Engineering student researches machine learning for language processing

Using computers to comb the vast sea of biomedical literature could be key to identifying relationships among concepts.

Featured photo
Clint Cuffy.

As part of Research Weeks (April 6–27) we are highlighting the work of six undergraduates whose work was made possible by VCU’s Undergraduate Research Opportunities ProgramGlobal Education OfficeDivision for Inclusive Excellence and guidance from faculty members.

Research Weeks takes place on both campuses and features a wide variety of projects in multiple disciplines.

See more stories by clicking on links in the “Related stories” section or learn more about the lineup of events for this year’s Research Weeks.


Clint Cuffy has always been interested in machine learning — the area of computer science in which computers use data to learn how to perform tasks, rather than being specifically programmed to do those tasks. But he lacked the opportunity to delve into the subject.

“It seemed like a daunting task without a finite starting point, especially when it comes to neural networks,” said the senior, who is majoring in computer science at the Virginia Commonwealth University School of Engineering. “Learning the inner workings and how to implement algorithmic approaches of modeling how the human mind works seemed far-fetched at best.”

Then Bridget McInnes, Ph.D., assistant professor in the Department of Computer Science, approached him with an opportunity to research machine learning with regard to natural language processing, and the rest is history, Cuffy said.

“My research project [‘Identifying relations in biomedical text for literature-based discovery’] entails using a neural network, an algorithm modeled after how the mind functions in regards to a-cyclical connected neurons, to learn unique relationships between concepts through predications and represent them in semantic space as concept vectors,” Cuffy said. “That is to say, considering an example such as ‘aspirin treats headaches,’ we can see the relationships between all three of these terms. ‘Aspirin’ and ‘headaches’ are related through the word ‘treats.’ Semantic similarity and relatedness defines how words can be similar to each other, such as ‘liver-organ,’ or related, such as ‘aspirin-headache,’ through predicate relationships. Using the previous examples, ‘liver is an organ,’ since liver is a more specific subset of an organ they are similar, but aspirin is not a headache so they are not similar. Since aspirin is used to treat headaches, they are related by the ‘treats’ predication.

“With this knowledge, we [use] a neural network that learns how to define representations of concepts in semantic space, in terms of similarity and relatedness, by the hypothesis words that can be defined by the context which surrounds it.”

Biomedical research publications are being published at an astounding rate, Cuffy noted. These publications could hold keys to potentially important relationships in literature-based discovery, but keeping up by reading a single document at a time and identifying possible relationships poses a daunting task, he said.

However, researchers have consequently found relationships among concepts through accidental or investigative reading of these publications. Attempts have been made to automate the process, but in order to identify meaningful relationships that are presently unknown, Cuffy and McInnes are building a foundation by identifying those that already exist within semantic space. They are training a neural network using data from the National Institutes of Health — which contains a Semantic Predication Database with more than 91.6 million examples of predication triplets — to generate term vectors that define the concepts and predicates with high levels of accuracy.

“The significance to this could be the key to unlocking more meaningful relationships,” Cuffy said. “Rather than investigative or accidental relationships being discovered, we could potentially automate this process.”

Providing undergraduate students the opportunity to conduct research is an important part of their education, McInnes said. “Experiential learning initiatives have been shown to aid in the development of undergraduates’ professional habits and promote scientific and critical thinking.” Cuffy said the project has further fueled his drive to see the limits of machine learning and its practicality. “Performing research at the undergraduate level is a blessing in disguise,” Cuffy said. “You find yourself exposed to information, briefly discussed or taught at the classroom level, taken steps further into practical application. … Research can be a very challenging, but rewarding, experience. Not only are you increasing your knowledge-set and learning invaluable information, but there is always the possibility of having a positive impact on the lives of others through your research.”

A study in unpredictability: VCU senior learns that when it comes to public health research, planning is only part of the process

Featured photo
Noelle Pooler.

As part of Research Weeks (April 6–27) we are highlighting the work of six undergraduates whose work was made possible by VCU’s Undergraduate Research Opportunities ProgramGlobal Education OfficeDivision for Inclusive Excellence and guidance from faculty members.

Research Weeks takes place on both campuses and features a wide variety of projects in multiple disciplines.

See more stories by clicking on links in the “Related stories” section or learn more about the lineup of events for this year’s Research Weeks.


