Personal profile
Research interests
I focus on designing scalable, interpretable algorithms to enable novel scientific discovery from biomedical imaging data at multiple scales ranging from diffuse optical tomography (DOT) to confocal and superresolution microscopy (SRM, STED, SMLM, dSTORM). I leverage and extend concepts from several fields: fuzzy computing (belief theory, information fusion) to simulation (discrete event simulators, agent based simulation), graph algorithms, vector fields, recurrent neural networks, and structural causal discovery from complex data.
Application domains range from degenerative (Alzheimer, ageing) to metabolic (diabetes) and infectious disease, with a specific focus on elucidating subcellular function from complex data. Whenever possible I like to design algorithms that push beyond the empirical resolution limits of modalities and that are adaptive or robust to complex noise models.
Biography
I started my research career developing a paralell discrete event simulator in C++ with the capability to switch at runtime between simulation paradigms enabling simulation designers to find automatic optima for their domain uses. In my Master's I combined distributed metaheuristics with hyperheuristics to enable symbolic regression for complex epidemiological simulations.
My doctorate focused on designing algorithms that extract interactions below observable empirical precision from superresolution microscopy.
In my postdoctoral fellowship I work on inferring equilibria from causal topological signatures in noisy biomedical imaging modalities.
Education/Academic qualification
Doctor of Science, Computational Reconstruction of Multiscale Interaction in Multichannel Superresolution Microscopy, Simon Fraser University
1 Sept 2017 → 30 Apr 2024
Award Date: 24 Apr 2024
Master in Science, Convergence of Symbolic Regression Using Metaheuristics (Computer Science), University of Antwerp
1 Sept 2015 → 30 Jun 2017
Award Date: 30 Jun 2017
Bachelor of Science, A Parallel Discrete Event Simulator in C++ (Computer Science), University of Antwerp
1 Sept 2012 → 30 Jun 2015
Award Date: 30 Jun 2015
Keywords
- QA75 Electronic computers. Computer science
- machine learning
- Image processing
- reconstruction
- uncertainty
- scalability
- vector fields
- graph algorithms
- QA76 Computer software
- simulation
- prediction
- RB Pathology
- Ageing
- Degenerative disease
- Mitochondria
- Protein Structure
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
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SDG 3 Good Health and Well-being
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Collaborations and top research areas from the last five years
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Closing the multichannel gap through computational reconstruction of interaction in super-resolution microscopy
Cardoen, B., Ben Yedder, H., Nabi, I. R. & Hamarneh, G., 9 May 2025, In: Patterns. 6, 5, 23 p., 101181.Research output: Contribution to journal › Review article › peer-review
Open Access -
Comparative Analysis of SPLICS and MCS-DETECT for Detecting Mitochondria-ER Contact Sites (MERCs)
Zheng, J., Cardoen, B., Ortiz-Silva, M., Hamarneh, G. & Nabi, I. R., Sept 2025, In: Contact. 8, 12 p., 25152564251313721.Research output: Contribution to journal › Article › peer-review
Open Access -
nERdy: network analysis of endoplasmic reticulum dynamics
Samudre, A., Gao, G., Cardoen, B., Joshi, B., Nabi, I. R. & Hamarneh, G., 5 Nov 2025, In: Communications Biology. 8, 15 p., 1529.Research output: Contribution to journal › Article › peer-review
Open AccessFile3 Downloads (Pure) -
SuperResNET: Model-Free Single-Molecule Network Analysis Software Achieves Molecular Resolution of Nup96
Li, Y. L., Khater, I. M., Hallgrimson, C., Cardoen, B., Wong, T. H., Hamarneh, G. & Nabi, I. R., 16 Mar 2025, In: Advanced Intelligent Systems. 7, 3, 14 p., 2400521.Research output: Contribution to journal › Article › peer-review
Open AccessFile -
AI analysis of super-resolution microscopy: Biological discovery in the absence of ground truth
Nabi, I. R., Cardoen, B., Khater, I. M., Gao, G., Wong, T. H. & Hamarneh, G., 5 Aug 2024, In: Journal of Cell Biology. 223, 8, 13 p., e202311073.Research output: Contribution to journal › Article › peer-review
Open Access