UQ MATH2504
Programming of Simulation, Analysis, and Learning Systems
(Semester 2 2024)
Unit 4: On data files, and basic numerics
In this unit we deal with data, numerics, and basic numerical algorithms. In terms of numerics, there other other courses at UQ that focus primarily on numerical mathematics. These include MATH3204 and COSC2500. Here we are only getting a taste of numerical mathematics from the viewpoint of programming. Also, in terms of data, later in this course (Units 6 and 7) we deal with data in a much broader context.
Data analysis
We first deal with files and file formats include binary, CSV, and JSON. We then discuss basic plotting and animation creation.
Files and file formats
A file is a collection of bytes, stored by your operating system on disk. It can also be transferred via the web.
Here we create a file with 5 ASCII characters 12345:
$ echo -n "12345" > my_file.txt
$ ls -l my_file.txt
-rw-r--r--@ 1 uqjnazar staff 5 1 Aug 09:34 my_file.txtHere we download Shakespeare's works from the web:
$ curl -o shakespeare.txt https://ocw.mit.edu/ans7870/6/6.006/s08/lecturenotes/files/t8.shakespeare.txt
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 5330k 100 5330k 0 0 6043k 0 --:--:-- --:--:-- --:--:-- 6036k
$ ls -l shakespeare.txt
-rw-r--r--@ 1 uqjnazar staff 5458199 1 Aug 09:45 shakespeare.txt
$ head -4 shakespeare.txt
This is the 100th Etext file presented by Project Gutenberg, and
is presented in cooperation with World Library, Inc., from their
Library of the Future and Shakespeare CDROMS. Project Gutenberg
often releases Etexts that are NOT placed in the Public Domain!!If a file is encoded as a text file, you can open it in an editor like VS Code and make sense of it. Otherwise it is binary and you cannot. Here we create a binary file of 20 bytes:
file = open("my_binary_file.dat","w") #Julia function to open a file. "w" means opening it for writing. write(file,Int8.(1:20)) #now f is the handle for the file close(file)
With VSCode, we can use the hexdump plugin to view the file (after you install the plugin - go to my_binary_file.dat in the VS code file explorer and choose Show Hexdump.
Offset: 00 01 02 03 04 05 06 07 08 09 0A 0B 0C 0D 0E 0F
00000000: 01 02 03 04 05 06 07 08 09 0A 0B 0C 0D 0E 0F 10 ................
00000010: 11 12 13 14 ....Another alternative is to use the hexdump Unix command:
$ hexdump my_binary_file.dat
0000000 01 02 03 04 05 06 07 08 09 0a 0b 0c 0d 0e 0f 10
0000010 11 12 13 14
0000014We won't deal much with binary files, but rather with files that can be interpreted as text. Within text files, one of the most common formats is CSV (Comma Separated Values). Another common format is JSON (Javascript Object Notation). We'll deal with both and in each case we'll use a Julia package that helps us work with such files. These are CSV.jl and JSON.j. We'll also use DataFrames.jl, much more of this package will be discussed in Units 6 and 7.
CSV Files
using DataFrames, CSV df = DataFrame( names = ["Jason", "Ella", "Kayley", "Emily"], ages = [23, 25, 13, 15], gender = [:male, missing, :female, :female]) println(df)
4×3 DataFrame
Row │ names ages gender
│ String Int64 Symbol?
─────┼────────────────────────
1 │ Jason 23 male
2 │ Ella 25 missing
3 │ Kayley 13 female
4 │ Emily 15 female
CSV.write("people.csv", df)
"people.csv"
In the REPL, if we enter the shell:
;
shell> ls -l people.csv
-rw-r--r-- 1 uqjnazar staff 74 1 Aug 10:35 people.csv
shell> cat people.csv
names,ages,gender
Jason,23,male
Ella,25,
Kayley,13,female
Emily,15,female
names,ages,gender
Jason,23,male
Ella,25,
Kayley,13,female
Emily,15,femaleThis form of the CSV file has a header row. There is also a form without
CSV.write("people_no_header.csv", df, header = false) sleep(3) # A crude way to let the OS settle with creating the file (otherwise Julia will beat it) readlines("people_no_header.csv") #A crude way to read lines of a file into a vector of strings
4-element Vector{String}:
"Jason,23,male"
"Ella,25,"
"Kayley,13,female"
"Emily,15,female"
Now that the have the files people.csv and people_no_header.csv we can read them and process them.
using DataFrames, CSV df_with_names = CSV.File("people.csv") |> DataFrame #In Julia f(x) |> g is like g(f(x)) println(df)
4×3 DataFrame
Row │ names ages gender
│ String Int64 Symbol?
─────┼────────────────────────
1 │ Jason 23 male
2 │ Ella 25 missing
3 │ Kayley 13 female
4 │ Emily 15 female
df_no_names = CSV.File("people_no_header.csv",header = false ) |> DataFrame println(df_no_names)
4×3 DataFrame
Row │ Column1 Column2 Column3
│ String7 Int64 String7?
─────┼────────────────────────────
1 │ Jason 23 male
2 │ Ella 25 missing
3 │ Kayley 13 female
4 │ Emily 15 female
n, p = size(df_with_names) @show n, p average_age = sum(df_with_names.ages)/n #notice we can access the field ages via ".ages" @show average_age;
(n, p) = (4, 3) average_age = 19.0
n, p = size(df_no_names) @show n, p average_age = sum(df_no_names[:,2])/n #Here we just access ages as the second column @show average_age;
(n, p) = (4, 3) average_age = 19.0
JSON Files
JSON files are much more structured than CSV files and are used for a variety of settings. As a real world application consider the Github Public API, this provides programmatic web access to github services so that source code and artefacts can be managed via software.
