About CML

 

 

Welcome to Computational Medicine Laboratory!

The Computational Medicine Laboratory (CML) is a multi disciplinary laboratory at the NYU’s Biomedical Engineering Department which mainly focuses on designing control, optimization, estimation, and signal processing algorithms for biomedical and neural engineering applications. CML is led by Dr. Rose Faghih, who has successfully collaborated with various medical doctors in different fields such as endocrinology, psychiatry, and gynecology over the last 10 years. CML focuses on medical cyber-physical systems research and develops biomedical signal processing and control algorithms for human-technology interactions, and prognosis, diagnosis, and treatment of pathological conditions related to neuroendocrine and neuropsychiatric disorders. CML brings the power of mathematical modeling to biomedical researchers and clinicians to aid in different pathological conditions.

2024 NEWS 

  • An open access book  on “Bayesian Filter Design for Computational Medicine: A State-Space Estimation Framework” authored by Dilranjan S. Wickramasuriya and Rose T. Faghih will be published by Springer in April, 2024. 
  • Rose was elected as an IEEE EMBS Administrative Committee (AdCom) Technical Representative, starting in 2024.
  • In January 2024, Rose was selected for the Second U.S.-Africa Frontiers of Science, Engineering, and Medicine Symposium which brings together outstanding young scientists, engineers, and medical professionals from the United States and the member countries of the African Union for a series of symposia to discuss exciting advances and opportunities in their fields.
  • Publications: A journal paper by CML students Saman Khazaei, Md. Rafiul Amin and Maryam Tahir with Rose as senior author on “Bayesian Inference of Hidden Cognitive Performance and Arousal States in Presence of Music” was published by IEEE Open Journal of Engineering in Medicine and Biology. Another paper co-authored by Samiul Alam and Saman with Rose as senior author on “Unveiling Productivity: The Interplay of Cognitive Arousal and Expressive Typing in Remote Work” was accepted by PLOS ONE.  
  • Rose is PI of the Early Stage NYU Discovery Research Fund for Human Health Award intended “to generate transformative, high-impact research on critical issues facing the world.” The proposed work titled “Multimodal Dynamic Biosensing for Quantification of Long COVID Symptom Progression” is multidisciplinary and involves co-PIs in NYU Langone Health
    – Dr. Susan Malone (NYU Rory Meyers School of Nursing)
    – Dr. Bradley Aouizerat (NYU School of Dentistry) and
    – Dr. Stuart Katz (NYU Grossman School of Medicine).
  • Rose is co-PI (PI: Yi Fang) on a $50,000 grant to organize the NYUAD Institute Dean Symposium: The First International Symposium on Artificial Intelligence for Engineering Innovations.