In her office at the 500 Academic Centre building on Virginia Commonwealth University’s Monroe Park Campus, Joann Richardson, Ph.D., has a framed thank you letter from a Jamaican woman who participated in a health study led by a VCU student.

“Thank you for choosing me to participate in the study,” the letter says. “I have learned so much about my health and now am educating my family from what I have learned from the survey. I have impacted other lives from it because they are eating properly, exercising and taking better care of themselves.”

Richardson, an associate professor in VCU’s Department of Kinesiology and Health Sciences, served as the faculty adviser for an Undergraduate Research and Creative Scholarship study that started in 2016. Last year, physical education and exercise science senior Noelle Pooler picked up where the original study left off. The purpose of the study was influencing attitudes and behaviors toward health, with an ultimate goal of preventing and controlling the development of hypertension and diabetes among rural, medically underserved Jamaican women of childbearing age.

Noncommunicable diseases are the leading cause of death globally, according to the World Health Organization. Jamaica’s Ministry of Health indicates that the diseases, which include hypertension and diabetes, account for about 60 percent of deaths among men and 75 percent of deaths among women. Pooler’s research focused on the fact that hypertension and diabetes can be reduced with educational interventions that change lifestyle risk factors. In her research proposal, she hypothesized that informing people about the seriousness, risks and preventive measures to control hypertension and diabetes could help their society and communities function optimally.

“The study was focused on empowering people through knowledge so that they can improve their health,” Pooler said.

Pooler traveled to Jamaica last summer to conduct the first phase of research. Prior to starting the Undergraduate Research Opportunities Program study, she had not conducted research independently.

“I was really overwhelmed at first,” she said.

Before traveling to Jamaica, the New Jersey native researched Jamaican culture and government to prepare for identifying with and relating to the study participants. “I wanted to be culturally competent when I arrived,” she said.

In Jamaica, she recruited 15 women to participate in the study. The women, who ranged in age from 15 to 44 years old, first completed a survey that quantified their knowledge about hypertension and diabetes. They then participated in an informational session — led by Pooler — about the effect of exercise and nutrition on development of the diseases. “Being able to empower someone with knowledge that way was very humbling,” Pooler said. The women were later asked to complete surveys that assessed the effectiveness of the informational session.

The second and third phases of the study involved collecting post-session surveys in the months following the information session, but Pooler ran into obstacles in completing those phases.

“The personality and nature of the Jamaican women is that they do better in a personal environment,” Richardson said. “Trying to do a study long distance just didn’t work for them.”

Though Pooler was not able to complete the study, she said she still learned a lot from participating.

“Dr. Richardson warned me in advance that the nature of public health research is that it is unpredictable,” Pooler said. “You have to be prepared to roll with the punches.”

While she does not foresee a future career in public health research, Pooler was grateful for the opportunity to learn more about the research experience and be immersed in a culture unfamiliar to her.

“Doing this research solidified the fact that I like working with people and want to work with a diverse population,” Pooler said. “It is important to have a diverse array of knowledge and experiences working with different types of people from different cultures.”

Infection detection: VCU student researcher is using the latest DNA sequencing technologies to pinpoint a malaria parasite

Analyzing DNA data of mosquitoes has been “an amazing window into the world of malaria research and its importance to global health,” Megan Mair said.

Featured photo
Megan Mair.

As part of Research Weeks (April 6–27) we are highlighting the work of six undergraduates whose work was made possible by VCU’s Undergraduate Research Opportunities ProgramGlobal Education OfficeDivision for Inclusive Excellence and guidance from faculty members.

Research Weeks takes place on both campuses and features a wide variety of projects in multiple disciplines.

See more stories by clicking on links in the “Related stories” section or learn more about the lineup of events for this year’s Research Weeks.


A Virginia Commonwealth University student researcher is perfecting methods of detecting a malaria parasite in mosquitoes in the Brazilian Amazon.

Megan Mair and mentor Luiz Shozo Ozaki, Ph.D., associate professor in the VCU Center for the Study of Biological Complexity, use the latest DNA sequencing technologies to identify plasmodium, the malaria parasite in anopheline mosquitoes. The insect transmits the parasite to humans.

