Publications

Uncertainty-Gated Min-Cost Flows for In Vivo NanoScale Synaptic Plasticity Tracking
Shashwat Kumar, Gabrielle I. Coste, Dasun Premathilaka, Richard L. Huganir, Austin R. Graves, Adam S. Charles, and Michael I. Miller
Preprint, 2025.
[arxiv]

Deep Geometric Framework to Predict Antibody-Antigen Binding Affinity
Nuwan Bandara, Dasun Premathilaka, Sachini Chandanayake, Sahan Hettiarachchi, Vithurshan Varenthirarajah, Aravinda Munasinghe, Kaushalya Madhawa, and Subodha Charles
Journal of Structural Biology, Volume 217, Issue 4, December 2025.
[paper]

Research

SynTrack: Nano-scale Synapse Tracking
- Formulated synapse tracking as a MAP estimation problem, with a fully-connected spatio-temporal graph to handle long-term occlusions.
- Advisor(s):
  - Dr. Richard L. Huganir (Professor), Johns Hopkins University, USA
  - Dr. Austin R. Graves (Assistant Research Professor), Johns Hopkins University, USA
  - Dr. Adam S. Charles (Assistant Professor), Johns Hopkins University, USA
  - Dr. Michael I. Miller (Professor), Johns Hopkins University, USA

– If the image is not clear, click here.

Deep Geometric Framework to Predict Antibody-Antigen Binding Affinity
- Proposed a deep geometric network that shares information between structure and sequence-based models via cross-attention to predict antibody–antigen binding affinity.
- Undergraduate Thesis Project [Thesis]
- Supervisor(s):
  - Dr. Subodha Charles (Senior Lecturer), University of Moratuwa, Sri Lanka
  - Dr. Aravinda Munasinghe (Senior Research Scientist), Pfizer Inc., USA
  - Dr. Kaushalya Madhawa (AI Scientist), University of Tokyo, Japan

– If the image is not clear, click here.

Multi-instance, Multi-task Learning for Cancer Histopathology Images
- Graduate Research Internship Project(s)
- Supervisor(s):
  - Dr. Lee Hwee Kuan (Head of Research Division), Bioinformatics Institute, A*STAR, Singapore
  - Tianyi Zhang (Research Officer), Bioinformatics Institute, A*STAR, Singapore

– For other projects, feel free to check out the Archive section.