We download the JSON file from the web for the repos of a particular github user and the use JSON.parse from the JSON.jl package to convert the JSON file into a hierarchical dictionary.
using HTTP, JSON web_request = HTTP.request("GET","https://api.github.com/users/paulbellette/repos") web_data = JSON.parse(String(web_request.body))
6-element Vector{Any}:
Dict{String, Any}("pulls_url" => "https://api.github.com/repos/PaulBellett
e/displaz/pulls{/number}", "mirror_url" => nothing, "keys_url" => "https://
api.github.com/repos/PaulBellette/displaz/keys{/key_id}", "html_url" => "ht
tps://github.com/PaulBellette/displaz", "comments_url" => "https://api.gith
ub.com/repos/PaulBellette/displaz/comments{/number}", "tags_url" => "https:
//api.github.com/repos/PaulBellette/displaz/tags", "svn_url" => "https://gi
thub.com/PaulBellette/displaz", "statuses_url" => "https://api.github.com/r
epos/PaulBellette/displaz/statuses/{sha}", "archive_url" => "https://api.gi
thub.com/repos/PaulBellette/displaz/{archive_format}{/ref}", "fork" => true
…)
Dict{String, Any}("pulls_url" => "https://api.github.com/repos/PaulBellett
e/Munkres.jl/pulls{/number}", "mirror_url" => nothing, "keys_url" => "https
://api.github.com/repos/PaulBellette/Munkres.jl/keys{/key_id}", "html_url"
=> "https://github.com/PaulBellette/Munkres.jl", "comments_url" => "https:/
/api.github.com/repos/PaulBellette/Munkres.jl/comments{/number}", "tags_url
" => "https://api.github.com/repos/PaulBellette/Munkres.jl/tags", "svn_url"
=> "https://github.com/PaulBellette/Munkres.jl", "statuses_url" => "https:
//api.github.com/repos/PaulBellette/Munkres.jl/statuses/{sha}", "archive_ur
l" => "https://api.github.com/repos/PaulBellette/Munkres.jl/{archive_format
}{/ref}", "fork" => true…)
Dict{String, Any}("pulls_url" => "https://api.github.com/repos/PaulBellett
e/PaulBellette.github.io/pulls{/number}", "mirror_url" => nothing, "keys_ur
l" => "https://api.github.com/repos/PaulBellette/PaulBellette.github.io/key
s{/key_id}", "html_url" => "https://github.com/PaulBellette/PaulBellette.gi
thub.io", "comments_url" => "https://api.github.com/repos/PaulBellette/Paul
Bellette.github.io/comments{/number}", "tags_url" => "https://api.github.co
m/repos/PaulBellette/PaulBellette.github.io/tags", "svn_url" => "https://gi
thub.com/PaulBellette/PaulBellette.github.io", "statuses_url" => "https://a
pi.github.com/repos/PaulBellette/PaulBellette.github.io/statuses/{sha}", "a
rchive_url" => "https://api.github.com/repos/PaulBellette/PaulBellette.gith
ub.io/{archive_format}{/ref}", "fork" => false…)
Dict{String, Any}("pulls_url" => "https://api.github.com/repos/PaulBellett
e/Pauls_Silly_Test_Repo/pulls{/number}", "mirror_url" => nothing, "keys_url
" => "https://api.github.com/repos/PaulBellette/Pauls_Silly_Test_Repo/keys{
/key_id}", "html_url" => "https://github.com/PaulBellette/Pauls_Silly_Test_
Repo", "comments_url" => "https://api.github.com/repos/PaulBellette/Pauls_S
illy_Test_Repo/comments{/number}", "tags_url" => "https://api.github.com/re
pos/PaulBellette/Pauls_Silly_Test_Repo/tags", "svn_url" => "https://github.
com/PaulBellette/Pauls_Silly_Test_Repo", "statuses_url" => "https://api.git
hub.com/repos/PaulBellette/Pauls_Silly_Test_Repo/statuses/{sha}", "archive_
url" => "https://api.github.com/repos/PaulBellette/Pauls_Silly_Test_Repo/{a
rchive_format}{/ref}", "fork" => false…)
Dict{String, Any}("pulls_url" => "https://api.github.com/repos/PaulBellett
e/SpatialGrids.jl/pulls{/number}", "mirror_url" => nothing, "keys_url" => "
https://api.github.com/repos/PaulBellette/SpatialGrids.jl/keys{/key_id}", "
html_url" => "https://github.com/PaulBellette/SpatialGrids.jl", "comments_u
rl" => "https://api.github.com/repos/PaulBellette/SpatialGrids.jl/comments{
/number}", "tags_url" => "https://api.github.com/repos/PaulBellette/Spatial
Grids.jl/tags", "svn_url" => "https://github.com/PaulBellette/SpatialGrids.
jl", "statuses_url" => "https://api.github.com/repos/PaulBellette/SpatialGr
ids.jl/statuses/{sha}", "archive_url" => "https://api.github.com/repos/Paul
Bellette/SpatialGrids.jl/{archive_format}{/ref}", "fork" => true…)
Dict{String, Any}("pulls_url" => "https://api.github.com/repos/PaulBellett
e/test_repo/pulls{/number}", "mirror_url" => nothing, "keys_url" => "https:
//api.github.com/repos/PaulBellette/test_repo/keys{/key_id}", "html_url" =>
"https://github.com/PaulBellette/test_repo", "comments_url" => "https://ap
i.github.com/repos/PaulBellette/test_repo/comments{/number}", "tags_url" =>
"https://api.github.com/repos/PaulBellette/test_repo/tags", "svn_url" => "
https://github.com/PaulBellette/test_repo", "statuses_url" => "https://api.
