About Me
My name’s Merna and I’m a PhD student in Machine Learning at Georgia Tech. I’m interested in research at the intersection of machine learning and healthcare, specifically in learning from limited and multimodal data. I was a Teaching & Research Assistant of Biomedical Engineering at Cairo University before that. I also hold a MSc. degree in Biomedical Engineering with a focus on machine learning for medical imaging.
I am most skilled in: Machine Learning and Research
Outside of academia, I enjoy hiking, drawing, reading, gaming and building Lego sets like the Bonsai Tree set.
Publications
- In Print
- Bibars, M., Salah, P. E., Eldeib, A., Elattar, M. A., & Yassine, I. A. (n.d.). “Cross-Modality Deep Transfer Learning: Application to Liver Segmentation in CT and MRI” In Waiter, G., Lambrou, T., Leontidis, G., Oren, N., Morris, T., Gordon, S. (eds) Medical Image Understanding and Analysis. MIUA 2023. Lecture Notes in Computer Science, vol “14122”. Springer, Cham. DOI
- Salah, P. E., Bibars, M., Eldeib, A., Ghanem, A. M., Gharib, A. M., Abd-Elmoniem, K. Z., Elattar, M. A., & Yassine, I. A. (n.d.). “Iterative Refinement Algorithm for Liver Segmentation Ground-Truth Generation using Fine-Tuning Weak Labels for CT and Structural MRI ”. In Waiter, G., Lambrou, T., Leontidis, G., Oren, N., Morris, T., Gordon, S. (eds) Medical Image Understanding and Analysis. MIUA 2023. Lecture Notes in Computer Science, vol 14122. Springer, Cham.DOI
- Accepted
- Zein, F. O., Issam, F., Hesham, M., Nawar, M., Nofal, Y. H., Bibars, M., & Sadek, I. 2023. “AI-Based Communication Tool for High-Functioning Autistic Children.” IEEE EMBS International Conference on Data Science and Engineering in Healthcare, Medicine and Biology. Portomaso, Malta
- In Preparation
- Bibars, M., Salah, P. E., Eldeib, A., Elattar, M. A., & Yassine, I. A., “Learning from Weak Labels: An Ablation Study of State-of-the-Art Deep Learning Models for CT and MRI Liver Segmentation.”
- Salah, P. E., Bibars, M., Eldeib, A., Ghanem, A. M., Gharib, A. M., Abd-Elmoniem, K. Z., Elattar, M. A., & Yassine, I. A. “Automatic Multiclass Liver Fibrosis Grading from Multiple MRE Strain-Encoded Images using ANN.”
Experience
Machine Learning, Georgia Institute of Technology
Graduate Research Assistant
2024 - Present
- Working on machine learning in digital pathology and telehealth
Biomedical & Systems Engineering, Cairo University
Teaching Assistant
2020 - 2024
- Designing and implementing course curricula.
- Supervising undergrads’ graduation projects
- Mentoring undergrads
Egypt – USA NIH Joint Project
Research Assistant
2021 - 2024
- Funded by Egypt’s Science and Technology Fund Institute. Project ID 45891- EG-US Cycle 20.
- “Developing Non-invasive Imaging Biomarkers for the Detection and Quantification of Inflammation in Hepatitis Infection”.
Education
Georgia Institute of Technology
Ph.D. in Machine Learning (Biomedical Engineering)
2024 - Present
Georgia Tech is one of the premier and top ten research universities in the United States. Its engineering and computing Colleges are the largest and among the highest-ranked in the nation.
Cairo University
MSc. Biomedical & Systems Engineering
2020 - 2023
Founded in 1908, Cairo University is the premier higher education institution in Egypt, and counts three Nobel Laureates among its graduates. It is the top university in Egypt.
Cairo University
BSc. Biomedical & Systems Engineering
2016 - 2020
- GPA: 4.0/4.0
- Rank: 1st
Skills
Tools & Languages
- Desktop development: C++, OOP, PyQt5, MATLAB Designer.
- Technical development: MATLAB, Python, R.
- Simulation: ROS, Webots, Gazebo.
- Machine Learning: Scikit-learn, Tensorflow, PyTorch, Jupyter.
- Image processing: OpenCV, SciPy, Numpy, MeVis Lab, ITKSnap, DICOM, NIFTI.
