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Time Series Analysis With Matlab Tutorials

This tutorial provides an overview of using MATLAB for time-series analysis. It introduces the MATLAB programming environment and basic functions. The tutorial is divided into three parts: Part A covers the MATLAB interface, Part B reviews basic mathematics concepts for time-series analysis, and Part C discusses similarity search, representations, distance measures and applications of time-series analysis in MATLAB. The tutorial uses Fisher's Iris dataset to demonstrate visualizing and exploring time-series data.

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Time Series Analysis With Matlab Tutorials

Uploaded by

bcrajasekaran

Available Formats

Download as PDF, TXT or read online on Scribd

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Tutorial | Time-Series with Matlab

Disclaimer
Feel free to use any of the following slides for educational purposes, however kindly acknowledge the source. We would also like to know how you have used these slides, so please send us emails with comments or suggestions.

HandsHands-On TimeTime-Series Analysis with Matlab

Michalis Vlachos and Spiros Papadimitriou

IBM T.J. Watson Research Center

Tutorial | Time-Series with Matlab

About this tutorial

Disclaimer

The goal of this tutorial is to show you that time-series research (or research in general) can be made fun, when it involves visualizing ideas, that can be achieved with concise programming. Matlab enables us to do that.
Will I be able to use this MATLAB right away after the tutorial? I am definitely smarter than her, but I am not a timetimeseries person, perper-se. I wonder what I gain from this tutorial tutorial

We are not affiliated with Mathworks in any way but we do like using Matlab a lot since it makes our lives easier Errors and bugs are most likely contained in this tutorial. We might be responsible for some of them.

Tutorial | Time-Series with Matlab

What this tutorial is NOT about

Moving averages Autoregressive models Forecasting/Prediction Stationarity Seasonality

Overview
PART A The Matlab programming environment PART B Basic mathematics Introduction / geometric intuition Coordinates and transforms Quantized representations Non-Euclidean distances PART C Similarity Search and Applications Introduction Representations Distance Measures Lower Bounding Clustering/Classification/Visualization Applications

Tutorial | Time-Series with Matlab

Why does anyone need Matlab?

Matlab enables the efficient Exploratory Data Analysis (EDA)
Science progresses through observation -- Isaac Newton
Isaac Newton

PART A: Matlab Introduction

The greatest value of a picture is that is forces us to notice what we never expected to see -- John Tukey

John Tukey

Tutorial | Time-Series with Matlab

Matlab
Interpreted Language Easy code maintenance (code is very compact) Very fast array/vector manipulation Support for OOP Easy plotting and visualization Easy Integration with other Languages/OSs Interact with C/C++, COM Objects, DLLs Build in Java support (and compiler) Ability to make executable files Multi-Platform Support (Windows, Mac, Linux) Extensive number of Toolboxes Image, Statistics, Bioinformatics, etc

History of Matlab (MATrix LABoratory)

The most important thing in the programming language is the name. I have recently invented a very good name and now I am looking for a suitable language. -- R. Knuth

Programmed by Cleve Moler as an interface for EISPACK & LINPACK

1957: Moler goes to Caltech. Studies numerical Analysis 1961: Goes to Stanford. Works with G. Forsythe on Laplacian eigenvalues. 1977: First edition of Matlab; 2000 lines of Fortran 80 functions (now more than 8000 functions) 1979: Met with Jack Little in Stanford. Started working on porting it to C 1984: Mathworks is founded
Video:http://www.mathworks.com/company/aboutus/founders/origins_of_matlab_wm.html

Cleve Moler

Tutorial | Time-Series with Matlab

Current State of Matlab/Mathworks

Matlab, Simulink, Stateflow Matlab version 7.3, R2006b Used in variety of industries
Aerospace, defense, computers, communication, biotech

Mathworks still is privately owned Used in >3,500 Universities, with >500,000 users worldwide 2005 Revenue: >350 M. 2005 Employees: 1,400+ Pricing:
starts from 1900$ (Commercial use), ~100$ (Student Edition)
Moneyis isbetter betterthan than Money poverty,if ifonly onlyfor for poverty, financialreasons reasons financial

Tutorial | Time-Series with Matlab

Matlab 7.3
R2006b, Released on Sept 1 2006
Distributed computing Better support for large files New optimization Toolbox Matlab builder for Java
create Java classes from Matlab

Who needs Matlab?

R&D companies for easy application deployment Professors Lab assignments
Matlab allows focus on algorithms not on language features

Students Batch processing of files

No more incomprehensible perl code!

Great environment for testing ideas

Demos, Webinars in Flash format

(http://www.mathworks.com/products/matlab/demos. html)

Quick coding of ideas, then porting to C/Java etc

Easy visualization Its cheap! (for students at least)

Tutorial | Time-Series with Matlab

Tutorial | Time-Series with Matlab Personally I'm always ready to learn, although I do not always like being taught. Sir Winston Churchill

Starting up Matlab
Commands like: cd pwd mkdir

Matlab Environment

Dos/Unix like directory navigation

Command Window: - type commands - load scripts

For navigation it is easier to just copy/paste the path from explorer E.g.: cd c:\documents\
Workspace: Loaded Variables/Types/Size

Tutorial | Time-Series with Matlab

Matlab Environment

Command Window: - type commands - load scripts

Workspace: Loaded Variables/Types/Size

Help contains a comprehensive introduction to all functions

Excellent demos and tutorial of the various features and toolboxes

Tutorial | Time-Series with Matlab

Starting with Matlab

Everything is arrays Manipulation of arrays is faster than regular manipulation with for-loops
a = [1 2 3 4 5 6 7 9 10] % define an array

Populating arrays
Plot sinusoid function
a = [0:0.3:2*pi] % generate values from 0 to 2pi (with step of 0.3) b = cos(a) cos(a) % access cos at positions contained in array [a] plot(a,b) plot(a,b) % plot a (x(x-axis) against b (y(y-axis)

Related: linspace(-100,100,15); % generate 15 values between -100 and 100

Tutorial | Time-Series with Matlab

Array Access
Access array elements
>> a(1) ans = 0 >> a(1:3) ans = 0 0.3000 0.6000

2D Arrays
Can access whole columns or rows

Lets define a 2D array

>> a = [1 2 3; 4 5 6] a = 1 4 >> a(2,2) ans = 5 2 5 3 6 >> a(1,:) ans = 1 >> a(:,1) ans = 1 4 2 3 Column-wise access Row-wise access

Set array elements

>> a(1) = 100 >> a(1:3) = [100 100 100] 100]

A good listener is not only popular everywhere, but after a while he gets to know something. Wilson Mizner

Tutorial | Time-Series with Matlab

Column-wise computation
For arrays greater than 1D, all computations happen column-by-column
>> a = [1 2 3; 3 2 1] a = 1 3 >> mean(a) mean(a) ans = 2.0000 2.0000 2.0000 2 2 3 1 >> max(a) max(a) ans = 3 >> sort(a) ans = 1 3 2 2 1 3 2 3

Concatenating arrays
Column-wise or row-wise

>> a = [1 2 3]; >> b = [4 5 6]; >> c = [a b] c = 1 2 3

Row next to row

>> a = [1;2]; >> b = [3;4]; >> c = [a b] c = 1 2 3 4

Column next to column

>> a = [1 2 3]; >> b = [4 5 6]; >> c = [a; b] c = 1 4 2 5 3 6

Row below row

>> a = [1;2]; >> b = [3;4]; >> c = [a; b] c = 1 2 3 4

Column below column

Tutorial | Time-Series with Matlab

Initializing arrays
Create array of ones [ones]
>> a = ones(1,3) a = 1 1 1 >> a = ones(2,2)*5; a = 5 5 5 5

Reshaping and Replicating Arrays

Changing the array shape [reshape] (eg, for easier column-wise computation)
>> a = [1 2 3 4 5 6] 6]; % make it into a column >> reshape(a,2,3) ans = 1 2 3 4 5 6 reshape(X,[M,N]): [M,N] matrix of columnwise version of X

>> a = ones(1,3)*inf a = Inf Inf Inf

Create array of zeroes [zeros] Good for initializing arrays

>> a = zeros(1,4) a = 0 0 0 0 >> a = zeros(3,1) + [1 2 3] 3] a = 1 2 3

Replicating an array [repmat]

>> a = [1 2 3]; >> repmat(a,1,2) ans = 1 2 3 1 2 3 repmat(X,[M,N]): make [M,N] tiles of X

>> repmat(a,2,1) repmat(a,2,1) ans = 1 2 1 2

3 3

Tutorial | Time-Series with Matlab

Useful Array functions

Last element of array [end]
>> a = [1 3 2 5]; >> a(end) ans = 5 >> a = [1 3 2 5]; >> a(enda(end-1) ans = 2

Useful Array functions

Find a specific element [find] **
>> a = [1 3 2 5 10 5 2 3]; >> b = find(a==2) b = 3 7

Length of array [length]

>> length(a) ans = 4 a= 1 3

Length = 4 2 5

Sorting [sort] ***

>> a = [1 3 2 5]; >> [s,i]=sort(a) s = 1 2 3 5 s= i = 1 3 2 4 i= 1 3 2 4 1 2 3 5 Indicates the index where the element came from a= 1 3 2 5

>> [rows, columns] = size(a) rows = 1 columns = 4

rows = 1

Dimensions of array [size]

columns = 4

Tutorial | Time-Series with Matlab

strcmp, scatter, hold on

Visualizing Data and Exporting Figures

Use Fishers Iris dataset
>> load fisheriris

Visualizing Data (2D)

>> >> >> >> >> >> >> >> idx_setosa = strcmp(species, setosa setosa); % rows of setosa data idx_virginica = strcmp(species, virginica virginica); % rows of virginica setosa = meas(idx_setosa,[1:2]); virgin = meas(idx_virginica,[1:2]); scatter(setosa(:,1), setosa(:,2)); % plot in blue circles by default hold on; scatter(virgin(:,1), virgin(:,2), rs ] squares[s ] for these rs); % red[r red[r] squares[s]

4 dimensions, 3 species Petal length & width, sepal length & width Iris:
virginica/versicolor/setosa
meas (150x4 array): Holds 4D measurements
... 'versicolor' 'versicolor' 'versicolor' 'versicolor' 'versicolor' 'virginica' 'virginica' 'virginica' 'virginica

idx_setosa
... 1 1 1 0 0 0

... species (150x1 cell array): Holds name of species for the specific measurement

An array of zeros and ones indicating the positions where the keyword setosa was found

... The world is governed more by appearances rather than realities --Daniel Webster

Tutorial | Time-Series with Matlab

scatter3

Tutorial | Time-Series with Matlab

Visualizing Data (3D)

>> idx_setosa = strcmp(species, setosa setosa); % rows of setosa data >> idx_virginica = strcmp(species, virginica virginica); % rows of virginica >> idx_versicolor = strcmp(species, versicolor versicolor); % rows of versicolor >> >> >> >> >> >> >> setosa = meas(idx_setosa,[1:3]); virgin = meas(idx_virginica,[1:3]); versi = meas(idx_versicolor,[1:3]); scatter3(setosa(:,1), setosa(:,2),setosa(:,3)); % plot in blue circles by default hold on; scatter3(virgin(:,1), virgin(:,2),virgin(:,3), rs ] squares[s ] for these rs); % red[r red[r] squares[s] scatter3(versi(:,1), virgin(:,2),versi(:,3), gx gx); % green xs