github.com/repos/PaulBellette/test_repo/statuses/{sha}", "archive_url" => "
https://api.github.com/repos/PaulBellette/test_repo/{archive_format}{/ref}"
, "fork" => false…)
length(web_data)
6
[(r["name"], r["language"]) for r in web_data]
6-element Vector{Tuple{String, Any}}:
("displaz", "C++")
("Munkres.jl", "Julia")
("PaulBellette.github.io", "HTML")
("Pauls_Silly_Test_Repo", "Julia")
("SpatialGrids.jl", "Julia")
("test_repo", nothing)
Basic scientific work environment
You can use Julia for plotting and statistics. We won't cover all the features of Plots.jl, but instead will show a few examples taken from SWJ which showcase plotting and animation. You may also use the image gallery, where in each case clicking on the example image gives you a link to self contained source code that plots the image. Note that in that source you can ignore (comment out) pyplot() which is a function which sets the backend of the plotting as Python's plotting package.
Simple direct plotting of functions:
using Plots plot([cos sin], label = ["cos" "sin"])
Multiple plots:
using Plots, LaTeXStrings, Measures f(x,y) = x^2 + y^2 f0(x) = f(x,0) f2(x) = f(x,2) xVals, yVals = -5:0.1:5 , -5:0.1:5 plot(xVals, [f0.(xVals), f2.(xVals)], c=[:blue :red], xlims=(-5,5), legend=:top, ylims=(-5,25), ylabel=L"f(x,\cdot)", label=[L"f(x,0)" L"f(x,2)"]) p1 = annotate!(0, -0.2, text("(0,0) The minimum\n of f(x,0)", :left, :top, 10)) z = [ f(x,y) for y in yVals, x in xVals ] p2 = surface(xVals, yVals, z, c=cgrad([:blue, :red]),legend=:none, ylabel="y", zlabel=L"f(x,y)") M = z[1:10,1:10] p3 = heatmap(M, c=cgrad([:blue, :red]), yflip=true, ylabel="y", xticks=([1:10;], xVals), yticks=([1:10;], yVals)) plot(p1, p2, p3, layout=(1,3), size=(1200,400), xlabel="x", margin=5mm)
Plotting data:
using DataFrames, CSV, Statistics, Dates, Plots, Measures resp = HTTP.request("GET","https://raw.githubusercontent.com/h-Klok/StatsWithJuliaBook/master/data/temperatures.csv") data = CSV.read(IOBuffer(String(resp.body)), DataFrame) brisbane = data.Brisbane goldcoast = data.GoldCoast diff = brisbane - goldcoast dates = [Date( Year(data.Year[i]), Month(data.Month[i]), Day(data.Day[i]) ) for i in 1:nrow(data)] fortnightRange = 250:263 brisFortnight = brisbane[fortnightRange] goldFortnight = goldcoast[fortnightRange] p1 = plot(dates, [brisbane goldcoast], label=["Brisbane" "Gold Coast"], c=[:blue :red], xlabel="Time", ylabel="Temperature") p2 = plot(dates[fortnightRange], [brisFortnight goldFortnight], label=["Brisbane" "Gold Coast"], c=[:blue :red], m=(:dot, 5, Plots.stroke(1)), xlabel="Time", ylabel="Temperature") p3 = plot(dates, diff, c=:black, ylabel="Temperature Difference",legend=false) p4 = histogram(diff, bins=-4:0.5:6, ylims=(0,140), legend = false, xlabel="Temperature Difference", ylabel="Frequency") plot(p1,p2,p3,p4, size = (800,500), margin = 5mm)
Creating animations:
using Plots function graphCreator(n::Int) vertices = 1:n complexPts = [exp(2*pi*im*k/n) for k in vertices] coords = [(real(p),imag(p)) for p in complexPts] xPts = first.(coords) yPts = last.(coords) edges = [] for v in vertices, u in (v+1):n push!(edges,(v,u)) end anim = Animation() scatter(xPts, yPts, c=:blue, msw=0, ratio=1, xlims=(-1.5,1.5), ylims=(-1.5,1.5), legend=:none) for i in 1:length(edges) u, v = edges[i][1], edges[i][2] xpoints = [xPts[u], xPts[v]] ypoints = [yPts[u], yPts[v]] plot!(xpoints, ypoints, line=(:red)) frame(anim) end gif(anim, "graph.gif", fps = 60) end graphCreator(16)
Basic statistical summaries
In terms of basic statistics associated with data you can use the in-built package Statistics as well as the external package StatsBase.jl:
using CSV, Statistics, StatsBase resp = HTTP.request("GET","https://raw.githubusercontent.com/h-Klok/StatsWithJuliaBook/master/data/temperatures.csv") data = CSV.read(IOBuffer(String(resp.body)), DataFrame)[:,4] # Take the fourth column println("Sample Mean: ", mean(data)) println("Harmonic <= Geometric <= Arithmetic ", (harmmean(data), geomean(data), mean(data))) println("Sample Variance: ",var(data)) println("Sample Standard Deviation: ",std(data)) println("Minimum: ", minimum(data)) println("Maximum: ", maximum(data)) println("Median: ", median(data)) println("95th percentile: ", percentile(data, 95)) println("0.95 quantile: ", quantile(data, 0.95)) println("Interquartile range: ", iqr(data),"\n") summarystats(data)
Sample Mean: 27.155405405405414 Harmonic <= Geometric <= Arithmetic (26.52181504074163, 26.84561900212437, 27.155405405405414) Sample Variance: 16.1253895583728 Sample Standard Deviation: 4.015643106449177 Minimum: 16.1 Maximum: 37.6 Median: 27.7 95th percentile: 33.0 0.95 quantile: 33.0 Interquartile range: 6.100000000000001 Summary Stats: Length: 777 Missing Count: 0 Mean: 27.155405 Std. Deviation: 4.015643 Minimum: 16.100000 1st Quartile: 24.000000 Median: 27.700000 3rd Quartile: 30.100000 Maximum: 37.600000
