Fast Interactive Machine Learning Enabled by GPUs
Mentor: Lee Cooper ( lee dot cooper at emory dot edu )
Overview: Enabling users to interact with large datasets via machine learning algorithms requires fast algorithm response times. This project will develop GPU pipelines for an active machine learning setting, where classification algorithms sift through millions of samples to select key examples for labeling by human experts. Increasing the speed of these pipelines will improve the user experience and the development of machine learning classifiers for cancer research. This pipeline will interact with a database containing millions of samples and their feature descriptions, and will feed results into a web framework in order to collect user feedback.
Programming Languages/Frameworks: C/C++, CUDA/OpenCL
Prerequisites: C++ programming skills, experience in CUDA/OpenCL , basic experience with machine learning algorithms
Level of Expertise: Intermediate.
Spatial Extensions to MongoDB
FAQ: Click here
Mentor: Ashish Sharma ( ashish dot sharma at emory dot edu )
Overview: In one of our projects we use MongoDB to manage shapes extracted from very high resolution (50Kx50K) digital pathology images. The resulting data is massive — >1B shapes from 100K images. When viewing and exploring these images, one would like to exploit the MongoDB 2d geospatial indexing system (2dspherical can't be used because it is in spherical coordinates). However the 2d index is limited because Mongo insists that it be the first index in a compound index (2d + image metadata). In this project you will create a custom 2d index that is appended to all documents and will extend Mongo's Java driver so that spatial queries can exploit your new 2d index.
Programming Languages/Frameworks: MongoDB, Java
Prerequisites: Java programming skills, experience with Mongo , experience in computational geometry or spatial query processing will be useful but is not a prerequisite.
Level of Expertise: Intermediate.
Develop a geospatial cache using HTML5 IndexedDB
FAQ: Click here
Mentor: Ashish Sharma ( ashish dot sharma at emory dot edu )
Overview: In our digital pathology platform (camicroscope.org), you would add a spatial cache using the browser's database. The presence of such a cache will give users the ability to use cached objects and avoid having to retrieve segmented objects from the remote web service
Programming Languages/Frameworks: Javascript
Prerequisites: Javascript, experience with HTML5 Indexed DB
Level of Expertise: Intermediate.
TCIA Data Exploration and Information Visualization
FAQ: Click here
Mentor: Ashish Sharma ( ashish dot sharma at emory dot edu )
Overview: The Cancer Imaging Archive provides access to a wealth of biomedical cancer imaging data. It contains over 26 million radiology images, pathology data, and clinical data. The existing web interface for searching the archive is extremely outdated. Recently a REST API for TCIA was implemented to allow programmatic query and download of the data. Using the new REST API this project would seek to create a new search interface to the data as an alternate way to explore the contents of TCIA, create dynamic dashboards that can be extended to support the exploration of TCIA data (similar to "http://nickqizhu.github.io/dc.js/"). In addition to searching the TCIA archive, this project could also include support to intuitively formulate queries that can federate data from other remote archives. Possible strategies could include Microsoft Pivotviewer which provides an interactive data exploration platform.
Programming Languages/Frameworks: Javascript, d3, crossfilter, HTML
Prerequisites: Extensive experience with jQuery. Experience/Coursework in HCI, visual interface development.
Level of Expertise: Intermediate.
Browser based Bulk Data Transfer
FAQ: Click here
Mentor: Ashish Sharma ( ashish dot sharma at emory dot edu )
Overview: Develop a web based system to transfer really large quantities of data — large is > 10s of GB. A possible strategy would involve maintaining an in-browser database that tracks the progress of data download, and can manage multiple download streams. Needless to say there will be a server side component that will be provided with a manifest of what needs to be downloaded.
Programming Languages/Frameworks: Javascript
Prerequisites: Javascript, experience with HTML5 Indexed DB
Level of Expertise: Intermediate.