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)

Fri 30 July 2021 by Dr. Dirk Colbry

Davin's Poster

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"

Genetic algorithms (GAs) find good solutions to search problems through a process inspired by evolution. Solutions are randomly selected …

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Nate Britton's Mid-Sure Project Presentation (Transfer learning)

Thu 29 July 2021 by Dr. Dirk Colbry

In the summer of 2021 Nate Britton worked with me as project titled "Reexamining Transfer Learning Image Segmentation Hypothesis by Scaling Up"

Image 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 …

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Making an Effective Video Presentation

Wed 30 June 2021 by Dr. Dirk Colbry

Texas A and M logo

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:

CCQH refernece

Here …

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Camtasia Studio tutorial

Wed 09 June 2021 by Dr. Dirk Colbry

Camtasia Logo

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 …

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SEE-Insight Research Group

Tue 25 May 2021 by Dr. Dirk Colbry

Title Slide for the SEE-Insight Overview Video

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 …

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Design of MTH314 - Matrix Algebra with Applications

Tue 09 February 2021 by Dr. Dirk Colbry

Example I was honored to be invited to give a presentation to the Math department about the redesign of MTH314 to focus more on applications in python. Here is my presentation:

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Using the Michigan Sate University Virtual Desktop System

Fri 04 December 2020 by Dr. Dirk Colbry

MSU VID 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 …

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Training Graduate Students Across Disciplines: Tools and Techniques for Developing Scientific Software

Fri 31 July 2020 by Dr. Dirk Colbry

US-RSE Research Software Engineering Association Logo

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.

Workshop Website

I had the pleasure to be a part of one of the panels and gave a short presentation on my work on …

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CyberAmbassadors:Results from Pilot Testing a New Professional Skills Curriculum

Tue 28 July 2020 by Dr. Dirk Colbry

PEARC20 Banner

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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