GSoC 2021 Project Idea 21.1: HDNet projects - Developing a Python-based codebase for analyzing stimulus prediction capabilities of neurons: improve the neural Maximum Entropy model

There are good theoretical reasons to believe that neurons learn to predict their input, but fewer experimental tests of this hypothesis. The mentor and co-mentor on this project have developed new methods for assessing the predictive capabilities of a large number of neurons from data using both information theoretic and a Bayesian framework. These methods have not yet been optimized and integrated into an existing, ever-growing codebase that will, upon release, allow other groups to easily assess the predictive capabilities of their neural populations.

One of the metrics for assessing stimulus prediction is based on the fitting of a Maximum Entropy model that probabilistically describes stimulus activity and the corresponding neural response. The student on this project is expected to be familiar with Python and Matlab, and either familiar with or eager to learn new techniques for Maximum Entropy model fitting. He or she will improve the neural Maximum Entropy model fit to data in two steps:

  • functions for Maximum Entropy model validation using pre-written Monte Carlo methods will be integrated into in the codebase
  • hyperparameters of Minimum Probability Flow, a powerful and relatively new algorithm for Maximum Entropy model fitting, will be optimized so that the model validation is improved

The result of this project will be a state-of-the-art, computationally efficient approach to parameter fitting of Maximum Entropy models that will on its own be useful to neuroscientists. The result of this project may be therefore integrated into HDNet (https://github.com/team-hdnet/hdnet) in addition to being released as part of the stimulus prediction package.

Mentor: Sarah Marzen
Co-mentor: Joost le Feber

Hi ! my name is Jiayi. I’m an undergrad student major in computer science and statistics. I have experience processing data in various projects using python. I’m very interested in this project and would love to contribute.

Hello I’m Vamsi from IIT Palakkad, currently in my 3rd year of study pursuing Computer Science And Engineering. I have experience in machine learning and reinforcement learning and I am interested in exploring this project. Can the mentors give me some starting steps to work with ?

@Jiayi , @Vamsi995 any specific/pointed queries/questions?

I’m sure the mentors would be happy to help.
Cheers!

Hi,

I’m Ranjana Nataraj, a third-year student BS-MS from IISER Pune, currently majoring in Biology with a minor in data science. I have been working in the computational neuroscience group of IISER Pune from my second year and have worked on projects where I learned the biophysics of neuronal network dynamics. I am proficient in Python and Matlab and am willing to develop new skills to aid me in the project. I found the project’s objective to be interesting and aligns with my current interest in the field. I would be grateful if I could be a part of this project, learn and contribute in any manner to GSOC.

Looking forward to hearing from you.

Ranjana Nataraj

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