CSEE Colloquium

An Integrated Machine Learning Framework for Analyzing Protein-Ligand Interaction Data

Dr. Huzefa Rangwala
Assistant Professor, Computer Science & Engineering
George Mason University

1:00 p.m., Friday, February 10, 2012, ITE 325B, UMBC

Proteins have a vast influence on the molecular machinery of life. Stunningly complex networks of proteins perform innumerable functions in every living cell.  Small organic molecules (a.k.a. ligands) can bind to different proteins and modulate (inhibit/activate) their functions. Understanding these interactions provides insight into the underlying biological processes and is useful for designing therapeutic drugs.

In this talk I will describe our work related to the analysis of information associated with proteins and their interacting molecule partners (protein-ligand activity matrix). The underlying hypothesis of our approach is that by extracting information from protein-ligand activity matrix, we are drawing bridges between the structure of chemical compounds (chemical space) and the structure of the proteins and their functions (biological space).  I will present an approach used for mining relational data, especially when the data is sparse and high dimensional. I will also present methods that are based on the principles of multi-task learning and semi-supervised learning.

Huzefa Rangwala is an Assistant Professor at the department of Computer Science & Engineering, George Mason University. He holds affiliate positions with the Department of Bioengineering and the Department of Bioinformatics & Computational Biology. He received his Ph.D. in Computer Science from the University of Minnesota in the year 2008. His core research interests include bioinformatics, machine learning, and high performance computing. Specifically, he is working on developing new data mining algorithms and applying them to the fields of genomics, structural bioinformatics, drug discovery and social media analysis.

Host: Dr. Marie desJardins

UMBC Cyber Defense Lab Research Meeting

Using data visualization techniques to support digital forensics

Tim Leschke

11:00am-12:15pm, Friday, Feb 3, 2012
ITE Room 228

Digital forensic examiners explore large datasets in search of evidence of a crime. In order to keep pace with the growing amount of data that is subject to a forensic examination, digital forensic examiners need to be more selective about the data they examine. One way to be selective about data is to focus attention at data that has changed-over-time. We present Change-Link, a data exploration tool which allows the user to see directories that have changed within an operating system. Our novel contributions are 1) the development of a segmented-box-and-whisker icon for representing change to individual directories, and 2) the first data visualization tool developed specifically for the domain of digital forensic data. We show that by using Change-Link to view change to a directory-tree structure, digital forensic examiners can enhance their ability to perform forensic examinations.

Tim Leschke is a Ph.D. student in the Computer Science program at UMBC.

Host: Professor Alan Sherman

A group of nearly 40 participants assembled yesterday afternoon at the UMBC 2012 Global Game Jam site. The Global Game Jam is an annual event where small teams design and create computer games over the course of one weekend. The teams will upload their final games to a central site by 3:00pm EST Sunday. Here’s a video stream live from the GAIM lab in 005 ECS.

If you are on campus tomorrow around 3:00pm, stop by the GAIM lab and see the final UMBC games demonstrated.

UMBC is a host for the 2012 Global Game Jam which takes place this coming weekend, January 27-29. This is a 48 hour event, where teams from around the world work to develop a complete game over one weekend. The first year had 54 sites in 23 countries. The second year had 124 sites in 34 countries. Last year was up to 169 sites. The UMBC site is open to participants at all skill levels and affiliations. Thanks to generous sponsorship by Next Century, there's no registration fee and food will be provided all weekend. However, you DO need to sign up in advance, just log into globalgamejam.org and select UMBC as your site.

The jam will start at 3:00pm on Friday, January 27th in the UMBC GAIM lab, room 005 in the ECS building with presentations by Microsoft about developing for the Windows Phone.  There will be some spiffy giveaways at the end of the weekend for teams that choose make a Windows Phone game.  The main event starts at 5:00pm with video keynote talks by Will Wright, Baiyon, Gonzalo Frasca, Brenda Garno Brathwaite and John Romero.  After these presentations, the theme for this year’s games will be announced, and participants will brainstorm game ideas and form into teams. For the rest of the weekend, each team will work to build a brand new computer game around the theme. At 3:00pm on Sunday, the final games must be uploaded and from 3-5, the group will review what was accomplished over the weekend.

For more information on the jam and how to participate, see the UMBC GAIM site.

Photo Courtesy Microsoft.com

Check out the CNET.com article where our very own Dr. Rick Forno, UMBC's Graduate Program Director of Cybersecurity, discusses how Microsoft security has progressed over the years.

CSEE Colloquium

An Integrated Machine Learning Framework for Analyzing Protein-Ligand Interaction Data

Dr. Huzefa Rangwala
Assistant Professor, Computer Science & Engineering
George Mason University

1:00 p.m., Friday, February 10, 2012, ITE 325B, UMBC

Proteins have a vast influence on the molecular machinery of life. Stunningly complex networks of proteins perform innumerable functions in every living cell.  Small organic molecules (a.k.a. ligands) can bind to different proteins and modulate (inhibit/activate) their functions. Understanding these interactions provides insight into the underlying biological processes and is useful for designing therapeutic drugs.

In this talk I will describe our work related to the analysis of information associated with proteins and their interacting molecule partners (protein-ligand activity matrix). The underlying hypothesis of our approach is that by extracting information from protein-ligand activity matrix, we are drawing bridges between the structure of chemical compounds (chemical space) and the structure of the proteins and their functions (biological space).  I will present an approach used for mining relational data, especially when the data is sparse and high dimensional. I will also present methods that are based on the principles of multi-task learning and semi-supervised learning.