Mair, a senior studying bioinformatics, is working with Ozaki and collaborators at the institutions Fiocruz Rondonia in Brazil, and the Liverpool School of Tropical Medicine in England, to determine if new DNA sequencing technologies can help better identify the malaria parasite than more commonly used methods. Researchers typically identify a particular protein or examine DNA fragments of the parasite, but this does not always paint a complete picture, Mair said.

“These methods have the potential to lead to false positives and false negatives due to lack of specificity,” she said. “If we can determine infection of the parasite based on sequencing reads, and if the cost and complexity of sequencing goes down in the next few years, this could be a sound method to utilize in the field.”

Mair said the work gave her a compelling experience in tropical diseases.

This has been an amazing window into the world of malaria research and its importance to global health.

“I had never put much thought into malaria research because it doesn’t affect a lot of people in the United States,” Mair said. “This has been an amazing window into the world of malaria research and its importance to global health.”

Mair analyzed DNA sequencing data of mosquitoes collected by colleagues in the village Vila Amazonas, a village in the Brazilian state of Rondonia, where in 2008 researchers attempted to eliminate malaria by directly eliminating the parasite in the human host. Ozaki and his collaborators are concurrently characterizing the genetic profile of two populations of mosquitoes captured before and after malaria was eliminated in the village.

Mair spent much of last summer sorting DNA sequences from more than 1,000 mosquitoes. She compared sequences from the total DNA of the mosquitoes to those in a database of plasmodium DNA to determine which mosquitoes were infected.

Mair and collaborators found additional confirmation that malaria elimination efforts in Vila Amazonas were effective. Before the disease was eliminated, there was higher incidence of the malaria parasite within mosquitoes.

The researchers are also confirming evidence they found of a species of malaria parasite not previously documented in the region.

“If that is true, this could really change the way malaria is treated in Brazil because that parasite isn’t currently screened for in humans,” Mair said. “We are hoping this isn’t the case. Hopefully, more DNA sequencing would confirm this with certainty.”

Mair said she would like to work with another graduate researcher in bioinformatics to continue interpreting the mosquito data. Ozaki said Mair’s technical skills and approach to scientific research will serve her well in this and future endeavors.

“Her computational skills are impressive. For instance, she is able to quickly write an algorithm to sort specific files from millions in a database,” he said. “What most impresses me is her inquisitive mind, new ideas and original conclusions.”

VCU student researcher explores dance as a method for combating racial inequalities and social constructs

Featured photo
Christine Wyatt.

As part of Research Weeks (April 6–27) we are highlighting the work of six undergraduates whose work was made possible by VCU’s Undergraduate Research Opportunities ProgramGlobal Education OfficeDivision for Inclusive Excellence and guidance from faculty members.

Research Weeks takes place on both campuses and features a wide variety of projects in multiple disciplines.

See more stories by clicking on links in the “Related stories” section or learn more about the lineup of events for this year’s Research Weeks.


Dance can be a vehicle for examining class and racial divides in the United States and healing those wounds, a Virginia Commonwealth University student researcher has found.

Christine Wyatt, a senior who majors in dance and choreography in the School of the Arts, employs the art form to improve dialogue about race and class and how the concepts inform American society and art. Wyatt includes Africanist-influenced movements in her work. She brings attention to the fact that Eurocentric approaches often dominate formal dance education in the U.S., even though dances of Africa and enslaved Africans in the Americas also have shaped the art form in this country.

Wyatt calls this investigative process “decolonizing dance.” In her eyes, dance education in the United States could help bring greater inclusivity to art and society. Decolonizing can be an abstract term that entails “undoing racial and class structures” within dance and society, Wyatt said.

“Decolonizing through dance is about undoing colonization in my daily life,” she said. “Colonization represents the concept of power struggles and dynamics that come up in dance. I found that when you’ve recognized there is an injustice, whether it’s in an entire education system or in a dance class, you have to recognize that it is flawed.”

To develop these ideas and practice them in her choreography and everyday life, in 2017 Wyatt attended the Summer Leadership Institute of the Urban Bush Women dance company. The Brooklyn-based group specializes in African-American dance theater and emphasizes community outreach and equity in dance. The Summer Leadership Institute teaches dancers, choreographers and activists to employ dance to empower themselves and the disenfranchised.

