Ph.D. Defense: “Kernel-based empirical bayesian classification method with applications to protein phosphorylation and non-coding RNA”, Mark Menor

Kernel-based empirical bayesian classification method with applications to protein phosphorylation and non-coding RNA

Mark Menor

 

Monday, June 2, 10:00am, POST 302

Abstract: With the advancement of high-throughput sequencing technologies, a new era of ‘big data’ biological research has dawned. However, the abundance of biological data presents many challenges in their analysis and it has proven very difficult to extract impor- tant information out of the data. One approach to this problem is to use the methods of machine learning.

In this dissertation, we describe novel probabilistic kernel-based learning methods and demonstrate their practical applicability by solving major bioinformatics problems at the transcriptome and proteome levels where the resulting tools are expected to help biologists further elucidate the important information contained in their data.

The proposed binary classification method, the Classification Relevance Units Machine (CRUM), employs the theory of kernel and empirical Bayesian methods to achieve non-linear classification and high generalization. We demonstrate the practical applicabil- ity of CRUM by applying it to the prediction of protein phosphorylation sites, which helps explain the mechanisms that control many biochemical processes.

Then we develop an extension of CRUM to solve multiclass problems, called the Multiclass Relevance Units Machine (McRUM). McRUM uses the error correcting output codes framework to decompose a multiclass problem into a set of binary problems. We devise a linear-time algorithm to aggregate the results into the final probabilistic multiclass prediction to allow for predictions in large scale applications. We demonstrate the practical applicability of the McRUM through a solution to the identification of mature microRNA (miRNA) and piwi-interacting RNA (piRNA) in small RNA sequencing datasets. This provides biologists a tool to help discover novel miRNA and piRNA to further understand the molecular processes of the organisms they study.

Committee: Kyungim Baek (Chairperson), Guylaine Poisson (Chairperson), Henri Casanova, Scott Robertson, and Gernot Presting

Ph.D. Proposal Defense: “Complex Multi-Agent Simulation of MSM HIV Transmission For Examining Concurrency”, Robert Puckett

Robert Puckett will be presenting his dissertation proposal on Friday, December 13, at 12noon in POST 318B (note the room is not the usual conference room).

Complex Multi-Agent Simulation of MSM HIV Transmission For Examining Concurrency

Abstract: The Human Immunodeficiency Virus (HIV) is a complex virus with a high rate of death, several modes of transmission, and long asymptomatic incubation period. Over time the virus weakens the host’s immune system leading to Acquired Immune Deficiency Syndrome (AIDS). Once progressed to AIDS, a body becomes susceptible to a range of opportunistic infections and cancers. In developed countries, HIV disproportionately affects men who have sex with men (MSM), primarily due to the practice of unprotected anal receptive (UAR) sex. Epidemic modeling helps researchers in developing hypotheses on the driving forces, testing intervention strategies, and predicting the course of the HIV epidemic. Although many models for HIV have been developed, HIV remains a difficult subject to model owing to complex transmission modes, limitations in data collection, and variability in human behavior. Instead of studying populations in aggregate, microsimulation techniques allow for the study of individuals over time. A multi-agent system (MAS) can be used to implement a microsimulation of HIV transmission among individual people existing within a complex network of sexual partners. Through simple rules governing agent interactions, complex behavior can emerge from the society of agents.

Of particular interest for study, the role of concurrent relationships as a driving force of epidemics has become a hotly debated topic in recent years. To reduce conflicting definitions in research and data collection, UNAIDS has formally defined concurrency as “overlapping sexual partnerships where sexual intercourse with one partner occurs between two acts of intercourse with another partner.” In 1998, Morris and Kretzschmar concluded from stochastic simulations that concurrent partnerships “dramatically increase the speed and pervasiveness of the epidemic spread.” Numerous subsequent publications by various authors have argued for and against the degree of impact for concurrency in HIV epidemics around the world. Thus, the role of concurrency is far from a settled subject.

In our research, we build and examine a multi-agent simulation of HIV transmission via concurrent relationships in a MSM community. Our simulation will illuminate some of the behavioral factors and sexual network characteristics that contribute to the spread of HIV. Principally, we believe that we will observe a profound impact from the acute HIV infection phase interacting with concurrent relationships to produce significantly larger epidemics. Insights gained from our simulation will aid policy makers in developing more useful HIV surveillance methods and intervention strategies.

Dissertation committee: Nancy Reed (chair), Tim Brown, JB Nation, Luz Quiroga, and Dennis Streveler

Brewer wins international sustainability award

Robert Brewer (PhD, Computer Science, 2013) has won the 2013 Graduate Student Research on Campus Sustainability Award from the Association for the Advancement of Sustainability in Higher Education (AASHE). He accepted the award on October 6, 2013, at AASHE’s annual conference and expo in Nashville, Tennessee. AASHE is an international organization providing resources and professional development for sustainable operations, research and education.

Brewer’s doctoral dissertation, titled “Fostering Sustained Energy Behavior Change and Increasing Literacy in a Student Housing Energy Challenge,” provides novel insights through two open source energy challenge software systems, an energy literacy assessment instrument, and the discovery of fundamental problems with the use of baselines for assessing energy competitions.

For more details, see the press release and his dissertation.

