Behavioral Syntax v 1.1

I’ve been contributing to a Python-based behavioral Turing Test that’s part of OpenWorm for a while now and Behavioral Syntax v 1.1 is almost ready so it’s time I announced its existence. The methods are based on the ‘Behavioral Syntax’ paper of Andre Brown et al. which attempts to describe the locomotion of C. Elegans in terms of a vocabulary of ‘worm shapes’ that are determined using K-means clustering.

the green segment designates the head

90 distinct postures are sufficient to account for 82% of postural variance so we
can map worm shapes from videos to these 90 postures with minimal loss of
information. And lo and behold! We now have a problem that amounts to comparing sequences and suddenly we can use methods from natural language processing and bioinformatics.

Now, I must add that this project was never intended to merely be a Python
version of Dr Brown’s Matlab code. From the beginning I planned to design
a fast behavioral Turing Test that would serve as a first pass filter. It would
automatically generate lab reports that would make it simple to assess whether
or not a simulated worm resembled a normal C. Elegans in its behavior.

The primary method I plan to use is bayesian classification using sub-models
such as minimal description length, grammatical inference, hierarchical
Markov models, and simpler things such as computing posture heat-map
similarity. A posture heat-map might be useful in a uniform setting such as
agar petri dishes off-food. Assuming that a standard search algorithm such
as Lévy flight search is in use, I would expect a certain pattern in the
occurrence of postures. You might think that Lévy flights would be off-limits
to my project since they represent continuous-time behavior but my plan is
actually to compare ‘continuous’ and ‘discrete’ models. It would be interesting
to see what kind of ‘false’ worms can actually fool a discrete Turing test.

Speaking of which, I’m actually planning to begin work on a ‘false worm’
repository. Initially these would be simple test cases to see whether the
Behavioral Turing test can actually be fooled by a random
piece-wise harmonic path on a flat surface. I can’t think of a better way to
see whether these tests actually have any value.

Stay tuned. In less than a week it should be possible for anybody to install the repository using pip.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s