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Modeling in Research

Simon D. Levy

Dept. of Computer Science

Program in Neuroscience

03 May 2011

I am never content until I have constructed

mechanical model of the subject I am

studying. If I succeed in making one, I

understand; otherwise I do not.

I often say that when you can measure what you are

speaking about, and express it in numbers, you know

something about it; but when you cannot measure it,

when you cannot express it in numbers, your knowledge

is of a meagre and unsatisfactory kind; it may be the

beginning of knowledge, but you have scarcely in your

thoughts advanced to the state of Science, whatever the

matter may be.

(1824 - 1907)

Radio has no future.

(1824 - 1907)

All models are wrong, but

some models are useful

– George Box

(1919 - )

What is Modeling?

to analyze complex, real-world

problems in order to make predictions

about what might happen with various

actions. (Shiflet & Shiflet 2006)

What is Modeling?

(from shodor.org)

CSCI 102

15%

40% 45%

(from shodor.org)

Modeling Tools

• Spreadsheets (Excel): Simple, easy to master,

transferrable skill

representation of model; limited to accumulating

quantities over time

transferrable, high-demand skill, hardest to learn

Modeling Tools

• Spreadsheets (Excel): Simple, easy to master,

transferrable skill

representation of model; limited to accumulating

quantities over time

transferrable, high-demand skill, hardest to learn

Enables modeling of very complex systems

(protein folding, weather) in reasonable time

Example #1: Modeling

Population Growth in Excel

and Vensim

Model

– Population P

– Initial population P0 = 100

– At each time step (minute, day, year), P

grows by 10%

Example #2: More Interesting

Vensim Models

• Two –compartment drug absorption

– Examine effect of different dosage regimens

– Examine effect of various inoculation schedules

– Examine effect of overfishing

Example #3: Modeling

Diffusion in Matlab

• Diffusion refers to any process in which a substance or

property spreads from one region to another: transfer of

heat, spread of dye in a liquid, motion of ants outward from a

nest, etc.

equations / systems dynamics – averages over large regions

of individuals.

cellular automata to model diffusion at the level of individual

ants, molecules, etc.

Initializing the System

• “Forest” is an n x n grid (lattice) of cells.

• Each cell is either empty (0) has a tree (1) or has

a burning tree (2).

• probTree = probability of

tree in cell

• probBurning = probability

n that the tree is burning

n

Updating Rules

• If a cell has a burning tree, the tree is gone at

t+1

• If a tree is adjacent to a burning tree, it catches

fire with a probability (1 – probImmune)

• A tree may also catch fire by being struck by

lightning: probLightning

HPC I: “Embarrassingly Parallel”

Problems on the GPU

• Graphics Processing Unit: The “brains” behind

awesome videogame graphics

HPC I: “Embarrassingly Parallel”

Problems on the GPU

• When each computation is independent of all

others (like pixels in a video game), we can

perform each one in a different thread, at the

same time

• Repeat the same operation on each pixel until it

exceeds some value, or repetitions max-out

• Color each pixel using fraction of max-out reached

HPC II: Parallel Algorithms on

Clusters

• N-Body Problem: Consider a large number N of

bodies interacting with each other through gravity

(e.g. galaxy of stars)

gravitational forces acting on it from all the others:

Gm1m2

F=

r2

where m1, m2 are the masses of two objects, r is the

distance between them, and G is Newton’s Gravitational

Constant.

€

The N-Body Problem

• Problem: for each of the N bodies, we must compute the

force between it and the other N -1 bodies: N*(N-1)/2 = (N2 –

N)/2 computations, which is proportional to N2 as N grows

large.

have relatively low mutual force.

and then treat each cluster as a single body acting on other

clusters. This approach lends itself nicely to the coarse-

grained parallelism we get on a computer cluster (like hbar).

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