Shamim Nemati

Title(s)Assistant Professor, Medicine
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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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 Overview 

    Collapse Research 
    Collapse Research Activities and Funding
    Enhanced Metadata Design, Architecture, and Learning (MeDAL) for Development of Generalizable Deep Learning-based Predictive Analytics from Electronic Health Records
    NIH R56LM013517Sep 25, 2020 - Aug 31, 2021
    Role: Principal Investigator
    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 K01ES025445Sep 30, 2015 - Jul 31, 2021
    Role: Principal Investigator
    Prediction of Adverse Events in the ICU
    NIH/NCATS L30 TR001819Sep 30, 2015 - Jul 31, 2020
    Role: Principal Investigator

    Collapse ORNG Applications 
    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A Locally Optimized Data-Driven Tool to Predict Sepsis-Associated Vasopressor Use in the ICU. Crit Care Med. 2021 Jul 01. Holder AL, Shashikumar SP, Wardi G, Buchman TG, Nemati S. PMID: 34259450.
      View in: PubMed   Mentions:    Fields:    
    2. DeepAISE - An interpretable and recurrent neural survival model for early prediction of sepsis. Artif Intell Med. 2021 Mar; 113:102036. Shashikumar SP, Josef CS, Sharma A, Nemati S. PMID: 33685592.
      View in: PubMed   Mentions: 1     Fields:    
    3. Contextual Embeddings from Clinical Notes Improves Prediction of Sepsis. AMIA Annu Symp Proc. 2020; 2020:197-202. Amrollahi F, Shashikumar SP, Razmi F, Nemati S. PMID: 33936391.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    4. Classifying Major Depressive Disorder and Response to Deep Brain Stimulation Over Time by Analyzing Facial Expressions. IEEE Trans Biomed Eng. 2021 02; 68(2):664-672. Jiang Z, Harati S, Crowell A, Mayberg HS, Nemati S, Clifford GD. PMID: 32746065.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    5. Predicting Progression to Septic Shock in the Emergency Department Using an Externally Generalizable Machine-Learning Algorithm. Ann Emerg Med. 2021 04; 77(4):395-406. Wardi G, Carlile M, Holder A, Shashikumar S, Hayden SR, Nemati S. PMID: 33455840.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    6. Development and Prospective Validation of a Deep Learning Algorithm for Predicting Need for Mechanical Ventilation. Chest. 2021 06; 159(6):2264-2273. Shashikumar SP, Wardi G, Paul P, Carlile M, Brenner LN, Hibbert KA, North CM, Mukerji SS, Robbins GK, Shao YP, Westover MB, Nemati S, Malhotra A. PMID: 33345948.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    7. Predicting Mortality in Critical Care Patients with Fungemia Using Structured and Unstructured Data. Annu Int Conf IEEE Eng Med Biol Soc. 2020 07; 2020:5459-5463. Baxter SL, Klie AR, Saseendrakumar BR, Ye GY, Hogarth M, Nemati S. PMID: 33019215.
      View in: PubMed   Mentions:
    8. AIDEx - An Open-source Platform for Real-Time Forecasting Sepsis and A Case Study on Taking ML Algorithms to Production. Annu Int Conf IEEE Eng Med Biol Soc. 2020 07; 2020:5610-5614. Amrollahi F, Shashikumar SP, Kathiravelu P, Sharma A, Nemati S. PMID: 33019249.
      View in: PubMed   Mentions:
    9. Development and Prospective Validation of a Transparent Deep Learning Algorithm for Predicting Need for Mechanical Ventilation. medRxiv. 2020 Jun 03. Shashikumar SP, Wardi G, Paul P, Carlile M, Brenner LN, Hibbert KA, North CM, Mukerji S, Robbins G, Shao YP, Malhotra A, Westover B, Nemati S. PMID: 32577682.
