For the last two decades, Human Brain Mapping (HBM) research has
flourished, generating tens of thousands of research papers that describe the
anatomical and functional structure of the human brain. This is mainly
accredited to the infiltration of fMRI research to every branch related to
neuroscience, from cognition, to decision making, neuro-economics, as well as
sensory perception and motor actions and planning. There is a huge amount of
data out there that is hardly indexed, and the number of fMRI papers is
increasing every year.
I believe that current technological tools, mainly web scraping,
crawlers and natural language processing (NLP) tools, have reached a point that
one can create an automatic tool that "reads" all these papers and
aggregate them in a single database according to anatomical as well as
functional structure.
In order to understand how to implement this project, as well as
how to use its products, a short explanation on fRMI research is in order. A
typical research begins with an experimental design, where the most basic one
is composed of two conditions, for example presenting the subject with a
picture of either a house or a face. Then the experiment begins inside the fMRI
research and is repeated many times per subject, as well as on many subjects,
in order to get a statistically significant result. Such a result is usually
described as: "area A was more active under condition X than condition
Y". This result thus suggests that area A is somehow involved in
processing condition X. For example, it was shown that an area called the
Fusiform Gyrus is more active when seeing faces than when seeing houses and
this result (with many others) suggests that the Fusiform Gyrus area is
involved in processing visual aspects of faces.
An example Abstract of an fMRI research paper (quite old):
"Using functional magnetic resonance
imaging (fMRI), we found an area in the fusiform gyrus in 12 of the 15 subjects
tested that was significantly more active when the subjects viewed faces than
when they viewed assorted common objects. This face activation was used to
define a specific region of interest individually for each subject, within
which several new tests of face specificity were run. In each of five subjects
tested, the predefined candidate “face area” also responded significantly more
strongly to passive viewing of (1) intact than scrambled two-tone faces, (2)
full front-view face photos than front-view photos of houses, and (in a
different set of five subjects) (3) three-quarter-view face photos (with hair
concealed) than photos of human hands; it also responded more strongly during
(4) a consecutive matching task performed on three-quarter-view faces versus
hands. Our technique of running multiple tests applied to the same region
defined functionally within individual subjects provides a solution to two
common problems in functional imaging: (1) the requirement to correct for
multiple statistical comparisons and (2) the inevitable ambiguity in the
interpretation of any study in which only two or three conditions are compared.
Our data allow us to reject alternative accounts of the function of the
fusiform face area (area “FF”) that appeal to visual attention,
subordinate-level classification, or general processing of any animate or human
forms, demonstrating that this region is selectively
involved in the perception of faces." From: Nancy Kanwisher, Josh McDermott, and Marvin M. Chun, "The Fusiform Face Area: A Module in Human
Extrastriate Cortex Specialized for Face Perception". The Journal of Neuroscience,
1 June 1997, 17(11):4302-4311
The first sentence has all the relevant information for the
project: an area "fusiform gyrus" and condition "subjects viewed faces than when they viewed
assorted common objects".
Furthermore, most papers have fMRI images that
show the exact area of activation, as well as standard 3D coordinates within
the brain call Talaraich coordinates. The project should thus first create an
indexed database of papers according to their coordinates and/or
function/condition; then using NLP tools to extract the meaning of the
area from many such papers. The product is thus a tool for future researchers
that can query such a database for a specific area they discover in their own
research and get not only proper citations for their papers (which is
important), but also a suggestion for the meaning of the areas they discovered.
If it works, the tool can be even more powerful; usually each experiment
results in several areas that are active, because more recent
experiments are much more complex and examine higher cognitive functions (e.g.
neuroeconomics). Hence, the tool can actually suggest a reconstruction
of the experiment all by itself. How? Given the active areas, the tool knows
and connects, via NLP and extensions, what function each area performs and
can integrate all of these into a hypothesis of the experiment that gave such
activation. This is a huge step in human brain mapping research and
neuroscience in general: it is akin to reading the inner as well as outer
environment of a person, solely from an fMRI scan (a little different from
recent "thought reading" experiments, which focus on much finer
details).
How to implement this project?
1. Crawlers in the internet can search specific sites of neuroscience-related
journals (not that many) and automatically scan for specific keywords: fMRI,
subjects, research, etc.
2. Once a candidate paper is found, the relevant areas are searched for
(again, not that many); or searching for Talaraich coordinates inside the
paper.
3. Milestone: An indexed 3D map/database of human brain papers.
4. Scanning all papers in the database for a description of the
experiment/condition.
5. Using state-of-the-art NLP tools to extract and index database of conditions/experiments
such that there would be overlap between papers.
6. Milestone: An indexed 3D map/database of the human brain function.