2023 NEWS 

  • Rose Received an NIH Maximizing Investigators’ Research Award for Early Stage Investigators
    This $1,825,840 five-year grant awarded by the National Institute of General Medical Sciences (NIGMS) on “MESH: Multimodal Estimators for Sensing Health“ aims to track four important indicators of health: inflammation, metabolism, fatigue and interoceptive awareness using  biochemical signals such as hormones and cytokines, and eye motion data for biomarker identification in health, disease and during emotional experiences. Read more in NYU News
  • NYU Tandon News shared a spotlight of CML since the lab’s move to NYU. CML research was also showcased in NYU Tandon’s The Unconventional Engineer on LinkedIn. 
  • Mindwatch update: CML graduate students and director Rose published “Regulation of Brain Cognitive Arousal and Performance States through Auditory, Gustatory, and Olfactory Stimulation with Wearable Monitoring” in Scientific Reports. This work has received vast international media attention in Yahoo News, EurekAlert!, The Independent, The Mirage, News Medical Life Science, SciTechDaily, Science Daily, and Medical Xpress, among others.
  • CML research on “A Bayesian Filtering Approach for Tracking Sympathetic Arousal and Cortisol-Related Energy From Marked Point Process and Continuous-Valued Observations” co-authored by former CML student Dilranjan Wickramasuriya and current CML student Saman Khazaei with Rose was published in IEEE Access. This work contributes a novel filter to combine continuous observations and marked point processes to estimate internal health states such as skin conductance-based cognitive arousal and cortisol-based energy state. This work was featured by NYU Tandon News and Medical Xpress. 
  • CML research on “Sparse Multichannel Decomposition of Electrodermal Activity With Physiological Priors” co-authored by former CML student Samiul Alam and current CML student Saman Khazaei with Rose was published in IEEE Open Journal of Engineering in Medicine and Biology. This work contributes a method of estimation of autonomic nervous system activation from concurrent skin conductance measurements from multiple sensors. 
  • Rose is co-PI (PI: Susan Malone) on a grant titled “Quantifying metabolically relevant hormonal rhythms and their association with glycemic control and behaviors in adults with prediabetes and short sleep durations in real world settings” funded by the New York University Research Development MEGA Grants Initiative to study the role of hormones in metabolic  and sleep disorders. 
  • CML has generated 12 open-source code repositories via GitHub. This includes (1) investigation of the relationship between cognitive performance and arousal, (2) closed loop energy regulation for patients with cortisol disorders and others.
  • The Computational Medicine Lab Won the First Place in the 2023 NYU Tandon Research Excellence Exhibit in Areas of Excellence category for the MINDWATCH Project.
  • NYU Service: Rose has been leading the efforts in creating the Biomedical Engineering Undergraduate Program for New York University which received internal approval from the Department of Biomedical Engineering and Tandon School of Engineering in 2023.  
  • Outreach: Rose was featured at the International Summer School on Bio-X: Data Science and Engineering in Medicine and Biology co-sponsored by NSF, IEEE Engineering in Medicine and Biology Society, and IEEE BRAIN in Crete. She gave presentations on “Smartwatch-Brain Interface Architectures for Mental Well-Being” and “Computational Medicine for Closed-Loop Therapy.”
  • Outreach: Rose was featured as a panelist for the “Women in Biomedical Engineering Panel 2: Nurturing the Next Generation Workforce in Healthcare: Balancing Academics, Industry, and Life” at the IEEE EMBS Inaugural Women in Biomedical Engineering Forum in Australia.
