Faculty PI

Dr. Pratik Shah

Dr. Pratik Shah is a medical technology expert in artificial intelligence and biological research.

Student Researchers

1. Betsy Tian, BS Electrical Engineering and Computer Science '25, MIT

   Summer 2022. Research in Machine Learning and Medicine with Pratik Shah at MIT

2. Bradley Bunch, BS Electrical Engineering and Computer Science '25, MIT

   Spring 2022. Research in Machine Learning and Medicine with Pratik Shah at MIT.

   More information about Bradley.

3. Weiduo (Amanda) Zhu, BS Electrical Engineering and Computer Science '25, MIT

   Spring 2022-Summer 2022. Research in Machine Learning and Medicine with Pratik Shah at MIT.

4. Audrey Xie, BS Electrical Engineering and Computer Science '24, MIT

   Fall 2020-Fall 2021. Research in Machine Learning and Medicine with Pratik Shah at MIT.

   More information about Audrey

   Publications with Dr. Pratik Shah:

   Uncertainty quantified deep learning for predicting dice coefficient of digital histopathology image segmentation

   Sambuddha Ghosal, Xie A and Shah P*

   ( *Senior author supervising research)

   arXiv:2011.05791 [stat.ML]

5. Steven Raphael, BS Electrical Engineering and Computer Science '24, MIT

   Summer 2020-Summer 2021. Research in Machine Learning and Medicine with Pratik Shah at MIT.

   More information about Steven.

6. Shree Mohan, BS Electrical Engineering and Computer Science '24, MIT

   Fall 2020-Summer 2021. Research in Machine Learning and Medicine with Pratik Shah at MIT.

   More information about Shree

7. Saketh Gabbita, BS Electrical Engineering and Computer Science '24, MIT

   Fall 2020-Summer 2021. Research in Machine Learning and Medicine with Pratik Shah at MIT.

8. Connor Anderson, BS Electrical Engineering and Computer Science '21, MIT

   Fall 2019-Spring 2020. Undergraduate Research in Machine Learning and Medicine with Pratik Shah at MIT.

   Now -MEng. candidate, Massachusetts Institute of Technology, Cambridge, MA.

   Publications with Dr. Pratik Shah:

   Automated end-to-end deep learning framework for classification and tumor localization from native non-stained pathology images

   Akram Bayat, Anderson C, Shah P*^♯

   (*Senior author supervising research, ^♯Selected for Deep-dive spotlight session)

   SPIE Proceedings. DOI: 10.1117/12.2582303

9. Michael Gilbert, BS Electrical Engineering and Computer Science '22, MIT

   Fall 2019-Spring 2020. Undergraduate Research in Machine Learning and Medicine with Pratik Shah at MIT.

   Now -Software engineer, NVIDIA, Boston, MA

10. Elizabeth Zhou, BS Electrical Engineering and Computer Science '21, MIT

    Fall 2019-Spring 2020. Undergraduate Research in Machine Learning and Medicine with Pratik Shah at MIT.

11. Sharon Wu, BS Computer Science and Molecular Biology '17, MIT

    2017. Undergraduate Research Opportunities Program trainee with Dr. Pratik Shah.
    UAP: Undergraduate Advanced Project: Microbial pathogenicity island prediction using convolutional neural network.
    Now - Ph.D. student, Molecular Cellular & Developmental Biology, University of Colorado, Boulder, CO.

    Publications with Dr. Pratik Shah:

    Near-infrared transillumination guides administration of dental 2D radiography and CBCT imaging

    Keith Angelino, Edlund D, Bhatia G, Wu S, Shah P*^♯

    (*Senior author supervising research, ^♯Selected for oral presentation)

    17^th annual IEEE International Conference on BioInformatics and BioEngineering. DOI: 10.1109/BIBE.2017.00-33

12. Alicia Chong Rodriguez, MS Integrated Design and Management '18, MIT

    2016-2017. MISTI-MIT Peru fund trainee with Dr. Pratik Shah.
    Now - Founder and CEO of Bloomer HealthTech. TED fellow, class of 2021.

