Abdul Muntakim Rafi

I am a Ph.D. candidate in Biomedical Engineering at the University of British Columbia. My current research focuses on decoding cis-regulatory logic using machine learning: building sequence-to-expression models, developing methods to interpret and rigorously evaluate their reliability, and continually improving these models through large-scale synthesis of informative DNA sequences and lab-in-the-loop experiments. I have supervised multiple Co-op students in the de Boer lab and am always on the lookout for motivated undergrads/high schoolers to join my research endeavors.

Abdul Muntakim Rafi

Education

2021 – Present
Ph.D. in Biomedical Engineering
University of British Columbia, Vancouver, Canada
2019 – 2021
MASc in Electrical Engineering
University of Windsor, Windsor, Canada
2014 – 2018
BSc in Electrical and Electronic Engineering
Bangladesh University of Engineering & Technology (BUET), Dhaka, Bangladesh

Publications

*Equal contribution    Corresponding author

Preprints / In Preparation

gRely: Reliability estimation of variant effect predictions for genome trained sequence-to-expression models
Abdul Muntakim Rafi, Gökçen Eraslan, Kipper Fletez-Brant
In preparation, 2026
Evaluation of active learning selection strategies and characterization of informative sequences for sequence-to-expression models
Justin Qian*, Abdul Muntakim Rafi*†, Emmanuel Cazottes*, Carl de Boer
In preparation, 2026
Yorzoi: Predicting RNA-seq coverage from DNA sequence in yeast
Timon Schneider, Abdul Muntakim Rafi, Cassandra Jensen, Daniella Liao, Yiren Zhao, Carl de Boer, Tom Ellis
bioRxiv, 2025
Detecting and avoiding homology-based data leakage in genome-trained sequence models
Abdul Muntakim Rafi, Brett Kiyota, Nozomu Yachie, Carl de Boer
bioRxiv, 2025

Journal Articles

Unraveling the regulatory dynamics of bidirectional promoters for modulating gene co-expression and metabolic flux in Saccharomyces cerevisiae
Zimo Jin, Yueming Dong, Abdul Muntakim Rafi, Mohsin MD Patwary, Catherine Xu, Morten H. Raadam, Carl de Boer, Codruta Ignea
Nucleic Acids Research, 2025
A community effort to optimize sequence-based deep learning models of gene regulation
Abdul Muntakim Rafi, Daria Nogina, Dmitry Penzar, Dohoon Lee, Danyeong Lee, Nayeon Kim, Sangyeup Kim, Dohyeon Kim, Yeojin Shin, Il-Youp Kwak, Georgy Meshcheryakov, Andrey Lando, Arsenii Zinkevich, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Eeshit Dhaval Vaishnav, Payman Yadollahpour, Random Promoter DREAM Challenge Consortium, Sun Kim, Jake Albrecht, Aviv Regev, Wuming Gong, Ivan V. Kulakovskiy, Pablo Meyer, Carl de Boer
Nature Biotechnology, 2024
Biochemical activity is the default DNA state in eukaryotes
Ishika Luthra, Xinyi E Chen, Cassandra Jensen, Asfar Lathif Salaudeen, Abdul Muntakim Rafi, Carl G de Boer
Nature Structural & Molecular Biology, 2024
LegNet: a best-in-class deep learning model for short DNA regulatory regions
Dmitry Penzar, Daria Nogina, Elizaveta Noskova, Arsenii Zinkevich, Georgy Meshcheryakov, Andrey Lando, Abdul Muntakim Rafi, Carl de Boer, Ivan V. Kulakovskiy
Bioinformatics, 2023
GIL: A Python package for designing custom indexing primers
Nicholas Mateyko, Omar Tariq, Xinyi E Chen, Will Cheney, Asfar Lathif Salaudeen, Ishika Luthra, Najmeh Nikpour, Abdul Muntakim Rafi, Hadis Kamali Deghan, Cassandra Jensen, Carl de Boer
Bioinformatics, 2023
RemNet: remnant convolutional neural network for camera model identification
Abdul Muntakim Rafi, Thamidul Islam Tonmoy, Uday Kamal, Jonathan Wu, Md Kamrul Hasan
Neural Computing and Applications, 2021

