Eftychios: Feb. 1

I'll be going over the following paper by Machens: Demixing population activity in higher cortical areas. Time permitting, I'll get into the more technical details of their approach described in this paper.

fast kalman filtering draft

hi all, any comments on this draft we just finished would be very welcome.

Carl Smith : Dec 15

This Wednesday I'll pick up where we left off last week when we covered graphical models, exponential families, and the basic ideas behind variational inference. This week I will go over variational inference in greater depth, and then describe some approximations to the variational problem that render it tractable: sum-product and the Bethe entropy approximation; mean field methods (time permitting); and convex approximations, in particular tree-reweighted belief propagation. The material is drawn from chapters 3, 4, 5, and 7 of the same paper.

Yashar Ahmadian : Dec 8

Designing optimal stimuli to control neuronal spike timing

We develop fast methods for optimal control of spike times by stimulating neurons. We 

adopt an approach based on models which describe how a stimulating agent (such as an 

injected electrical current, or a laser light interacting with caged neurotransmitters or pho- 

tosensitive ion channels) affect the spiking activity of neurons. Based on these models, we 

solve the reverse problem of finding the best time-dependent modulation of the input, sub- 

ject to hardware limitations as well as physiologically inspired safety measures, that makes 

the neuron emit a spike train which with highest probability will be close to a target spike 

train. We adopt fast convex constrained optimization methods to solve this problem. Our 

methods can potentially be implemented in real time and are also generalizable to the case 

of many cells, suitable for neural prosthesis applications. Using biologically sensible param- 

eters and constraints, our method finds stimulation patterns that generate very precise spike 

trains in simulated experiments. We also tested the intracellular current injection method 

on pyramidal cells in mouse cortical slices, achieving sub-milisecond spike timing precision 

and high reliability with constrained currents.

cosyne abstracts

hey, our submitted cosyne abstracts are here - any feedback on any of these would be very welcome.

Carl Smith : Dec 1

"This week I plan to present topics from the first half (chapters 1-5) of Wainwright and Jordan's "Graphical Models, Exponential Families, and Variational Inference". I will emphasize the ideas of 1) conjugate duality between partition function and negative entropy, and 2) nonconvexity in mean field approaches to inference. I will present the following week on some combination of ideas from the second half of the same paper, related papers by Wainwright, and related stuff Liam and I have been working on, depending on time and what people are interested in after the first hour."

Getting started with Git

If you have a large shared software project and want an easy way to manage collaboration, branch off different versions of the project and generally keep things organized, you need a version control system. Git is the one I know (Mercurial and Subversion are also popular choices) and the one other people in the group are using, so it's the one I'll go over here.

Download git here: http://git-scm.com/download

Set up an ssh public key and register an account at github.com: http://help.github.com/mac-key-setup/ (apologies to non-Mac users)

Enter the following at the terminal (with obvious substitutions):

PATH=$PATH:/usr/local/git/bin/

export PATH

git config --global user.name "Your Name"

git config --global user.email your.email@something.com

To pull a repository called "repo" from user "person":

mkdir repo (or what have you)

cd repo

git init

git remote add origin git@github.com:person/repo.git

git pull origin master

In particular, every call of "git pull origin master" pulls the currest master version off github. Be sure you're working with the current version before trying to push local changes, or you might get conflicts. To commit changes, either call

git add files_that_changed

git commit

or

git commit -a

which commits all changed files. Committing brings up a text editor where you describe any changes made. Be aware, if you don't write anything the commit will be aborted. Then to push your changes from the local machine to github just type

git push

and that's it! Things get messier when working with branches, checkouts and merges, but for 90% of what I do the above suffices. The web abounds with tutorials and a quick reference sheet can be found here.