      View in: PubMed   Mentions:
    10. Detecting heart failure using wearables: a pilot study. Physiol Meas. 2020 05 04; 41(4):044001. Shah AJ, Isakadze N, Levantsevych O, Vest A, Clifford G, Nemati S. PMID: 32163936.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    11. Assessing Contribution of Higher Order Clinical Risk Factors to Prediction of Outcome in Aneurysmal Subarachnoid Hemorrhage Patients. AMIA Annu Symp Proc. 2019; 2019:848-856. Tabaie A, Nemati S, Allen JW, Chung C, Queiroga F, Kuk WJ, Prater AB. PMID: 32308881.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    12. Early Prediction of Sepsis From Clinical Data: The PhysioNet/Computing in Cardiology Challenge 2019. Crit Care Med. 2020 02; 48(2):210-217. Reyna MA, Josef CS, Jeter R, Shashikumar SP, Westover MB, Nemati S, Clifford GD, Sharma A. PMID: 31939789.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    13. Addressing the Credit Assignment Problem in Treatment Outcome Prediction using Temporal Difference Learning. Pac Symp Biocomput. 2020; 25:43-54. Harati S, Crowell A, Mayberg H, Nemati S. PMID: 31797585.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    14. Classifying Depression Severity in Recovery From Major Depressive Disorder via Dynamic Facial Features. IEEE J Biomed Health Inform. 2020 03; 24(3):815-824. Harati S, Crowell A, Huang Y, Mayberg H, Nemati S. PMID: 31352356.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    15. Ventricular ectopic beat detection using a wavelet transform and a convolutional neural network. Physiol Meas. 2019 06 04; 40(5):055002. Li Q, Liu C, Li Q, Shashikumar SP, Nemati S, Shen Z, Clifford GD. PMID: 30970338.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    16. Deep learning in the cross-time frequency domain for sleep staging from a single-lead electrocardiogram. Physiol Meas. 2018 12 21; 39(12):124005. Li Q, Li Q, Liu C, Shashikumar SP, Nemati S, Clifford GD. PMID: 30524025.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    17. Multiscale network dynamics between heart rate and locomotor activity are altered in schizophrenia. Physiol Meas. 2018 10 30; 39(11):115001. Reinertsen E, Shashikumar SP, Shah AJ, Nemati S, Clifford GD. PMID: 30222594.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    18. An open source benchmarked toolbox for cardiovascular waveform and interval analysis. Physiol Meas. 2018 10 11; 39(10):105004. Vest AN, Da Poian G, Li Q, Liu C, Nemati S, Shah AJ, Clifford GD. PMID: 30199376.
      View in: PubMed   Mentions: 19     Fields:    Translation:Humans
    19. A comparison of entropy approaches for AF discrimination. Physiol Meas. 2018 07 06; 39(7):074002. Liu C, Oster J, Reinertsen E, Li Q, Zhao L, Nemati S, Clifford GD. PMID: 29897343.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    20. It Is About Time: Extinguishing the Fire of Acute Kidney Injury. Crit Care Med. 2018 07; 46(7):1187-1189. Josef CS, Nemati S. PMID: 29912099.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    21. Depression Severity Classification from Speech Emotion. Annu Int Conf IEEE Eng Med Biol Soc. 2018 Jul; 2018:5763-5766. Harati S, Crowell A, Mayberg H, Nemati S. PMID: 30441645.
      View in: PubMed   Mentions:
    22. A Deep Deterministic Policy Gradient Approach to Medication Dosing and Surveillance in the ICU. Annu Int Conf IEEE Eng Med Biol Soc. 2018 Jul; 2018:4927-4931. Lin R, Stanley MD, Ghassemi MM, Nemati S. PMID: 30441448.
      View in: PubMed   Mentions:
    23. A FHIR-Enabled Streaming Sepsis Prediction System for ICUs. Annu Int Conf IEEE Eng Med Biol Soc. 2018 Jul; 2018:4093-4096. Henry JR, Lynch D, Mals J, Shashikumar SP, Holder A, Sharma A, Nemati S. PMID: 30441256.
      View in: PubMed   Mentions:
    24. How is the Doctor Feeling? ICU Provider Sentiment is Associated with Diagnostic Imaging Utilization. Annu Int Conf IEEE Eng Med Biol Soc. 2018 Jul; 2018:4058-4064. Ghassemi MM, Al-Hanai T, Raffa JD, Mark RG, Nemati S, Chokshi FH. PMID: 30441248.
      View in: PubMed   Mentions:
    25. Doubly-Robust Estimation of Effect of Imaging Resource Utilization on Discharge Decisions in Emergency Departments. Annu Int Conf IEEE Eng Med Biol Soc. 2018 Jul; 2018:3256-3259. Tabaie A, Chokshi FH, Holder AL, Nemati SN. PMID: 30441086.
      View in: PubMed   Mentions:
    26. 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. Nemati S. PMID: 29538119.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    27. An Interpretable Machine Learning Model for Accurate Prediction of Sepsis in the ICU. Crit Care Med. 2018 04; 46(4):547-553. Nemati S, Holder A, Razmi F, Stanley MD, Clifford GD, Buchman TG. PMID: 29286945.