Jordan Takayama wins UROP award

Jordan Takayama, ICS undergraduate honors student, has won funding from the University of Hawaii Undergraduate Research Opportunities (UROP) program. His research project is entitled “Making game design as easy as gaming: Creating an administrative interface to the Kukui Cup.” The research will involve creation of an administrative “wizard” for configuring the Makahiki serious game framework, and evaluating its effectiveness through qualitative case studies of users.

The award will cover software licenses, conference travel, and participant compensation.  Jordan is advised by Professor Philip Johnson.

ICS Ph.D. Defense: Robert Brewer, “Fostering Sustained Energy Behavior Change and Increasing Energy Literacy In A Student Housing Energy Challenge”

Fostering Sustained Energy Behavior Change and Increasing Energy Literacy In A Student Housing Energy Challenge, Robert Brewer

Wednesday, March 13, 3:00pm, POST 302

Abstract: We designed the Kukui Cup challenge to foster energy conservation and increase energy literacy. Based on a review of the literature, the challenge combined a variety of elements into an overall game experience, including: real-time energy feedback, goals, commitments, competition, and prizes.

We designed a software system called Makahiki to provide the online portion of the Kukui Cup challenge. Energy use was monitored by smart meters installed on each floor of the Hale Aloha residence halls on the University of Hawai’i at Manoa campus.

In October 2011, we ran the UH Kukui Cup challenge for the over 1000 residents of the Hale Aloha towers. To evaluate the Kukui Cup challenge, I conducted three experiments: challenge participation, energy literacy, and energy use.

Many residents participated in the challenge, as measured by points earned and actions completed through the challenge website. I measured the energy literacy of a random sample of Hale Aloha residents using an online energy literacy questionnaire administered before and after the challenge. I found that challenge participants’ energy knowledge increased significantly compared to non-challenge participants. Positive self-reported energy behaviors increased after the challenge for both challenge participants and non-participants, leading to the possibility of passive participation by the non-challenge participants.

I found that energy use varied substantially between and within lounges over time. Variations in energy use over time complicated the selection of a baseline of energy use to compare the levels during and after the challenge. The best team reduced its energy use during the challenge by 16%. However, team energy conservation did not appear to correlate to participation in the challenge, and there was no evidence of sustained energy conservation after the challenge. The problems inherent in assessing energy conservation using a baseline call into question this common practice.

My research has generated several contributions, including: a demonstration of increased energy literacy as a result of the challenge, the discovery of fundamental problems with the use of baselines for assessing energy competitions, the creation of two open source software systems, and the creation of an energy literacy assessment instrument.

Committee: Philip Johnson (chair), Martha Crosby, Scott Robertson, Daniel Suthers, and Anthony Kuh

CIS Ph.D. Defense: Blanca Polo, “The Virtual Critical Studio: Implementing studio based learning techniques in an online introductory programming course to address common programming errors and misconceptions

Date: Monday, February 25th, 2013, Time: 11:00am, Location: POST 302

Abstract: Student programming errors, online education and studio-based learning (SBL) in computer science education have all been topics of recent research efforts. This study expands on this research applying this knowledge to proactively help students overcome their difficulties. This project coins the term virtual critical studio (VCS), and proposes it for proactive online teaching. The VCS consists of three components, the studio-based-learning pedagogy, the precise and critical timing and content of the VCS sessions and the virtual nature of the implementation environment. The implementation of VCS aims to provide a better quality of online computer science courses by promoting student-student interaction focused on the discussion of problematic curriculum issues.

Data collected prior to the application of VCS provided insights into common programming errors that were later used to create the assignments for the VCS sessions. This study compares online vs. VCS incarnations of the same course. In addition, it observes and analyzes the content of VCS sessions

The VCS like its predecessor SBL, has shown the potential to help novice programmers overcome their difficulties. The effects of this treatment show that students have an optimistic state of mind before, during and after VCS sessions. These effects do not exist for the control group. This research provides a unique insight into the VCS process including the identification of “learning moments”, student-student interaction and the building of camaraderie.

Seminar: Mike Gowanlock, “Habitability within the Milky Way galaxy”

Studies of the habitability of the Earth, the Solar System and beyond indicate that life may exist in a variety of environments, some of which were previously thought too hostile for life. In this talk I will discuss my research on the Galactic Habitable Zone, which is described in terms of the spatial and temporal dimensions of the Galaxy that may favour the development of complex life. Monday, August 27, 4:30pm, POST 126

Studies of the habitability of the Earth, the Solar System and beyond indicate that life may exist in a variety of environments, some of which were previously thought too hostile for life. Overlap in the studies of extrasolar planets and the habitability of numerous environments indicates that there might be an increasingly large number of habitable regions in the universe for life to thrive. Initial studies of habitability in newly discovered environments offer an exciting opportunity to begin to understand the parameter space that defines the carrying capacity for life in these environments. In this talk I will discuss my research on the Galactic Habitable Zone, which is described in terms of the spatial and temporal dimensions of the Galaxy that may favour the development of complex life.

Mike Gowanlock is pursuing his Ph.D. in computer science and works in the fields of astrobiology and high performance computing. He is interested in the computational methods that enable scientific simulations, in particular, those that are applied to his work on the habitability of our Galaxy.

All are welcome to attend. Since next Monday is Labor Day, our monthly first Monday social hour at Manoa Gardens will follow Mike’s talk.