GD. Data Fusion for Improved Respiration Rate Estimation. EURASIP J Adv Signal Process. 2010; 2010:926305. PMID: 20806056.
      View in: PubMed
    47. Fagg AH, Hatsopoulos NG, de Lafuente V, Moxon KA, Nemati S, Rebesco JM, Romo R, Solla SA, Reimer J, Tkach D, Pohlmeyer EA, Miller LE. Biomimetic brain machine interfaces for the control of movement. J Neurosci. 2007 Oct 31; 27(44):11842-6. PMID: 17978021.
      View in: PubMed
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