Wyatt said she used the skills learned in the program to express her racial identity in her choreography and to work collaboratively with other dancers. For 10 days, internationally and racially diverse participants questioned what race and power structures mean in American society and how these barriers manifest in artistic communities.

“We went through the process of discussing what are prejudice, discrimination and racism,” she said. “We asked questions such as, Does race exist? During the conversation, Urban Bush Women provided a lot of historical context and information for the digging we were doing.”

Wyatt will express her musings in MEANS WITHIN, the Spring 2018 Senior Project Concert, which is the culmination of her education in dance and choreography. Wyatt and seven student choreographers will showcase pieces performed by VCU dancers that explore how people deal with constructs and challenges. Wyatt’s work “Ti’ed” alludes to the colloquial pronunciation of the word tired, which represents the speaker being so exhausted, he or she drops the ‘r’ sound. Wyatt intends to expose the social, psychological and political sources of fatigue felt by the disenfranchised. The piece is inspired by civil and voting rights activist Fannie Lou Hamer, who coined the phrase “I’m sick and tired of being sick and tired.”

Wyatt said VCU is the ideal place to premiere “Ti’ed” and to begin pushing for social change.

“The thing that drew me to VCU was we make it real. In dance, we find out what that means on a very deep level,” she said. “We are constantly making ourselves better through dance, building community and finding community. For me, that is what making it real has been at VCU.”

For Ronald Romero, researching the links between discrimination and health is personal

Featured photo
Ronald Romero.

As part of Research Weeks (April 6–27) we are highlighting the work of six undergraduates whose work was made possible by VCU’s Undergraduate Research Opportunities ProgramGlobal Education OfficeDivision for Inclusive Excellence and guidance from faculty members.

Research Weeks takes place on both campuses and features a wide variety of projects in multiple disciplines.

See more stories by clicking on links in the “Related stories” section or learn more about the lineup of events for this year’s Research Weeks.


As a research assistant in the Discrimination and Health Lab in the Department of Psychology in Virginia Commonwealth University’s College of Humanities and Sciences, Ronald Romero is helping investigate the role of discrimination in racial and ethnic health disparities.

Romero, a senior psychology major, is working on several projects. One is examining the psychological mechanisms that underlie the link between perceived discrimination and weight outcomes among first-generation Latinx immigrants in the community. Another is exploring the dynamics of patient-physician communication in family medicine clinics among black patients with Type 2 diabetes.

“My experience on these projects in the lab has been nothing short of amazing,” Romero said. “I have learned crucial skills having to do with correlational and experimental study designs as well as gaining knowledge as to how the process of psychological research is carried out, as well as what it takes to run a successful experiment.”

Romero was born in Venezuela and immigrated to the United States at a young age. As a researcher, his work to better understand the effects of discrimination is deeply personal.

“As an immigrant to this country, I’ve seen and experienced discrimination, oppression and marginalization in many forms,” he said. “With the knowledge that I’ve gained as a psychology student, I want to help vulnerable people who don’t have the resources to defend themselves, such as immigrants.”

After graduation this spring, he plans to continue pursuing research opportunities and will eventually attend graduate school. Ultimately, he intends to complete a doctoral program in social or health psychology in order to influence policies that address the many health disparities faced by ethnic and racial minority groups.

“I’ve been in a tricky situation my whole life because legally I am labeled an outsider, but my entire life I can only recall my American experiences,” he said. “It has been hard growing up as I’ve had to grow with American peers sharing their experiences and embracing their culture knowing deep down what my true roots are.”

Romero’s job in the Discrimination and Health Lab is part of a work-study research assistant program through the Undergraduate Research Opportunities Program in the VCU Office of Research and Innovation.

He was recruited for the position by Nao Hagiwara, Ph.D., an assistant professor of psychology who leads the lab. She met Romero when he took her Social Psychology course in fall 2016.

“Ronald stood out in this large class for his enthusiasm for learning and striking intellectual abilities,” she said. “So I asked him to join my Discrimination and Health Lab in the subsequent semester.”

Since joining the team, Romero has played an important role in the lab’s work.

“In our lab, we examine the underlying psychological processes and consequences of stereotyping, prejudice and discrimination,” she said. “Over the last 1.5 years, Ronald has been involved in a number of projects related to this core research question.