  • Other outreach: Rose was identified by the NYU Tandon School of Engineering as one among Tandon’s agents of optimism. She was also invited to present CML’s research work on the MINDWATCH project at the NYU Tandon Dean’s Luncheon and Alumni Awards Ceremony. Rose presented her career path at a UMD REU Outreach event.
  • Engagement with National Academies: Rose was invited by the National Academy of Engineering (NAE) to the 2023 EU-US Frontiers of Engineering Symposium (EU-US FOE), organized by NAE and the European Council of Applied Sciences, Technologies, and Engineering hosted by Nokia Bell Labs. EU-US FOE includes 60 early-career engineers from EU and US universities, industry, and government. 
  • Rose joined the PNAS Nexus Editorial Board as a Board of Reviewing Editors (BoRE) member. PNAS Nexus is published by the National Academy of Sciences in partnership with Oxford University Press.
  • Rose joined the IEEE Transactions on Neural Systems and Rehabilitation Engineering (TNSRE) Board as an Associate Editor. IEEE TNSRE is an IEEE journal on the interaction of biomedical engineering, neuroscience and clinical research.
  • Rose served on the program committee for the second CPS Rising Stars Workshop in 2023.
  • Patent granted in April 2023: Faghih, R. T., E. N. Brown, and A. K. Styer. System and method for automated ovarian follicular monitoring, 2023. US Patent 11,622,744.
  • Filed provisional patent: Faghih, R. T., R. Reddy, and S. Khazaei. A system and method for estimating emotional valence based on measurements of respiration, 2023. US Patent App 63/514,825.
  • Filed provisional patent: Faghih, R. T. and S. Khazaei. Systems and methods for estimating interoceptive awareness state using eye-tracking measurements, 2023. US Patent App 63/584,814.
  • Rose gave multiple talks such as University of Bristol Integrative Neuroscience & Endocrinology Seminar, MIT Neural Signal Processing Seminar, Tufts University Biomedical Engineering Seminar and American College of Sports Medicine Greater New York Chapter “AI in Exercise Science” Seminar.
  • Rose gave an invited talk on  “A Mathematical Framework for Decoding and Regulating Cognitive Arousal using Smartwatches of the Future” at the mini-symposium on “Dynamical Modeling for Neurotechnology Applications” in IEEE Engineering in Medicine and Biology Conference 2023 held in Sydney, Australia.
  • CML students and postdoc had oral and poster presentations in  IEEE Engineering in Medicine and Biology Conference 2023 held in Sydney, Australia on: 1. The estimation of emotional valence state from respiration signal, 2. The effect of treatment on leptin in premenopausal obese women, 3. The changes in cortisol secretion during cardiac surgery, and 4. The effect of cardiac surgery on cytokine expression in the inflammatory response.
  • Ph.D. student Saman Khazaei presented an invited talk at a special session on “Enabling Closed-Loop Technologies for Mental Health: Biobehavioral Sensor Informatics and Just-in-Time Interventions,” based on the MINDWATCH project, at the 2023 IEEE-EMBS International Conference on Biomedical and Health Informatics. 
  • Rose was Interviewed by Various Media Outlets as a Wearables Expert: She explained the ability of wearables such as MINDWATCH to improve quality of health and reduce hospitalizations in Renal and Urology News. 
  • Several journal articles were published by CML this year, in journals including Scientific Reports, IEEE Transactions on Biomedical Engineering, Frontiers in Computational Neuroscience, IEEE Access, Frontiers in neuroscience, IEEE Open Journal of Engineering in Medicine and Biology, Frontiers in Endocrinology, PLoS Computational Biology, and Journal of the Endocrine Society. CML research was presented at 2022 IEEE Healthcare Innovations and Point of Care Technologies (HI-POCT). 
  • CML welcomed new Masters’ student, Qing Xiang.

