Jinani Sooriyaarachchi

I am a final-year PhD candidate (graduating in December 2024) specialized in Computational Neuroscience and Machine Learning at McGill University, in the Department of Physiology under the supervision of Dr. Curtis Baker. My research is aimed at the long-term objective of understanding the visual processing carried out by an early visual cortex neuron. Towards this end, I develop elaborate machine learning models to estimate the evoked neuronal spiking activities recorded in the primary visual cortex in response to natural image stimuli. I’m always happy to take on projects involved in studying how the brain works to learn principles that allow us to make better AI.

Main Research Interests:

  • Machine Learning
  • Computational Neuroscience
  • Electrophysiology
  • System Identification
  • Computational Modelling
  • Bio-signal Processing
Download CV



Research

Cortical state effects on responses of primary visual cortex neurons: A machine learning approach

PhD Thesis | McGill University, Canada

In the field of visual neuroscience, computational models of a visual cortex neuron are useful for understanding its functional role within the mammalian brain. A successful model will be able to accurately predict a neuron's responses to any visual image. Understanding the activity of a single visual cortex neuron is especially challenging for model development because brain responses vary for repeated presentations of the same stimulus as a result of "brain-state" fluctuations (e.g., sleep, arousal, attention) that can affect large populations of neurons.
Thus, the goal of my work is to develop novel computational models for single neurons that considers both brain-state and visual input, and alternative possible interactions between them, that can be used to evaluate neuronal responses in the visual cortex. The resulting models are expected to outperform existing models in terms of predictive accuracy, computational optimization and give new insights into the effects of brain-state fluctuations on visual perception. Ultimately, my work will provide a better understanding of the basic visual system that will contribute to developing treatment strategies for visual impairments caused by visual cortex pathology.

MusicID: A Brainwave-Based User Authentication System for Internet of Things

Internship project | Data61-CSIRO, Australia

MusicID is an authentication solution for smart devices that uses music-induced brainwave patterns as a behavioral biometric modality. This work experimentally analyse data collected from real users whilst they are listening to two forms of music: 1) a popular English song and 2) individual's favorite song and shows that an accuracy over 98% for user identification and an accuracy over 97% for user verification can be achieved by using data collected from a 4-electrode commodity brainwave headset. Further MusicID shows that a single electrode is able to provide an accuracy of approximately 85% and the use of two electrodes provides an accuracy of approximately 95%. As already shown by commodity brain-sensing headsets for meditation applications, including dry electroencephalogram electrodes in smart headsets are feasible and MusicID has the potential of providing an entry point and continuous authentication framework for upcoming surge of smart devices mainly driven by augmented reality (AR)/virtual reality (VR) applications.

Removing subject dependencies on Non-Invasive Blood Glucose Measurement using Hybrid Techniques

Final year project | University of Moratuwa, Sri Lanka

Diabetes mellitus is a major health problem which requires regular glucose monitoring and invasive blood glucose measuring systems with acceptable accuracies are currently used for these measurements. Several non-invasive blood glucose measurement techniques are reported in research literature, but most of them are not commercially available due to low accuracy or dependency on individual physiological parameters. This work presents a hybrid technique to measure blood glucose levels non-invasively using a combination of multi-wavelength near infrared (NIR) spectroscopy and bio-impedance spectroscopy. Physiological parameters of individuals and other environmental factors that affect non-invasive glucose measurements have been identified and compensated to make the device work on any person without the requirement of complicated further calibrations. The measured parameters, along with the glucose levels of human subjects obtained from a commercial blood glucose meter is used to train a machine learning model (Random Forest regression algorithm). The trained system (with a training set of 315 data samples and a a test set of 80 data samples) predicted the blood glucose levels non-invasively with an accuracy of 90.7%.

Other Projects

1. A Model-to-Brain mapping: Modelling ventral visual stream with AlexNet

Summer project | Neromatch Academy

2. WIMU based performance and injury analysis system for Sri Lankan Cricket team

Research | Center for Biomedical Innovation

3. Shimmer IMU based gait analysis system

Research | Center for Biomedical Innovation

4. A server monitoring/alarming system using Nagios

Implementation | Axiata Digital Labs & CAT telecom-Thailand

5. VeinViewer: An Affordable Vein Imaging Device

Research | University of Moratuwa


Education

PhD in Physiology (Thesis) - Specialized in Computational Neuroscience and Machine Learning