“Ronald is a hard-working, bright student who is eager to learn,” she added. “I truly admire his strong motivation, great work ethic and competency.”

NOBCChE: Last meeting of the semester!

The VCU chapter of the National Organization for the Professional Advancement of Black Chemists and Chemical Engineers  invites you to our last meeting of the semester ! it will be held this Wednesday, April 18, 2018 from 7 p.m. to 8:30 p.m. in Temple Rm. 3309. We are an academic organization that showcases excellence in STEM and provides opportunities to learn of co-ops and internships, build a network, be a competitive applicant, and enhance professional development while also promoting inclusivity and diversity.

This Wednesday, April 18, 2018 from 7 p.m. to 8:30 p.m. in Temple Rm. 3309. We will have graduate students from various departments in STEM, along with the ACS VA Section Younger Chemists Committee (YCC) to share upcoming events you can participate in and answer any questions you may have in moving forward academically. We will also have fun activities to make you a stronger interviewee!  ..and food! a.k.a. pizza and RedEye Cookie Co. !

If you have any questions please email us at nobcchevcu@gmail.com

You are invited!! VCU Poster Symposium for Undergraduate Research and Creativity!

We are very excited to invite you all to visit our undergraduates as they present their research and scholarly endeavors at our 10th(!) Annual Poster Symposium for Undergraduate Research and Creativity taking place on Wed. April 25thin the Commonwealth Ballrooms and Richmond Salons of the Student Commons. Session 1: 10:30-12pm, Session 2: 1-2:30pm.  Remarks and awards at 12:30pm.  Our students have put together some fantastic posters profiling their work from the past academic year, and nothing would mean more to them than to be able to share it with our community!  We have nearly 300 students eager to answer your questions and tell you about their research.

At 12:30pm we will host remarks from Vice President for Research Development, Dr. John Ryan, and will be awarding our outstanding faculty members for their mentorship of our undergraduates.  We will also announce our annual VCU Launch awards for first-year and second-year students who have produced research posters that exhibit remarkable rigor and vision.

We thank you for your continuing support of undergraduate research at VCU and hope that you will join us at this special event, part of VCU Student Research Weeks!

Events exploring VCU research on opioids and women’s health will highlight Student Research Weeks

A snapshot of the 300-plus research posters presented during the Undergraduate Research and Creativity symposium.
A snapshot of the 300-plus research posters presented during the Undergraduate Research and Creativity symposium.

Undergraduate and graduate students will grow as scholars when they share and promote their research at the eighth annual Student Research Weeks, April 6-27. Students enrolled in the university’s more than 200 degree programs in multiple disciplines will present their research to faculty and peers during symposiums and other events.

The goal is for students to network and learn from other researchers, and practice engaging the community with their work, said Herbert Hill, director of undergraduate research opportunities in the Office of Research and Innovation.

“VCU Research Weeks is about providing our students, both graduate and undergraduate, with a platform to share their work with their peers and the broader community,” Hill said. “One of the core outcomes of research is dissemination, sharing challenges, progress and discoveries in the effort to advance knowledge as a whole.”

The following is a schedule of VCU Research Weeks events, which are free and open to the public:


School of Education Research Colloquium
Oliver Hall, 1015 W. Main St.
April 6

Keynote speaker Jennifer Piver-Renna will share how research can change the conversation around education policy in Virginia, offering an inside perspective on how research and data can influence state policy decisions. Other sessions will include presentations of faculty and student research.

 

Angelica De Jesus, graduate student in the Department of Psychology, presented her research on body image problems and parental weight comments and how they predict Latino young adults’ depressive symptoms during the 10th Annual Women’s Health Research Day poster session.
Angelica De Jesus, graduate student in the Department of Psychology, presented her research on body image problems and parental weight comments and how they predict Latino young adults’ depressive symptoms during the 10th Annual Women’s Health Research Day poster session.

14th annual Women’s Health Research Day
Hermes A. Kontos Medical Science Building, auditorium, 1217 E. Marshall St.
April 12

Women’s Health Research Day is a celebration and promotion of research activities in women’s health at VCU. A plenary symposium will cover topics such as women and substance use disorders, using e-cigarettes during pregnancy, opioid use during pregnancy and PTSD-related drinking.