    Recognitions:

    • Taking on gender gaps in health care and technology

      Graduate student Alicia Chong Rodriguez uses her engineering skills to empower women.

    • Meet the 2021 class of TED Fellows

      Health care technology entrepreneur Alicia Chong Rodriguez makes smart medical devices that gather often overlooked data on heart disease in women, a frequently misdiagnosed and under-researched killer.uses her engineering skills to empower women.

13. Yachi (Judy) Chang, BS Computer Engineering '16, MIT

    2015. Undergraduate Research Opportunities Program trainee with Dr. Pratik Shah.
    UAP: Undergraduate Advanced Project: Virtual reality in healthcare.
    Now - Software engineer Square.

Postdoctoral Associates

1. Akram Bayat, Ph.D. Computer Science '18, University of Massachusetts Boston

   Summer 2019-Summer 2020. Postdoctoral Associate with Pratik Shah at MIT.

   Recognition:

   • MIT NEWS article on research contributions to computational staining research published in JAMA Network
   • Selection of SPIE medical imaging conference publication for Deep-Dive session
   Publications with Dr. Pratik Shah:

   1. Automated end-to-end deep learning framework for classification and tumor localization from native non-stained pathology images

      Akram Bayat, Anderson C, Shah P*^♯

      (*Senior author supervising research, ^♯Selected for Deep-dive spotlight session)

      SPIE Proceedings. DOI: 10.1117/12.2582303

   2. Use of deep learning to develop and analyze computational hematoxylin and eosin staining of prostate core biopsy images for tumor diagnosis

      Aman Rana, Lowe A, Lithgow M, Horback K, Janovitz T, Da Silva A, Tsai H, Shanmugam V, Bayat A, Shah P*

      (*Senior author supervising research)

      JAMA Network. DOI: 10.1001/jamanetworkopen.2020.5111

2. Sambuddha Ghosal, Ph.D. Mechanical Engineering with a minor in Electrical Engineering '19, Iowa State University

   Fall 2019-Spring 2022. Postdoctoral Associate with Pratik Shah at MIT.

   Now - Data scientist digital field testing, Bayer AG, St Louis, MO

   Publications with Dr. Pratik Shah:

   1. A deep-learning toolkit for visualization and interpretation of segmented medical images

      Sambuddha Ghosal and Shah P*

      ( *Senior author supervising research)

      Cell Reports Methods 1, 100107, 2021

   2. Uncertainty quantified deep learning for predicting dice coefficient of digital histopathology image segmentation

      Sambuddha Ghosal, Xie A and Shah P*

      ( *Senior author supervising research)

      arXiv:2011.05791 [stat.ML]

3. Hyung-Jin Yoon, Ph.D. Mechanical Engineering and MS Applied Mathematics '19, University of Illinois at Urbana-Champaign

   Summer 2019-Summer 2020. Postdoctoral Associate with Pratik Shah at MIT.

   Now - University of Nevada, Reno, NV

   Publication: Early estimations of antibiotic therapies by constrained deep learning. Under preparation, 2023.

Research Collaborators

1. Muthuraman Alagappan, MD

   Chief Medical Director at Notable Health and attending physician at UCSF.

2. Alarice Lowe, MD

   Associate Professor - University Medical Line, Pathology, Stanford Hospitals and Clinics

3. Rohit Karnik, Ph.D

   Professor- Department of Mechanical Engineering, Massachusetts Institute of Technology

4. United States FDA

   The Office of Science and Engineering Laboratories, Center for Devices and Radiological Health.

Graduate Students

1. Mary Tellers Strawser, Ph.D. '22, MIT

   Ph.D. in Mechanical Engineering, 2022. Department of Mechanical Engineering, Massachusetts Institute of Technology. Co-advisor.

   Now - Senior Engineer II · Werfen North America, Bedford, MA

2. Emily Hanhauser

   Department of Mechanical Engineering, Massachusetts Institute of Technology. Co-advisor

Research Staff

1. Aman Rana, BS and MS Robotics Engineering, Worcester Polytechnic Institute

   2017-2019. Senior Research Support Associate with Pratik Shah at MIT.
   Now - Applied Research Scientist at Amazon, Cambridge, MA.