Department of Physiology-McGill University, Canada | 2021 - 2024
GPA 4.0/4.0
Thesis Topic A machine learning approach to understand the cortical state effects on responses of primary visual cortex neurons.
Supervisor Dr. Curtis L. Baker
Scientific presentations 6 oral presentations, 5 international presentations, 11 national presentations
Awards 5 fellowships and 3 best presentation awards, 1 hackathon
Courses
  • PSYC 526 Advances in Visual Perception (Grade: A)
  • NEUR 631 Principles of Neuroscience 2 (Grade: A)
  • NEUR 503 Computational Neuroscience (Grade: A)

MSc in Physiology (Thesis)- Fast-tracked to PhD

Department of Physiology-McGill University, Canada | 2020-2021
GPA 4.0/4.0
Thesis Topic A machine learning approach to understand the cortical state effects on responses of primary visual cortex neurons.
Supervisor Dr. Curtis L. Baker

BSc in Engineering (Honours)

Biomedical Engineering-University of Moratuwa, Sri Lanka | 2014-2018
GPA 3.94/4.2 (First Class)
Included in Dean’s List in all the semesters
Ranked 2nd highest GPA holder in Biomedical Engineering
Courses
  • EN 2550 Fundamentals of Image processing and Machine Vision
  • EN 2110 Electronics
  • EN 2570 Digital Signal Processing
  • EN 4563 Robotics
  • BM 4111 Medical Electronics and Instrumentation
  • BM 3121 Medical Imaging
  • BM 2020 Human Anatomy and Physiology 
  • MA 2013 Differential Equations
  • MA 2023 Calculus
  • MA 4043 Neural Network and Fuzzy Logic

Deep Learning - Interactive Track and Course Project

Neuromatch Academy | Summer 2022

Diploma in Management Accounting - Foundation Level

Chartered Institute of Management Accountants (CIMA)

Certificate in Business Accounting - Operational Level

Chartered Institute of Management Accountants (CIMA)

Publications

Journal Articles

  1. J. Sooriyaarachchi, S. Seneviratne, K. Thilakarathna and A. Y. Zomaya, ”MusicID: A Brainwave-based User Authentication System for Internet of Things,” in IEEE Internet of Things Journal, doi: 10.1109/JIOT.2020.3044726.
  2. J. Sooriyaarachchi, Chang'an Zhan, Curtis L. Baker Jr., ”Cortical state contributions to response variability in the early visual cortex: A system identification approach,” bioRxiv 2024.09.17.613530; doi: https://doi.org/10.1101/2024.09.17.613530
  3. Philippe Nguyen * , Jinani Sooriyaarachchi *, Qianyu Huang, Curtis L. Baker Jr., (2024) ”Estimating receptive fields of simple and complex cells in early visual cortex: A convolutional neural network model with parameterized rectification. PLOS Computational Biology 20(5): e1012127.”, https://doi.org/10.1371/journal.pcbi.1012127 (* shared first authors)
  4. K. D. Pathirage, P. Roopasinghe, J. Sooriyaarachchi, R. Weththasinghe and N. D. Nanayakkara, ”Removing subject dependencies on Non-Invasive Blood Glucose Measurement using Hybrid Techniques,” 2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Berlin, Germany, 2019, pp. 7197-7200.

Scientific Presentations

    International Conferences

  1. J. Sooriyaarachchi, C. Zhan, C. Baker, “Cortical State Effects Vary Across Different Neuronal Subclasses in the Primary Visual Cortex”, Society for Neuroscience Annual Meeting (SFN23), Nov 2023
  2. J. Sooriyaarachchi, C. Zhan, C. Baker, “Cortical State Effects Vary Across Different Neuronal Subclasses in the Primary Visual Cortex”, Annual computational neuroscience conference (CNS23), July 2023
  3. J. Sooriyaarachchi, C. Zhan, C. Baker, “Cortical state effects on receptive field responses of early visual cortex neurons”, Society for Neuroscience Annual Meeting (SFN22), Nov 2022
  4. J. Sooriyaarachchi, C. Zhan, C. Baker, “Cortical state effects on responses of primary visual cortex neurons: A system identification approach.”, Active vision symposium (University of Rochester), May 2022
  5. J. Sooriyaarachchi, C. Zhan, C. Baker, “Brain state effects on responses of early visual cortex neurons: A system identification approach”, Society for Neuroscience Annual Meeting (SFN21), Nov 2021
  6. National Conferences