Changing Plots Visually

Zoom out

Zoom in

Create line

Computersare are Computers useless.They Theycan can useless. onlygive giveyou you only answers answers

Create Arrow
7 6 5 4 3 2 1 4.5 4 3.5 3 2.5 2 4 4.5 5 5.5 6 6.5 7 7.5 8

>> grid on; % show grid on axis >> rotate3D on; % rotate with mouse

Select Object

Add text

Tutorial | Time-Series with Matlab

Changing Plots Visually

Add titles Add labels on axis Change tick labels Add grids to axis Change color of line Change thickness/ Linestyle etc

Changing Plots Visually (Example)

Change color and width of a line

A Right click C

Tutorial | Time-Series with Matlab

Changing Plots Visually (Example)

The result

Changing Figure Properties with Code

GUIs are easy, but sooner or later we realize that coding is faster
>> a = cumsum(randn(365,1)); % random walk of 365 values

Other Styles:
3 2 1 0 -1 -2 -3 3 2 1 0 -1 -2 -3 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100

If this represents a years worth of measurements of an imaginary quantity, we will change: x-axis annotation to months Axis labels Put title in the figure Include some greek letters in the title just for fun

Real men do it command-line --Anonymous

Tutorial | Time-Series with Matlab

Changing Figure Properties with Code

Axis annotation to months
>> >> >> axis tight; % irrelevant but useful... xx = [15:30:365]; set(gca, xtick xtick,xx)

Changing Figure Properties with Code

Axis annotation to months
>> set(gca, set(gca,xticklabel xticklabel,[ ,[Jan Jan; ... Feb Feb;Mar Mar])

The result

Real men do it command-line --Anonymous

Tutorial | Time-Series with Matlab

Changing Figure Properties with Code

Axis labels and title
>> title( title(My measurements (\ (\epsilon/\ epsilon/\pi) pi)) Other latex examples: \alpha, \beta, e^{-\alpha} etc

Saving Figures
Matlab allows to save the figures (.fig) for later processing

>> ylabel( ylabel(Imaginary Quantity Quantity)

.fig can be later opened through Matlab >> xlabel( xlabel(Month of 2005 2005)

Real men do it command-line --Anonymous

You can always put-off for tomorrow, what you can do today. -Anonymous

Tutorial | Time-Series with Matlab

Exporting Figures

Exporting figures (code)

You can also achieve the same result with Matlab code

Export to: emf, eps, jpg, etc

Matlab code:
% extract to color eps print -depsc myImage.eps; myImage.eps; % from commandcommand-line print(gcf, print(gcf,-depsc depsc,myImage myImage) % using variable as name

Tutorial | Time-Series with Matlab

Visualizing Data - 2D Bars

1 2 3 4

Visualizing Data - 3D Bars

data
10 8 6 4 2 0 1 2

colormap
7 5 4 4 2 1 0 0.0198 0.0397 0.0595 0.0794 0.0992 1.0000 1.0000 1.0000 1.0000 0 0.0124 0.0248 0.0372 0.0496 0.0620 ... 0.7440 0.7564 0.7688 0.7812
3

colormap

10 9 8 6 6 3
3 5 6 3

8 6 6 5 3 2

0 0.0079 0.0158 0.0237 0.0316 0.0395 0.4738 0.4817 0.4896 0.4975

bars
time = [100 120 80 70]; % our data h = bar(time); bar(time); % get handle cmap = [1 0 0; 0 1 0; 0 0 1; .5 0 1]; % colors colormap(cmap); colormap(cmap); % create colormap cdata = [1 2 3 4]; % assign colors set(h,'CDataMapping','direct','CData',cdata); set(h,'CDataMapping','direct','CData',cdata);

data = [ 10 8 7; 9 6 5; 8 6 4; 6 5 4; 6 3 2; 3 2 1]; bar3([1 2 3 5 6 7], data); c = colormap(gray); colormap(gray); % get colors of colormap c = c(20:55,:); % get some colors colormap(c); colormap(c); % new colormap

Tutorial | Time-Series with Matlab

Visualizing Data - Surfaces

data
10 9 8 7 6 5 4 3 2 1 10 8 6 4 2 0 0 2 6 4 8 10

Creating .m files
Standard text files
10

1 1

Script: A series of Matlab commands (no input/output arguments) Functions: Programs that accept input and return output

9 10 1 10

The value at position x-y of the array indicates the height of the surface

Right click

data = [1:10]; data = repmat(data,10,1); % create data surface(data,'FaceColor',[1 1 1], 'Edgecolor ', [0 0 1]); % plot data 'Edgecolor', view(3); grid on; % change viewpoint and put axis lines

Tutorial | Time-Series with Matlab

cumsum, num2str, save

Creating .m files

Creating .m files
The following script will create: An array with 10 random walk vectors
M editor

Will save them under text files: 1.dat, , 10.dat

myScript.m

Double click

Sample Script

A 1 2 3 4 5

cumsum(A) 1 3 6
10 15

a = cumsum(randn(100,10)); % 10 random walk data of length 100 for i=1:size(a,2), % number of columns data = a(:,i) ; fname = [num2str(i) .dat .dat]; % a string is a vector of characters! save(fname, data data,-ASCII ASCII); % save each column in a text file end Write this in the M editor

A random walk time-series

-5

90 100

and execute by typing the name on the Matlab command line

Tutorial | Time-Series with Matlab

Functions in .m scripts
When we need to: Organize our code Frequently change parameters in our scripts
keyword output argument function name input argument

Cell Arrays
Cells that hold other Matlab arrays Lets read the files of a directory
>> f = dir( dir(*.dat *.dat) % read file contents f = 15x1 struct array with fields: name date bytes isdir for i=1:length(f), a{i} = load(f(i).name); N = length(a{i}); plot3([1:N], a{i}(:,1), a{i}(:,2), ... r-, Linewidth Linewidth, 1.5); grid on; pause; 600 500 cla; 400 end
300 200 100 0 1000 1500

Struct Array 1 2 3 4 5

function dataN = zNorm(data) % ZNORM zNormalization of vector % subtract mean and divide by std if (nargin <1), % check parameters (nargin<1), error( error(Not enough arguments arguments); end data = data mean(data); mean(data); % subtract mean data = data/std(data ); % divide by std data/std(data); dataN = data;

Help Text (help function_name)

name date bytes isdir

f(1

).n

e am

Function Body

function [a,b] = myFunc(data, x, y) % pass & return more arguments

Tutorial | Time-Series with Matlab

Reading/Writing Files
Load/Save are faster than C style I/O operations But fscanf, fprintf can be useful for file formatting or reading non-Matlab files
fid = fopen('fischer.txt', 'wt'); for i=1:length(species), fprintf(fid, '%6.4f %6.4f %6.4f %6.4f %s\ %s\n', meas(i,:), species{i}); end fclose(fid);

Flow Control/Loops
if (else/elseif) , switch
Check logical conditions

while
Execute statements infinite number of times

for
Execute statements a fixed number of times

Output file:

Elements are accessed column-wise (again)

x = 0:.1:1; y = [x; exp(x)]; fid = fopen('exp.txt','w'); fprintf(fid,'%6.2f %12.8f\ %12.8f\n',y); fclose(fid);
0 1 0.1 1.1052 0.2 1.2214 0.3 1.3499 0.4 0.4 1.4918 0.5 1.6487 1.6487 0.6 1.8221 0.7 2.0138

break, continue return

Return execution to the invoking function

Life is pleasant. Death is peaceful. Its the transition thats troublesome. Isaac Asimov

Tutorial | Time-Series with Matlab

tic, toc, clear all

Tutorial | Time-Series with Matlab

For-Loop or vectorization?
clear all; tic; for i=1:50000 a(i) a(i) = sin(i); sin(i); end toc elapsed_time = 5.0070

Pre-allocate arrays that store output results No need for Matlab to resize everytime Functions are faster than scripts Compiled into pseudocode Load/Save faster than Matlab I/O functions After v. 6.5 of Matlab there is for-loop vectorization (interpreter)

Matlab Profiler
Find which portions of code take up most of the execution time Identify bottlenecks Vectorize offending code

clear all; a = zeros(1,50000); tic; for i=1:50000 a(i) a(i) = sin(i); sin(i); end toc

elapsed_time = 0.1400

clear all; tic; i = [1:50000]; a = sin(i); sin(i); toc; toc;

elapsed_time = 0.0200

Vectorizations help, but not so obvious how to achieve many times

Time not importantonly life important. The Fifth Element

Tutorial | Time-Series with Matlab

Hints &Tips
There is always an easier (and faster) way
Typically there is a specialized function for what you want to achieve

Debugging

Beware of bugs in the above code; I have only proved it correct, not tried it -- R. Knuth

Not as frequently required as in C/C++ Set breakpoints, step, step in, check variables values
Set breakpoints

Learn vectorization techniques, by peaking at the actual Matlab files:

edit [fname], eg edit mean edit princomp

Matlab Help contains many vectorization examples

Tutorial | Time-Series with Matlab

Debugging

Eitherthis thisman manis is Either deador ormy mywatch watch dead hasstopped. stopped. has

Tutorial | Time-Series with Matlab

Advanced Features 3D modeling/Volume Rendering

Very easy volume manipulation and rendering

Full control over variables and execution path F10: step, F11: step in (visit functions, as well)
A

F10 C

Tutorial | Time-Series with Matlab

Advanced Features Making Animations (Example)

Create animation by changing the camera viewpoint
3 2 1 3 2 1 0 -1 -2 -3 -1 0 1 2 3 4 100 100 1 2 3 4 50 0 -1 -2 0 -3 0

Advanced Features GUIs

Built-in Development Environment Buttons, figures, Menus, sliders, etc

3 2 1 0 -1 -2 -3 0
50

Several Examples in Help Directory listing

50 100 -1 0 1 2 3 4

Address book reader GUI with multiple axis

-1

azimuth = [50:100 99:99:-1:50]; % azimuth range of values for k = 1:length(azimuth), plot3(1:length(a), a(:,1), a(:,2), 'r', 'Linewidth',2); grid on; view(azimuth(k),30); % change new M(k) M(k) = getframe; getframe; % save the frame end movie(M,20); % play movie 20 times See also:movie2avi

Tutorial | Time-Series with Matlab

Advanced Features Using Java

Matlab is shipped with Java Virtual Machine (JVM) Access Java API (eg I/O or networking) Import Java classes and construct objects Pass data between Java objects and Matlab variables

Advanced Features Using Java (Example)

Stock Quote Query
Connect to Yahoo server http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do? objectId=4069&objectType=file
disp('Contacting YAHOO server using ...'); disp(['url = java.net.URL(' java.net.URL(' urlString ')']); end; url = java.net.URL(urlString); java.net.URL(urlString); try stream = openStream(url); openStream(url); ireader = java.io.InputStreamReader(stream); java.io.InputStreamReader(stream); breader = java.io.BufferedReader(ireader); java.io.BufferedReader(ireader); connect_query_data= connect_query_data= 1; %connect made; catch connect_query_data= connect_query_data= -1; %could not connect case; disp(['URL: disp(['URL: ' urlString]); urlString]); error(['Could not connect to server. It may be unavailable. Try again later.']); stockdata={}; stockdata={}; return; end

Tutorial | Time-Series with Matlab

Matlab Toolboxes
You can buy many specialized toolboxes from Mathworks Image Processing, Statistics, Bio-Informatics, etc There are many equivalent free toolboxes too: SVM toolbox
http://theoval.sys.uea.ac.uk/~gcc/svm/toolbox/

In case I get stuck

help [command] (on the command line) eg. help fft Menu: help -> matlab help Excellent introduction on various topics Matlab webinars

Ivehad hada awonderful wonderful Ive evening.But Butthis this evening. wasntit it wasnt

http://www.mathworks.com/company/events/archived_webinars.html?fp

Wavelets
http://www.math.rutgers.edu/~ojanen/wavekit/

Google groups comp.soft-sys.matlab You can find *anything* here Someone else had the same problem before you!