- Web development: HTML, CSS, JS, Bootstrap, Angular, Ionic.
- Database: SQL
- Project Management: Agile workflow, Jira.
Soft Skills
- Languages: Arabic, English.
- Literature review.
- Time-management.
- Teamwork.
- Leadership.
- Communication, and presentation skills.
MSc. Thesis
Iterative Refinement of Liver Segmentation Across Modalities As Accurate Preprocessing Step For Hepatic Tissue Analysis
Deep Learning, TensorFlow, PyTorch, MeVisLab, ITKSnap, DICOM, NIFTI
Iterative refinement of weak annotations created by MeVisLab to segment the liver from MR images in order to grade liver fibrosis.
Projects
- Graduation Project : “Intention Decoding for Mode Switching of Upper-Limb Prosthetic Hand Using Computer Vision: An Evaluation Study using Simulation”. ROS, Gazebo, Webots, Python, C++, Simulation, Deep Learning (PyTorch) (Acc 99%), Transfer Learning.
- Liver Segmentation: CT volumes, LiTS Kaggle Dataset. U-net (93% Dice Metric)
- Pneumonia classification: X-ray 6 datasets. VGG-16, ResNet, Inception, VGG-16 (Acc 98.5%). GitHub
- Egyptian Liver Fibrosis Grade Prediction: Tabular data. Pre-processing/cleaning, features engineering, features selection, Random Forest, KNN, Bagging, Linear SVM (Acc 59.2%)
- LSVT (Lee Silverman Voice Treatment) classification: Accuracy (94.62%), features reduced from 310 to 6, Naïve Bayes & KNN classifiers, sequential forward feature selection, MATLAB. GitHub
- Self-driving car: real-time lane detection & following, obstacle avoidance. Image processing (filtering, edge detection, segmentation), Python, OpenCV, Ultrasound module, Arduino. GitHub
- Computer Vison: Python, OpenCV, PyQt5. GUI, Canny edge detection, Hough Transforms, Noise addition and filtering, Template Matching.
- MRI Simulator: Simulate MRI sequences on digital phantoms. Python, GUI, PyQt5, threading. GitHub
- Alzheimer smart care system: sensors in home (FSR, flowmeter, thermistor, IR sensor), android application for patient & caregiver, Arduino C OOP (data acquisition and analysis). Patient monitoring.
- Blood bank: Web app. HTML5, CSS3, Bootstrap, NodeJS, Angular, MySQL. Bank database (donations & transfusions). Web access. Front-end GitHub.
- Attendance System: Mobile app, flutter, face recognition, QR code.
- Infection time: Timeframes for infection spread in a matrix. Data structures (queue, linked list), C++.
- Equalizer: Music equalizer. MATLAB, MATLAB Designer, digital filters, DSP.
- Signal Compressor: Lossy, lossless signals (ECG, audio, 1-D US) compression algorithms. MATLAB, MATLAB Designer.
Designed Courses
Algorithms in Medicine
2021 - 2024
Biomedical Image Processing
2020 - 2022
Advanced Topics in Image Processing & Computer Vision
2022 - 2022
Activities & Honors
- Best Oral Paper Presenter MIUA conference 2023
- IEEE EMBS student chapter undergraduate research mentor 2023-2024
- SBME AI club moderator and coordinator 2021-2022
- Technical intern at Al Ahlyia company for medical equipment trading & distribution 2019
- BEAT student activity (scientific committee member) 2019
- Dean award for exceptional performance and top rank in the school year 2018
- Model student award 2016
Conferences
- 27th International Medical Image Understanding and Analysis (MIUA) Conference - Presenter 2023
- 9th Cairo International Biomedical Engineering Conference (CIBEC) – Attendee 2018
- 3rd IEEE International Students’ Conference (ISC) - Attendee 2017
MOOCS
- Deep Learning.AI Supervised Machine Learning: Regression and Classification Course Certificate
- Imperial College: Getting started with TensorFlow 2 Course Certificate
- Deep Learning.AI: Neural Networks and Deep Learning Course Certificate
- Deep Learning.AI: Convolutional Neural Networks Course Certificate
- Johns Hopkins: Data Scientist’s Toolbox Course Certificate