yaminarefeen@gmail.com

I am on the academic job market! [Research Statement]

Research

Journal Publications

Diffusion probabilistic generative models for accelerated, in-NICU permanent magnet neonatal MRI

Yamin Arefeen, Brett Levac, Bhairav Patel, Chang Ho, Jonathan Tamir

Magnetic Resonance in Medicine (2025)

[paper]

Robust multi-coil MRI reconstruction via self-supervised denoising

Asad Aali, Marius Arvinte, Sidharth Kumar, Yamin Arefeen, Jonathan Tamir

Magnetic Resonance in Medicine (2025)

[paper] [code]

A Benchmark of Domain-Adapted Large Language Models for Generating Brief Hospital Course Summaries

Asad Aali, Dave Van Veen, Yamin Arefeen, Jason Hom, Christian Bluethgen, Eduardo Pontes Reis, Sergios Gatidis, Namuun Clifford, Joseph Daws, Arash Tehrani, Jangwoon Kim, Akshay Chaudhari

Journal of the American Medical Informatics Association (2024)

Zero-DeepSub: Zero-Shot Deep Subspace Reconstruction for Rapid Multiparametric Quantitative MRI Using 3D-QALAS

Yohan Jun, Yamin Arefeen, Jaejin Cho, Shohei Fujita, Xiaoqing Wang, Ellen Grant, Borjan Gagoski, Camilo Jaimes, Michael Gee, Berkin Bilgic

Magnetic Resonance in Medicine (2024)

[paper] [code]

Latent Signal Models: Learning Compact Representations of Signal Evolution for Improved Time-Resolved, Multi-contrast MRI

Yamin Arefeen, Junshen Xu, Molin Zhang, Zijing Dong, Fuyixue Wang, Jacob White, Berkin Bilgic, Elfar Adalsteinsson

Magnetic Resonance in Medicine (2023)

[paper] [code]

Stochastic-offset-enhanced restricted slice excitation and 180° refocusing designs with spatially non-linear ΔB0 shim array fields

Molin Zhang, Nicolas Arango, Yamin Arefeen, Georgy Guryev, Jason P. Stockmann, Jacob White, Elfar Adalsteinsson

Magnetic Resonance in Medicine (2023)

[paper]

Scan Specific Artifact Reduction in K-space (SPARK) Neural Networks Synergize with Physics-based Reconstruction to Accelerate MRI

Yamin Arefeen, Onur Beker, Jaejin Cho, Heng Yu, Elfar Adalsteinsson, Berkin Bilgic

Magnetic Resonance in Medicine (2022)

[paper] [code]

Conference Proceedings

A Generative Diffusion Model to Solve Inverse Problems for Robust in-NICU Neonatal MRI

Yamin Arefeen, Brett Levac, Jonathan Tamir

IEEE International Conference on Image Processing (2025)

[paper]

Diffusion probabilistic generative models for accelerated in-nicu, permanent magnet neonatal MRI reconstruction

Yamin Arefeen, Brett Levac, Jonathan Tamir

In proceedings of the International Society for Magnetic Resonance in Medicine (2025)

Training diffusion probabilistic models with limited data for accelerated MRI reconstruction with application to stroke MRI

Sidharth Kumar, Yamin Arefeen, Hamidreza Saber, Jonathan Tamir

In proceedings of the International Society for Magnetic Resonance in Medicine (2025)

INFusion: Diffusion Regularized Implicit Neural Representations for 2D and 3D accelerated MRI reconstruction

Yamin Arefeen, Brett Levac, Zach Stoebner, Jonathan Tamir

Asilomar Conference on Signals Systems and Computers (2024)

[paper] [code]

Parallel Imaging Reconstruction in Public Datasets Biases Downstream Analysis in Retrospective Sampling Studies

Evan Frenklak, Yamin Arefeen, Jon Tamir

In the proceedings of the International Society for Magnetic Resonance in Medicine (2024)

GSURE Denoising enables training of higher quality generative priors for accelerated Multi-Coil MRI Reconstruction

Asad Aali, Marius Arvinte, Sidharth Kumar, Yamin Arefeen, Jonathan Tamir

In the proceedings of the International Society for Magnetic Resonance in Medicine (2024)

Improved T1 and T2 mapping in 3D-QALAS using temporal subspaces and flip angle optimization enabled by auto-differentiation

Yamin Arefeen, Borjan Gagoski, Yohan Jun, Berkin Bilgic, Elfar Adalsteinsson

In proceedings of the International Society for Magnetic Resonance in Medicine (2023)

[code]

Zero-Shot Self-Supervised Joint Temporal Image and Sensitivity Map Reconstruction via Linear Latent Space

Molin Zhang, Junshen Xu, Yamin Arefeen, Elfar Adalsteinsson

Medical Imaging with Deep Learning (2023)

[paper]