Speech Processing
http://www.ee.ic.ac.uk/hp/staff/dmb/voicebox/voicebox.html

Bayesian Networks
http://www.cs.ubc.ca/~murphyk/Software/BNT/bnt.html

Tutorial | Time-Series with Matlab

Overview of Part B
1. 2. Introduction and geometric intuition Coordinates and transforms Eightpercent percentof of Eight successis isshowing showing success up. up. 3. 4. Fourier transform (DFT) Wavelet transform (DWT) Incremental DWT Principal components (PCA) Incremental PCA Piecewise quantized / symbolic Vector quantization (VQ) / K-means Dynamic time warping (DTW)

PART B: Mathematical notions

Quantized representations

Non-Euclidean distances

Tutorial | Time-Series with Matlab

What is a time-series
Definition: Definition:A Asequence sequenceof ofmeasurements measurementsover overtime time
Medicine Stock Market Meteorology Geology Astronomy Chemistry Biometrics Robotics
64.0 62.8 62.0 66.0 62.0 32.0 86.4 ... 21.6 45.2 43.2 53.0 43.2 42.8 43.2 36.4 16.9 10.0 ECG

Applications
Images
Image

Shapes

Motion capture

Sunspot Color Histogram

600 400 200 0 400 50 100 150 200 250

Acer platanoides

200

100

150

200

250

800 600 400 200 0 50 100 150 200 250

Earthquake

Time-Series
Salix fragilis time

more to come

Tutorial | Time-Series with Matlab

Time Series
value

x5 x2 x6 x3 x1 x4 time
3

9 8 6 4 1

x = (3, 8, 4, 1, 9, 6)

time

Sequence of numeric values Finite: N-dimensional vectors/points Infinite: Infinite-dimensional vectors

Tutorial | Time-Series with Matlab

Mean
Definition:

Variance
Definition:

From now on, we will generally assume zero mean mean normalization:

or, if zero mean, then

From now on, we will generally assume unit variance variance normalization:

Tutorial | Time-Series with Matlab

Mean and variance

Why and when to normalize

Intuitively, the notion of shape is generally independent of
Average level (mean) Magnitude (variance)
variance

mean

Unless otherwise specified, we normalize to zero mean and unit variance

Tutorial | Time-Series with Matlab

Variance = Length
Variance of zero-mean series:

Covariance and correlation

Definition

Length of N-dimensional vector (L2-norm):

or, if zero mean and unit variance, then So that:

||x |

Tutorial | Time-Series with Matlab

Correlation and similarity

How strong is the linear relationship between xt and yt ? For normalized series,

Correlation = Angle
Correlation of normalized series:

residual

Cosine law:

slope

2.5 2 1.5 1

2.5

= -0.23

2 1.5 1

= 0.99

So that:
x

CAD

BEF

0.5 0

-0.5 -1 -1.5 -2 -2.5 -2 -1 0 1 2

x.y
FRF

FRF

Tutorial | Time-Series with Matlab

Correlation and distance

For normalized series,

Ergodicity
Example

Assume I eat chicken at the same restaurant every day and Question: How often is the food good?
Answer one:

i.e., correlation and squared Euclidean distance are linearly related.

Answer two:

Answers are equal ergodic

If the chicken is usually good, then my guests today can safely order other things.
||x || -y

x.y y

Tutorial | Time-Series with Matlab

Ergodicity
Example

Stationarity
Example

Ergodicity is a common and fundamental assumption, but sometimes can be wrong: Total number of murders this year is 5% of the population If I live 100 years, then I will commit about 5 murders, and if I live 60 years, I will commit about 3 murders non-ergodic! Such ergodicity assumptions on population ensembles is commonly called racism.

Is the chicken quality consistent?

Last week: Two weeks ago: Last month: Last year:

Answers are equal stationary

Tutorial | Time-Series with Matlab

Autocorrelation
Definition:

Time-domain coordinates
6 4 2 1.5

3.5

Is well-defined if and only if the series is (weakly) stationary Depends only on lag , not time t
-0.5

-0.5 -2

+ 1.5

+ -2

+ 2

+ 3.5

Tutorial | Time-Series with Matlab

Time-domain coordinates
6 4 2 1.5 1

Orthonormal basis
Set of N vectors, { e1, e2, , eN }
Normal: ||ei|| = 1, for all 1 i N Orthogonal: eiej = 0, for i j

3.5

-0.5 -2

Describe a Cartesian coordinate system

Preserve length (aka. Parseval theorem) Preserve angles (inner-product, correlations)

x1 -0.5

42 + x

x3 + 1.5

x4 + -2

+ x 25

66 + x

x7 + 3.5

18 + x

Tutorial | Time-Series with Matlab

Orthonormal basis
Note that the coefficients xi w.r.t. the basis { e1, , eN } are the corresponding similarities of x to each basis vector/series:

Orthonormal bases
The time-domain basis is a trivial tautology:
Each coefficient is simply the value at one time instant

What other bases may be of interest? Coefficients may correspond to:

6 4 1.5 2 1 -0.5 -2 3.5

Frequency (Fourier) Time/scale (wavelets)

=
-0.5

+ e1

+ e2

Features extracted from series collection (PCA)

Tutorial | Time-Series with Matlab

Frequency domain coordinates

Preview
6 4 2 1.5 1

Time series geometry

Summary

Basic concepts:
Series / vector
3.5

Mean: average level Variance: magnitude/length

-0.5 -2

Correlation: similarity, distance, angle Basis: Cartesian coordinate system

5.6

+ -2.2

+ 2.8

- 4.9

+ -3

+ 0.05

Tutorial | Time-Series with Matlab

Time series geometry

Preview Applications

Overview
1. 2. Introduction and geometric intuition Coordinates and transforms 3. 4. Fourier transform (DFT) Wavelet transform (DWT) Incremental DWT Principal components (PCA) Incremental PCA Piecewise quantized / symbolic Vector quantization (VQ) / K-means Dynamic time warping (DTW)

The quest for the right basis Compression / pattern extraction

Filtering Similarity / distance Indexing Clustering Forecasting Periodicity estimation Correlation

Quantized representations

Non-Euclidean distances

Tutorial | Time-Series with Matlab

Frequency

Frequency and time

.
One cycle every 20 time units (period)
period = 8 period 20? Why is the

= 0

Its not 8, because its similarity (projection) to a period-8 series (of the same length) is zero.

Tutorial | Time-Series with Matlab

Frequency and time

.
= 0
period = 10 period = 40

.
= 0 Why is the cycle 20? Its not 40, because its similarity (projection) to a period-40 series (of the same length) is zero.

Why is the cycle 20? Its not 10, because its similarity (projection) to a period-10 series (of the same length) is zero.

and so on

Tutorial | Time-Series with Matlab

Frequency

Fourier transform - Intuition

Frequency

Fourier transform - Intuition

To find the period, we compared the time series with sinusoids of many different periods Therefore, a good description (or basis) would consist of all these sinusoids This is precisely the idea behind the discrete Fourier transform
The coefficients capture the similarity (in terms of amplitude and phase) of the series with sinusoids of different periods

Technical details:
We have to ensure we get an orthonormal basis Real form: sines and cosines at N/2 different frequencies Complex form: exponentials at N different frequencies

Tutorial | Time-Series with Matlab

Fourier transform
Real form

Fourier transform

Real form Amplitude and phase

For odd-length series,

Observe that, for any fk, we can write

where The pair of bases at frequency fk are are the amplitude and phase, respectively. plus the zero-frequency (mean) component

Tutorial | Time-Series with Matlab

Fourier transform

Real form Amplitude and phase

Fourier transform
Complex form

It is often easier to think in terms of amplitude rk and phase k e.g.,

The equations become easier to handle if we allow the series and the Fourier coefficients Xk to take complex values:

1 0.5 0 -0.5 -1 0 10 20 30 40 50 60 70 80

Matlab note: fft omits the scaling factor and is not unitaryhowever, ifft includes an scaling factor, so always ifft(fft(x)) == x.

Tutorial | Time-Series with Matlab

Fourier transform
Example
2 GBP 1 0 -1 2 GBP 1 0 -1 2 GBP 1 0 -1

Other frequency-based transforms

Discrete Cosine Transform (DCT)
1 frequency 2 frequencies

Matlab: dct / idct

Modified Discrete Cosine Transform (MDCT)

3 frequencies

2 GBP 1 0 -1

5 frequencies

2 GBP 1 0 -1

10 frequencies

2 GBP 1 0 -1

20 frequencies

Tutorial | Time-Series with Matlab

Frequency and time

e.g., .

period = 20

0 0 etc

Quantized representations

period = 10

What is the cycle now?

Non-Euclidean distances

No single cycle, because the series isnt exactly similar with any series of the same length.

Tutorial | Time-Series with Matlab

Frequency and time

Fourier is successful for summarization of series with a few, stable periodic components However, content is smeared across frequencies when there are
Frequency shifts or jumps, e.g.,

Frequency and time

If there are discontinuities in time/frequency or frequency shifts, then we should seek an alternate description or basis Main idea: Localize bases in time
Short-time Fourier transform (STFT) Discrete wavelet transform (DWT)

Discontinuities (jumps) in time, e.g.,

Tutorial | Time-Series with Matlab

Frequency and time

Intuition

Frequency and time

Intuition

What if we examined, e.g., eight values at a time?

What if we examined, e.g., eight values at a time? Can only compare with periods up to eight.
Results may be different for each group (window)

Tutorial | Time-Series with Matlab

Frequency and time

Intuition

Wavelets
Intuition

Main idea
Use small windows for small periods
Remove high-frequency component, then

Use larger windows for larger periods

Twice as large

Can adapt to localized phenomena Fixed window: short-window Fourier (STFT)

How to choose window size?

