Publications

A research program in interpretable biomedical AI.

Selected manuscripts and a complete scholarly record spanning biomedical representation learning, computational genomics, medical imaging, explainable AI, and biological data science.

Google Scholar Academic CV

Current Manuscripts & Preprints

5 current works
  1. 01
    Mostafa S, Jiang Y, Zou J, Massoud TF, Alizadeh AA, Diehn M, Xing L, Islam MT
    Vision-Based Deep Learning of Biomedical Tabular Data via Self-Supervised Cartographic Representation.
    Nature Communications· Under review · 2026
  2. 02
    Mostafa S, Zou J, Alizadeh AA, Diehn M, Xing L, Islam MT
    Language-Encoded Structural Topology Enables Generalizable Foundation Models for Graph-Structured Data.
    Nature Computational Science· Under review · 2026
  3. 03
    Mostafa S, Diehn M, Alizadeh AA, Xing L, Islam MT
    Transformation of Biological Networks into Images via Semantic Cartography for Visual Interpretation and Scalable Deep Analysis.
    Nature Biomedical Engineering· Under review · 2026
  4. 04
    Xue Y*, Mostafa S*, Zou J, Liao J, Diehn M, Alizadeh AA, Xing L, Islam MT
    Knowledge Graph Modulated Deep Learning for Limited-Sample Clinical Data Analysis.
    Nature Biomedical Engineering· Preparing for submission · 2026* Equal contribution
  5. 05
    Yesiloglu R, Mostafa S, Zou J, Alizadeh A, Wu J, Xing L, Adeli E, Islam MT
    A Vision Foundation Model for Single-Cell Biology via Spatial Gene Cartography.
    Nature· Preparing for submission · 2026

Recent Preprints & Conference Abstracts

3 selected works
  1. 01
  2. 02
    Mostafa S, Xue Y, Islam MT
    Biologically Informed Graph Neural Network Construction via Pathway-Based Gene-Interaction Graphs.
    Joint AAPM | COMP Annual Meeting· 2026Conference abstract
  3. 03
    Rahman A, Mostafa S, Xing L, Islam MT
    GenoIntig: A Structure-Preserving Deep Learning Pipeline for Single-Cell RNA-seq Integration.
    TechRxiv· 2025Single-cell integration

Cancer and Biomedical AI

1 paper
  1. 01
    Rahman A, Rahman A, Mostafa S, Islam MT
    Cross-Cancer Computational Framework for Immune-Dysregulated Ecosystem Discovery and Therapeutic Prioritization.
    Proc. IEEE CBMS · 2026

Neurological Disorder Diagnosis & Medical Imaging

6 papers
  1. 01
    Yin W, Mostafa S, Wu F-X
    Diagnosis of Autism Spectrum Disorder Based on Functional Brain Networks with Deep Learning.
    Journal of Computational Biology 28(2) · 2021 162 citations
  2. 02
    Mostafa S, Tang L, Wu F-X
    Diagnosis of Autism Spectrum Disorder Based on Eigenvalues of Brain Networks.
    IEEE Access 7 · 2019 98 citations IF 4.64 · Q1
  3. 03
    Tang L, Mostafa S, Wu F-X
    A Network Clustering-Based Feature Selection Strategy for Classifying Autism Spectrum Disorder.
    BMC Medical Genomics 12:153 · 2019 13 citations
  4. 04
    Jahan F, Shifat SM, Anannya FZ, Mostafa S, Hasan MM
    Dementia Patient Health, Prescriptions ML Dataset: LightGBM Classification of XAI-based LIME and SHAP for Dementia Detection.
    Proc. NSysS · 2024
  5. 05
    Mostafa S, Yin W, Wu F-X
    Autoencoder-Based Methods for Diagnosis of Autism Spectrum Disorder.
    ICCABS, LNCS 12029 · 2019 26 citations
  6. 06
    Guo H, Yin W, Mostafa S, Wu F-X
    Diagnosis of ASD from rs-fMRI Images Based on Brain Dynamic Networks.
    ISBRA, LNCS 12304 · 2020

Plant Phenomics & Agricultural AI

3 papers
  1. 01
    Mostafa S, Mondal D, Panjvani K, Kochian L, Stavness I
    Explainable Deep Learning in Plant Phenotyping.
    Frontiers in AI: AI in Food, Agriculture, Water 6 · 2023 80 citations
  2. 02
    Mostafa S, Mondal D, Beck M, Bidinosti C, Henry C, Stavness I
    Leveraging Guided Backpropagation to Select Convolutional Neural Networks for Plant Classification.
    Frontiers in AI 5 · 2022 23 citations IF 3.77 · Q2
  3. 03
    Mostafa S, Mondal D, Beck M, Bidinosti C, Henry C, Stavness I
    Visualizing Feature Maps for Model Selection in Convolutional Neural Networks.
    ICCV Workshops · 2021 Acceptance 25%

Software Engineering & Methodological CS

6 papers
  1. 01
    Mostafa S, Cynthia ST, Roy B, Mondal D
    Feature Transformation for Improved Software Bug Detection Models.
    Journal of Systems and Software 219 · 2025 IF 3.7 · Q1
  2. 02
    Mostafa S, Fahim MANI, Hossain ABMA
    A New Chaos-Based Medical Image Encryption Scheme.
    ICIEV · 2017 7 citations
  3. 03
    Fahim MANI, Mostafa S, Tasnim J, Hossain ABMA
    Alignment of 3-D Scanning Data for Polygonal Mesh based on Modified Triangulation.
    ICIEV · 2017
  4. 04
    Mostafa S, Fahim MANI, Tasnim J
    An Approach to Effective 3D Reconstruction Based on Point Cloud Merging.
    IEEE WIECON-ECE · 2016
  5. 05
    Jahiruzzaman M, Fahim MANI, Mostafa S, Hossain ABMA
    An Adaptive Reconfigurable Radix-2n FFT/IFFT Architecture.
    IEEE ICIEV · 2016
  6. 06
    Zahan N, Hossain ABMA, Mostafa S
    Simulation Study on Nonlinear Ultrasound Imaging Using Different Realistic Synthetic Phantoms.
    IEEE WIECON-ECE · 2015

Book Chapter

1 paper
  1. 01
    Mostafa S, Wu F-X
    Diagnosis of Autism Spectrum Disorder with Convolutional Autoencoder and Structural MRI Images.
    Neural Engineering Techniques for ASD, Academic Press · 2021 59 citations