Numerics
We now focus on floating point numbers. This is the Double-precision floating-point format. Before we get into the details, here are some illustrations on how it is represented in memory:
function pretty_print_float(x::Float64) bits = bitstring(x) println("Sign: ", bits[1]) println("Exponent: ", bits[2:12]) println("Significand: ", bits[13:64]) end x = 15.324 @show typeof(x) @show sizeof(x) @show bitstring(x); pretty_print_float(x) ex = exponent(x) sig = significand(x) @show ex, sig @show 2^ex * sig;
typeof(x) = Float64 sizeof(x) = 8 bitstring(x) = "01000000001011101010010111100011010100111111011111001110110 11001" Sign: 0 Exponent: 10000000010 Significand: 1110101001011110001101010011111101111100111011011001 (ex, sig) = (3, 1.9155) 2 ^ ex * sig = 15.324
And this is the Single-precision floating-point format:
function pretty_print_float(x::Float32) #Notice this is a second method of pretty_print_float bits = bitstring(x) println("Sign: ", bits[1]) println("Exponent: ", bits[2:9]) println("Significand: ", bits[10:32]) end x = 15.324f0 @show typeof(x) @show sizeof(x) @show bitstring(x); pretty_print_float(x) ex = exponent(x) sig = significand(x) @show ex, sig @show 2^ex * sig;
typeof(x) = Float32 sizeof(x) = 4 bitstring(x) = "01000001011101010010111100011011" Sign: 0 Exponent: 10000010 Significand: 11101010010111100011011 (ex, sig) = (3, 1.9155f0) 2 ^ ex * sig = 15.324f0
We would ideally like to represent any number on the real line ${\mathbb R}$ via a finite number of bits with the computer. However, this is not possible and any numerical representation of a number $x \in {\mathbb R}$ is only approximated via a number $\tilde{x} \in {\mathbb F}$ where ${\mathbb F}$ is the set of floating point numbers. Each such floating point number is represented as,
\[ \tilde{x} = \pm (1+f) 2^e, \]
where $e$ is a (signed) integer called the exponent and $1+f$ is the mantissa (or significand). The value $f$ is represented as,
\[ f = \sum_{i=1}^d b_i 2^{-i}, \]
where $b_i \in \{0,1\}$ and $d$ is a fixed positive integer counting the number of bits used for the mantissa.
Hence the mantissa, $1+f$, lies in the range $[1,2)$ and is represented in binary form. By multiplying the equation above by $2^{-d}$ we have,
\[ f = 2^{-d} \Big(\sum_{i=1}^d b_i 2^{d-i} \Big) = 2^{-d} z. \]
Hence $z \in \{0,1,2,\ldots,2^d-1\}$. This means that between $2^e$ and ending just before $2^e-1$ there are exactly $2^d$ evenly spaced numbers in the set ${\mathbb F}$.
Exercise: Take $d=3$. What are the floating point numbers with $e=0$? How about with $e=1$? How about with $e=-1$?
Exercise: Take $d=2$. Determine ${\mathbb F} \cap [-5,5]$.
Observe now that the smallest element of ${\mathbb F}$ that is greater than $1$ is $1+2^{-d}$. This motivates defining machine epsilon as $\varepsilon_{\text{mach}} = 2^{-d}$.
The IEEE 754 double precision standard has $d=52$ bits and single precision (Float32) has $d=23$ bits. Hence with Float64 variables we have
\[ \varepsilon_{\text{mach}} = 2^{-52} \approx 2.2 \times 10^{-16}. \]
@show eps() #Default is for Float64 @show eps(Float32) @show eps(Float16)
eps() = 2.220446049250313e-16 eps(Float32) = 1.1920929f-7 eps(Float16) = Float16(0.000977) Float16(0.000977)
@show 2^(-52) @show 2^(-23) @show 2^(-10);
2 ^ -52 = 2.220446049250313e-16 2 ^ -23 = 1.1920928955078125e-7 2 ^ -10 = 0.0009765625
We can suppose there is some (mathematical) function $\text{fl}: {\mathbb F} \to {\mathbb R}$ where $\text{fl}(x)$ takes a real number $x$ and maps it to the nearest $\tilde{x}$ in ${\mathbb F}$. For positive $x$ it lies in the interval $[2^e,2^{e+1})$ where the spacing between the elements is $2^{e-d}$. Hence $|\tilde{x} - x| \le \frac{1}{2} 2^{e-d}$. We can now consider the relative error between $\tilde{x}$ and $x$:
\[ \frac{|\tilde{x} - x|}{|x|} \le \frac{2^{e-d-1}}{2^e} \le \frac{1}{2} \varepsilon_{\text{mach}}. \]
An equivalent statement states that for any $x \in {\mathbb R}$ (within the range of the exponent), there is a $\varepsilon$ where $|\varepsilon| \le \frac{1}{2} \varepsilon_{\text{mach}}$ and,
\[ \text{fl}(x) = x (1+ \varepsilon). \]
Here is an example that looks at the irrational square roots of $\{1,2,3,\ldots,100\}$ and estimates the $\varepsilon$ associated with $\text{fl}(x)$ for each of these square roots. The example does this for Float32 values and uses Float64 as an approximation of the absolute truth. The two black bars are at $\pm \frac{1}{2} \varepsilon_{\text{mach}}$.