Repeat recursively

Technical details
Need to ensure we get an orthonormal basis

Variable windows: wavelets

Tutorial | Time-Series with Matlab

Wavelets
Intuition

Wavelets

Intuition Tiling time and frequency

Scale (frequency)

Time

Scale (frequency)

Frequency

Time

Fourier, DCT,

STFT

Wavelets

Tutorial | Time-Series with Matlab

Wavelet transform
Pyramid algorithm

High pass

High pass Low pass Low pass

Tutorial | Time-Series with Matlab

Wavelet transform
Pyramid algorithm

High pass

x w0
High pass

w2
High pass Low pass

High pass Low pass

Low pass

w3 v3

Low pass

Tutorial | Time-Series with Matlab

Wavelet transforms
General form

Wavelet transforms
Other filters examples
Haar (Daubechies-1)

A high-pass / low-pass filter pair

Example: pairwise difference / average (Haar) In general: Quadrature Mirror Filter (QMF) pair
Orthogonal spans, which cover the entire space

Better frequency isolation Worse time localization

Daubechies-2

Additional requirements to ensure orthonormality of overall transform

Daubechies-3

Use to recursively analyze into top / bottom half of frequency band

Daubechies-4

Wavelet filter, or Mother filter (high-pass)

Scaling filter, or Father filter (low-pass)

Tutorial | Time-Series with Matlab

Wavelets
Example Wavelet coefficients (GBP, Haar)
2 1 0 -1 500 1 W1 0 -1 1 W2 0 -1 2 W3 0 -2 2 W4 0 -2 5 W5 0 -5 10 W6 0 -10 20 V6 0 -20 5 10 15 20 25 30 35 40 5 10 15 20 25 30 35 40 10 20 30 40 50 60 70 80 20 40 60 80 100 120 140 160 50 100 150 200 250 300 100 200 300 400 500 600 200 400 600 800 1000 1200 1000 1500 2000 2500 1 D1 0 -1 1 0 -1 1 0 -1 2 0 -2 5 0 -5 5 0 -5 20 0 -20 5 10 15 20 25 30 35 40 45 5 10 15 20 25 30 35 40 45 A6 10 20 30 40 50 60 70 80 20 40 60 80 100 120 140 160 50 100 150 200 250 300 D4 100 200 300 400 500 600 200 400 600 800 1000 1200 2 1 0 -1 500 1000 1500 2000 2500 GBP

Wavelets
Example Wavelet coefficients (GBP, Daubechies-3)
2 1 0 -1 500 0.1 0 -0.1 -0.2 -0.3 500 0.2 0 -0.2 500 0.4 0.2 0 -0.2 -0.4 0.4 0.2 0 -0.2 -0.4 0.5 0 -0.5 500 0.5 0 -0.5 2 1 0 -1 500 1000 1500 2000 2500 D6 1000 1500 2000 2500 500 1000 1500 2000 2500 0.2 0 -0.2 -0.4 0.5 0 -0.5 0.5 0 -0.5 2 1 0 -1 500 1000 1500 2000 2500 500 1000 1500 2000 2500 D3 1000 1500 2000 2500 0.2 0 -0.2 -0.4 500 1000 1500 2000 2500 D2 1000 1500 2000 2500 1000 1500 2000 2500 0 -0.2 -0.4 -0.6 0.2 0 -0.2 -0.4 -0.6 500 1000 1500 2000 2500 GBP

Multi-resolution analysis (GBP, Haar)

2 1 0 -1

Multi-resolution analysis (GBP, Daubechies-3)

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Tutorial | Time-Series with Matlab

Wavelets
Example Multi-resolution analysis (GBP, Haar)
2 1 0 -1 500 0.1 0 -0.1 -0.2 -0.3 500 0.2 0 -0.2 500 0.4 0.2 0 -0.2 -0.4 0.4 0.2 0 -0.2 -0.4 0.5 0 -0.5 500 0.5 0 -0.5 2 1 0 -1 500 1000 1500 2000 2500 D6 500 D3 D2 2 1 0 -1 500 1500 1000 2000 1000 1500 2000 2500 0.2 0 -0.2 -0.4 1500 500 0.2 1000 1500 1000 1500 2 1 0 -1 GBP

Wavelets
Matlab Multi-resolution analysis (GBP, Daubechies-3)

Wavelet GUI: wavemenu

2500

Analysis levels are orthogonal,

DiDj = 0, for i j
2000 2500 500 0 -0.2 -0.4 -0.6 0.2 0 -0.2 -0.4 -0.6 2000 2500 500

1000

1500

2000

Single level: dwt / idwt Multiple level: wavedec / waverec

wmaxlev

Haar analysis: simple, piecewise constant

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Wavelet bases: wavefun

2 500 1 1000 0 -1 1000 1500 1500

Daubechies-3 analysis: 0 less artifacting

2000 2500 -0.2 -0.4 0.5 0 -0.5 500 2000 2500 1000 0.5 0 -0.5 2 1 0 -1 500 1000 1500 2000 2500 1500 500 1000 2000 1500 2500 2000 2500 500 1000 1500 2000 2500

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Tutorial | Time-Series with Matlab

Other wavelets
Only scratching the surface Wavelet packets
All possible tilings (binary) Best-basis transform

More on wavelets
Signal representation and compressibility
100

Partial energy (GBP)

100

Partial energy (Light)

Quality (% energy)

Quality (% energy)
Time FFT Haar DB3
0 2 4 6 8 10

Overcomplete wavelet transform (ODWT), aka. maximum-overlap wavelets (MODWT), aka. shiftinvariant wavelets

Further reading: 1. Donald B. Percival, Andrew T. Walden, Wavelet Methods for Time Series Analysis, Cambridge Univ. Press, 2006. 2. Gilbert Strang, Truong Nguyen, Wavelets and Filter Banks, Wellesley College, 1996. 3. Tao Li, Qi Li, Shenghuo Zhu, Mitsunori Ogihara, A Survey of Wavelet Applications in Data Mining, SIGKDD Explorations, 4(2), 2002.

Time FFT Haar DB3

0 5 10 15

Compression (% coefficients)

Tutorial | Time-Series with Matlab

More wavelets
Keeping the highest coefficients minimizes total error (L2-distance) Other coefficient selection/thresholding schemes for different error metrics (e.g., maximum per-instant error, or L1-dist.)
Typically use Haar bases

Quantized representations

Further reading: 1. Minos Garofalakis, Amit Kumar, Wavelet Synopses for General Error Metrics, ACM TODS, 30(4), 2005. 2.Panagiotis Karras, Nikos Mamoulis, One-pass Wavelet Synopses for Maximum-Error Metrics, VLDB 2005.

Non-Euclidean distances

Tutorial | Time-Series with Matlab

Wavelets

Incremental estimation

Wavelets

Incremental estimation

Tutorial | Time-Series with Matlab

Wavelets

Incremental estimation

Wavelets

Incremental estimation

Tutorial | Time-Series with Matlab

Wavelets

Incremental estimation

Wavelets

Incremental estimation

post-order traversal

Tutorial | Time-Series with Matlab

Wavelets

Incremental estimation

Overview
:
1. 2. Introduction and geometric intuition Coordinates and transforms
constant factor: filter length

Forward transform
O(1) time (amortized)

Post-order traversal of wavelet coefficient tree O(logN) buffer space (total)

Fourier transform (DFT) Wavelet transform (DWT) Incremental DWT Principal components (PCA) Incremental PCA Piecewise quantized / symbolic Vector quantization (VQ) / K-means Dynamic time warping (DTW)

3. 4.

Inverse transform:
Same complexity

Pre-order traversal of wavelet coefficient tree

Quantized representations

Non-Euclidean distances

Tutorial | Time-Series with Matlab

Time series collections

Overview

Time series collections

Some notation:

Fourier and wavelets are the most prevalent and successful descriptions of time series. Next, we will consider collections of M time series, each of length N.
What is the series that is most similar to all series in the collection? What is the second most similar, and so on

values at time t, xt i-th series, x(i)

Tutorial | Time-Series with Matlab

Principal Component Analysis

Example
Exchange rates (vs. USD)
2 0 -2 2 0 -2 2 0 -2 2 0 -2 2 0 -2 2 0 -2 2 0 -2 2 0 -2 2 0 -2 2 0 -2 2 0 -2 2 0 -2 500 1000 Time 1500 2000 2500

Principal component analysis

u1
0.05 0 -0.05

Principal components 1-4

( 0)
CAD

AUD

= 48% + 33% = 81% + 11% = 92% + 4% = 96%

BEF

0 -0.05 0.05 0 -0.05 0.05 0 -0.05 500 1000 Time 1500 2000 2500

SEK
40
GBP 2 0 -2

FRF

CAD

AUD
2 0 -2 FRF

DEM

x(2) = 49.1u1 + 8.1u2 + 7.8u3 + 3.6u4 + 1

i,2

JPY

Best basis : { u1, u2, u3, u4 }

ESP

0.05

2 0 -2

First two principal components

2 0 -2

NZL

Coefficients of each time series w.r.t. basis { u1, u2, u3, u4 } :

NLG

NZL
0
2 0 -2 NLG

CHF
2 0 -2

ESP

-10

SEK

-20
JPY

2 0 -2

CHF

GBP

-30

-20

-10

i,1

Tutorial | Time-Series with Matlab

Principal Component Analysis

Matrix notation Singular Value Decomposition (SVD)

Principal Component Analysis

Matrix notation Singular Value Decomposition (SVD)

X = UVT X U VT
x(1) x(2) x(M)

X = UVT X U VT
v1 M x(1) x(2) x(M)

u1 u2

1 2 3

u1 u2

v2 1 2 3 vk

DEM

BEF

2 0 -2

time series

basis for time series

coefficients w.r.t. basis in U (columns)

time series

basis for time series

basis for measurements (rows) coefficients w.r.t. basis in U (columns)

Tutorial | Time-Series with Matlab

Principal Component Analysis

Matrix notation Singular Value Decomposition (SVD)

Principal component analysis

Properties Singular Value Decomposition (SVD)

X = UVT X U
1
x(1) x(2) x(M)

V are the eigenvectors of the covariance matrix XTX, since

VT
v1

u1 u2

.
k

U are the eigenvectors of the Gram (inner-product) matrix XXT, since

vk basis for measurements (rows) Further reading: 1. Ian T. Jolliffe, Principal Component Analysis (2nd ed), Springer, 2002. 2. Gilbert Strang, Linear Algebra and Its Applications (4th ed), Brooks Cole, 2005.

scaling factors time series basis for time series

Tutorial | Time-Series with Matlab

Kernels and KPCA

What are kernels? Usual definition of inner product w.r.t. vector coordinates is xy = i xiyi However, other definitions that preserve
NZL CAD AUD

Multidimensional scaling (MDS)

Exchange rates
SEK ESP GBP

Kernels are still Euclidean in some sense

We still have a Hilbert (inner-product) space, even though it may not be the space of the original data
FRF BEF DEM NLG CHF

the fundamental properties are possible Why kernels? We no longer have explicit coordinates
Objects do not even need to be numeric

For arbitrary similarities, we can still find the eigendecomposition of the similarity matrix
Multidimensional scaling (MDS) Maps arbitrary metric data into a low-dimensional space
CAD AUD

JPY

But we can still talk about distances and angles Many algorithms rely just on these two concepts

Exchange rates
SEK ESP GBP

NZL

FRF BEF DEM NLG CHF

Further reading: 1. Bernhard Schlkopf, Alexander J. Smola, Learning with Kernels: Support Vector Machines, Regularization, Optimization and Beyond, MIT Press, 2001.

JPY

Tutorial | Time-Series with Matlab

Principal components
Matlab

PCA on sliding windows

Empirical orthogonal functions (EOF), aka. Singular Spectrum Analysis (SSA) If the series is stationary, then it can be shown that
The eigenvectors of its autocovariance matrix are the Fourier bases The principal components are the Fourier coefficients

pcacov princomp [U, S, V] = svd(X) [U, S, V] = svds(X, k)

Further reading: 1. M. Ghil, et al., Advanced Spectral Methods for Climatic Time Series, Rev. Geophys., 40(1), 2002.