  7. J. Sooriyaarachchi, C. Zhan, C. Baker, “Cortical State Effects Vary Across Different Neuronal Subclasses in the Primary Visual Cortex”, The New VISTAs in Vision Research (CVR23), Dec 2023
  8. J. Sooriyaarachchi, C. Zhan, C. Baker, “Cortical State Effects Vary Across Different Neuronal Subclasses in the Primary Visual Cortex”, McGill Ophthalmology Grand rounds talk, Nov 2023
  9. J. Sooriyaarachchi, C. Baker, “Cortical State Effects Vary Across Different Neuronal Subclasses in the Primary Visual Cortex” - McGill Ophthalmology Research Day, May 2023
  10. J. Sooriyaarachchi, C. Baker, “Cortical state effects on receptive field responses of early visual cortex neurons”, Graduate Research Day - Department of Physiology, McGill University, May 2023
  11. J. Sooriyaarachchi, C. Zhan, C. Baker, “Cortical State Effects Vary Across Different Neuronal Subclasses in the Primary Visual Cortex”, Biological and biomedical engineering symposium (BBMESS), May 2023
  12. J. Sooriyaarachchi, C. Zhan, C. Baker, “Cortical state effects on responses of primary visual cortex neurons: A system identification approach”, Brain Repair and Integrative Neuroscience (BRaIN) seminar talk, Feb 2023
  13. J. Sooriyaarachchi, C. Zhan, C. Baker, “Improved accuracy in estimating responses of early visual cortex neurons with CNNs incorporating cortical state dynamics.”, Montreal AI and Neuroscience (MAIN), Dec 2022
  14. J. Sooriyaarachchi, C. Zhan, C. Baker, “Cortical state effects on responses of primary visual cortex neurons: A system identification approach.”, Vision Health Research Network (VHRN), Nov 2022
  15. J. Sooriyaarachchi, C. Baker, “Cortical state effects on receptive field responses of early visual cortex neurons”, Graduate Research Day - Department of Physiology, McGill University, May 2022
  16. J. Sooriyaarachchi, C. Zhan, C. Baker, “Cortical state effects on responses of primary visual cortex neurons: A system identification approach.”, Montreal AI and Neuroscience (MAIN), Nov 2021
  17. J. Sooriyaarachchi, C. Baker, “Receptive Field Estimation of Primary Visual Cortex (V1) Neurons: A System Identification Approach Incorporating Cortical State” - McGill Ophthalmology Research Day, Oct 2021
  18. J. Sooriyaarachchi, C. Baker, “Incorporating Brain States in V1 Receptive Field Estimation”, Graduate Research Day - Department of Physiology, McGill University, May 2021
  19. K. D. Pathirage, P. Roopasinghe, J.J. Sooriyaarachchi, R. Weththasinghe and N. D. Nanayakkara, “Non-Invasive Blood Glucose Measurement”, Expose Exhibition-University of Moratuwa, Jan 2019
  20. J.J. Sooriyaarachchi, M. Athif, L.K.Rathnayaka, “Real-time EEG signal capturing with BIOPAC system”, Brain-Computer Interface (BCI) workshop – IEEE Engineering and Biology Society- University of Moratuwa Sri Lanka, Jun 2018
  21. J.J. Sooriyaarachchi, M. Athif, L.K.Rathnayaka, “Physiological signal measurements with BIOPAC system”, Expose Exhibition-University of Moratuwa, May 2017
  22. J.J. Sooriyaarachchi, M. Athif, L.K.Rathnayaka, D. Anojan, “VeinViewer: An Affordable Vein Imaging Device”, Expose Exhibition-University of Moratuwa, March 2016

Skills

Programming Advanced level in Python and Matlab (data analysis and visualization), conda, git
Machine Learning Advanced level in regression, clustering, dimensionality reduction, neural nets, deep learning and transfer learning using Tensorflow, Keras, Scikit-Learn, PyTorch libraries
Bio-signal processing Electrophysiology, EEG, EMG and ECG data acquisition and processing
Research Skills Data acquisition, Data analysis and visualization, Statistical analysis, Neurophysi- ology techniques, Participant recruitment and screening, Ethics applications, Scientific communications
Operating Systems Linux, Windows, Mac
Project Management and Leadership Skills Leading and mentoring multidisciplinary teams of biomedical engineers and computer scientists.


