Shawn T. O'Neil

Way back in 2013, I wrote a music theory explorer using the Java-based processing.org framework.

The monarchr package makes it easy to work with Knowledge Graph (KG) data in R.

Opaiui (oh-pie-you-eye) provides a rapid prototyping framework for LLM-backed chat applications based on Pydantic.AI and Streamlit.

In this study, published in npj Digital Medicine, I apply an unsupervised learning technique known as Latent Dirichlet Allocation (LDA) to identify condition clusters across millions of patients in the N3C database.

What if an AI could perform a literature review for you?

Since starting a new position with the TISLab in early 2020, my primary effort has been as Training Coordinator with the National COVID Cohort Collaborative, or N3C.

DS@OSU was a project I had the priveledge of co-leading (along with Dr.

TidyTensor is an R package for inspecting and manipulating tensors (multidimensional arrays). i It provides an improved print() function for summarizing structure, named tensors, conversion to data frames, and high-level manipulation functions.

My CV.

Sometimes you just get tired of paying AWS & Digital Ocean.

In an earlier post we considered machine learning “models” as functions producting predictions from data, and training models to be the production of these functions with higher-order functions.

I recently ran across this excellent article explaining gradient boosting in the context of regression trees.

I’ve been studying up on deep learning recently (I know, trendy), and I learned something along the way that I think is just incredible.1 First, a little background: deep learning models are artificial neural networks, represented as potentially thousands…

This book is based on a workshop I taught a few times at OSU, meant to introduce computer science theory to biologists.

Read Online at Open Oregon State (Open-Access & Free!)

I’ve been teaching an evening class at the Oregon State University Craft Center in “3D modeling and printing.”

I’m (usually) a fan of the R programming language, though in a few ways it lacks features computer scientists expect.

These were made between 2012 and 2015, some at a studio in Marquette, MI, and some at the Notre Dame Glass Club.

There’s a pretty cool app called Codea, which is a programming IDE similar processing.org, but in Lua, on the iPad.

I don’t know what made me think it would be a good idea to lug my heavy camera up to the top of South Sister to see the sunrise, but the photos at least turned out ok.

Climate change is likely to have profound impacts on ecological systems, but in some important cases we’re still a long way from understanding exactly what those impacts might be.

So, I was on TV once.

A timelapse video of me making a marble at the Oregon State University Craft Center.

Distributing large data files to all the nodes on a computing network is an important problem in large-scale scientific computing.

Back in my day, the word “theory” meant something.

TimelapseThing is a Python script that includes a number of tools for working with timelapse image series (in JPG format).

Work in borosilicate glass, mostly done between 2011 and 2013 at the University of Notre Dame Glass Club.

Assessing the quality and completeness of transcriptome assemblies is a challenge.

By Shawn O’Neil and Katie Drueen.

When working with sequencing datasets of ecological interest, an interesting problem is how to tease out the genetic diversity present in the population being sequenced.

Some extended family got married in Jamaica, I did some photography for them.

A few fun things I don’t want to lose.

I did this project with Mike Olson, a Notre Dame graduate student.

This class was very interesting; we studied some of the basics of online algorithms as well as some applications to computational finance.

Much of the research I performed during my Master’s was on the newsvendor problem, which deals with attempting to guess the demand for short-lived products so as to maximize profits.

Machine learning methods and inventory management were a focus in my Master’s work.

This was a project I did for Cryptography, which implemented a digital cash scheme as a web service.

I did this project with Allison Regier.

I also studied formal logic, under the direction of the amazing Don Faust.

Some code from a very cool computer graphics class, mostly in Java.

Just a few things from my undergrad algs class.

I really enjoyed the survey of programming topics and paradigms this class offered.

I took a Theory of Knowledge class as an undergraduate, and thoroughly enjoyed it.

Once upon a time, I knew how to use Unix sockets.

This one was a long time in the making.

Some old code files from my undergraduate CS222 Data Structures class.

In my earlier programming career, I was very interested in cellular automata and Braitenberg vehicles.

The second iteration of the headphone amp was the same internal design, packed into a slightly smaller, sleeker container.

A few old code files from my undergraduate CS122 class; these are all written as Java applets (as was the fashion at the time), so I’m just making the code available.