Inferring Connectivity in Neural Spike Train Recordings

EE376A (Winter 2019)

By Ethan Shen (ezshen), Eli Pugh (epugh), Vamsi Varanasi (vamsijv), and Mac Klinkachorn (sirapopk)

Importance of Neural Connectivity

Simulated neural data is of vital importance to understanding the function of the brain as well as for the development of potential interventions. Synchronization of different neurons and connectivity are two key parameters that govern how a portion of the brain behaves. In particular, gross behavior results from synchronized neurons firing together over the period of time during which the behavior is observed. Thus, predicting connectivity and synchronization from neural firing patterns, or “spike trains” is key to understanding the underlying structure of the biological neural network. Here, we use information theoretic measures to quantify connectivity of a population of neurons given their spike trains. We aim to use our methods to quantify synchronization between different subsets of the neural population to better understand the dynamics of our system.

Check out our paper and code!


For the outreach activity, our group designed a decoding/encoding game for the students to play. For younger participants(around 6-8 years old), we let them translate the Ascii code on the board into short words or vice versa by providing them with a key and some guidance on how they should partition the code. For older participants (around 8-11 years old), we give out multiple cards containing sequences with different patterns. For example, there are sequences containing: 1111111, 111000111, 10101010101,10011010111 etc.  We then ask the students to observe the pattern in the series and try to come up with a way to concatenate it. The participants were quick to recognized that there are repeated elements and we explained to them the concept of entropy and information in each code.

Throughout the process, we faced several challenges. We realized that the students come from different backgrounds ranging from 5-11 years old. Therefore, we need to come up with the variations of the activities right on the spot to help students learn the best. Also, we improvise a lot during the event to make the activity exciting for the students and keep them engaged. We offered candy to those who completed the challenges in order to bring more kids to our station and give them some gratification upon finishing.

Our most popular game was a binary code on the board with a key that mapped binary strings of length three to eight different letters. The kids had to match each block of three 0’s and 1’s in the “code” until they spelled out “CODEBREAKER”. It took some kids longer than others, but it was really cool to see them figure out by themselves how to match the blocks of binary to each letter. The excitement of finishing and seeing “CODEBREAKER” was very apparent.

The outreach was an extremely fulfilling and intellectually challenging experience. We learned how to convey important material in simple ways, and it turns out that by preparing for the outreach event our team got a better understanding of the material in the class. We really enjoyed interacting with the students and seeing them have fun while developing some information theory intuition.

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