Welcome to my website! I am Joseph, a graduate student in the School of Electrical Engineering and Computer Science at Oregon State University in Corvallis, Oregon. I am currently working towards my PhD in computer science under the supervision of Professor David Hendrix. Since joining OSU in 2019, I have worked on developing deep learning models for scientific discovery in the field of molecular biology. I am always interested in hearing about internship opportunities and chances to collaborate with other researchers, so please reach out if you would like to talk!

My Research

Broadly, I build machine learning systems with the aim of discovering new biological rules at the cellular and molecular levels. I am most interested in domain-specific modifications of deep learning for biological sequence data, which can present unique challenges to established techniques. Biological sequences bear some similarity to natural language – both are ordered sequences of discrete characters. However, RNA, DNA, and proteins can be many times larger than human sentences, with a much sparser vocabulary. Architectures from NLP are often a suitable starting point, but my work seeks to improve their efficiency and tailor their operation with principled inductive biases. Explainable AI is another area of interest, as many current methods assume a continuous problem space that is not valid for nucleotides and fail to capture the kind of causal information needed for hypothesis generation and laboratory validation of salient patterns.

At the moment, I am focusing on translational regulation – the ability of cells to precisely tune the levels of available proteins during translation. I am developing a deep learning classifier system to distinguish messenger RNA and long noncoding RNA. My model incorporates the mechanics of translation as a simple but biologically meaningful inductive bias. At the same time, I am investigating interpretive techniques to mine the learned representations for insight into the sequence patterns governing translational regulation. A primer on translational regulation and the current state of my ongoing research can be found in my Qualifying Exam, which I passed in October 2021. During the rest of my PhD, I hope to integrate my work on RNA sequences with other -omics datatypes such as Ribo-Seq, scRNA-seq, and various functional genomic assays. I am eager to solve problems in both fundamental biology and applications to human health and plant genomics.

Background and Personal Interests

I am originally from Colorado, and before coming to Oregon State, I graduated from the University of Tulsa in Oklahoma with a B.S. in CS. In my spare time, music is one of my biggest passions : I enjoy playing the guitar, singing, and have even composed a few songs of my own. I try to lift weights regularly, am learning to play tennis, and enjoy hiking and skiing in the outdoors of both the Pacific Northwest and Colorado.