Department of Biomedical Informatics, Emory University

Biomedical research to advance healthcare

Technologies
python, javascript, java, bash, Colab
Topics
cloud, data integration, workflows, data security, ML/AL
Biomedical research to advance healthcare
Biomedical Informatics is a multidisciplinary field that is motivated by our desire to improve diagnosis, clinical care, and human health, through novel computational approaches to use (and learn from) biomedical and clinical data. We use our expertise in computer science and informatics by developing various enabling tools, technologies, and algorithms to solve specific biomedical and clinical applications. And in doing so help advance our understanding of disease and treatment, and also develop useful software and applications. Members of the department work in a variety of areas that range from machine learning, healthcare middleware that leverages cloud computing, clinical information systems, clinically oriented image analysis, and biomedical knowledge modeling. The driving applications for the various ongoing projects include cancer research, organ transplant, HIV, medical imaging, radiation therapy, and clinical data analytics. All development work that is undertaken is free and open-source. We have had a diverse set of successful GSoC projects in the past. In previous years, GSoC contributors have worked on diverse projects such as: geospatial systems for exploring microscopy environments that leveraged Hadoop; GPU accelerated pipelines for computational analysis of digitized biopsies; interactive visualization platforms for viewing massive images (>1GB); systems for data agnostic sharing of biomedical research datasets; Apache Drill based data integration and de-duplication platform for SQL and NoSQL databases; CNN based high throughput analysis of digitized biopsies; A GUI for Tensorflow; integrated architectures for biomedical data integration and federation; and information visualization of heterogeneous medical data. Many of these projects have been published in reputable journals and presented at major conferences. Some of the projects proved to be so successful that they were adopted in major national/international biomedical research initiatives.
2024 Program

Successful Projects

Contributor
timisanjo
Mentor
Mahmoud Zeydabadinezhad
Organization
Department of Biomedical Informatics, Emory University
A Framework for Unsupervised Deep Clustering
Not only can clustering in itself be a useful task to solve, features learnt from deep clustering algorithms can also be used in downstream tasks...
Contributor
Sarper
Mentor
Özgür Kara, Babak Mahmoudi, Mahmoud Zeydabadinezhad
Organization
Department of Biomedical Informatics, Emory University
A GUI of Foundational Model Toolbox for Image Segmentation
This proposal highlights some key points and expected results of the project. The project proposes developing an open-source Graphical User Interface...
Contributor
Shreyas S
Mentor
Babak Mahmoudi, Mahmoud Zeydabadinezhad
Organization
Department of Biomedical Informatics, Emory University
Development of an Open-Source EEG Foundation Model
The project's core objective is to develop an open-source foundational model for EEG data analysis, using deep learning techniques and extensive...
Contributor
Mete
Mentor
Özgür Kara, Babak Mahmoudi, Mahmoud Zeydabadinezhad
Organization
Department of Biomedical Informatics, Emory University
Development of a Graphical User Interface for Time Series Toolbox Using Deep Learning
Time series data has wide application across numerous sectors including healthcare, finance, and environmental studies, offering profound insights...
Contributor
Muhammad Ubadah Tanveer
Mentor
Reza Sameni
Organization
Department of Biomedical Informatics, Emory University
Python Expansion of the Open Source Electrophysiological Toolbox
This project aims to enhance the Open Source Electrophysiological Toolbox (OSET) by expanding its Python capabilities. The goal is to create a...