2022 NEWS

  • NYU Biomedical Engineering welcomed Rose.
  • CML research work on the estimation of emotional valence from facial electromyogram measurements in Frontiers in Neuroscience. This work was completed as part of a course project for the graduate course titled “State-Space Estimation with Physiological Applications.”
  • Rose outlined the potential of wearables in determining the stress for The Washington Post.
  • Rose and CML alumni discussed the role of wearable technology on mental health in their interview on verywellmind.
  • Mindwatch update: CML graduate student Rafiul Amin and Rose published a near real-time algorithm for inferring nervous system activation using skin conductance in PLOS Computational Biology. This work has received vast media attention and has been outlined by Yahoo news , MSN, Gadgets and Wearables, Global Health News Wire, News Azi, The Mirage, News Medical Life Science, Medical Republic, and Medical Xpress.
  • Mindwatch update: CML graduate student Dilranjan Wickramasuriya and Rose published an algorithm for utilizing cognitive arousal events (e.g., skin conductance response events) pertaining to physiological response to emotions (e.g., sweat secretion) in order to estimate the levels of hidden internal states (e.g., autonomous nervous system activation) in IEEE Transactions of Biomedical Engineering (TBME). 
    This work was featured by NYU Tandon News and Medical Xpress. 
  • Rose served as an expert panelist at the  2022 National Science Foundation Cyber Physical Systems Principal Investigator meeting as part of the mini-workshop on “Artificial Intelligence (AI) for healthcare“, and 2022 IEEE Healthcare Innovations – Point of Care Technologies (HI-PoCT) conference on the challenges and opportunities in the point-of-care technologies. 
  • Rose presented CML’s research at many invited talks and research seminars, including at NYU Center for Urban Science and Progress (CUSP) (video), NYU Science Talks Science Talk on Intelligent Bio-X Interfaces, NYU Biomedical Engineering Colloquium, University of Houston Biomedical Engineering Seminar, Psychoneuroendocrinology and Immunology Research Consortium Seminar at the University of Arkansas’s department of  Psychological Science and MIT Neural Signal Processing Seminar.
  • Rose was inducted into the inaugural class of the Early Career Distinguished Alumni (ECDA) Society at the A. James Clark School of Engineering, University of Maryland, College Park. Read in UMD News here. The announcement reads, “The ECDA Society recognizes the innovations, leadership, and impact made by Maryland Engineering alumni 40 years and under. The chosen alumni are at the forefront of their respective fields and have demonstrated excellence in leadership, innovation, entrepreneurship, and service.” Earlier this year, UMD reported on Rose’s move to NYU. 
  • CML paper on “Sparse system identification of leptin dynamics in women with obesity”  has been described by Medical Xpress and labroots. The paper studied the differences in leptin hormone dynamics before and after treatment in obese women, and the causality relationship between leptin and the stress hormone, cortisol. Read in UH News.
  • UMD Department of Electrical and Computer Engineering spotlighted Rose’s career at NYU.
  • Research by CML students was spotlighted at  IEEE Engineering in Medicine and Biology Conference  (EMBC).
  • Research by Rose and students of CML in collaboration with researchers at the National Institute of Health studied the effects of disruption of sleep on the secretion of growth hormone in pubertal children. This work was published in the Journal of Endocrine Society and is part of a body of CML research pertaining to the study of neuroendocrinal hormones in various populations.
  • CML research work titled “Enhancement of closed-loop cognitive stress regulation using supervised control architectures“ in the IEEE Journal of Open Engineering in Biology and Medicine. This work was covered by  Medical Xpress.
  • CML Public Dataset: A new dataset, “A Wearable Exam Stress Dataset for Predicting Cognitive Performance in Real-World Settings,” comprising physiological signals measured using wearables to estimate stress was generated by CML. Research based on this dataset has been published in IEEE Healthcare Innovations in Point of Care Technology (HIPOCT) and can be accessed here.
  • Ph.D. student Saman Khazaei gave a presentation on “Decoding a Neurofeedback-Modulated Performance State in Presence of a Time-Varying Process Noise Variance” at the 2022 IEEE Asilomar Conference held last November.
  • Ph.D. student Saman Khazaei presented research on cognitive arousal estimation from wearables at 48th Annual Northeast Bioengineering Conference (NEBEC 2022) and NYU Langone Medical AI Seminar Series.
  • This year, CML welcomed new members to CML: Saman Khazaei (graduate student), Revanth Reddy (graduate student), and Vidya Raju (postdoctoral associate).
  • Outreach: CML participated in 2022 “Women in STEM Campus Tour” with the aim of encouraging girls from the Poly Prep High School to consider engineering as a future career path. CML lab member Saman Khazaei spoke with them about the MINDWATCH project. 

    2021 NEWS 
  • CML Doctoral students (Fekri Azgomi, H and Amin, M.R) have had a live presentation at the National Science Foundation’s Cyber-Physical Systems (CPS) Principal Investigators’ meeting regarding the MINDWATCH project.
  • Rose contributed as an author of a book published by Frontiers in Neuroscience. The book is comprised of multiple papers which mainly investigate deep brain stimulation (DBS).
  • CML published several journal papers including IEEE Transactions on Biomedical Engineering, IEEE Access, Frontiers in neuroscienceand PLoS ONE. These research works involved seizure state tracking using Electroencephalography (EEG) Data, designing a closed-loop system for stress regulation using fuzzy logic control, closed- loop fuzzy energy regulation, and robust point-process Granger causality analysis.
  • Three conference papers were published in the Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) which characterize the cognitive arousal and performance states, and their relationship using non-invasive data such as skin conductance variation, Functional near-infrared spectroscopy (fNIRS) data, and reaction times.  
  • Four CML students graduated in 2021. Md. Rafiul Amin defended his thesis “Scalable and Robust Inference of Sparse Brain Signals via Personalized Physiological System Identification“.  Hamid Fekri Azgomi defended his thesis “Closed-Loop Regulation of Internal Brain States using Wearable Brain Machine Interface Architectures with Real-World Experimental Implementation.” Luciano Branco defended his thesis “Closed-Loop Control of Brain States using Physiological Signals from Wearable Devices“. Saman Khazaei defended his thesis “Bayesian Decoder Design for Investigation of Cognitive Arousal and Performance Using Physiological and Behavioral Data“. 
  • Rose was elevated to IEEE senior member.
  • CML collaboration with McGovern Medical School at UTHealth Leads To New Epilepsy Research.
  • New CML publication describes an approach for management of Cushing’s disease.
  • CML paper outlines the possibility of using your smartwatch to reduce stress.
  • CML students give a live presentation at the NSF’s Cyber-Physical Systems Principal Investigators’ meeting.