Tutorial | Time-Series with Matlab

Principal components
Incremental estimation

PCA via SVD on X 2

Singular values 2

NM
kk

recap:

(diagonal)
Nk

Energy / reconstruction accuracy

Left singular vectors U 2

Basis for time series Eigenvectors of Gram matrix XXT

Quantized representations

Right singular vectors V 2

Basis for measurements space Eigenvectors of covariance matrix XTX

Non-Euclidean distances

Tutorial | Time-Series with Matlab

Principal components
Incremental estimation

Principal components
Incremental estimation Example

PCA via SVD on X 2

recap: First series

VT
30oC

kk (diagonal) Singular X values 2 U

Energy / reconstruction accuracy

Left singular vectors U 2 (1 (2 (M

x )x
)

vk 20oC

Right singular vectors V 2

Basis for measurements space Eigenvectors of covariance matrix XTX

Series x(1)

uk . = u1 u2 Basis for time series Eigenvectors of Gram matrix XXT x

)

Nk 2

v1 v2

First three values Other values

Tutorial | Time-Series with Matlab

Principal components
Incremental estimation Example

First series
30oC

Correlations:
30oC

Second series
Series x(2) Series x(2)

Lets take a closer look at the first three measurementpairs

20oC

First three values Other values

20oC

30oC

Series x(1)

First three values Other values

Tutorial | Time-Series with Matlab

Principal components
Incremental estimation Example

30oC

Series x(2)

20oC

e ffs

pa ci in

O(M) numbers for the slope, and One number for each measurementpair (offset on line = PC)
First three values Other values

Series x(2)

m co

ne po

First three lie (almost) on a line in the space of nt measurement-pairs

30oC

Other pairs also follow the same pattern: they lie (approximately) on this line

20oC

30oC

20oC

30oC

Series x(1)

First three values Other values

Tutorial | Time-Series with Matlab

Principal components
Incremental estimation Example

Principal components

Incremental estimation Example (update)

For each new point

30oC

For each new point

30oC

error

Project onto current line Estimate error

Series x(2)

error

Project onto current line Estimate error Rotate line in the direction of the error and in proportion to its magnitude

Series x(2)

20oC

O(M) time

20oC

30oC

Series x(1)

New value

20oC

30oC

Series x(1)

New value

Tutorial | Time-Series with Matlab

Principal components

Incremental estimation Example (update)

Principal components
Incremental estimation Example

For each new point

30oC

The line is the first principal component (PC) direction This line is optimal: it minimizes the sum of squared projection errors

Project onto current line Estimate error Rotate line in the direction of the error and in proportion to its magnitude

Series x(2)

20oC

30oC

Series x(1)

Tutorial | Time-Series with Matlab

Principal components

Incremental estimation Update equations

Principal components

Incremental estimation Complexity

For each new point xt and for j = 1, , k : yj := vjTxt j2 j + yj2 ej := x yjwj vj vj + (1/
2 j )

O(Mk) space (total) and time (per tuple), i.e., Independent of # points Linear w.r.t. # streams (M) Linear w.r.t. # principal components (k)

(proj. onto vj) (energy j-th eigenval.) (error) yjej (update estimate) (repeat with remainder)

xt xt yjvj

xt e1

v1 updated v1 y1

Tutorial | Time-Series with Matlab

Principal components

Incremental estimation Applications

Overview
1. 2. Introduction and geometric intuition Coordinates and transforms 3. Fourier transform (DFT) Wavelet transform (DWT) Incremental DWT Principal components (PCA) Incremental PCA Piecewise quantized / symbolic Vector quantization (VQ) / K-means Dynamic time warping (DTW)

Incremental PCs (measurement space)

Incremental tracking of correlations Forecasting / imputation Change detection

Quantized representations

Further reading: 1. Sudipto Guha, Dimitrios Gunopulos, Nick Koudas, Correlating synchronous and asynchronous data streams, KDD 2003. 2. Spiros Papadimitriou, Jimeng Sun, Christos Faloutsos, Streaming Pattern Discovery in Multiple Time-Series, VLDB 2005. 3. Matthew Brand, Fast Online SVD Revisions for Lightweight Recommender Systems, SDM 2003.

Non-Euclidean distances

Tutorial | Time-Series with Matlab

Piecewise constant (APCA)

So far our windows were pre-determined
DFT: Entire series STFT: Single, fixed window DWT: Geometric progression of windows

Piecewise constant
Example APCA (k=10)
2 1 0 -1

Within each window we sought fairly complex patterns (sinusoids, wavelets, etc.) Next, we will allow any window size, but constrain the pattern within each window to the simplest possible (mean)

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APCA (k=21)
2 1 0 -1

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APCA (k=41)
2 1 0 -1

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Tutorial | Time-Series with Matlab

Piecewise constant (APCA)

Divide series into k segments with endpoints

Piecewise constant
Example APCA (k=10)
2 1 0

Constant length: PAA Variable length: APCA

-1

Represent all points within one average mj, 1 j k, thus minimizing

2 1 0 -1

Single-level Haar smooths, 2 , for all 1 j k if tj+1-tj = segment with their

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APCA (k=21) / Haar (level 7, 21 coeffs)

1 0 -1

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APCA (k=41) / Haar (level 6, 41 coeffs)

2 1 0 -1

Further reading: 1. Kaushik Chakrabarti, Eamonn Keogh, Sharad Mehrotra, Michael Pazzani, Locally Adaptive Dimensionality Reduction for Indexing Large Time Series Databases, TODS, 27(2), 2002.

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Tutorial | Time-Series with Matlab

Piecewise constant
Example APCA (k=10)
2 1 0 -1

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APCA (k=21) / Haar (level 7, 21 coeffs)

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APCA (k=21) / Haar (level 7, 21 coeffs)

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APCA / Haar (top-21 out of 7 levels)

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APCA (k=15) / Daubechies-3 (level 7, 15 coeffs)

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Tutorial | Time-Series with Matlab

k/h-segmentation
Again, divide the series into k segments (variable length) For each segment choose one of h quantization levels to represent all points
Now, mj can take only h k possible values

Symbolic aggregate approximation (SAX)

Quantization of values Segmentation of time based on these quantization levels More in next part

APCA = k/k-segmentation (h = k)

Further reading: 1. Aristides Gionis, Heikki Mannila, Finding Recurrent Sources in Sequences, Recomb 2003.

Tutorial | Time-Series with Matlab

K-means / Vector quantization (VQ)

APCA considers one time series and
Groups time instants Approximates them via their (scalar) mean

Vector Quantization / K-means applies to a collection of M time series (of length N)

Groups time series Approximates them via their (vector) mean

Quantized representations

Non-Euclidean distances

Tutorial | Time-Series with Matlab

K-means

K-means
Partitions the time series x(1), , x(M) into groups, Ij, for 1 j k .

All time series in the j-th group, 1 j k, are represented by their centroid, mj . Objective is to choose mj so as to minimize the overall squared distortion,

m1
1-D on values + contiguity requirement: APCA

Tutorial | Time-Series with Matlab

K-means

m2 Objective implies that, given Ij, for 1 j k,

i.e., mj is the vector mean of all points in cluster j. m1

Tutorial | Time-Series with Matlab

K-means
1. Start with arbitrary cluster assignment. 2. Compute centroids. 3. Re-assign to clusters based on new centroids. 4. Repeat from (2), until no improvement.

K-means
Example

Exchange rates
50

ESP SEK GBP

PCs
0.05 0 -0.05 0.05 0 -0.05

CAD

AUD

k=2
20

i,2

1 0 -1

Finds local optimum of D. Matlab: [idx, M] = kmeans(X, k)

DEM NZL
0

FRF BEF NLG CHF

2 1 0 -1

2 1 0 -1 -10 2 1 0 -1 2 0 -2 2 0 -2 50 60

k=4

-20

JPY

-30

-20

-10

i,1

Tutorial | Time-Series with Matlab

K-means in other coordinates

An orthonormal transform (e.g., DFT, DWT, PCA) preserves distances. K-means can be applied in any of these coordinate systems. Can transform data to speed up distance computations (if N large)

K-means and PCA

Further reading: 1. Hongyuan Zha, Xiaofeng He, Chris H.Q. Ding, Ming Gu, Horst D. Simon, Spectral Relaxation for K-means Clustering, NIPS 2001.

Tutorial | Time-Series with Matlab

Dynamic time warping (DTW)

So far we have been discussing shapes via various kinds of features or descriptions (bases) However, the series were always fixed Dynamic time warping:
Allows local deformations (stretch/shrink) Can thus also handle series of different lengths

Quantized representations

Non-Euclidean distances

Tutorial | Time-Series with Matlab

Dynamic time warping (DTW)

Euclidean (L2) distance is or, recursively, Dynamic time warping distance is

Dynamic time warping (DTW)

Each cell c = (i,j) is a pair of indices whose corresponding values will be compared, (xi yj)2, and included in the sum for the distance
y[1:j]

Euclidean path:
i = j always Ignores off-diagonal cells

where x1:i is the subsequence (x1, , xi)

shrink x / stretch y stretch x / shrink y

x[1:i]

Tutorial | Time-Series with Matlab

Dynamic time warping (DTW)

DTW allows any path Examine all paths:
shrink x / stretch y
(i-1, j) y[1:j]

Dynamic time-warping
Fast estimation

Standard dynamic programming: O(N2) Envelope-based technique

Introduced by [Keogh 2000 & 2002] Multi-scale, wavelet-like technique and formalism by [Salvador et al. 2004] and, independently, by [Sakurai et al. 2005]

(i, j)

stretch x / shrink y

(i-1, j-1) (i, j-1)

x[1:i]

Standard dynamic programming to fill in tabletop-right cell contains final result

Further reading: 1. Eamonn J. Keogh, Exact Indexing of Dynamic Time Warping, VLDB 2002. 2. Stan Salvador, Philip Chan, FastDTW: Toward Accurate Dynamic Time Warping in Linear Time and Space, TDM 2004. 3. Yasushi Sakurai, Masatoshi Yoshikawa, Christos Faloutsos, FTW: Fast Similarity Under the Time Warping Distance, PODS 2005.

Tutorial | Time-Series with Matlab

Dynamic time warping

Fast estimation Summary

Non-Euclidean metrics
Create lower-bounding distance on coarser granularity, either at
Single scale Multiple scales

Use to prune search space

x[1:i]

Tutorial | Time-Series with Matlab

Timeline of part C
Introduction TimeTime-Series Representations Distance Measures Lower Bounding Clustering/Classification/Visualization Applications

PART C: Similarity Search and Applications

Tutorial | Time-Series with Matlab

Applications (Image Matching)

Cluster 1
Many types of data can be converted to time-series
Image

Applications (Shapes)
Recognize type of leaf based on its shape

Ulmus carpinifolia

Acer platanoides

Salix fragilis

Tilia

Quercus robur

Color Histogram
600 400 200 0 400 50 100 150 200 250

Convert perimeter into a sequence of values

Cluster 2

200

100

150

200

250

800 600 400 200 0 50 100 150 200 250

Time-Series Special thanks to A. Ratanamahatana & E. Keogh for the leaf video.