non_squares = setdiff(1:100,[i^2 for i in 1:100]) x̃ = sqrt.(Float32.(non_squares)) #x + \tilde + [TAB] x = sqrt.(non_squares) #Lets treat 64 bit as infinite precision ϵ = x̃ ./ x .- 1 #\epsilon + [TAB] scatter(non_squares,ϵ,legend=false,xlabel = "Attempt", ylabel="Approximation of ϵ") plot!([(x)->0.5*eps(Float32) (x)->-0.5eps(Float32)], c=:black,ylim=(-0.7*eps(Float32), 0.7*eps(Float32)))
Going back to Float64 (double precision) we have 52 bits in the mantissa. $11$ bits for the exponent $e$ and a single sign bit. This makes $64$ bits. There are also some special values:
bitstring(0/0) #NaN
"0111111111111000000000000000000000000000000000000000000000000000"
bitstring(1/0) #Inf
"0111111111110000000000000000000000000000000000000000000000000000"
bitstring(-1/0) #-Inf
"1111111111110000000000000000000000000000000000000000000000000000"
Numerical inaccuracy issues
Due to the approximate nature of the floating point numbers there are a range of numerical issues that can arise. The most simple being that some number are not exactly represented, e.g.
@show big(0.1)
big(0.1) = 0.1000000000000000055511151231257827021181583404541015625 0.1000000000000000055511151231257827021181583404541015625
This approximate nature also leads to associativity of addition of floating point numbers not being guaranteed, e.g.
@show (0.1 + 0.2) + 0.3 == 0.1 + (0.2 + 0.3)
(0.1 + 0.2) + 0.3 == 0.1 + (0.2 + 0.3) = false false
but this is not usually a big error
@show (0.1 + 0.2) + 0.3 ≈ 0.1 + (0.2 + 0.3) @show (0.1 + 0.2) + 0.3 - (0.1 + (0.2 + 0.3))
(0.1 + 0.2) + 0.3 ≈ 0.1 + (0.2 + 0.3) = true ((0.1 + 0.2) + 0.3) - (0.1 + (0.2 + 0.3)) = 1.1102230246251565e-16 1.1102230246251565e-16
Also small numbers can get "absorbed" into a larger number
@show (1e9 + 1e-9) == 1e9
1.0e9 + 1.0e-9 == 1.0e9 = true true
Obviously repeated addition can compound errors, for example
a = 0.1 x = 0.0 n = 1e6 for i = 1 : n global x += a end error = a*n - x @show error
error = -1.3328826753422618e-6 -1.3328826753422618e-6
There are many examples of such errors and when used in complex operations these errors can lead to the violation of expected mathematical results, e.g.
using LinearAlgebra x = [ones(10,6) zeros(10)] eigen_values, eigen_vectors = eigen(x'*x) fraction_bad = sum(eigen_values .< 0)/length(eigen_values) @show fraction_bad
fraction_bad = 0.2857142857142857 0.2857142857142857
Numerical derivatives
These errors are particularly bad when considering a finite difference approximation to a derivative
\[ f'(x) \approx \frac{f(x+h) - f(x)}{h} \]
Mathematically we would expect that the error in the mathematical approximation should go to zero as $h$ approaches zero. However floating point errors increase (difference of close numbers divided by a small number) so there is an optimal value for the finite difference step size that reduces the total approximation error.
diff_forward(f, x; h = sqrt(eps())) = (f(x+h) - f(x))/h f(x) = sin(x^2) f_der(x) = 2x*cos(x^2) #Here we know the analytic derivative x0, x1 = 0.5, 5 h_range = 10 .^ (-14:0.01:-2) errs0 = [abs(diff_forward(f, x0; h = h) - f_der(x0))/abs(f_der(x0)) for h in h_range] errs1 = [abs(diff_forward(f, x1; h = h) - f_der(x1))/abs(f_der(x1)) for h in h_range] plot(h_range,[errs0 errs1], yaxis = :log,xaxis = :log, xlabel="h",ylabel="Absolute relative error", label = ["x = $x0" "x = $x1"], c = [:red :blue], legend = :bottomright)
Brief intro to automatic differentiation
Doing finite differences suffers from numerical accuracy issues. Doing finite differences for functions of the type $y = f(x)$ where $y \in {\mathbb R}$ and $x \in {\mathbb R}^{\tilde{n}}$ where $ n > 1$ also suffers from a computational complexity issue as $O(n)$ function evaluations are also required. A modern approach to this is called automatic differentiation, where floating point precision accuracy for the derivative is achieved and $O(1)$ function evaluations are required. This works by the cunning application of the chain rule and a special numerical type called a Dual Number. We won't go into details here but this is supported by various Julia packages.
using Zygote @show gradient((x,y) -> 3x + 4y + 1, 0,0)
gradient(((x, y)->begin
#= /Users/uqjnazar/git/ProgrammingCourse-with-Julia-SimulationA
nalysisAndLearningSystems/markdown/lecture-unit-4.jmd:4 =#
3x + 4y + 1
end), 0, 0) = (3.0, 4.0)
(3.0, 4.0)
Numerical integration
Numerical integration finds many useful applications in Applied Mathematics, Statistics, Science and Engineering. The standard problem is to find a numerical estimate of the definite integral of some function. Numerical methods for the approximate integration of univariate functions are usually referred to as quadrature methods and higher dimensional problems are referred to as cubature methods. As a starting point consider the 1D integral of the function $f(x)$ from $x=a$ to $x=b$
\[ \int _{a}^{b}f(x)dx \]
A simple method for estimating the integral is to use the Reimann sum at some finite width to approximate the integral, i.e.