    2020 NEWS 
  • Rose received the NSF CAREER Award for her proposal entitled “MINDWATCH: Multimodal Intelligent Noninvasive brain state Decoder for Wearable AdapTive Closed-loop arcHitectures.” She proposed using smartwatch-like devices to infer brain states that are typically inaccessible except via neurotechnologies such as electroencephalography (EEG). Instead, tiny variations in sweat secretions and changes in heart (pulse) rates can be used to infer some of this information, and eventually be used to provide closed-loop therapy for patient care. Read more
  • Rose is selected as one of the visionaries in list of MIT Technology Review Innovators Under 35. The recognition highlighted her idea of sensor-laden wrist-watches that could monitor states of the brain traditionally accessed via neuroimaging technologies such as EEG. 
  • UH Cullen college of engineering outlined Rose’s selection in MIT Technology Review 2020 Innovator Under 35. 
  • Futuroprossimo, an Italian futurology magazine, highlighted Rose as one of the three MIT Technology Review’s 2020 Innovators Under 35 female awardees, who work on an innovation that has the highest potential for a future Nobel prize.  
  • Rose was selected For 2020-21 Interstellar Initiative, a program by the New York Academy of Science and the Japan Agency for Medical Research and Development.  The program seeks to bring together promising young researchers from different countries to address major research challenges related to healthy longevity.
  • Rose received a 2020 Research Excellence and Teaching Excellence Awards from the University of Houston’s Cullen College of Engineering.
  • Rose is featured by the IEEE Women in Engineering Magazine as a “Woman to Watch”.
  • Medical Xpress presented Rose’s research with the aim of improving mental health treatment.
  • Students in Rose’s “State-space Estimation with Physiological Applications” class completed a number of projects in modeling the spread of COVID-19 infections in different parts of the world and created several YouTube videos to disseminate the knowledge to the general public. Read more
  • Educational Impact: CML continued its public outreach virtually during the pandemic by posting videos onto its YouTube channel. The videos drew attention to senior design projects, class projects, and several others, meant as brief tutorials for teaching concepts related to controls.
  • UMD Department of Electrical and Computer engineering covered Rose’s work on the MINDWATCH project.
  • Rose received a NSF CAREER Award for her MINDWATCH Proposal.
  • IEEE Women in Engineering (WIE) Magazine recently highlighted Rose as a “Woman to Watch.” Her career from her student days to an assistant professor, her love for writing poetry, and some of her outreach activities were described in an article published in the IEEE Women in Engineering Magazine June issue.
  • Rose’s work was featured by the IEEEXplore. IEEE drew attention to CML’s work on tracking brain states based on tiny variations in sweat secretions. 
  • CML published research work in journals including IEEE Transactions on Biomedical Engineering (two papers, one on cortisol regulation and another one on sympathetic nervous system activation), IEEE Access, and PLoS ONE. The published work involved sparse recovery with skin conductance and cortisol data and state estimation based on skin conductance and heart rate data.
  • Rose presented CML’s research findings at several invited talks including the Medical Wearables Conference, University of Maryland IEEE Leadership Seminar, MIT Technology Review’s Conference on Emerging Technologies, MIT Neural Signal Processing Seminar, and University of Texas Health Science IoT and Aging in Place Workshop.
  • CML Ph.D. student Hamid Fekri has been selected for the UH Cullen College of Engineering Future Faculty Program. The program is intended to prepare top-performing Ph.D. students for a successful career in academia.
  • Jon Genty received a Summer Undergraduate Research Fellowship (SURF) for his summer research at CML. Jon’s work involves analyzing growth hormone and skin conductance data to investigate applications to disease diagnosis.
  • CML graduate students presented posters at two conferences organized by Rice University: the Theoretical and Computational Neuroscience Conference, and the Ken Kennedy Institute Data Science Virtual Conference. The posters featured some of CML’s latest work on sparse deconvolution, estimation, and control with regard to recovering unobserved brain states from peripheral physiological signals.
  • Four CML students graduated in 2020. Dilranjan Wickramasuriya successfully defended his PhD thesis in December 2020 as the first PhD graduate of CML. Srinidhi Parshi and Divesh Pednekar successfully defended their M.S. theses in May 2020 as the first two M.S. graduates of CML. Jon Genty successfully defended his undergraduate Honors thesis in November 2020. 