Tutorial | Time-Series with Matlab

Applications (Motion Capture)

Motion-Capture (MOCAP) Data (Movies, Games) Track position of several joints over time 3*17 joints = 51 parameters per frame

Applications (Video)
Video-tracking / Surveillance Visual tracking of body features (2D time-series) Sign Language recognition (3D time-series)
Video Tracking of body feature over time (Athens1, Athens2)

MOCAPdata data MOCAP myprecious precious my

Tutorial | Time-Series with Matlab

Time-Series and Matlab

Time-series can be represented as vectors or arrays Fast vector manipulation
Most linear operations (eg euclidean distance, correlation) can be trivially vectorized

Easy visualization Many built-in functions Specialized Toolboxes

Becoming Becoming sufficiently sufficiently familiar familiar with with something something is is a a substitute substitute for for understanding understanding it. it.

PART II: Time Series Matching Introduction

Tutorial | Time-Series with Matlab

Basic Data-Mining problem

Todays databases are becoming too large. Search is difficult. How can we overcome this obstacle? Basic structure of data-mining solution: Represent data in a new format Search few data in the new representation Examine even fewer original data Provide guarantees about the search results Provide some type of data/result visualization

Basic Time-Series Matching Problem

Distance
query D = 7.3

Linear Scan: Objective: Compare the query with all sequences in DB and return the k most similar sequences to the query. Database Databasewith withtime-series: time-series: Medical Medicalsequences sequences Images, Images,etc etc Sequence SequenceLength:100-1000pts Length:100-1000pts DB Size: 1 TByte DB Size: 1 TByte

D = 10.2

D = 11.8

D = 17

D = 22

Tutorial | Time-Series with Matlab

What other problems can we solve?

Clustering: Place time-series into similar groups

Hierarchical Clustering
Very generic & powerful tool Provides visual data grouping

Pairwise distances
D1,1 D2,1

Classification: To which group is a time-series most similar to?

query ? ? ? DM,N

1. Merge objects with smallest distance 2. Reevaluate distances 3. Repeat process

Z = linkage(D); H = dendrogram(Z);

Tutorial | Time-Series with Matlab

Partitional Clustering
Faster than hierarchical clustering Typically provides suboptimal solutions (local minima) Not good performance for high dimensions

K-Means Demo

1.4 1.2 1

K-Means Algorithm: 1. Initialize k clusters (k specified by user) randomly. 2. Repeat until convergence 1. Assign each object to the nearest cluster center. 2. Re-estimate cluster centers.

0.9

0.8 0.6 0.4 0.2 0 -0.2 -0.4

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0.1

0.2

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1.5

See: kmeans

Tutorial | Time-Series with Matlab

K-Means Clustering for Time-Series

So how is kMeans applied for Time-Series that are high-dimensional? Perform kMeans on a compressed dimensionality

Classification
Typically classification can be made easier if we have clustered the objects Class A
0.4

0.2

Original sequences

Compressed sequences
0.4

Clustering space

-0.2

0.2

Project query in the new space and find its closest cluster

-0.4

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So, query Q is more similar to class B

-0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8

Class B

-0.2

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Tutorial | Time-Series with Matlab

Nearest Neighbor Classification

We need not perform clustering before classification. We can classify an object based on the class majority of its nearest neighbors/matches.

Example
Elfs

Hobbits

10 9 8 7 6 5 4 3 2 1 1 2 3 4 5 6 7 8 9 10
Height

Hair Length

What do we need?
1. Define Similarity 2. Search fast Dimensionality Reduction (compress data)

Tutorial | Time-Series with Matlab

Notion of Similarity I
Solution to any time-series problem, boils down to a proper definition of *similarity*

All All models models are are wrong, wrong, but but some some are are useful useful

PART II: Time Series Matching Similarity/Distance functions

Similarity is always subjective. (i.e. it depends on the application)

Tutorial | Time-Series with Matlab

Notion of Similarity II
Similarity depends on the features we consider (i.e. how we will describe or compress the sequences)

Metric and Non-metric Distance Functions

Distance functions Metric Euclidean Distance Correlation Properties
Positivity: 0 Positivity:d(x,y) d(x,y) 0and andd(x,y)=0, d(x,y)=0,if ifx=y x=y Symmetry: d(x,y)= =d(y,x) d(y,x) Symmetry:d(x,y) Triangle d(x,z) d(x,y) d(x,y)+ +d(y,z) d(y,z) TriangleInequality: Inequality:d(x,z) If Ifany anyof ofthese theseis isnot not obeyed obeyedthen thenthe thedistance distance is a non-metric is a non-metric

Non-Metric Time Warping LCSS

Tutorial | Time-Series with Matlab

Triangle Inequality
Triangle TriangleInequality: Inequality:d(x,z) d(x,z) d(x,y) d(x,y)+ +d(y,z) d(y,z)

Triangle Inequality (Importance)

Triangle TriangleInequality: Inequality:d(x,z) d(x,z) d(x,y) d(x,y)+ +d(y,z) d(y,z)
Assume: d(Q,bestMatch) = 20 d(Q,B) =150

z x y
Metric distance functions can exploit the triangle inequality to speed-up search

Q A B C

and

Then, since d(A,B)=20 d(Q,A) d(Q,B) d(B,A) d(Q,A) 150 20 = 130 So we dont have to retrieve A from disk

Intuitively, if: - x is similar to y and, - y is similar to z, then, - x is similar to z too.

A A B C 0 20 110

B 20 0 90

C 110 90 0

Tutorial | Time-Series with Matlab

Non-Metric Distance Functions

Euclidean Distance
Most widely used distance measure

Man similar to bat?? Bat similar to batman Batman similar to man

Matching Matchingflexibility flexibility

Robustness Robustnessto tooutliers outliers Stretching Stretchingin intime/space time/space Support Supportfor fordifferent differentsizes/lengths sizes/lengths

Definition: L2 =

(a[i] b[i])
i =1

100

Speeding-up Speeding-upsearch searchcan canbe be

difficult difficult

L2 = sqrt(sum((asqrt(sum((a-b).^2)); % return Euclidean distance

Tutorial | Time-Series with Matlab

Euclidean Distance (Vectorization)

Question: If I want to compare many sequences to each other do I have to use a for-loop? Answer: No, one can use the following equation to perform matrix computations only

Data Preprocessing (Baseline Removal)

average value of A average value of B

||A-B|| = sqrt (
A: DxM matrix

||A||2

||B||2

- 2*A.B ) result
D1,1 D2,1 DM,N

M sequences Of length D

B: DxN matrix Result is MxN matrix

aa= .*b); ab=a'*b; aa=sum(a.*a); sum(a.*a); bb=sum(b bb=sum(b.*b); ab=a'*b; d = sqrt(repmat(aa',[1 size(bb,2)]) + repmat(bb,[size(aa,2) 1]) - 2*ab ); 2*ab);

a = a mean(a); mean(a);

Tutorial | Time-Series with Matlab

Data Preprocessing (Rescaling)

Dynamic Time-Warping (Motivation)

Euclidean distance or warping cannot compensate for small distortions in time axis. A B C Solution: Allow for compression & decompression in time According to Euclidean distance B is more similar to A than to C

a = a ./ std(a); std(a);

Tutorial | Time-Series with Matlab

Dynamic Time-Warping
First used in speech recognition for recognizing words spoken at different speeds ---Maat--llaabb------------------Same idea can work equally well for generic time-series data

Dynamic Time-Warping (how does it work?)

The intuition is that we copy an element multiple times so as to achieve a better matching

Euclidean Euclideandistance distance T1 T1= =[1, [1,1, 1,2, 2,2] 2] d d= =1 1 T2 T2= =[1, [1,2, 2,2, 2,2] 2]
One-to-one linear alignment

----Mat-lab--------------------------

Warping Warpingdistance distance T1 T1= =[1, [1,1, 1,2, 2,2] 2] d d= =0 0 T2 T2= =[1, [1,2, 2,2, 2,2] 2]
One-to-many non-linear alignment

Tutorial | Time-Series with Matlab

Dynamic Time-Warping (implementation)

It is implemented using dynamic programming. Create an array that stores all solutions for all possible subsequences.

Dynamic Time-Warping (Examples)

So does it work better than Euclidean? Well yes! After all it is more costly..
Dynamic Time Warping

Euclidean Distance
18 16 7 13 14 3 9 6 2 15 11 19 10 20 17 5 12 8 4 1

c(i,j) (( A Bj))+ i, c(i,j) = =D D A i ,B j + min{ i-1, j-1) i-1, jj)), ,c( i, min{c( c( i-1, j-1), ,c( c( i-1, c( ij ,-1) j-1)}}
Recursive equation

18 20 17 13 16 14 12 19 15 11 3 9 8 7 5 6 2 10 4 1

MIT arrhythmia database

Tutorial | Time-Series with Matlab

Dynamic Time-Warping (Can we speed it up?)

Complexity is O(n2). We can reduce it to O(n) simply by restricting the warping path.

Dynamic Time-Warping (restricted warping)

Camera-Mouse dataset

The restriction of the warping path helps: A. Speed-up execution B. Avoid extreme (degenerate) matchings C. Improve clustering/classification accuracy Classification Accuracy
Camera Mouse

A
We now only fill only a small portion of the array

Australian Sign Language Minimum Bounding Envelope (MBE)

10% warping is adequate

Warping Length

Tutorial | Time-Series with Matlab

Longest Common Subsequence (LCSS)

With Time Warping extreme values (outliers) can destroy the distance estimates. The LCSS model can offer more resilience to noise and impose spatial constraints too.
ignore majority of noise

Longest Common Subsequence (LCSS)

LCSS is more resilient to noise than DTW.

Disadvantages of DTW: A. All points are matched

ignore majority of noise

B. Outliers can distort distance C. One-to-many mapping

match match

Advantages of LCSS: Matching within time and in space

Everything that is outside the bounding envelope can never be matched match match

A. Outlying values not matched B. Distance/Similarity distorted less C. Constraints in time & space

Tutorial | Time-Series with Matlab

Longest Common Subsequence (Implementation)

Similar dynamic programming solution as DTW, but now we measure similarity not distance.

Distance Measure Comparison

Dataset
Camera-Mouse

Method
Euclidean DTW LCSS

Time (sec)
34 237 210 2.2 9.1 8.2 2.1 9.3 8.3

Accuracy
20% 80%

100%
33% 44%

ASL

Euclidean DTW LCSS

46%
11% 15%

ASL+noise Can also be expressed as distance

Euclidean DTW LCSS

31%

LCSS offers enhanced robustness under noisy conditions

Tutorial | Time-Series with Matlab

Distance Measure Comparison (Overview)

Method Euclidean DTW LCSS Complexity O(n) O(n*) O(n*) Elastic Matching 2 3 3 One-to-one Matching 3 2 3 Noise Robustness 2 2 3

PART II: Time Series Matching Lower Bounding

Tutorial | Time-Series with Matlab

Basic Time-Series Problem Revisited

Compression Dimensionality Reduction

Project all sequences into a new space, and search this space instead (eg project timeseries from 100-D space to 2-D space)

Feature 1

Objective: Instead of comparing the query to the original sequences (Linear Scan/LS) , lets compare the query to simplified versions of the DB timeseries.

