About



I am a PhD candidate at RMIT University with a strong background in computer engineering and applied artificial intelligence. My current research focuses on deep learning for medical imaging, specifically developing AI models for tumour tracking and radiotherapy guidance. Before this, I was involved in deep learning–based bioinformatics research, working on nanopore sequencing and selective genomics—broadening my exposure to AI applications in life sciences. Prior to academia, I worked in the software industry for several years, contributing to scalable microservices, cloud-based applications, and AI-driven solutions.

With hands-on experience in AI/ML, full-stack development, and cloud platforms like Azure, I bring a blend of research insight and engineering practicality.

Contact Me @ Linkedin | Github | Google Scholar | Stackoverflow

Interests

  • Artificial Intelligence & Machine Learning
  • Computer Vision in Medical Imaging
  • Bioinformatics
  • Data Driven Astronomy
  • Full Stack Development

Education

  • Doctor of Philosophy

    Royal Melbourne Institute of Technology, Melbourne

    2024 — Present

  • M.Phil in Computer Engineering

    University of Peradeniya, Kandy

    2020 — 2023

  • BSc(Hons) in Computer Engineering

    University of Peradeniya, Kandy

    2015 — 2020

Work Experience

  • PhD Candidate

    Royal Melbourne Institute of Technology, Melbourne

    • Deep Learning based lung tumour motion tracking in Stereotatic body radiotherapy
    Mar. 2024 — Present

  • Software Engineer

    WSO2 LLC, Colombo

    • Implementing Ballerina FHIR Conformance APIs.
    • Generating, restructuring and maintaining Ballerina FHIR Packages.
    • Implementing Package and Template Generator Tools.
    • Feature implementations, test cases and issue fixes of Ballerina HL7 and FHIR Transformation Packages and their prebuilt APIs.
    • Implemented element select feature in FHIRPath package.
    • Engaging in Customer PoC Demonstrations & allocations.
    • Involved in fixing bugs, improving the code base of WSO2 healthcare solutions.
    • Prepared documentation for customers as well as internal purposes.
    • Worked as a release manager to release Ballerina packages.
    • Domain Research (OpenEHR spec, FHIR Consent Management for Choreo).
    • Assisting junior team members with their issues.
    Jan. 2022 — Feb. 2024

  • AI & Software Engineer

    Infinity Innovators Pvt Ltd, Colombo

    • Developed Flask-based Microservices.
    • Developed ReactJS Single Page Applications.
    • Computer Vision Research.
    • Integrated Single Sign On with Azure AD + Federation.
    • Deployed Web Apps on Azure App Services.
    • Deployed Static Web Frontends on Azure Blob Storage.
    • Implemented CI/CD Pipelines on Azure DevOps.
    • Automated Cloud Infrastructure Deployment with Azure ARM Templates (IaC).
    • PostgreSQL Schema Designing, Implementation and Deployment on Cloud.
    Aug. 2020 — Jan. 2022

  • Trainee Software Engineer

    Proavos Labs Pvt Ltd

    • Developed important functionalities in Avtra Passenger Service System
    • Technologies: Java, Spring Boot and Oracle
    Feb. 2019 — July 2019

Publications

  • DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing

    Senanayake, A., Gamaarachchi, H., Herath, D. and Ragel, R.

    BMC Bioinformatics

    [Paper]

    Jan. 2023

  • Genopo: a nanopore sequencing analysis toolkit for portable Android devices

    Samarakoon, H., Punchihewa, S., Senanayake, A., Hammond, M., Stevanovski, I., Ferguson, J., Ragel, R., Gamaarachchi, H., Deveson, I.

    The Nature

    [Paper]

    Sep. 2020

Projects

  • Deep Learning based lung tumour motion tracking during stereotatic body radiotherapy

    Technologies: Python, Pytorch, TIGRE

    Contribution: Implementation of a new technique based on DL to track lung tumour motion during radiotherapy

    March. 2024 - Present

  • DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing

    Technologies: TensorFlow, Python, SLOW5, FAST5, Bash

    Contribution: Implemented a DL based framework called DeepSelectNet for realtime selective sequencing of DNA strands during sequencing

    [Github]

    Nov. 2020 - Nov. 2023

  • Online Assessment & Proctoring Platform (Infinity Innovators Pvt Ltd)

    Technologies: ReactJS, Python, PostgreSQL, Computer Vision, Azure (Cloud, DevOps, AD)

    Contribution: Developed microservices, Implemented SSO with Azure AD, CI/CD with Azure DevOps, Deployment to Azure Cloud

    2020 — 2022

  • Arogya – A Health Service Platform

    Technologies: Android, Node.js, React.js, Git

    Contribution: Team Leader, Design of the system, Collaborative development of Arogya mobile app, Developed the backend

    [Github]

    2020

  • Mobile Genomics – Bioinformatics Project

    Technologies: Java, Android, C, Vaadin, Maven, Git

    Contribution: Developed the f5n-server and the MinIt module in the f5n Android app

    [Github]

    2019

  • Flexibus – e-Ticketing Platform

    Technologies: Android, React Native, SQL, Node.js, Git

    Contribution: Developed conductor-side app and the backend

    [Github]

    2019

  • Radiobook – NLP Project

    Technologies: Stanford CoreNLP, Text-to-Speech, Maven, Git

    Contribution: Developed a TTS module to read textbooks with different voices, Fine-tuned Stanford CoreNLP

    [Github]

    2018

  • Automated Fishing Bot - Embedded Systems

    Technologies: Node.js, Express, Angular.js, JavaScript, HTML, CSS, MongoDB, Arduino, Raspberry Pi, Git

    Contribution: Developed the frontend and backend for the Server, (REST APIs, Middlewares, Web App, Database, Validations), Programed relay node to server data push module, Implemented MQTT protocol for relay node – server communication.

    [Github]

    2018

  • Packet Forwarding Simulator – Network Software Project

    Technologies: Java, JavaFX, GraphStream, Git, Maven

    Contribution: Developed the UI/UX for the simulator, Integrated UI with the simulator, Conducted software testing, and handled deployment

    [Github]

    2017

Achievements & Activities

  • Brainstorm, UoM

    2019

  • ihack 4.0v, UCSC

    Runners up (Radiobook Project)

    2018

  • 4IR Hackathon, SLASSCOM

    2018

  • ACES Hackathon, UoP

    2018

  • ACES Hackathon, UoP

    2017

  • Dramsoc, Ceylon Dramatic Society

    Team award for best crew

    2016

  • G.C.E Advanced Level Examination

    Passed all 4 subjects sat with 3 distinction (A) and a very good pass(B)

    2014

  • Vice Secretary of Sinhala Literary Union, Trinity College, Kandy

    2013

  • K.B Sangakkara Memorial Scholarship

    Awarded for the academically promising top students in the A/L section

    2013

  • Best Students Prize, Education Ministry of Central Province

    For top performances in G.C.E O/L examination in central province, Sri Lanka

    2012

  • G.C.E Ordinary Level Examination

    Passed all 9 subjects sat with distinctions (A) for all

    2011

Certifications & Memberships

  • Microsoft Certified: Azure Fundementals

    2022 - Present

  • Associate Member of Engineering Council of Sri Lanka

    2021 - Present