\[ \int _{a}^{b}f(x)dx \approx (b - a)f\left(\frac{a+b}{2}\right) \]
This can be improved by using interpolating polynomials of successively higher orders to more closely follow the function (called Newton-Cotes formulas). Fox example, for a 1st order polynomial we get the trapezoid rule
\[ \int _{a}^{b}f(x)dx \approx (b - a)\left(\frac{f(a)+f(b)}{2}\right) \]
and for a second order polynomial we get Simpson's Rule
\[ \int _{a}^{b}f(x)dx \approx \frac{b - a}{6}\left[f(a)+4f\left(\frac{a+b}{2}\right)+f(b)\right] \]
and so on and so on. In general the error of these methods reduces as the order of the polynomial increases. However an important special case is when the function is smooth is periodic, here midpoint and trapezoid rules have excellent convergence properties (beating the higher order methods), see below
using SpecialFunctions function riemann_sum(f, a, b, method = "midpoint") if method == "midpoint" return (b - a)*f((a + b)/2) elseif method == "simpsons" return (b-a) / 6 * (f(a) + 4*f((a+b)/2) + f(b)) else @error("unsupported method given") end end f1(x) = exp(10*cos(x)) f2(x) = exp(x) #from 0 to 2π integral_f1 = 2π*besseli(0,10) integral_f2 = exp(2π) - 1 #use a map to implement midpoint method on successively finer grid f1_int_midpoint = Float64[] f1_int_simpsons = Float64[] f2_int_midpoint = Float64[] f2_int_simpsons = Float64[] n_range = 1 : 100 for n in n_range dx = 2π/n xs = 0 .+ dx * (0 : n-1 ) f1_int_mid = sum(map(x -> riemann_sum(f1, x, x+dx), xs)) f1_int_simp = sum(map(x -> riemann_sum(f1, x, x+dx, "simpsons"), xs)) push!(f1_int_midpoint, f1_int_mid) push!(f1_int_simpsons, f1_int_simp) f2_int_mid = sum(map(x -> riemann_sum(f2, x, x+dx), xs)) f2_int_simp = sum(map(x -> riemann_sum(f2, x, x+dx, "simpsons"), xs)) push!(f2_int_midpoint, f2_int_mid) push!(f2_int_simpsons, f2_int_simp) end p1 = plot(log.(abs.(f2_int_midpoint .- integral_f2)), xlabel = "n", ylabel = "log abs error", label = "midpoint f2") plot!(p1, log.(abs.(f2_int_simpsons .- integral_f2)), xlabel = "n", ylabel = "log abs error", label = "simpsons f2") p2 = plot(log.(abs.(f1_int_midpoint .- integral_f1)), xlabel = "n", ylabel = "log abs error", label = "midpoint f1") plot!(p2, log.(abs.(f1_int_simpsons .- integral_f1)), xlabel = "n", ylabel = "log abs error", label = "simpsons f1") plot(p1,p2)
The wild success of the simple integration methods for smooth periodic function methods explains why the Fast Fourier Transform sees such widespread use in Science and Engineering (for example in the JPEG compression algorithm, well its close cousin the DCT).
Higher dimensional integration methods (cubature) methods follow a similar approach but due to the poor scaling of computational complexity with dimension tend to feature advance adaptive methods to resize the grid the integral is performed on. See for example the rate of error increase with dimension in the following integral of a multivariate normal distribution using a state of the art integration method:
using HCubature M = 4.5 maxD = 10 f(x) = (2*pi)^(-length(x)/2) * exp(-(1/2)*x'x) for n in 1:maxD a = -M*ones(n) b = M*ones(n) I,e = hcubature(f, a, b, maxevals = 10^7) println("n = $(n), integral = $(I), error (estimate) = $(e)") end
n = 1, integral = 0.9999932046537504, error (estimate) = 4.3658478221519914 e-10 n = 2, integral = 0.9999864091389511, error (estimate) = 1.4879076431478765 e-8 n = 3, integral = 0.999979614080429, error (estimate) = 1.4899542970993485e -8 n = 4, integral = 0.9999728074508325, error (estimate) = 4.4447365683649473 e-7 n = 5, integral = 0.9999659361030514, error (estimate) = 2.329466913486385e -5 n = 6, integral = 0.9999639124757704, error (estimate) = 0.0003937954462610 3876 n = 7, integral = 1.0001623151630605, error (estimate) = 0.0031506650163379 626 n = 8, integral = 1.0074827348433584, error (estimate) = 0.0232757416645974 14 n = 9, integral = 1.2233043761463294, error (estimate) = 0.3731125349186626 n = 10, integral = 0.4286620931616117, error (estimate) = 0.220897606036683 15
Differential Equations
Differential equations are the backbone of physical modelling in Science and Engineering and hence a vast amount of literature to the numerical solution of differential equations has been produced. Partial Differential Equations require some special care for numerical analysis and won't be covered here. Ordinary Differential Equations are much more approachable (particularly initial value problems). In fact Julia features a state of the art library for the solution of Ordinary (and Stochastic) Differential Equations in DifferentialEquations.jl. A simple example is given below for a "spring-mass_damper" second order ODE.