A B C

Feature 2 query query

One can also organize the low-dimensional points into a hierarchical index structure. In this tutorial we will not go over indexing techniques.

This ThisDB DBcan cantypically typically fit fitin inmemory memory

Question: When searching the original space it is guaranteed that we will find the best match. Does this hold (or under which circumstances) in the new compressed space?

Tutorial | Time-Series with Matlab

Concept of Lower Bounding

You can guarantee similar results to Linear Scan in the original dimensionality, as long as you provide a Lower Bounding (LB) function (in low dim) to the original distance (high dim.) GEMINI, GEneric Multimedia INdexIng
So, for projection from high dim. (N) to low dim. (n): Aa, Bb etc

Generic Search using Lower Bounding

simplified DB Answer Superset original DB Final Answer set

D (a,b) <= Dtrue(A,B) D LB LB (a,b) <= D true(A,B)

Projection onto X-axis

C B C
0 1 2 3

Verify against original DB

EF
4 5

D F E
1 2 3 4 5 0 1

False alarm (not a problem)

Projection on some other axis

B C
2 3

simplified query

EF
4 5

0 0

False dismissal (bad!)

query

Find everything within range of 1 from A

Tutorial | Time-Series with Matlab

Lower Bounding Example

sequences query

Lower Bounding Example

sequences query

Tutorial | Time-Series with Matlab

Lower Bounding Example

sequences

Lower Bounding Example

sequences

Lower Bounds
4.6399 37.9032 19.5174 72.1846 67.1436 78.0920 70.9273 63.7253 1.4121

True Distance
46.7790 108.8856 113.5873 104.5062 119.4087 120.0066 111.6011 119.0635 17.2540 BestSoFar

Tutorial | Time-Series with Matlab

Lower Bounding the Euclidean distance

There are many dimensionality reduction (compression ) techniques for time-series data. The following ones can be used to lower bound the Euclidean distance.

Fourier Decomposition
Decompose a time-series into sum of sine waves
DFT: IDFT:

Everysignal signalcan can Every berepresented representedas as be asuperposition superpositionof of a sinesand andcosines cosines sines (alasnobody nobody (alas believesme) me) believes

20 40 60 80 100 120

DFT

DWT

SVD

APCA

PAA

PLA

Figure by Eamonn Keogh, Time-Series Tutorial

Tutorial | Time-Series with Matlab

Tutorial | Time-Series with Matlab X(f)

-0.3633 -0.6280 + 0.2709i -0.4929 + 0.0399i -1.0143 + 0.9520i 0.7200 - 1.0571i -0.0411 + 0.1674i -0.5120 - 0.3572i 0.9860 + 0.8043i -0.3680 - 0.1296i -0.0517 - 0.0830i -0.9158 + 0.4481i 1.1212 - 0.6795i 0.2667 + 0.1100i 0.2667 - 0.1100i 1.1212 + 0.6795i -0.9158 - 0.4481i -0.0517 + 0.0830i -0.3680 + 0.1296i 0.9860 - 0.8043i -0.5120 + 0.3572i -0.0411 - 0.1674i 0.7200 + 1.0571i -1.0143 - 0.9520i -0.4929 - 0.0399i -0.6280 - 0.2709i

Fourier Decomposition
Decompose a time-series into sum of sine waves
DFT: IDFT:

x(n)
-0.4446 -0.9864 -0.3254 -0.6938 -0.1086 -0.3470 0.5849 1.5927 -0.9430 -0.3037 -0.7805 -0.1953 -0.3037 0.2381 2.8389 -0.7046 -0.5529 -0.6721 0.1189 0.2706 -0.0003 1.3976 -0.4987 -0.2387 -0.7588

Fourier Decomposition
How much space we gain by compressing random walk data?

Reconstruction using 1coefficients

-5 50 100 150 200 250

1 coeff > 60% of energy 10 coeff > 90% of energy

fa = fft(a); fft(a); % Fourier decomposition fa(5:end) = 0; % keep first 5 coefficients (low frequencies) reconstr = real(ifft(fa)); real(ifft(fa)); % reconstruct signal Life is complex, it has both real and imaginary parts.

Tutorial | Time-Series with Matlab

Fourier Decomposition
How much space we gain by compressing random walk data?

Reconstruction using 2coefficients

Reconstruction using 7coefficients

-5 50 100 150 200 250

1 coeff > 60% of energy 10 coeff > 90% of energy

Tutorial | Time-Series with Matlab

Fourier Decomposition
How much space we gain by compressing random walk data?

Fourier Decomposition
How much space we gain by compressing random walk data?
Error 1500 1 0.95 Energy Percentage

Reconstruction using 20coefficients 1000 5 500

0.9 0.85 0.8 0.75 0.7

-5 50 100 150 200 250 0 20 40 60 80 Coefficients 100 120

0.65 20 40 60 80 Coefficients 100 120

1 coeff > 60% of energy 10 coeff > 90% of energy

Tutorial | Time-Series with Matlab

Fourier Decomposition
Which coefficients are important? We can measure the energy of each coefficient Energy = Real(X(fk))2 + Imag(X(fk))2
Most of data-mining research uses first k coefficients: Good for random walk signals (eg stock market) Easy to index Not good for general signals

Fourier Decomposition
Which coefficients are important? We can measure the energy of each coefficient Energy = Real(X(fk))2 + Imag(X(fk))2
Usage of the coefficients with highest energy: Good for all types of signals Believed to be difficult to index CAN be indexed using metric trees

fa = fft(a); fft(a); % Fourier decomposition N = length(a); length(a); % how many? fa = fa(1:ceil(N/2)); % keep first half only mag = 2*abs(fa).^2; % calculate energy

Tutorial | Time-Series with Matlab

Tutorial | Time-Series with Matlab X(f)

0 -0.6280 + 0.2709i

Code for Reconstructed Sequence

a = load('randomWalk.dat'); a = (a(a-mean(a))/std(a); fa = fft(a); maxInd = ceil(length(a)/2); N = length(a); energy = zeros(maxIndzeros(maxInd-1, 1); E = sum(a.^2); for ind=2:maxInd, fa_N = fa; fa_N(ind+1:Nfa_N(ind+1:N-ind+1) = 0; r = real(ifft(fa_N)); % copy fourier % zero out unused % reconstruction % until the middle % zz-normalization

Code for Plotting the Error

a = load('randomWalk.dat'); a = (a(a-mean(a))/std(a); fa = fft(a); maxInd = ceil(length(a)/2); N = length(a); energy = zeros(maxIndzeros(maxInd-1, 1); E = sum(a.^2); for ind=2:maxInd, fa_N = fa; fa_N(ind+1:Nfa_N(ind+1:N-ind+1) = 0; r = real(ifft(fa_N)); % zz-normalization This is the same % until the middle

keep

-0.4929 + 0.0399i -1.0143 + 0.9520i 0.7200 - 1.0571i -0.0411 + 0.1674i -0.5120 - 0.3572i 0.9860 + 0.8043i -0.3680 - 0.1296i -0.0517 - 0.0830i

% energy of a

-0.9158 + 0.4481i 1.1212 - 0.6795i

Ignore

0.2667 + 0.1100i 0.2667 - 0.1100i 1.1212 + 0.6795i -0.9158 - 0.4481i -0.0517 + 0.0830i -0.3680 + 0.1296i 0.9860 - 0.8043i -0.5120 + 0.3572i -0.0411 - 0.1674i 0.7200 + 1.0571i -1.0143 - 0.9520i -0.4929 - 0.0399i -0.6280 - 0.2709i

% copy fourier % zero out unused % reconstruction

energy(indenergy(ind-1) = sum(r.^2); % energy of reconstruction error(inderror(ind-1) = sum(abs(rsum(abs(r-a).^2); % error end E = ones(maxIndones(maxInd-1, 1)*E; error = E - energy; ratio = energy ./ E; subplot(1,2,1); % left plot plot([1:maxIndplot([1:maxInd-1], error, 'r', 'LineWidth',1.5); subplot(1,2,2); % right plot plot([1:maxIndplot([1:maxInd-1], ratio, 'b', 'LineWidth',1.5);

end

plot(r, 'r','LineWidth',2); hold on; plot(a,'k'); title(['Reconstruction using ' num2str(indnum2str(ind-1) 'coefficients']); set(gca,'plotboxaspectratio', [3 1 1]); axis tight pause; % wait for key cla; % clear axis keep

Tutorial | Time-Series with Matlab

Lower Bounding using Fourier coefficients

Parsevals Theorem states that energy in the frequency domain equals the energy in the time domain:

Lower Bounding using Fourier coefficients -Example

x y or, that Euclidean distance

If we just keep some of the coefficients, their sum of squares always underestimates (ie lower bounds) the Euclidean distance:

Note the normalization

x = cumsum(randn(100,1)); y = cumsum(randn(100,1)); euclid_Time = sqrt(sum((xsqrt(sum((x-y).^2));

120.9051

Keeping 10 coefficients the distance is: 115.5556 < 120.9051

fx = fft(x)/sqrt(length(x)); fft(x)/sqrt(length(x)); fy = fft(y)/sqrt(length(x)); fft(y)/sqrt(length(x)); euclid_Freq = sqrt(sum(abs(fx - fy).^2));

120.9051

Tutorial | Time-Series with Matlab

Fourier Decomposition

Wavelets Why exist?

Similar concept with Fourier decomposition Fourier coefficients represent global contributions, wavelets are localized

O(nlogn) O(nlogn)complexity complexity Tried Triedand andtested tested Hardware Hardwareimplementations implementations Many Manyapplications: applications: compression compression smoothing smoothing periodicity periodicitydetection detection

Not Notgood goodapproximation approximationfor for bursty burstysignals signals Not Notgood goodapproximation approximationfor for signals signalswith withflat flatand andbusy busy sections sections (requires (requiresmany manycoefficients) coefficients) Fourier is good for smooth, random walk data, but not for bursty data or flat data

Tutorial | Time-Series with Matlab

Wavelets (Haar) - Intuition

Wavelet coefficients, still represent an inner product (projection) of the signal with some basis functions. These functions have lengths that are powers of two (full sequence length, half, quarter etc)
c-d00 c+d00 D

Wavelets in Matlab
Specialized Matlab interface for wavelets

An arithmetic example X = [9,7,3,5] Haar = [6,2,1,-1]

etc

c = 6 = (9+7+3+5)/4 c + d00 = 6+2 = 8 = (9+7)/2 c - d00 = 6-2 = 4 = (3+5)/2 etc

Haar coefficients: {c, d00, d10, d11,}

Tutorial | Time-Series with Matlab

Code for Haar Wavelets

a = load('randomWalk.dat'); a = (a% z(a-mean(a))/std(a); z-normalization maxlevels = wmaxlev(length(a),'haar'); [Ca, La] = wavedec(a,maxlevels,'haar'); % Plot coefficients and MRA for level = 1:maxlevels cla; subplot(2,1,1); plot(detcoef(Ca,La,level)); axis tight; title(sprintf('Wavelet coefficients Level %d',level)); subplot(2,1,2); plot(wrcoef('d',Ca,La,'haar',level)); axis tight; title(sprintf('MRA Level %d',level)); pause; end % TopTop-20 coefficient reconstruction [Ca_sorted, Ca_sortind] = sort(Ca); Ca_top20 = Ca; Ca_top20(Ca_sortind(1:endCa_top20(Ca_sortind(1:end-19)) = 0; a_top20 = waverec(Ca_top20,La,'haar'); figure; hold on; plot(a, 'b'); plot(a_top20, 'r');

