2.1 Neural Encoding

Created: March 17, 2021 9:35 PM Status: Open Updated: April 26, 2021 4:48 PM

What is neural code?

Information from the environment is transformed from one form to another into sensory signals which are represented in our brain
This means we should be able to interpret these representations by analyzing neural signals, this requires discovering the form in which this information is represented in our heads

functional magnetic resonance imaging is used as a diagnostic tool in hospitals
This technique allows us to record from a persons brain while they're performing some task, as long as that task does not require moving around
The person is placed inside a scanner with their head in the center of a large magnet
The scanner measures spatial perturbations in the magnetic field, which are caused by changes in blood oxygenation
As different parts of the brain become active, blood flows to those areas that support the underlying neural activity
This provides a measure of activity over regions of the scale of about a cubic millimeter

This method has a faster response time because it captures the changes in the electrical fields of the underlying neural circuits directly
Some implementations are caps covered by electrodes which making contact with the scalp
The downside of EEG is it tends to be a very noisy signal, since there are many contributions to the recorded signal
Still, methods like fMRI and EEG are very exciting because, although they cannot record the activity of individual neurons, they're non-invasive and so they can be used on healthy, awake human subjects

Used to access the activity of single neurons when direct access to neural tissue is possible
Consists of electronics and amplifiers for amplifying the tiny voltage signals extracted from individual neurons
Each electrode is about 10 microns across, roughly the size of a single neuron
One can record from many neurons simultaneously with the slices of brain tissue

Cells contain a calcium indicator that changes its fluorescent properties when bound to calcium
Since calcium enters the cell during action potentials, this signal acts as a record of cell firing
Using fiber optics, deeper regions of the brain can be recorded

Although continuously varying membrane potentials can encode information, even in spiking cells, action potentials, or spikes, are canonically considered to be the “currency” of the central nervous system
As such, the raster plot portrays only the times of these action potentials
The raster plot is not a suitable visualization device for non-spiking cells (such as rods and cones)
A vertical bar in the raster plot indicates a strong response, meaning that one cell fires very reliably at a particular time during the stimulus presentation, and suggesting that the cell is responding to the particular feature of the stimulus that occurs at that time
Weaker responses are represented by thin red bars (where the cell fires during some iterations but not others)
As such, a weak response indicates that there is something about the feature (orientation of a bar of light in the video for example) that the cell likes, but is not the feature it responds to best (the orientation is off by a few degrees from what the cell prefers, for example)

Encoding: how does a stimulus cause a pattern of responses
- Quasi mechanistic models
- \(P(Response | Stimulus)\)
Decoding: what do responses tell us about the stimulus
- How do we reconstruct what the brain is doing, so that a person could control a prosthetic arm in the same way that they control their own arm
- \(P(Stimulus | Response)\)
The notation P(X|Y) denotes the probability of a random variable X given that random variable Y has been fixed (everything to the right of the | is assumed given)
This is called a conditional probability distribution
If X is independent of Y, then P(X|Y) = P(X)

The meaning of s depends on the nature of the stimulus
While for simple stimuli such as moving bars of light, a relevant stimulus parameter can be easy to define, complex stimuli, such as faces can be very difficult to “parameterize” in a meaningful way