using DifferentialEquations, LinearAlgebra, Plots k, b, M = 1.2, 0.3, 2.0 A = [0 1; -k/M -b/M] initX = [8., 0.0] tEnd = 50.0 tRange = 0:0.1:tEnd manualSol = [exp(A*t)*initX for t in tRange] linearRHS(x,Amat,t) = Amat*x prob = ODEProblem(linearRHS, initX, (0,tEnd), A) sol = solve(prob) p1 = plot(first.(manualSol), last.(manualSol), c=:blue, label="Manual trajectory") p1 = scatter!(first.(sol.u), last.(sol.u), c=:red, ms = 5, msw=0, label="DiffEq package") p1 = scatter!([initX[1]], [initX[2]], c=:black, ms=10, label="Initial state", xlims=(-7,9), ylims=(-9,7), ratio=:equal, xlabel="Displacement", ylabel="Velocity") p2 = plot(tRange, first.(manualSol), c=:blue, label="Manual trajectory") p2 = scatter!(sol.t, first.(sol.u), c=:red, ms = 5, msw=0, label="DiffEq package") p2 = scatter!([0], [initX[1]], c=:black, ms=10, label="Initial state", xlabel="Time", ylabel="Displacement") plot(p1, p2, size=(800,400), legend=:topright)
There is a great similarity in the basic method for the numerical solution of ODES and the numerical integration methods outlined above. For example consider the following initial value ODE problem
\[ \frac{d y}{dt} = f(y,t), \qquad \text{and} \qquad y(0) = y_0. \]
where $f: {\mathbb R}^n \to {\mathbb R}^n$ and we seek solutions on some time horizon from $t = 0$ to $t = a$.
The most basic approximation method to the derivative is using the approximation
\[ \frac{d y}{dt} \approx \frac{y(t + h) - y(t)}{h} \]
which when applied recursively yields a basic numerical method called Euler's Method.
\[ y(t+h) = y(t) + h f\big(y(t)\big), \]
A popular Higher Order Method are the Runge-Kutta Methods. These use intermediate points to approximate the derivative that have coefficients chosen to reduce the approximation error. The 4th order Runge-Kutta mthod is of the form
\[ y(t+h) = y(t) + \frac{h}{6}(k_1 + 2k_2 + 2k_3 +k_4), \]
where,
\[ \begin{align*} k_{1} &=f\left(y(t)\right) \\ k_{2} &=f\left(y(t) + h \, \frac{k_{1}}{2}\right), \\ k_{3} &=f\left(y(t) + h \, \frac{k_{2}}{2}\right) \\ k_{4} &=f\left(y(t) + h\, k_{3}\right) . \end{align*} \]
Note that if we consider the Fundamental Theorem of Calculus we can recognise that Eulers method and the RK4 method are similar to the Midpoint rule and Simpsons rule for numerical integration.
Matrix operations
You can expect any scientific programming environment to have in-built linear algebra support and Julia does not fall short. See the Linear Algebra documentation. Like MATLAB, and NumPy for Python you can do any sensible operation you would expect on matrices and vectors. This includes solving linear equations, factorizing matrices in various ways (e.g. LU, QR, SVD), computing eigenvalues, and much more.
Almost any linear algebra system uses BLAS and LAPACK under the hood. This is a collection of highly optimized routines for linear algebra. Julia does the same.
Here are some basics:
using LinearAlgebra A = [1 2; 3 4] #A matrix of integers
2×2 Matrix{Int64}:
1 2
3 4
A = [1.0 2; 3 4] #A matrix of Float64 values
2×2 Matrix{Float64}:
1.0 2.0
3.0 4.0
B = inv(A)
2×2 Matrix{Float64}:
-2.0 1.0
1.5 -0.5
B*A
2×2 Matrix{Float64}:
1.0 0.0
2.22045e-16 1.0
In Julia's linear algebra we use I for the identity.
I
UniformScaling{Bool}
true*I
I*A
2×2 Matrix{Float64}:
1.0 2.0
3.0 4.0
I == inv(A)*A #Will be false due to numerical error
false
I ≈ inv(A)*A #\approx + [TAB] shorthand for isapprox()
true
One of the most verstile linear algebra tools is the function "\", sometimes called the left division operator.
help?> \
search: \
\(x, y)
Left division operator: multiplication of y by the inverse of x on the left. Gives floating-point results for integer
arguments.
Examples
≡≡≡≡≡≡≡≡≡≡
julia> 3 \ 6
2.0
julia> inv(3) * 6
2.0
julia> A = [4 3; 2 1]; x = [5, 6];
julia> A \ x
2-element Vector{Float64}:
6.5
-7.0
julia> inv(A) * x
2-element Vector{Float64}:
6.5
-7.0
...As shown in th documentation above it is used to "solve" systems of linear equations. However, it can also find least squares solutions to overdetermined systems of equations.
We won't cover all of the linear algebra capabilities but rather use them as they are needed throughout the course. However, let's consider a single example of least squares fitting. Take this very simple dataset of 5 points. The least squares line has an intercept of 0.945 and a slope of 0.716.
using DataFrames, GLM, Statistics, LinearAlgebra, CSV, HTTP resp = HTTP.request("GET","https://raw.githubusercontent.com/h-Klok/StatsWithJuliaBook/master/data/L1L2data.csv") data = CSV.read(IOBuffer(String(resp.body)), DataFrame) xVals, yVals = data.X, data.Y modelJ = lm(@formula(Y ~ X), data) b0, b1 = coef(modelJ) @show b0, b1 scatter(xVals, yVals, legend=false,xlim=(0,10),ylim=(0,10), xlabel = "X values", ylabel = "Y values") plot!([0,10], [b0, b0 + 10*b1])
(b0, b1) = (0.9449358690844778, 0.7164971251658554)
This least squares line minimizes (assume $n=5$),
\[ \sum_{i=1}^n (y_i - \beta_0 - \beta_1 x_i)^2. \]
This is just like minimizing $\|A \beta - y\|^2$, where $\beta$ is the vector of $\beta_0$ and $\beta_1$ in this case, and $A$ is an $n\times 2$ matrix where the first column has 1's and the second column has the values of the variable $x$.
