Department of Biomedical Informatics (BMI), Emory University School of Medicine

Data science and integrative biomedical research to advance healthcare

Technologies
python, java, tensorflow, medical imaging, deeplearning
Topics
cloud, distributed systems, science and medicine, data integration, workflows
Data science and integrative biomedical research to advance healthcare

Biomedical Informatics (BMI) 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 students 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.

2021 Program

Successful Projects

Contributor
Aryan Verma
Mentor
Monjoy Saha
Organization
Department of Biomedical Informatics (BMI), Emory University School of Medicine
CovCT: Development of an AI-based Android Application for distinguishing COVID-19 and Pneumonia using Computed Tomography Images and generate reports for analysis
Development of an AI-based Android Application for distinguishing COVID-19 and Pneumonia using Computed Tomography Images.The project aims at...
Contributor
Shubham Awasthi
Mentor
Mark Arnold, Pradeeban Kathiravelu, Babak Mahmoudi
Organization
Department of Biomedical Informatics (BMI), Emory University School of Medicine
A Frontend For Loopsim Framework To Model Workflows With Closed Loops
LoopSim framework aims to facilitate workflows with loops i.e workflows without specific start and end services. LoopSim requires an interface to...
Contributor
Nishchal Singi
Mentor
Imon Banerjee, Judy Gichoya, Pradeeban Kathiravelu
Organization
Department of Biomedical Informatics (BMI), Emory University School of Medicine
A frontend for Niffler DICOM framework for machine learning pipelines and processing workflows
This project aims to develop a potential frontend for Niffler. Niffler is currently a command-line tool where the user has to download it in their...
Contributor
Özgür Kara
Mentor
Babak Mahmoudi, Parisa Sarikhani
Organization
Department of Biomedical Informatics (BMI), Emory University School of Medicine
Graphical User Interface for OpenAI Gym
The project is aiming to develop a GUI for the simulations of reinforcement learning so that users, particularly, the researchers can be able to test...
Contributor
Viraj Patel
Mentor
Monjoy Saha
Organization
Department of Biomedical Informatics (BMI), Emory University School of Medicine
Tensorflow GUI
Tensorflow GUI will help everyone from beginners to professionals in their day to day work. People who are new to the field of deep learning can use...
Contributor
Chinmay Vibhute
Mentor
Pradeeban Kathiravelu, Hari Trivedi, Ramon Correa
Organization
Department of Biomedical Informatics (BMI), Emory University School of Medicine
A Testing Framework for Niffler DICOM frameworks for Continuous Integration
This Project aims to develop unit and integration tests for the Niffler modules and implement automated testing using Continuous Integration. The...