MS Thesis Defense

Integrating Domain Knowledge in Supervised Machine Learning
to Assess the Risk of Breast Cancer Using Genomic Data

Aniket Bochare

9:00am Friday 29 June 2012, ITE 325b

Breast cancer is the most common form of cancer in women. Breast cancer comprises 22.9% of the invasive cancers in women and 16% of all the female cancers. Currently, treatment decisions are based primarily on clinical parameters, with little use of genomic data. Our study takes into consideration the data of postmenopausal women of European descent and their single nucleotide polymorphism (SNP) information to assess the risk of developing breast cancer. We used various supervised machine learning and data mining techniques to generate a model for predicting risk of breast cancer using only genomic data.

In this research we propose an approach to select the nine best SNPs using various feature selection algorithms to improve binary classification accuracy and validate our results with the existing literature. The machine learning model generated without the domain knowledge yields poor prediction results. After the addition of the domain knowledge of the 11 SNPs into the original training set we performed classification using the best features obtained by feature selection techniques. The machine learning model generated using both the domain knowledge and the feature selection techniques performed much better compared to the naive approach of classification.

Committee: Drs. Yelena Yesha (chair), Anupam Joshi, Aryya Gangopadhyay and Micheal Grasso

Each year, the Alumni Association Scholarship program helps amazing students succeed at UMBC. Over the next few weeks, we’ll be sharing some of their stories with you. This week, meet scholarship recipient Gift Jayakar ’12.
A famous English poet/playwright once asked: What’s in a name?
For new grad Gift Jayakar ’12, his first name is so much more than a moniker. To him, “gift” is the way of life he lead as a student at UMBC — and it’s a philosophy that will follow him into medical school and beyond.
“As a son of a pastor and a public school teacher, I could have chosen a career in education or religion,” said Jayakar, who has family and friends in India. “My friend’s death in the 2004 Asian tsunami gave me a direction. I decided to pursue a career in helping people as a doctor.”
Jayakar, who majored in biological sciences and minored in sociology and emergency health services, will start medical school in India this fall, with the hope of becoming a cardiothoracic surgeon. Uncertain about what he wanted to study at UMBC early on, he found his roots after stumbling into an EHS class his second semester.
“I just wanted to try it out. And I loved it,” said Jayakar, who jumped at the chance to participate in research at the University of Maryland, Baltimore department of immunology, and volunteer with Maryland Shock Trauma and the emergency room of St. Agnes Hospital through a partnership with the Shriver Center.
He was also incredibly active in numerous activities on campus, including serving as a senator in the Student Government Association and assistant speaker of the SGA Senate; serving as president of the Interdisciplinary Studies Council of Majors; and playing an active role in UMBC’s pre-med society, the Relay for Life, tennis club and other groups.
“Of all the leadership and community service positions I’ve held, I value my experience with UMBC Student Government Association the most. It helped me gain a lot of confidence and realize that I can make changes to the community,” he said.
“I learn a lot when I’m involved in service. I’ve learned patience, responsibility, commitment, and punctuality after being involved in service. To me these are life-time lessons that classroom alone can never teach.”
After the 2004 tsunami in India, Jayakar and his father volunteered as missionaries to help the victims, but he left wishing he could have done more. After med school, he hopes to someday build a hospital there where people can be treated for free.
“It’s so simple,” he says of his philanthropic philosophy. “Society gives you so many opportunities to live the life you want to live. It our responsibility — 0ur duty — to give back.”

Each year, the Alumni Association Scholarship program helps amazing students succeed at UMBC. Over the next few weeks, we’ll be sharing some of their stories with you. This week, meet scholarship recipient Gift Jayakar ’12.

A famous English poet/playwright once asked: What’s in a name?

For new grad Gift Jayakar ’12, his first name is so much more than a moniker. To him, “gift” is the way of life he lead as a student at UMBC — and it’s a philosophy that will follow him into medical school and beyond.

“As a son of a pastor and a public school teacher, I could have chosen a career in education or religion,” said Jayakar, who has family and friends in India. “My friend’s death in the 2004 Asian tsunami gave me a direction. I decided to pursue a career in helping people as a doctor.”

Jayakar, who majored in biological sciences and minored in sociology and emergency health services, will start medical school in India this fall, with the hope of becoming a cardiothoracic surgeon. Uncertain about what he wanted to study at UMBC early on, he found his roots after stumbling into an EHS class his second semester.

“I just wanted to try it out. And I loved it,” said Jayakar, who jumped at the chance to participate in research at the University of Maryland, Baltimore department of immunology, and volunteer with Maryland Shock Trauma and the emergency room of St. Agnes Hospital through a partnership with the Shriver Center.