School of Dentistry Clinic and Research Day
VCU School of Dentistry, Crockett Lounge, 520 N. 12 St.
April 19

School of Dentistry students will present research that demonstrates how they progress the practice of dentistry and dental hygiene from 9:30 a.m. to 2:30 p.m. Prizes will be awarded for the best poster presentations.

VCU Political Science 12th annual Student Research Conference
April 20
University Student Commons, 907 Floyd Ave.

VCU undergraduate and graduate students and students from across Virginia and overseas will present research and facilitate roundtable discussions on topics related to general fields of government and public affairs. Topics will include American government, public policy, international relations, comparative government and politics, political theory and research methods. Research may share connections to sociology, ethics, religious studies, philosophy, economics and history. The conference will be held from 8:30 a.m. to 4:30 p.m.

Graduate Research Symposium and Exhibit
April 24
University Student Commons, 907 Floyd Ave.

Five VCU experts in opioid related research will discuss how to combat the epidemic during a panel discussion. A poster presentation of graduate level research will cover opiate addiction and other topics in multiple disciplines. The event has a thematic tie to “Dreamland,” VCU’s 2017 Common Book.

Poster Symposium for Undergraduate Research and Creativity
April 25
University Student Commons, 907 Floyd Ave.

The symposium is a chance for many VCU undergraduates to showcase the results of their first major research endeavor. Students in multiple disciplines in the arts, sciences and humanities will present their research. The event is often a culmination of an undergraduate academic career, and marks the end of a year’s worth of exploration for a research project.

 Graduate Recruitment Fair
April 25
University Student Commons, 907 Floyd Ave.

The fair will coincide with the Poster Symposium for Undergraduate Research and Creativity. Undergraduates from all disciplines are invited to attend for information related to opportunities at VCU and other institutions. Recruiters from other universities will be in attendance.

 National Science Foundation Research Fellowship information session
April 26
University Student Commons, 907 Floyd Ave.

The VCU National Scholarship Office will be hosting an information session for the NSF’s Graduate Research Fellowship Program. Jeff Wing, director of the VCU National Scholarship Office, will share information about the application process. Juniors and seniors who are planning to pursue graduate degrees in STEM fields are encouraged to attend, as are first-year students.

Fulbright Scholarship information session
April 26
University Student Commons, 907 Floyd Ave.

The VCU National Scholarship Office will host an information session for students interested in the Fulbright U.S. Student Program, which includes funding to study, conduct research or teach English in more than 140 nations.

Barry M. Goldwater Scholarship information session
April 26
University Student Commons, 907 Floyd Ave.

The VCU National Scholarship Office is hosting an information session for students interested in the Goldwater Scholarship. The purpose of the Goldwater program is to provide a continuing source of highly qualified scientists, mathematicians and engineers by awarding scholarships to college students who intend to pursue research careers in these STEM fields.

 School of Social Work Research Symposium
April 27
University Student Commons, 907 Floyd Ave.

Graduate and undergraduate students from the VCU School of Social Work will present their research and scholarly projects in the form of posters and oral presentations at the annual symposium, held from 10 a.m to 2 p.m.

School of Engineering Senior Design Expo
April 27
VCU Siegel Center, 1200 W. Broad St.

Undergraduates in the School of Engineering will share capstone senior projects with the greater Richmond community to raise awareness of the profession among middle and high school students. Senior design teams will demonstrate their prototypes, which are a culmination of eight months of effort. In all, 88 student teams will participate in the expo, which has become a signature event for the university.

At the School of Social Work Research Symposium in 2014, Grace Dawson discusses her team's research project, “Comparing the Effectiveness of Foster Parent Training Programs Through Satisfaction.”
At the School of Social Work Research Symposium in 2014, Grace Dawson discusses her team’s research project, “Comparing the Effectiveness of Foster Parent Training Programs Through Satisfaction.”

Currently recruiting undergraduates: MINDFULNESS FOR HEALTHCARE PROFESSIONAL STUDENTS AND TRAINEES

 

Why Participate?

1.      Receive free training in mindfulness, meditation, and yoga

2.      Entered to win $100 in compensation

3.      Receive personalized feedback report on psychological and cognitive functioning at study end

4.     Help advance research to improve healthcare professional education and well-being