Work Experience

Consultant: AAVAA, Montreal, Canada

2022/12 - 2023/03
  • Developed an approach to denoise EEG signals with a higher accuracy for a commercial grade BCI device.
  • Implemented an UMAP based clustering algorithm to cluster eye blinks to reject noisy eye blinks in a BCI application.
  • Implemented an algorithm to calibrate eye blink signals extracted from EEG to standardize eye blinks of a specific user using BCI to control a commercial grade device developed in the company.

Research Assistant: Center for Biomedical Innovation, Sri Lanka

2020/01 - 2020/09
  • Developed an IMU Based Gait Analysis system (based on Matlab and ShimmerIMU).
  • Conducted clinical trials with scoliosis patients.
  • Managed project teams working on gait analysis with the national cricket team.
  • Collaborated with Shimmer Research.
  • Recruited and trained new research employees.

Senior Executive - Software Engineer: Axiata Digital Labs, Sri Lanka

2019/01 - 2019/10
  • Developed and installed a server monitoring/alarming system at CAT Telecom (Thailand).
  • Developed a system to authenticate users purchasing SIM cards at Dialog Telecom (Sri Lanka).
  • Worked on a web service proxy to convert from SOAP APIs to REST APIs.
  • Collaborated with CAT Telecom (Thailand) and Huawei (China).

Research Trainee: DATA61-CSIRO, Australia

2017/08 - 2018/01
  • Developed a machine learning based biometric authentication system using music-induced EEG.
  • Wrote and managed the ethics approval for collecting EEG from human subjects.
  • Tested the authentication system with human subjects.
  • Presented and published the research in IEEE-Internet of Things journal.
  • Managed time to deliver a successful authentication system in less than six months.
  • Collaborated with the University of Sydney.

Leadership

2024 | Mentor, Scientista program, McGill University, Canada

2016 | Control Board External Relations Manager, AIESEC Colombo-South, University of Moratuwa, Sri Lanka
2015 | Department Representative, Biomedical Engineering, University of Moratuwa, Sri Lanka
2015 | Project manager, AIESEC Colombo-South, University of Moratuwa, Sri Lanka

2012-2013 | Senior Prefect, School: Sujatha Vidyalaya, Matara, Sri Lanka
2010-2011 | Junior Prefect, School: Sujatha Vidyalaya, Matara, Sri Lanka


Awards

Fonds de recherche du Québec - Santé (FRQS) doctoral fellowship

2022 - 2026 | 84,000 CAD

Awarding organization: Fonds de recherche du Québec, Canada

  • Third place in FRQS fellowship competition (category: neuroscience) providing four years of PhD funding

NeuroSphere Neurotech Hackathon Challenge Award

2024 | 3,000 CAD

Awarding organization: NeuroSphere-HBHL

  • natHacks neurotech Hackathon

The Applied AI Institute Award for best poster presentation

2022/12 | 400 CAD

Awarding organization: The Applied AI Institute, Canada

  • Awarded at the Montreal AI and Neuroscience (MAIN22) conference

Faculty of Medicine Internal Studentship

2022/09 - 2023/09 | 12,000 CAD

Awarding organization: Faculty of Medicine and Health Sciences, McGill University

  • Awarded to the top ranked graduate students in Faculty of Medicine and Health Sciences

Max E. and Jane K. Childress Entrance Fellowships in Physiology

2021/09 - 2022/09 | 38,000 CAD

Awarding organization: Department of Physiology, McGill University

  • Awarded to the top ranked students accepted to PhD program

Max Stern Recruitment Fellowship in Physiology

2020/09 - 2021/09 | 27,000 CAD

Awarding organization: Department of Physiology, McGill University

  • Awarded to the top ranked students accepted to MSc program

Best oral presentation - Physiology Graduate Research Day

2021/05 and 2024/05 | 50 CAD

Awarding organization: Department of Physiology, McGill University

Dean's List in 8/8 semesters

2014 - 2018

Awarding organization: University of Moratuwa, Sri Lanka

  • Awarded to the students with GPA > 3.8

Mahapola Higher Education Scholarship

2014 - 2018 | 240,000LKR

Awarding organization: University Grants Commission, Sri Lanka

  • G.C.E. Advanced Level 2013 - Physical science Z-Score: 2.7109 (3'A passes), Island Rank:15, District Rank:2


Contact

I'm currently looking for work opportunities in the field of NeuroAI after my graduation (December 2024), please contact me by email at [email protected] or [email protected]