      View in: PubMed   Mentions: 85     Fields:    Translation:Humans
    28. 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. Holder AL, Overton E, Lyu P, Kempker JA, Nemati S, Razmi F, Martin GS, Buchman TG, Murphy DJ. PMID: 28906286.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    29. Multiscale network representation of physiological time series for early prediction of sepsis. Physiol Meas. 2017 Nov 30; 38(12):2235-2248. Shashikumar SP, Li Q, Clifford GD, Nemati S. PMID: 29091053.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    30. Early sepsis detection in critical care patients using multiscale blood pressure and heart rate dynamics. J Electrocardiol. 2017 Nov - Dec; 50(6):739-743. Shashikumar SP, Stanley MD, Sadiq I, Li Q, Holder A, Clifford GD, Nemati S. PMID: 28916175.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    31. Benchmarking heart rate variability toolboxes. J Electrocardiol. 2017 Nov - Dec; 50(6):744-747. Vest AN, Li Q, Liu C, Nemati S, Shah A, Clifford GD. PMID: 28965961.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    32. 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. Reinertsen E, Nemati S, Vest AN, Vaccarino V, Lampert R, Shah AJ, Clifford GD. PMID: 28489609.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    33. 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. Sands SA, Mebrate Y, Edwards BA, Nemati S, Manisty CH, Desai AS, Wellman A, Willson K, Francis DP, Butler JP, Malhotra A. PMID: 27559818.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    34. THE TRAINING OF NEXT GENERATION DATA SCIENTISTS IN BIOMEDICINE. Pac Symp Biocomput. 2017; 22:640-645. Garmire LX, Gliske S, Nguyen QC, Chen JH, Nemati S, VAN Horn JD, Moore JH, Shreffler C, Dunn M. PMID: 27897014.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansPHPublic Health
    35. 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. Lehman LH, Mark RG, Nemati S. PMID: 27959829.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    36. Monitoring and detecting atrial fibrillation using wearable technology. Annu Int Conf IEEE Eng Med Biol Soc. 2016 Aug; 2016:3394-3397. Nemati S, Ghassemi MM, Ambai V, Isakadze N, Levantsevych O, Shah A, Clifford GD. PMID: 28269032.
      View in: PubMed   Mentions:
    37. Optimal medication dosing from suboptimal clinical examples: a deep reinforcement learning approach. Annu Int Conf IEEE Eng Med Biol Soc. 2016 Aug; 2016:2978-2981. Nemati S, Ghassemi MM, Clifford GD. PMID: 28268938.
      View in: PubMed   Mentions:
    38. Discriminating clinical phases of recovery from major depressive disorder using the dynamics of facial expression. Annu Int Conf IEEE Eng Med Biol Soc. 2016 Aug; 2016:2254-2257. Harati S, Crowell A, Mayberg H, Jun Kong , Nemati S. PMID: 28268777.
      View in: PubMed   Mentions:
    39. A Visualization of Evolving Clinical Sentiment Using Vector Representations of Clinical Notes. Comput Cardiol (2010). 2015 Sep; 2015:629-632. Ghassemi MM, Mark RG, Nemati S. PMID: 27774487.
      View in: PubMed   Mentions:
    40. Patient Prognosis from Vital Sign Time Series: Combining Convolutional Neural Networks with a Dynamical Systems Approach. Comput Cardiol (2010). 2015; 42:1069-1072. Lehman LW, Ghassemi M, Snoek J, Nemati S. PMID: 27790623.
      View in: PubMed   Mentions:
    41. Hemodynamic Monitoring Using Switching Autoregressive Dynamics of Multivariate Vital Sign Time Series. Comput Cardiol (2010). 2015; 42:1065-1068. Lehman LH, Nemati S, Mark RG. PMID: 27774489.
      View in: PubMed   Mentions:
    42. Machine Learning and Decision Support in Critical Care. Proc IEEE Inst Electr Electron Eng. 2016 Feb; 104(2):444-466. Johnson AE, Ghassemi MM, Nemati S, Niehaus KE, Clifton DA, Clifford GD. PMID: 27765959.
      View in: PubMed   Mentions:
    43. Semisupervised ECG Ventricular Beat Classification With Novelty Detection Based on Switching Kalman Filters. IEEE Trans Biomed Eng. 2015 Sep; 62(9):2125-34. Oster J, Behar J, Sayadi O, Nemati S, Johnson AE, Clifford GD. PMID: 25680203.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    44. Accumulated deep sleep is a powerful predictor of LH pulse onset in pubertal children. J Clin Endocrinol Metab. 2015 Mar; 100(3):1062-70. Shaw ND, Butler JP, Nemati S, Kangarloo T, Ghassemi M, Malhotra A, Hall JE. PMID: 25490277.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    45. Quantifying the ventilatory control contribution to sleep apnoea using polysomnography. Eur Respir J. 2015 Feb; 45(2):408-18. Terrill PI, Edwards BA, Nemati S, Butler JP, Owens RL, Eckert DJ, White DP, Malhotra A, Wellman A, Sands SA. PMID: 25323235.