SubZero: Subspace Zero-Shot MRI Reconstruction

Heng Yu, Yamin Arefeen, Berkin Bilgic

In proceedings of the International Society for Magnetic Resonance in Medicine (2023)

[code]

Zero-DeepSub: Zero-Shot Deep Subspace Reconstruction for Multiparametric Quantitative MRI Using QALAS

Yohan Jun, Yamin Arefeen, Jaejin Cho, Xiaoqing Wang, Michael Gee, Borjan Gagoski, Berkin Bilgic

In proceedings of the International Society for Magnetic Resonance in Medicine (2023)

[code]

Learning compact latent representations of signal evolution for improved shuffling reconstruction

Yamin Arefeen, Junshsen Xu, Molin Zhang, Jacob White, Berkin Bilgic, Elfar Adalsteinsson

In proceedings of the International Society for Magnetic Resonance in Medicine (2022), Magna Cum Laude Awarded

Improved acquisition efficiency in T2-weighted fetal MRI with optimized variable flip angles and prospective wave-encoding

Yamin Arefeen, Borjan Gagoski, Berkin Bilgic, Ellen Grant, Elfar Adalsteinsson

In proceedings of the International Society for Magnetic Resonance in Medicine (2022)

Design of Novel RF Pulse for Fetal MRI Refocusing Trains using Rank Factorization (SLfRank) to Reduce SAR and Improve Image Acquisition Efficiency

Sebastian Diaz, Yamin Arefeen, Borjan Gagoski, Ellen Grant, Elfar Adalsteinsson

In proceedings of the International Society for Magnetic Resonance in Medicine (2022)

Zero-Shot Self-Supervised Learning for 2D T2-shuffling MRI reconstruction

Molin Zhang, Junshen Xu, Yamin Arefeen, Elfar Adalsteinsson

In proceedings of the International Society for Magnetic Resonance in Medicine (2022)

Predicting Critical Biogeochemistry of the Southern Ocean for Climate Monitoring

Ellen Park, Jae Deok Kim, Nadege Aoki, Yumeng Melody Cao, Yamin Arefeen, Matthew Beveridge, David Nicholson, Iddo Drori

Tackling Climate Change with Machine Learning workshop at NeurIPS (2022)

[paper]

Rapid fetal HASTE imaging using variable flip angles and simultaneous multislice wave-LORAKS

Yamin Arefeen, Tae Hyung Kim, Justin Haldar, Ellen Grant, Borjan Gagoski, Berkin Bilgic, Elfar Adalsteinsson

In proceedings of the International Society for Magnetic Resonance in Medicine (2021), Summa Cum Laude Awarded

Towards Accelerating 3D 1H-MRSI Using Randomly Undersampled Spatial and Spectral Spirals with Low-rank Subspaces

Yamin Arefeen, Borjan Gagoski, Elfar Adalsteinsson

In proceedings of the International Society for Magnetic Resonance in Medicine (2021)

Extending Scan-specific Artifact Reduction in K-space (SPARK) to Advanced Encoding and Reconstruction Schemes

Yamin Arefeen, Onur Beker, Heng Yu, Elfar Adalsteinsson, Berkin Bilgic

In proceedings of the International Society for Magnetic Resonance in Medicine (2021)

eRAKI: Fast Robust Artificial neural networks for K-space Interpolation (RAKI) with Coil Combination and Joint Reconstruction

Heng Yu, Zijing Dong, Yamin Arefeen, Congyu Liao, Kawin Setsompop, Berkin Bilgic

In proceedings of the International Society for Magnetic Resonance in Medicine (2021)

Single-shot T2-weighted Fetal MRI with variable flip angles, full k-space sampling, and nonlinear inversion: towards improved SAR and sharpness

Yamin Arefeen, Borjan Gagoski, Esra Turk, Ellen Grant, Jacob White, Kawin Setsompop, Elfar Adalsteinsson

In proceedings of the International Society for Magnetic Resonance in Medicine (2020)

Improving cartesian single-shot 2D T2 shuffling and reducing radial streaking artifacts with golden angle radial T2 shuffling

Yamin Arefeen, Fei Han, Borjan Gagoski, Jacob White, Elfar Adalsteinsson

In proceedings of the International Society for Magnetic Resonance in Medicine (2020)

Refined-subspaces for two iteration single shot T2-Shuffling using dictionary matching

Yamin Arefeen, Nick Arango, Siddharth Iyer, Borjan Gagoski, Kawin Setsompop, Jacob White, Elfar Adalsteinsson

In proceedings of the International Society for Magnetic Resonance in Medicine (2019)

Real-time, data-driven system to learn parameters for multisite pacemaker beat detection

Yamin Arefeen, Philip Taffet, Daniel Zdeblick, Jorge Quintero, Greg Harper, Behnaam Aazhang, Joseph Cavallaro, Mehdi Razavi

In proceedings of the 51st Asilomar Conference on Signals, Systems, and Computers (2017)

[proceedings]

Thank you to Vasilios Mavroudis for the template