   Recognitions:

   • MIT NEWS article on research contributions to computational staining research published in JAMA Network
   Publications with Dr. Pratik Shah:

   1. Use of deep learning to develop and analyze computational hematoxylin and eosin staining of prostate core biopsy images for tumor diagnosis

      Aman Rana, Lowe A, Lithgow M, Horback K, Janovitz T, Da Silva A, Tsai H, Shanmugam V, Bayat A, Shah P*

      (*Senior author supervising research)

      JAMA Network. DOI: 10.1001/jamanetworkopen.2020.5111

   2. Automated process incorporating machine learning segmentation and correlation of oral diseases with systemic health

      Gregory Yauney, Rana A, Javia P, Wong L, Muftu A, Shah P*

      (*Senior author supervising research)

      41st IEEE International Engineering in Medicine and Biology Conference. DOI: 10.1109/EMBC.2019.8857965

   3. Digital reconstruction of teeth using near-infrared light

      Keith Angelino, Yauney G, Rana A, Muftu A, Edlund D, Shah P*

      (*Senior author supervising research)

      41st IEEE International Engineering in Medicine and Biology Conference. DOI: 10.1109/EMBC.2019.8857734

   4. Computational histological staining and destaining of prostate core biopsy RGB images with generative adversarial neural networks

      Aman Rana, Yauney G, Lowe A, Shah P*

      (*Senior author supervising research)

      17th IEEE International Conference of Machine Learning and Applications. DOI: 10.1109/ICMLA.2018.00133

   5. Machine learning algorithms for classification of microcirculation images from septic and non-septic patients

      Perikumar Javia, Rana A, Shapiro NI, Shah P*

      (*Senior author supervising research)

      17th IEEE International Conference of Machine Learning and Applications. DOI: 10.1109/ICMLA.2018.00097

   6. Automated segmentation of gingival diseases from oral images

      Aman Rana, Yauney G, Wong L, Muftu A, Shah P*

      (*Senior author supervising research)

      IEEE-NIH 2017 Special Topics Conference on Healthcare Innovations and Point-of-Care Technologies. DOI: 10.1109/HIC.2017.8227605

2. Gregory Yauney, BS Computer Science, Brown University

   2016-2018. Technical Associate with Dr. Pratik Shah at MIT.
   Now - Ph.D. Student Computer Science Department, Cornell University, Ithaca, NY.

   Recognitions:

   • MIT NEWS article on research contributions to deep learning and medical research
   Publications with Dr. Pratik Shah:

   1. Automated process incorporating machine learning segmentation and correlation of oral diseases with systemic health

      Gregory Yauney, Rana A, Javia P, Wong L, Muftu A, Shah P*

      (*Senior author supervising research)

      41st IEEE International Engineering in Medicine and Biology Conference. DOI: 10.1109/EMBC.2019.8857965

   2. Digital reconstruction of teeth using near-infrared light

      Keith Angelino, Yauney G, Rana A, Muftu A, Edlund D, Shah P*

      (*Senior author supervising research)

      41st IEEE International Engineering in Medicine and Biology Conference. DOI: 10.1109/EMBC.2019.8857734

   3. Reinforcement learning with action-derived rewards for chemotherapy and clinical trial dosing regimen selection

      Gregory Yauney, Shah P*

      (*Senior author supervising research)

      Proceedings of the 3rd Machine Learning for Healthcare Conference. PMLR 85:161-226

   4. Technology-enabled examinations evaluated jointly with routine health screenings: an observational study at the 2015 Kumbh Mela in India

      Pratik Shah*^†, Yauney G^†, Gupta O, Patalano V, Mohit M, Merchant R, Subramanian SV

      (*Senior author supervising research, ^†Contributed equally)

      The British Medical Journal Open. PMID: 29678964

   5. Computational histological staining and destaining of prostate core biopsy RGB images with generative adversarial neural networks

      Aman Rana, Yauney G, Lowe A, Shah P*

      (*Senior author supervising research)

      17th IEEE International Conference of Machine Learning and Applications. DOI: 10.1109/ICMLA.2018.00133

