IEEE HPEC 2021 Presentation
Tue 21 September 2021 by Dr. Dirk Colbry
Nicholas Grabill, Kai Pinckard and I presented our most recent work on the SEE-Segment Project at the IEEE HPEC Converence. This is work that both students conducted during the summer of 2020 as part of the XSEDE Empower program.
Scaling of Evolutionary Search of Algorithm Space to Speed-Up Scientific ImageUnderstanding Workflows
Scientific image understanding is an integral part of many research workflows. Studies in everything from self-driving cars to the makeup of cells rely on image understanding through computer vision techniques. Unfortunately, almost every new scientific question requires a new algorithm to be developed by researchers. Exploring the possible algorithms (and their parameters) to find one that fits a particular scientific problem requires time and a broad understanding of the many options available. For this reason, many scientists resort to making measurements "by hand" instead of making the considerable investment required to develop a tool that can automate their specialized workflow. This paper explores the scaling of a tool (SEE-Segment) that searches the "algorithm space" of possible image segmentation algorithms and their parameters for solutions to unique scientific problems. The goal is to have the researchers do this manual annotation of their images ("measure by hand") using a Graphical User Interface front end while the SEE-Segment program searches through the algorithms and their parameters on the back end. In the best case, the SEE-Segment tool finds a good candidate algorithm that can be used on the remaining images in the researcher's data-set. In the worst case, the researchers annotate their images as they would without the tool. Unfortunately, the search space for different segmentation algorithms and their parameters is quite large and non-linear. This research leverages the pleasantly parallel nature of Genetic Algorithms and explores the use of large-scale computing to speed up the search both on a local HPC and on the cloud using Kubernetes.
Davin Lin's Final Project Presentation (SEE-Classify)
In the summer of 2021 Davin Lin worked with me as part of the ICER/ACERS REu program on his project titled "Simple Evolutionary Exploration in Classification Algorithms for Supervised Learning"
read moreGenetic algorithms (GAs) find good solutions to search problems through a process inspired by evolution. Solutions are randomly selected …
Nate Britton's Mid-Sure Project Presentation (Transfer learning)
In the summer of 2021 Nate Britton worked with me as project titled "Reexamining Transfer Learning Image Segmentation Hypothesis by Scaling Up"
read moreImage segmentation is a process in which an image is separated into foreground (areas of interest) and background regions. Image segmentation is used as a first step in …
Making an Effective Video Presentation
I was asked to give an second of two "effective presentation" tutorials to a group of REU students at Texas A&M. This second part covers how to make an effective presentation with a focus on scientific introductions. I pulled heavily from the CCQH method described here:
Here …
read moreCamtasia Studio tutorial
I was asked to give an "effective presentation" tutorial to a group of REU students at Texas A&M. As I talked with the organizers we thought it would be helpful to do a two part tutorial. The first is more of a technical, hands-on workshop on how to use …
read moreSEE-Insight Research Group
This week we had a bunch of new students join the SEE-Insight research group. I put together a quick introductory presentation for them. I thought it came out fairly well so I decided to post in here in case anyone is interested in learning more about what our group is …
read moreDesign of MTH314 - Matrix Algebra with Applications
Using the Michigan Sate University Virtual Desktop System
Michigan State University (MSU) has a Virtual Desktop System that is accessible to students and staff. If you have an account you can access it from here:
I find it is a great for when I need to do something in windows or I need a backup …
read moreTraining Graduate Students Across Disciplines: Tools and Techniques for Developing Scientific Software
On Friday during the last day of PEARC20 there was a wonderful Research Software Engineers Community Workshop (US-RSE) to discuss building and sustaining software development community.
I had the pleasure to be a part of one of the panels and gave a short presentation on my work on …
read moreCyberAmbassadors:Results from Pilot Testing a New Professional Skills Curriculum
I was pleased to present the most resent paper form our CyberAmbassador Project entitled "CyberAmbassadors: Results from Pilot Testing a New Professional Skills Curriculum" By Astri Briliyanti, Julie Wilson Rojewski, Katy Luchini-Colbry, and Dirk Colbry. This paper wwas given the best paper award in the PEARC 2020 “People involved in …
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