Huzefa Rangwala is an Assistant Professor at the department of Computer Science & Engineering, George Mason University. He holds affiliate positions with the Department of Bioengineering and the Department of Bioinformatics & Computational Biology. He received his Ph.D. in Computer Science from the University of Minnesota in the year 2008. His core research interests include bioinformatics, machine learning, and high performance computing. Specifically, he is working on developing new data mining algorithms and applying them to the fields of genomics, structural bioinformatics, drug discovery and social media analysis.

Host: Dr. Marie desJardins

Dr. Finin has been a faculty member of UMBC’s Computer Science and Electrical Engineering Department for over twenty years. A member of UMBC’s Ebiquity research group, Dr. Finin’s research is in Artificial Intelligence.

Congratulations to Dr. Tim Finin, who was just named this year’s Presidential Research Professor. The appointment, which lasts from the beginning of July 2012 through June 2015, is awarded to faculty members whose outstanding scholarship and excellent teaching have stood out at UMBC.

“I’m very honored to be selected,” says Dr. Finin of the award. He credits his research success to the collaborative research environment at UMBC and the talented students and professors that he has worked with over the years. “I feel like I’ve been lucky to be here at UMBC because having a good set of colleagues and students to work with is the reason for [this] success.”

Through his research in Artificial Intelligence, Dr. Finin is constantly searching for answers to the question: “How can we make [software] systems more intelligent?” He has applied his research to the increasingly popular areas of Mobile Computing, Social Computing and Security. Recently, Dr. Finin has been working on a project that looks at the potential of smartphones to understand a user’s context. The project– a collaborative effort with fellow CSEE professor, Dr. Joshi–is being sponsored by the National Science Foundation (NSF). More information about Dr. Finin’s research can be found in his research profile.

Finin’s appointment as Presidential Research Professor, comes with a $2,500 allowance, and a $2,500 per semester gift to the Computer Science and Electrical Engineering Department, to be used towards enhancing teaching and research. A formal award ceremony will take place this Spring to celebrate Dr. Finin and the other recipients of 2012 Presidential Faculty and Staff Awards.

Attention rising Junior and Senior Undergraduate and Graduate students interested in Information Assurance: Thursday, January 12 is the deadline to apply for a scholarship through the Information Assurance Scholarship Program (IASP).

The scholarship is great for students who are interested in pursuing careers in Information Assurance for the Federal Government.  Each recipient will receive full tuition, room and board, books,and stipend.  In return, the recipient must  work for DoD (for pay) for one year for year of scholarship.  Each recipient will also engage in a summer internship at DoD  (for pay).

Interested applicants should contact Dr. Alan Sherman (Sorry, you need javascript to view this email address. ) to be guided through the application process. For more information about the program, and for an application form, visit UMBC's Center for Information Security and Assurance website.

In an exciting close finish, UMBC placed 2nd with 5 points at the 2011 Pan-American Intercollegiate Team Chess Championship, held Dec 27-30 in Dallas-Fort Worth, TX. Also advancing to the President's Cup (Final Four of College Chess) are Univ. of Texas at Dallas [UTD] (1st place with 6 points), Texas Tech (3rd place with 4.5 points), and New York Univ. (4th place with 4.5 points). Top-rated Univ. of Texas Brownsville [UTB] finished 5th with 4 points, failing to make the cut for the Final Four.  UMBC's only loss was to UTD, in Round 5.  In Round 6, UTD defeated UTB, clinching clear first place in this six-round team Swiss championship open to any university team from North, South, or Central America.

UMBC's International Grandmaster Giorgi Margvelashvili won top player on Board 2, and UMBC's  Adithya Balasubramanian won the prize for top alternate. Also playing for UMBC were GM Leonid Kritz (captain), IM Sasha Kaplan, WGM Sabina Foisor, and alternate Benjamin Krause. Supporting the UMBC team in Texas was Associate Director GM Sam Palatnik.

Twenty-eight teams entered this annual championship, known as the "World Series of College Chess." Princeton placed 16, Yale 24.  Each team comprised four players and up to two alternates. UMBC has won or tied for first place a record nine times at the Pan-Am.

For complete results, see http://swchess.com/sce/tourney/PanAms11/Colres.htm
For some of the games, see www.monroi.com

An article in last week's Wall Street Journal, Interns Are Latest Target In Battle for Tech Talent, focused on the increased interest in hiring summer interns in the Bay area.

"Bay Area tech companies, already in a fierce fight for full-time hires, are now also battling to woo summer interns. Technology giants like Google Inc. have been expanding their summer-intern programs, while smaller tech companies are ramping up theirs in response—sometimes even luring candidates away from college."

The motivation for companies is simple. Their growth depends on a steady stream of new hires with good skills and work habits. Hiring prospects as summer interns is a "try before you buy" strategy, giving the company lots of information to decide whether to extend an offer for a full-time position after graduation.

Meanwhile, Facebook Inc. plans to hire 625 interns for next summer, up from 550 this year. Google hired 1,000 engineering interns this past summer, up 20% from the previous year. Yolanda Mangolini, Google's director of talent and outreach programs, says the company is still figuring out its target for 2012, based on its overall staffing plan. Google generally extends offers to the majority of its intern class, Ms. Mangolini says. "It is one of the primary ways we find full-time hires."

While the WSJ story focused on Bay area companies, the situation is similar throughout the country and applies not only to companies, but also government agencies. It you are pursuing a computing-related program, now is the time to aggressively explore internship opportunities for the summer.

Graduate students and undergraduates who are currently juniors or seniors planning on going into graduate school will get the most interest, but there will be opportunities for current sophomores and even freshmen as well. If you want start working on lining up a great summer internship, your first stop should be the Career Services Center.