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.”