      View in: PubMed   Mentions: 64     Fields:    Translation:Humans
    46. Model-based estimation of loop gain using spontaneous breathing: a validation study. Respir Physiol Neurobiol. 2014 Sep 15; 201:84-92. Gederi E, Nemati S, Edwards BA, Clifford GD, Malhotra A, Wellman A. PMID: 25038522.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    47. A physiological time series dynamics-based approach to patient monitoring and outcome prediction. IEEE J Biomed Health Inform. 2015 May; 19(3):1068-76. Lehman LW, Adams RP, Mayaud L, Moody GB, Malhotra A, Mark RG, Nemati S. PMID: 25014976.
      View in: PubMed   Mentions: 23     Fields:    Translation:Humans
    48. 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. Nemati S, Edwards BA, Lee J, Pittman-Polletta B, Butler JP, Malhotra A. PMID: 23811194.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    49. A simplified method for determining phenotypic traits in patients with obstructive sleep apnea. J Appl Physiol (1985). 2013 Apr; 114(7):911-22. Wellman A, Edwards BA, Sands SA, Owens RL, Nemati S, Butler J, Passaglia CL, Jackson AC, Malhotra A, White DP. PMID: 23349453.
      View in: PubMed   Mentions: 70     Fields:    Translation:Humans
    50. Tracking progression of patient state of health in critical care using inferred shared dynamics in physiological time series. Annu Int Conf IEEE Eng Med Biol Soc. 2013; 2013:7072-5. Lehman LW, Nemati S, Adams RP, Moody G, Malhotra A, Mark RG. PMID: 24111374.
      View in: PubMed   Mentions:
    51. Learning outcome-discriminative dynamics in multivariate physiological cohort time series. Annu Int Conf IEEE Eng Med Biol Soc. 2013; 2013:7104-7. Nemati S, Lehman LW, Adams RP. PMID: 24111382.
      View in: PubMed   Mentions:
    52. Transfer entropy estimation and directional coupling change detection in biomedical time series. Biomed Eng Online. 2012 Apr 13; 11:19. Lee J, Nemati S, Silva I, Edwards BA, Butler JP, Malhotra A. PMID: 22500692.
      View in: PubMed   Mentions: 21     Fields:    
    53. Discovering shared cardiovascular dynamics within a patient cohort. Annu Int Conf IEEE Eng Med Biol Soc. 2012; 2012:6526-9. Nemati S, Lehman LW, Adams RP, Malhotra A. PMID: 23367424.
      View in: PubMed   Mentions:
    54. Discovering shared dynamics in physiological signals: application to patient monitoring in ICU. Annu Int Conf IEEE Eng Med Biol Soc. 2012; 2012:5939-42. Lehman LW, Nemati S, Adams RP, Mark RG. PMID: 23367281.
      View in: PubMed   Mentions:
    55. Model-based characterization of ventilatory stability using spontaneous breathing. J Appl Physiol (1985). 2011 Jul; 111(1):55-67. Nemati S, Edwards BA, Sands SA, Berger PJ, Wellman A, Verghese GC, Malhotra A, Butler JP. PMID: 21474696.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    56. T-wave alternans patterns during sleep in healthy, cardiac disease, and sleep apnea patients. J Electrocardiol. 2011 Mar-Apr; 44(2):126-30. Nemati S, Malhotra A, Clifford GD. PMID: 21163493.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    57. A nonparametric surrogate-based test of significance for T-wave alternans detection. IEEE Trans Biomed Eng. 2011 May; 58(5):1356-64. Nemati S, Abdala O, Monasterio V, Yim-Yeh S, Malhotra A, Clifford GD. PMID: 20409986.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    58. An artificial vector model for generating abnormal electrocardiographic rhythms. Physiol Meas. 2010 May; 31(5):595-609. Clifford GD, Nemati S, Sameni R. PMID: 20308774.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    59. Data Fusion for Improved Respiration Rate Estimation. EURASIP J Adv Signal Process. 2010; 2010:926305. Nemati S, Malhotra A, Clifford GD. PMID: 20806056.
      View in: PubMed   Mentions:
    60. Biomimetic brain machine interfaces for the control of movement. J Neurosci. 2007 Oct 31; 27(44):11842-6. 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. PMID: 17978021.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimals
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