Caroline Casey - Week 1 - Complex Systems Group: Neural Networks - University of Pennsylvania

I started working in Dr. Bassett's Networking Lab in the Bioengineering Department of the University of Pennsylvania on Wednesday, June18! So far, I am loving the lab and the project I am working on. Dr. Bassett is so nice, encouraging and an overall great mentor to me in the lab. There are five other people in the lab and they all have their own individual projects within the Networking Lab. We all sit at individual desks in a big room where we work from about 10:00 a.m. to 5:00 p.m.; however, I start working at 9:00 a.m. Since this is a computer based lab, we all sit at our desks and don't talk to each other much, however, when we do talk, everyone is so nice. I have been so engaged and interested in my work that I don't mind that their isn't much interaction.

On my first day, Dr. Bassett gave me an in-depth introduction to the first part of my project. The lab is interested in how people learn motor skills, so they taught 20 subjects 6 arpeggio sequences to play on a keyboard (however, we only analyze 2 of the sequences). Curiously, they noticed that some subjects played the arpeggio sequences very proficiently at home, but played them much slower when placed in the MRI during the 3 different MRI scanning sessions. My task is to use Matlab in order to identify whether there is a correlation between the amount of interference observed and certain parts of the brain and to then create a network to illustrate the results. There are many steps I have to take in order to accomplish this task. First, I have to conduct a t-test with all the behavior data (data of the time it takes for the subjects to complete the sequences) and the t-values I get represents the Interference (I) value. Next, I have to average all the adjacency matrices of the brain data of the different trials that the subjects conducted on each of the sessions. Next, I have to determine whether or not there is a correlation between the parts of the brain and the amount of interference. Then, I have to determine the significant edges, which are the edge weights that have a p value less than 0.05. The nodes of this network are the parts of the brain and the edges represent the connections between the different regions. Finally, I visualize the data into a network.

On the first day, I read from the Introductions to Networks textbook and read some more articles as well. On the second day, I met with Dr. Bassett and she gave me all the data and told me to try to figure out how to complete the t-test with all the behavior data (there is a lot of behavior data, 40 184-230x8 matrices!) and then all of the other data manipulations. At first, I was nervous about figuring out how to complete the tasks on Matlab, but I discovered how to complete a t-test and completed that step successfully! I also started averaging all the matrices of the brain data on Thursday. On Friday, I finished averaging all the matrices and then compiled all the individual matrices into a 6216x20 matrix compiled by using individual vectors of the brain data for each of the 20 subjects. I then moved on to figuring out how to do correlations with the different data sets. I am still working on figuring out how to do the correlation, it is a bit confusing, but with a little help from Dr. Bassett, I will figure it out.

An example of some of my work.

This is an adjacency matrix of brain data. The matrix is symmetric, therefore, the bottom portion can be set to zero to save computation time and memory space.

I really like Dr. Bassett's hands-off approach to the project, however, if I have any questions or need help (after first spending a long time figuring out how to do a task by myself), she is very willing to help me. I feel like I learn the most about Matlab through investigating the program by myself. I am becoming very comfortable with Matlab and I actually really love working with the computer, programming specifically! I am very interested in my project, it has very interesting implications for understanding more about learning and the brain.

Everyone in my lab is so nice and relaxed, I was even invited to attend a Phillies game on Monday! Unfortunately, I couldn't go because the times didn't work out, but hopefully there will be another opportunity to get together with the other lab members. I really love the experience, I am discovering a genuine interest for computers and networking. I couldn't have asked for a better lab to be a part of for the summer!