Archie: a tool for detecting, monitoring, and preserving architecturally significant code. - Mehdi Mirakhorli; Ahmed Fakhry; Artem Grechko; Mateusz Wieloch; Jane Cleland-Huang (SIGSOFT FSE, 2014)

Integrative analysis of the connectivity and gene expression atlases in the mouse brain. - Shuiwang Ji; Ahmed Fakhry; Houtao Deng (NeuroImage, 2014)

Leveraging Traceability to Reveal the Tapestry of Quality Concerns in Source Code. - Xiaoli Lian; Ahmed Fakhry; Li Zhang 029; Jane Cleland-Huang (SST@ICSE, 2015)

Global analysis of gene expression and projection target correlations in the mouse brain. - Ahmed Fakhry; Tao Zeng; Hanchuan Peng; Shuiwang Ji (Brain Informatics, 2015)

Deep models for brain EM image segmentation: novel insights and improved performance. - Ahmed Fakhry; Hanchuan Peng; Shuiwang Ji (Bioinform., 2016)

Machine Learning Methods for Brain Image Analysis. - Ahmed Fakhry (2016)

Feature and Intensity Based Medical Image Registration Using Particle Swarm Optimization. - Mohamed Abdel-Basset; Ahmed Fakhry; Ibrahim M. El-Henawy; Tie Qiu 001; Arun Kumar Sangaiah (J. Medical Syst., 2017)

Residual Deconvolutional Networks for Brain Electron Microscopy Image Segmentation. - Ahmed Fakhry; Tao Zeng; Shuiwang Ji (IEEE Trans. Medical Imaging, 2017)

Arabic text clustering using improved clustering algorithms with dimensionality reduction. - Arun Kumar Sangaiah; Ahmed Fakhry; Mohamed Abdel-Basset; Ibrahim M. El-Henawy (Clust. Comput., 2019)

Virufy: Global Applicability of Crowdsourced and Clinical Datasets for AI Detection of COVID-19 from Cough. - Gunvant R. Chaudhari; Xinyi Jiang 002; Ahmed Fakhry; Asriel Han; Jaclyn Xiao; Sabrina Shen; Amil Khanzada (CoRR, 2020)

2-Levels of clustering strategy to detect and locate copy-move forgery in digital images. - Mohamed Abdel-Basset; Gunasekaran Manogaran; Ahmed Fakhry; Ibrahim M. El-Henawy (Multim. Tools Appl., 2020)

A Multi-Branch Deep Learning Network for Automated Detection of COVID-19. - Ahmed Fakhry; Xinyi Jiang 002; Jaclyn Xiao; Gunvant R. Chaudhari; Asriel Han (Interspeech, 2021)

Virufy: A Multi-Branch Deep Learning Network for Automated Detection of COVID-19. - Ahmed Fakhry; Xinyi Jiang 002; Jaclyn Xiao; Gunvant R. Chaudhari; Asriel Han; Amil Khanzada (CoRR, 2021)

GENER: A Parallel Layer Deep Learning Network To Detect Gene-Gene Interactions From Gene Expression Data. - Ahmed Fakhry; Raneem Khafagy; Adriaan-Alexander Ludl (CoRR, 2023)

Open Domain Knowledge Extraction for Knowledge Graphs. - Kun Qian 002; Anton Belyi; Fei Wu; Samira Khorshidi; Azadeh Nikfarjam; Rahul Khot; Yisi Sang; Katherine Luna; Xianqi Chu; Eric Choi; Yash Govind; Chloe Seivwright; et al. (CoRR, 2023)

Enhancing Few-Shot Video Anomaly Detection with Key-Frame Selection and Relational Cross Transformers. - Ahmed Fakhry; Jong Taek Lee (AVSS, 2024)

Deep Learning for Video Fluoroscopic Swallowing Study Analysis: A Survey on Classification, Detection, and Segmentation Techniques. - Ahmed Fakhry; Sarah Mary Antony; Eunhee Park 002; Jong Taek Lee (IEEE Access, 2025)

Drone Video Anomaly Detection by Future Segmentation Prediction and Spatio- Temporal Relational Modeling. - Ahmed Fakhry; Janghoon Lee; Jong Taek Lee (IEEE Access, 2025)