    2019 NEWS 
  • Rose was selected in the 2019 National Academy of Engineering’s U.S. Frontiers of Engineering Symposium.
  • Invited Talks: Rose presented CML’s research findings at several  invited talks including the Institute for Computational Medicine Distinguished Seminar Series at the Johns Hopkins University, the Biomedical Engineering Seminar at the University of Connecticut, Technology Collaboration Center Wearable Technologies Workshop at NASA Johnson Space Center, Industrial Engineering Seminar at the University of Houston, and the Invited Special Session on Wearable Sensor Informatics for Cardiopulmonary Monitoring at the IEEE Conference on Biomedical and Health Informatics. Read more
  • CML reported in Frontiers in Neuroscience that a closed-loop brain stimulator, based on sweat response, can be developed for those who suffer an array of neuropsychiatric disorders. This research was covered by UH News, Science Daily, Psych Central, EurekAlert, New Medical, Biospace, Neuroscience News and other online news portals. Read more
  • Multiple journal papers were accepted for publication in the IEEE Transactions on Biomedical Engineering (TBME) and IEEE Access.  Read more
  • CML members attended the IEEE Engineering in Medicine and Biology Conference (EMBC) in Germany and gave six presentations there. Read more
  • CML research describes a method for those who suffer an array of neuropsychiatric disorders.
  • CML members presented five papers at the Asilomar Conference on Signals, Systems, and Computers and the IEEE-EMB Special Topics Conference on Healthcare Innovations and Point-of-Care Technologies at the National Institute of Health. Three of these presentations were projects from the “State-Space Estimation with Physiological Applications” course designed and taught by Rose where two CML Ph.D. students served as teaching assistants. Moreover, another paper was based on one of the summer  National Science Foundation Research Experiences for Undergraduates projects at CML. Read more
  • Srinidhi Parshi came second at the ECE  Department’s Graduate Research Conference and received the 7×24 Exchange International South Texas Award.
  • Srinidhi Parshi received the National Science Foundation student travel award at the IEEE Biomedical and Health Informatics Conference.
  • Dilranjan Wickramasuriya received an Honorable Mention Award for his poster at the Graduate Research Showcase.
  • Dilranjan Wickramasuriya, Hamid Fekri, and Md. Rafiul Amin received the Cullen Fellowship Travel Grants to attend IEEE conferences.
  • A team of undergraduate senior design students mentored at CML came second in the ECE Department’s capstone design competition.
  • Undergraduate Samantha Havens received a Summer Undergraduate Research Fellowship for her research at CML.
  • Outreach: CML hosted over 80 girls at CML as a part of the Chevron Girls Engineering the Future event.