He was also incredibly active in numerous activities on campus, including serving as a senator in the Student Government Association and assistant speaker of the SGA Senate; serving as president of the Interdisciplinary Studies Council of Majors; and playing an active role in UMBC’s pre-med society, the Relay for Life, tennis club and other groups.

“Of all the leadership and community service positions I’ve held, I value my experience with UMBC Student Government Association the most. It helped me gain a lot of confidence and realize that I can make changes to the community,” he said.

“I learn a lot when I’m involved in service. I’ve learned patience, responsibility, commitment, and punctuality after being involved in service. To me these are life-time lessons that classroom alone can never teach.”

After the 2004 tsunami in India, Jayakar and his father volunteered as missionaries to help the victims, but he left wishing he could have done more. After med school, he hopes to someday build a hospital there where people can be treated for free.

“It’s so simple,” he says of his philanthropic philosophy. “Society gives you so many opportunities to live the life you want to live. It our responsibility — 0ur duty — to give back.”

Beth Wells, assistant vice provost for Academic Affairs, earned designation in April as a Board Certified Coach by the Center for Credentialing and Education.

UMBC recently asked its students a simple question: How does UMBC inspire you? But, instead of essay response customary for scholarship competitions, students were challenged to answer in video form.

As you might imagine, our students truly delivered. Twenty-seven students entered the UMBC Change the World Video Contest, which was sponsored by the Office of Undergraduate Admissions in conjunction with their award-winning Super Heroes campaign.

The winner, incoming sophomore Deanna Zare, submitted a video that picked up on the super hero theme and highlighted ways UMBC has helped her become a student leader:

“Everyone knows that UMBC is ranked the number one up and coming university, but not everyone realizes how this inspires underdogs or Retrievers just like me,” she explains in the intro.

Zare won a $3,000 scholarship for her efforts. Two runners-up won $1,000 scholarships, and four honorable mention winners took home prize packs from the UMBC Book Store. Great job, everyone!

Watch all of the submitted videos here.

Last night I received the following update from Kim Smith who has been at the Rio+20 events this past week:

Each day at Rio+20 brings volumes of new information about the state of our planet, the actions of civil society, and the conflicts between the governments. It is hard to reconcile my feelings between the contrasts of meeting so many amazing people who give me hope for the future and learning about the growing devastation of ecosystems and wondering, truly, if we will be able to respond fast enough. Not only do our governments have to lead a coherent and collaborative effort to create systems that facilitate major changes quickly, but our media must give accurate and solution-based information in order to educate, empower, and engage our citizens in actions to make a difference. There really is no other option and there is no time to wait. It is unfortunate that the US, Canada, Russia, and Venezuela are obstructing much of the progress.

I truly believe that higher education must be a leader in these efforts but we will not be effective unless we have a systems-based approach where our political, economic and social institutions work closely in collaboration with education across all ages and in much more applied and practical ways. The Higher Education Sustainability Initiative, launched by UNESCO and led by UN Asst Secretary Elizabeth Thompson, is a start, as it raises the recognition of higher education’s contributions to sustainable development efforts.

More of the issues themselves have been addressed by the non-profits. From struggling ocean ecosystems ("our blue heart") and mountain top removal to the extinction of indigenous cultures and the status of farmers, NGOs are leading the actions at the People's Summit, a huge civil society event coinciding with the Rio Summit. In the last few days, I have been fortunate to hear Vandana Shiva, Marina Silva, a woman from La Via Campesina, Sylvia Earle, Ted Turner, a team from the TARA ocean research project, and Ban Ki-Moon himself. They are all calling for global change.

This culminated yesterday in a huge march, with 1000s of NGO activists, students, and professors protesting in the streets. So intense, with countless signs, costumes, and voices. I feel blessed to have happened upon the education protests in Cinelandia. According to some students from another Brasilian state, the students and professors are really struggling with funding and resources, given World Bank structural loan adjustments. While we all make calls for sustainable education, many people are frustrated that the mission is not backed up with resource support.

I have been on the search for Hillary Clinton, who arrived yesterday. I hope to hand her information on our education efforts, but I cannot promise I will be able to connect with her. All of the world leaders are followed closely by security. They have actually given students and workers several days off in Rio to simply lighten the load on the transportation systems in town. The cavalcades for the delegates are particularly disruptive, with huge police escorts.

Despite all if the traffic, I cannot speak more highly of the kindness and hospitality of the Cariocas (Rio residents). I rarely have no trouble finding a place, as Brasilians will often go out of their way to help you and some even walk you to your destination.