Planarity has been successfully exploited to design faster and more accurate approximation algorithms for many graph optimization problems. The celebrated theorem of Kuratowski completely characterizes planar graphs as those excluding K_5 and K_{3,3} as minors. Kuratowski's theorem allows one to generalize planar graphs to H-minor-free graphs: those that exclude a...
MicroRNAs are a highly conserved class of small endogenous RNA, about ~22nt in length, involved in post-transcriptional gene silencing and have prominent roles in disease and development. Though the process of microRNA discovery was once an arduous task, the advent of high throughput sequencing technology has resulted in novel microRNAs...
Ensuring correctness of real-world software applications is a challenging task. Testing can be used to find many bugs, but is typically not sufficient for proving correctness or even eliminating entire classes of bugs. However, formal proof and verification techniques tend to be very heavy weight and are simply not available...
We explore the application of deep learning to the disparate fields of natural language processing and computational biology. Both the sentences uttered by humans as well as the RNA and protein sequences found within the cells of their bodies can be considered formal languages in computer science, as sets of...
This paper reports the findings of two studies conducted at Oregon State University. The first set of studies compares use of header comments versus mnemonic procedure and function names by programmers performing tasks relating to modification tasks. The second study compares the use of header comments versus in-line comments when...
Software developers frequently need to perform code maintenance tasks, but doing so requires time-consuming navigation through code. A variety of tools are aimed at easing this navigation by using models to predict places in the code that a developer might want to visit, and then providing shortcuts so that the...
This project aims at building a Java application and a Java applet that would simulate a Stern-Gerlach laboratory in Quantum Mechanics. The project provides a tool for allowing the student to quickly design and run on the computer screen a number of experiments involving spin systems. This application could be...
Researchers have hypothesized that if we could estimate the probability that a fault in a code component will a cause a failure, we could use this estimate to improve the fault-detection effectiveness of code-coverage-based testing. If this hypothesis could be supported, it would motivate further research in this area and...
An important impact of the genome technology revolution will be the elucidation of mechanisms of cancer pathogenesis, leading to improvements in the diagnosis of cancer and the selection of cancer treatment. Integrated with current well-studied massive knowledge and findings about the role of protein-coding mutations in cancer, demystifying the functional...
Tensegrity structures are composed of pure compressional elements that are connected via a network of pure tensional elements. The concept of tensegrity promises numerous advantages to the field of robotics. Tensegrity robots are, however, notoriously difficult to control due to their oscillatory nature and nonlinear interaction between the components. Multiagent...