Open Access Senior Thesis
Bachelor of Science
© 2017 Caitlin R Lienkaemper
How does the brain encode the spatial structure of the external world?
A partial answer comes through place cells, hippocampal neurons which
become associated to approximately convex regions of the world known
as their place fields. When an organism is in the place field of some place
cell, that cell will fire at an increased rate. A neural code describes the set
of firing patterns observed in a set of neurons in terms of which subsets
fire together and which do not. If the neurons the code describes are place
cells, then the neural code gives some information about the relationships
between the place fields–for instance, two place fields intersect if and only if
their associated place cells fire together. Since place fields are convex, we are
interested in determining which neural codes can be realized with convex
sets and in finding convex sets which generate a given neural code when
taken as place fields. To this end, we study algebraic invariants associated
to neural codes, such as neural ideals and toric ideals. We work with a
special class of convex codes, known as inductively pierced codes, and seek
to identify these codes through the Gröbner bases of their toric ideals.
Lienkaemper, Caitlin, "Toric Ideals, Polytopes, and Convex Neural Codes" (2017). HMC Senior Theses. 106.