   6. Convolutional neural network for combined classification of fluorescent biomarkers and expert annotations using white light images

      Gregory Yauney, Angelino K, Edlund D, Shah P*^♯

      (*Senior author supervising research, ^♯Selected for oral presentation)

      17^th annual IEEE International Conference on BioInformatics and BioEngineering. DOI: 10.1109/BIBE.2017.00-37

   7. Automated segmentation of gingival diseases from oral images

      Aman Rana, Yauney G, Wong L, Muftu A, Shah P*

      (*Senior author supervising research)

      IEEE-NIH 2017 Special Topics Conference on Healthcare Innovations and Point-of-Care Technologies. DOI: 10.1109/HIC.2017.8227605

   8. Clinical validation and assessment of a modular fluorescent imaging system and algorithm for rapid detection and quantification of dental plaque

      Pratik Shah*^†, Angelino K^†, Edlund D, Mohit M, Yauney G

      (*Senior author supervising research, ^†Contributed equally)

      BMC Oral. PMID: 29284461

3. Keith Angelino, BS and MS Biomedical Engineering, Case Western Reserve University

   2016-2018. Technical Associate with Dr. Pratik Shah at MIT.
   Now - At startup.

   Publications with Dr. Pratik Shah:

   1. Digital reconstruction of teeth using near-infrared light

      Keith Angelino, Yauney G, Rana A, Muftu A, Edlund D, Shah P*

      (*Senior author supervising research)

      41st IEEE International Engineering in Medicine and Biology Conference. DOI: 10.1109/EMBC.2019.8857734

   2. Near-infrared transillumination guides administration of dental 2D radiography and CBCT imaging

      Keith Angelino, Edlund D, Bhatia G, Wu S, Shah P*^♯

      (*Senior author supervising research, ^♯Selected for oral presentation)

      17^th annual IEEE International Conference on BioInformatics and BioEngineering. DOI: 10.1109/BIBE.2017.00-33

   3. Near-infrared imaging for detecting caries and structural deformities in teeth

      Keith Angelino, Edlund D and Shah P*

      (*Senior author supervising research)

      Journal of Translational Engineering in Health and Medicine. PMID: 28507826

   4. Clinical validation and assessment of a modular fluorescent imaging system and algorithm for rapid detection and quantification of dental plaque

      Pratik Shah*^†, Angelino K^†, Edlund D, Mohit M, Yauney G

      (*Senior author supervising research, ^†Contributed equally)

      BMC Oral. PMID: 29284461

   5. Convolutional neural network for combined classification of fluorescent biomarkers and expert annotations using white light images

      Gregory Yauney, Angelino K, Edlund D, Shah P*^♯

      (*Senior author supervising research, ^♯Selected for oral presentation)

      17^th annual IEEE International Conference on BioInformatics and BioEngineering. DOI: 10.1109/BIBE.2017.00-37

4. Perikumar Javia, BS and MS Computer Engineering, Arizona State University

   2018-2019. Research specialist with Dr. Pratik Shah at MIT.

   Now - Software engineer at Google

   Publications with Dr. Pratik Shah:

   Machine learning algorithms for classification of microcirculation images from septic and non-septic patients

   Perikumar Javia, Rana A, Shapiro NI, Shah P*

   (*Senior author supervising research)

   17th IEEE International Conference of Machine Learning and Applications. DOI: 10.1109/ICMLA.2018.00097

5. Gaurav Bhatia, MS Electrical Engineering, University of Houston

   2016-2017. Senior research support associate with Dr. Pratik Shah at MIT.
   Now - Electrical Engineer at Harbor Design and Manufacturing, Baltimore, MD.

   Publications with Dr. Pratik Shah:

   Near-infrared transillumination guides administration of dental 2D radiography and CBCT imaging

   Keith Angelino, Edlund D, Bhatia G, Wu S, Shah P*^♯

   (*Senior author supervising research, ^♯Selected for oral presentation)

   17^th annual IEEE International Conference on BioInformatics and BioEngineering. DOI: 10.1109/BIBE.2017.00-33