Conference Papers

Lung cancer tumor region segmentation using recurrent 3D-DenseUNet
Uday Kamal, Abdul Muntakim Rafi, Rakibul Hoque, Jonathan Wu, Md Kamrul Hasan
MICCAI 2020
Understanding Global Reaction to the Recent Outbreaks of COVID-19: Insights from Instagram Data Analysis
Abdul Muntakim Rafi*, Shivang Rana*, Rajwinder Kaur*, Jonathan Wu, Pooya Moradian Zadeh
IEEE International Conference on Systems, Man, and Cybernetics, 2020
L2-Constrained RemNet for Camera Model Identification and Image Manipulation Detection
Abdul Muntakim Rafi, Jonathan Wu, Md. Kamrul Hasan
Advances in Image Manipulation Workshop, ECCV 2020
Application of DenseNet in Camera Model Identification and Post-processing Detection
Abdul Muntakim Rafi, Uday Kamal, Rakibul Hoque, Abid Abrar, Sowmitra Das, Robert Laganiere, Md Kamrul Hasan
CVPR 2019
Image-based Bengali Sign Language Alphabet Recognition for Deaf and Dumb Community
Abdul Muntakim Rafi, Nowshin Nawal, Nur Sultan Nazar Bayev, Lusain Nima, Celia Shahnaz, Shaikh Anowarul Fattah
IEEE GHTC 2019

Selected Talks

Characterizing homology-induced data leakage and memorization in genome-trained sequence models 2026
  • Models, Inference & Algorithms (MIA) Seminar, Broad Institute of MIT and Harvard, Cambridge, United States
  • MASSIV 1.0: The Meeting for Advanced Synthetic Biology and Systems Bioengineering, Vancouver, Canada
  • UBC Life Sciences Symposium 2026, Vancouver, Canada (upcoming)
From inflated benchmarks to trustworthy predictions: addressing reliability in genomic models 2025
  • Biomedical Horizons Seminar Series, IBM Thomas J. Watson Research Center, New York, United States
Detecting and avoiding homology-based data leakage in genome-trained sequence models 2024–2025
  • AI in Molecular Biology, Keystone Symposia, Santa Fe, United States
  • ISMB/ECCB 2025, Liverpool, United Kingdom
  • Kipoi Seminar (online)
  • IGVF Consortium, Machine Learning Focus Group Journal Club (online)
  • Deep Learning in Genomics Journal Club, Johns Hopkins University (online)
  • Kundaje Lab Journal Club, Stanford University, Stanford, United States
  • Kelley group Journal Club, Calico Life Sciences, South San Francisco, United States
Beyond the genome: engineering and modeling synthetic DNA to uncover cis-regulatory logic 2025
  • Tom Ellis Lab, Imperial College London, London, United Kingdom
A community effort to optimize sequence-based deep learning models of gene regulation 2025
  • Genentech, internal seminar (online)
  • Biological Data Science, Cold Spring Harbor Laboratory, New York, United States
  • London SynBio Network Meeting, Imperial College London, London, United Kingdom
Evaluation and optimization of sequence-based gene regulatory deep learning models 2024
  • Pacific Northwest Yeast Club Meeting, Fred Hutchinson Cancer Center, Seattle, United States
Predicting gene expression using random promoter sequences – Challenge Overview 2022
  • 14th RECOMB/ISCB Conf. on Regulatory & Systems Genomics with DREAM Challenges, Las Vegas, United States
Tumor segmentation from CT scans using deep learning 2021
  • Guest lecture, ELEC 8280: Image Processing, University of Windsor, Windsor, Canada
L2-constrained RemNet for camera model identification and image manipulation detection 2020
  • Advances in Image Manipulation Workshop, ECCV 2020 (online)
Lung cancer tumor region segmentation using recurrent 3D-DenseUNet 2020
  • Second International Workshop on Thoracic Image Analysis, MICCAI 2020 (online)
IEEE SPS Video and Image Processing Cup 2018 – Final Round 2018
  • IEEE International Conference on Image Processing (ICIP), Athens, Greece
Shongket: Bengali sign language alphabet interpreter for the deaf community in Bangladesh 2018
  • 4th IEEE WIECON-ECE Conference, Thailand (online)

Work Experience

Developed reliability estimation methods for sequence-to-expression model predictions.
Joined Lanner through the Mitacs Accelerate, which is Canada's premiere research internship program. Here, I worked on efficient inference of different AI-driven applications in edge devices.
Joined IFIVEO through the Mitacs Accelerate. Here, my task has been to perform activity recognition in order to measure and improve manufacturing floor production processes using deep learning based vision systems. I have collected data from manufacturing floors, supervised the annotation process, and deployed deep learning models using Amazon Sagemaker.
Worked on designing a real-time Sign2Text translator for Bangla Sign Language.

Teaching Experience

  • BIOL 234: Fundamentals of Genetics
  • ELEC 8330: Computational Intelligence
  • GENG 2320: Engineering Software Fundamentals

Selected Awards

Four Year Doctoral Fellowship (4YF)
University of British Columbia
SBME Graduate Support Initiative Entrance Award
School of Biomedical Engineering, UBC
Stem Cell Network International Travel Award
Stem Cell Network, Canada
JXTX + CSHL Biological Data Science Scholarship
Cold Spring Harbor Laboratory