How to create neural circuit diagrams (updated)


My diagrams are always a mess, but maybe I could start following this advice a little more carefully?

Diagrams of even simple circuits are often unnecessarily complex, making understanding brain connectivity maps difficult…Encoding several variables without sacrificing information, while still maintaining clarity, is a challenge. To do this, exclude extraneous variables—vary a graphical element only if it encodes something relevant, and do not encode any variables twice…

For neural circuits such as the brainstem auditory circuits, physical arrangement is a fundamental part of function. Another topology that is commonly necessary in neural circuit diagrams is the laminar organization of the cerebral cortex. When some parts of a circuit diagram are anatomically correct, readers may assume all aspects of the figure are similarly correct. For example, if cells are in their appropriate layers, one may assume that the path that one axon travels to reach another cell is also accurate. Be careful not to portray misleading information—draw edges clearly within or between layers, and always clearly communicate any uncertainty in the circuit.

Update: Andrew Giessel pointed me to this collection of blog posts from Nature Methods on how to visualize biological data more generally. Recommended!

#Cosyne2016, by the numbers


Cosyne is the systems and computational neuroscience conference held every year in Salt Lake City and Snow Bird. It is a pretty good representation of the direction the community is heading…though given the falling acceptance rate you have to wonder how true that will stay especially for those on the ‘fringe’. But 2016 is in the air so it is time to update the Cosyne statistics.

I’m always curious about who is most active in any given year and this year it is Xiao-Jing Wang who I dub this year’s Hierarch of Cosyne. I always think of his work on decision-making and the speed-accuracy tradeoff. He has used some very nice modeling of small circuits to show how these tasks could be implemented in nervous systems. Glancing over his posters, though, and his work this year looks a bit more varied.

Still, it is nice to see such a large clump of people at the top: the distribution of posters is much flatter this year than previously which suggests a bit of

Here are the previous ‘leaders’:

  • 2004: L. Abbott/M. Meister
  • 2005: A. Zador
  • 2006: P. Dayan
  • 2007: L. Paninski
  • 2008: L. Paninski
  • 2009: J. Victor
  • 2010: A. Zador
  • 2011: L. Paninski
  • 2012: E. Simoncelli
  • 2013: J. Pillow/L. Abbott/L. Paninski
  • 2014: W. Gerstner
  • 2015: C. Brody
  • 2016: X. Wang


If you look at the total number across all years, well, Liam Paninski is still massacring everyone else. At this rate, even if Pope Paninski doesn’t submit any abstracts over the next few years and anyone submits six per year… well it will be a good half a decade before he could possibly be dethroned.

The network diagram of co-authors is interesting, as usual. Here is the network diagram for 2016 (click for PDF):


And the mess that is all-time Cosyne:



I was curious about this network. How connected is it? What is its dimensionality? If you look at the eigenvalues of the adjacency matrix, you get:


I put the first two eigenvectors at the bottom of this post, but suffice it to say the first eigenvector is basically Pouget vs. Latham! And the second is Pillow vs Paninski! So of course, I had to plot a few people in Pouget-Pillowspace:


(What does this tell us? God knows, but I find it kind of funny. Pillowspace.)

Finally, I took a bunch of abstracts and fed them through a Markov model to generate some prototypical Cosyne sentences. Here are abstracts that you can submit for next year:

  • Based on gap in the solution with tighter synchrony manifested both a dark noise [and] much more abstract grammatical rules.
  • Tuning curves should not be crucial for an approximate Bayesian inference which would shift in sensory information about alternatives
  • However that information about 1 dimensional latent state would voluntarily switch to odor input pathways.
  • We used in the inter vibrissa evoked responses to obtain time frequency use of power law in sensory perception such manageable pieces have been argued to simultaneously [shift] acoustic patterns to food reward to significantly shifted responses
  • We obtained a computational capacity that is purely visual that the visual information may allow ganglion cells [to] use inhibitory coupling as NMDA receptors, pg iii, Dynamical State University
  • Here we find that the drifting gratings represent the performance of the movement.
  • For example, competing perceptions thereby preserve the interactions between network modalities.
  • This modeling framework of goal changes uses [the] gamma distribution.
  • Computation and spontaneous activity at the other stimulus saliency is innocuous and their target location in cortex encodes the initiation.
  • It is known as the presentation of the forepaw target reaction times is described with low dimensional systems theory Laura Busse Andrea Benucci Matteo Carandini Smith-Kettlewell Eye Research.

Note: sorry about the small font size. This is normally a pet peeve of mine. I need to get access to Illustrator to fix it and will do so later…

The first two eigenvectors:

ev1 ev2

Punctuation in novels

Faulkner versus McCarthy

I found some beautiful posters that showed the punctation in different novels the other day. I was immediately curious if I could do something similar and wrote a little script (code here) to extract the punctation and print out a compressed representation of my favorite novels.

Then, like any proper scientist, I looked at the data and did some simple stats. Go see on Medium!

Here are a few of the (almost) full sets of punctuation from a couple of novels. For Pride And Prejudice, note the zoom-in versus the zoom-out:




Here are the files for Pride and Prejudice (alternate), A Doll’s House, and Romeo and Juliet.

Please let me know in the comments how totally I was wrong in my Medium analysis, and if there is anything you would like to see.

Update: Here a couple I thought were interesting. First, part of the Tractatus Logico Philosophicus:


And then Ulysses, the difference between the beginning of the book (first) and the end of the book (second):



Posted in Art

The ballerina illusion

No matter how hard I try, I cannot get the spinning dancer illusion to flip. Looks like someone has found a much more powerful version of the illusion:


What I especially like about this version of the illusion is I can totally get why it is happening. There aren’t great depth cues so there is a powerful prior that if you can see a face then that face is looking in your direction – hence direction flipping.

(via kottke)

Posted in Art