It can be shown that the minimizer is a solution of the normal equations,
\[ A^TA \beta = A^T y. \]
n = length(xVals) A = [ones(n) xVals] #This is sometimes called the design matrix
5×2 Matrix{Float64}:
1.0 2.9
1.0 4.3
1.0 5.2
1.0 6.9
1.0 8.3
Let's check that the normal equations are indeed solved by the solution b0 and b1 computed above:
β=[b0,b1] #computed via lm() above lhs_normal_equations = A'A*β rhs_normalequations = A'*yVals lhs_normal_equations - rhs_normalequations
2-element Vector{Float64}:
-3.552713678800501e-15
-2.842170943040401e-14
Now for the fun of it, and to see several linear algebra features, we'll compute $\beta$ using 9 alternative methods and in the process see quite a few LinearAlgebra functions including dot, pinv, qr, svd, and Diagonal. As you can see from the output. In all cases, these different methods of computing the least squares estimates yields the same coefficients. Note that the first two approaches are specific to "simple linear regression" (a single independent variable). However the other approaches will in general work with multiple independent variables as long as the columns of $A$ are linearly independent. The SVD and gradient descent approach will also work in case $A$ is is not a full rank matrix.
# Approach A - Using specific formulas for simple linear regression xBar, yBar = mean(xVals),mean(yVals) sXX, sXY = ones(n)'*(xVals.-xBar).^2 , dot(xVals.-xBar,yVals.-yBar) b1A = sXY/sXX b0A = yBar - b1A*xBar # Approach B - Using specific formulas for simple linear regression b1B = cor(xVals,yVals)*(std(yVals)/std(xVals)) b0B = yBar - b1B*xBar # Approach C - Solving the normal equations using b0C, b1C = A'A \ A'yVals # Approach D Adag = inv(A'*A)*A' b0D, b1D = Adag*yVals # Approach E b0E, b1E = pinv(A)*yVals # Approach F b0F, b1F = A\yVals # Approach G F = qr(A) Q, R = F.Q, F.R b0G, b1G = (inv(R)*Q')*yVals # Approach H F = svd(A) V, Sp, Us = F.V, Diagonal(1 ./ F.S), F.U' b0H, b1H = (V*Sp*Us)*yVals # Approach I - Gradient Descent - we won't describe here η = 0.002 b, bPrev = [0,0], [1,1] while norm(bPrev-b) >= √eps() global bPrev = b global b = b - η*2*A'*(A*b - yVals) end b0I, b1I = b[1], b[2] println(round.([b0A,b0B,b0C,b0D,b0E,b0F,b0G,b0H,b0I],digits=3)) println(round.([b1A,b1B,b1C,b1D,b1E,b1F,b1G,b1H,b1I],digits=3))
[0.945, 0.945, 0.945, 0.945, 0.945, 0.945, 0.945, 0.945, 0.945] [0.716, 0.716, 0.716, 0.716, 0.716, 0.716, 0.716, 0.716, 0.716]
Sparsity
A very useful data structure for dealing with large matrices is a Sparse Matrix. The idea is that only the non zero elements of a matrix are kept and typical linear algebra methods and extended for this special type. These types of matrices arise very frequently in the numerical solution of PDEs from the finite difference approximation of certain operators, in applications of graph theory where the edges are sparse and also in Statistics and Machine Learning where the Inverse Covariance Matrix often has a special sparse structure.
Consider the following imaginary social network
using SparseArrays, Random, Arpack, LinearAlgebra, InteractiveUtils n_people = 10000 Random.seed!(0) rows = Int[] columns = Int[] for i = 1 : n_people for j = i + 1 : n_people is_friend = rand() < 100/n_people if is_friend push!(rows, i) push!(columns, j) push!(rows, j) push!(columns, i) end end end friend_matrix = sparse(rows, columns, 1) big_zeros = zeros(n_people, n_people) #show size in memory of sparse adjacency matrix varinfo(r"friend_matrix") varinfo(r"big_zeros") #now you want to do some spectral graph theory on the network to discover clusters of friends @time eigs(friend_matrix) #don't even try to take eigenvalues of a dense matrix this size O(n^2.4ish)!!!!
1.651698 seconds (5.07 M allocations: 347.752 MiB, 1.13% gc time, 51.74% compilation time) ([100.85219904099397, -19.934428552838963, -19.925178341628452, 19.92106976 2397682, -19.889223092302032, 19.873857670630578], [0.009167875448341583 0. 013200487543342118 … 0.0013695849151978284 -0.0001051438225039006; 0.010039 490340577967 0.001413882977560496 … -0.0033840322738105427 -0.0119460766560 83682; … ; 0.01156160261084242 0.014922646436773062 … -0.004423989864127105 -0.00032088072679284114; 0.011076245564527729 0.004536735392501429 … -0.00 7470250314075448 0.0006368598623093374], 6, 85, 1021, [0.1977001335000457, 0.18438035930957805, 0.013740450934548456, 0.050893358193371964, -0.0944524 8955496342, 0.12281353815792316, 0.08524851500938076, 0.059582811469092806, 0.266339573646308, 0.026740123506682367 … 0.05589457204412348, 0.1105223 9439235473, -0.2406016949789472, -0.11878966205239706, 0.030119308258795035 , 0.14379538839181505, 0.031469385975261666, -0.0886096654335993, -0.142708 82913323038, 0.3031398679986816])