PAA (Piecewise Aggregate Approximation)

also featured as Piecewise Constant Approximation Represent time-series as a sequence of segments Essentially a projection of the Haar coefficients in time
Reconstruction using 1coefficients 2 1 0 -1 -2 50 100 150 200 250

Tutorial | Time-Series with Matlab

PAA (Piecewise Aggregate Approximation)

Tutorial | Time-Series with Matlab

PAA (Piecewise Aggregate Approximation)

Tutorial | Time-Series with Matlab

PAA (Piecewise Aggregate Approximation)

PAA Matlab Code

function data = paa(s, numCoeff) % PAA(s, numcoeff) % s: sequence vector (Nx1 or Nx1) % numCoeff: number of PAA segments % data: PAA sequence (Nx1) N = length(s); segLen = N/numCoeff; % length of sequence % assume it's integer % % % % break in segments average segments expand segments make column

sN = reshape(s, segLen, numCoeff); avg = mean(sN); data = repmat(avg, segLen, 1); data = data(:);

numCoeff

Tutorial | Time-Series with Matlab

PAA Matlab Code

function data = paa(s, numCoeff) % PAA(s, numcoeff) % s: sequence vector (Nx1 or Nx1) % numCoeff: number of PAA segments % data: PAA sequence (Nx1)

N=8 segLen = 2

N = length(s); segLen = N/numCoeff;

% length of sequence % assume it's integer

N=8 segLen = 2

sN = reshape(s, segLen, numCoeff); avg = mean(sN); data = repmat(avg, segLen, 1); data = data(:);

% % % %

break in segments average segments expand segments make column

numCoeff

s sN

numCoeff

1 2

3 4

5 6

7 8

Tutorial | Time-Series with Matlab

PAA Matlab Code

function data = paa(s, numCoeff) % PAA(s, numcoeff) % s: sequence vector (1xN) % numCoeff: number of PAA segments % data: PAA sequence (1xN)

N=8 segLen = 2

N = length(s); segLen = N/numCoeff;

% length of sequence % assume it's integer % % % % break in segments average segments expand segments make row

N=8 segLen = 2

sN = reshape(s, segLen, numCoeff); avg = mean(sN); data = repmat(avg, segLen, 1); data = data(:);

sN = reshape(s, segLen, numCoeff); avg = mean(sN); 2 data = repmat(avg, segLen, 1); data = data(:) data(:);

s sN avg

numCoeff

s sN avg

numCoeff
1.5 3.5 3.5 5.5 5.5 7.5 7.5

1 2 1.5

3 4 3.5

5 6 5.5

7 8 7.5

1 2 1.5

3 4 3.5

5 6 5.5

7 8 7.5

data

1.5

Tutorial | Time-Series with Matlab

PAA Matlab Code

function data = paa(s, numCoeff) % PAA(s, numcoeff) % s: sequence vector (1xN) % numCoeff: number of PAA segments % data: PAA sequence (1xN) N = length(s); segLen = N/numCoeff; % length of sequence % assume it's integer % % % % break in segments average segments expand segments make row

APCA (Adaptive Piecewise Constant Approximation)

PAA

Segments of equal size

Not all haar/PAA coefficients are equally important Intuition: Keep ones with the highest energy Segments of variable length APCA is good for bursty signals PAA requires 1 number per segment, APCA requires 2: [value, length]
E.g. 10 bits for a sequence of 1024 points

N=8 segLen = 2

sN = reshape(s, segLen, numCoeff); avg = mean(sN); data = repmat(avg, segLen, 1); data = data(:) data(:);

APCA

s sN avg

numCoeff
1.5 3.5 3.5 1.5 5.5 5.5 3.5 7.5 7.5 3.5

Segments of variable size

1 2 1.5

3 4 3.5

5 6 5.5

7 8 7.5

data data

1.5 1.5

5.5

7.5

Tutorial | Time-Series with Matlab

Wavelet Decomposition

Piecewise Linear Approximation (PLA)

Approximate a sequence with multiple linear segments First such algorithms appeared in cartography for map approximation Many implementations Optimal Greedy Bottom-Up Greedy Top-down Genetic, etc You can find a bottom-up implementation here: http://www.cs.ucr.edu/~eamonn/TSDMA/time_series_toolbox/

O(n) O(n)complexity complexity Hierarchical Hierarchicalstructure structure Progressive Progressivetransmission transmission Better Betterlocalization localization Good Goodfor forbursty burstysignals signals

Most Mostdata-mining data-miningresearch research still stillutilizes utilizesHaar Haarwavelets wavelets because of their simplicity. because of their simplicity.

Many Manyapplications: applications: compression compression periodicity periodicitydetection detection

Tutorial | Time-Series with Matlab

Piecewise Linear Approximation (PLA)

Approximate a sequence with multiple linear segments First such algorithms appeared in cartography for map approximation

Piecewise Linear Approximation (PLA)

Approximate a sequence with multiple linear segments First such algorithms appeared in cartography for map approximation

Tutorial | Time-Series with Matlab

Piecewise Linear Approximation (PLA)

Approximate a sequence with multiple linear segments First such algorithms appeared in cartography for map approximation

Piecewise Linear Approximation (PLA)

Approximate a sequence with multiple linear segments First such algorithms appeared in cartography for map approximation

Tutorial | Time-Series with Matlab

Piecewise Linear Approximation (PLA)

Approximate a sequence with multiple linear segments First such algorithms appeared in cartography for map approximation

Piecewise Linear Approximation (PLA)

O(nlogn) O(nlogn)complexity complexityfor for bottom bottomup upalgorithm algorithm Incremental Incrementalcomputation computation possible possible Provable Provableerror errorbounds bounds Applications Applicationsfor: for: Image Image//signal signal simplification simplification Trend Trenddetection detection

Visually Visuallynot notvery verysmooth smoothor or pleasing. pleasing.

Tutorial | Time-Series with Matlab

Singular Value Decomposition (SVD)

SVD attempts to find the optimal basis for describing a set of multidimensional points Objective: Find the axis (directions) that describe better the data variance

Singular Value Decomposition (SVD)

Each time-series is essentially a multidimensional point Objective: Find the eigenwaves (basis) whose linear combination describes best the sequences. Eigenwaves are data-dependent.
eigenwave 0

AMxn = UMxr * rxr * VTnxr

Factoring of data array into 3 matrices

eigenwave 1

each of length n
eigenwave 3

eigenwave 4

y We need 2 numbers (x,y) for every point

y Now we can describe each point with 1 number, their projection on the line

M sequences

[U,S,V] = svd(A) svd(A)

New axis and position of points (after projection and rotation)

A linear combination of the eigenwaves can produce any sequence in the database

Tutorial | Time-Series with Matlab

Code for SVD / PCA

A = cumsum(randn(100,10)); % zz-normalization A = (A(A-repmat(mean(A),size(A,1),1))./repmat(std(A),size(A,1),1); [U,S,V] = svd(A,0); % Plot relative energy figure; plot(cumsum(diag(S).^2)/norm(diag(S))^2); set(gca, 'YLim', [0 1]); pause; % TopTop-3 eigenvector reconstruction A_top3 = U(:,1:3)*S(1:3,1:3)*V(:,1:3)'; % Plot original and reconstruction figure; for i = 1:10 cla; subplot(2,1,1); plot(A(:,i)); title('Original'); axis tight; subplot(2,1,2); plot(A_top3(:,i)); title('Reconstruction'); axis tight; pause; end

Singular Value Decomposition

Optimal Optimaldimensionality dimensionality reduction reductionin inEuclidean Euclidean distance distancesense sense SVD SVDis isa avery verypowerful powerfultool tool in inmany manydomains: domains: Websearch Websearch(PageRank) (PageRank)

Cannot Cannotbe beapplied appliedfor forjust just one onesequence. sequence.A Aset setof of sequences sequencesis isrequired. required. Addition Additionof ofa asequence sequencein in database databaserequires requires recomputation recomputation Very Verycostly costlyto tocompute. compute. 2n), O(Mn22 Time: n), O(Mn )} )} Time:min{ min{O(M O(M2 Space: Space:O(Mn) O(Mn)
M Msequences sequencesof oflength lengthn n

Tutorial | Time-Series with Matlab

Symbolic Approximation
Assign a different symbol based on range of values Find ranges either from data histogram or uniformly

Symbolic Approximations

c c b
0

c b
Linear Linearcomplexity complexity After Aftersymbolization symbolizationmany many tools toolsfrom frombioinformatics bioinformatics can canbe beused used Markov Markovmodels models Suffix-Trees, Suffix-Trees,etc etc Number Numberof ofregions regions (alphabet (alphabetlength) length)can canaffect affect the quality of the quality ofresult result

b a
20

a
40 60 80 100 120

baabccbc
You can find an implementation here: http://www.ise.gmu.edu/~jessica/sax.htm

Tutorial | Time-Series with Matlab

Multidimensional Time-Series
Catching momentum lately Applications for mobile trajectories, sensor networks, epidemiology, etc

Ari,are areyou yousure surethe the Ari, world is not 1D? world is not 1D?

Multidimensional MBRs
Find Bounding rectangles that completely contain a trajectory given some optimization criteria (eg minimize volume)

Lets see how to approximate 2D trajectories with Minimum Bounding Rectangles

Aristotle

On my income tax 1040 it says "Check this box if you are blind." I wanted to put a check mark about three inches away. - Tom Lehrer

Tutorial | Time-Series with Matlab

Comparison of different Dim. Reduction Techniques

So which dimensionality reduction is the best?

Fourieris is Fourier good good APCAis is APCA better better PAA! PAA! thanPAA! PAA! than Chebyshev Chebyshev isbetter better is thanAPCA! APCA! than The The futureis is future symbolic! symbolic!

1993

2000

2001

2004

2005

Absence of proof is no proof of absence. - Michael Crichton

Tutorial | Time-Series with Matlab

Comparisons
Lets see how tight the lower bounds are for a variety on 65 datasets
Average Lower Bound

A. No approach is better on all datasets B. Best coeff. techniques can offer tighter bounds C. Choice of compression depends on application
Note: similar results also reported by Keogh in SIGKDD02

PART II: Time Series Matching Lower Bounding the DTW and LCSS

Median Lower Bound

Tutorial | Time-Series with Matlab

Lower Bounding the Dynamic Time Warping

Recent approaches use the Minimum Bounding Envelope for bounding the DTW Create Minimum Bounding Envelope (MBE) of query Q Calculate distance between MBE of Q and any sequence A One can show that: D(MBE(Q) D(MBE(Q),A) < DTW(Q,A)

Lower Bounding the Dynamic Time Warping

LB by Keogh approximate MBE and sequence using MBRs LB = 13.84
Q A

MBE(Q)

LB = sqrt(sum([[A > U].* [A-U]; [A < L].* [L-A]].^2)); One Matlab command! U LB by Zhu and Shasha approximate MBE and sequence using PAA However, this representation is uncompressed. Both MBE and the DB sequence can be compressed using any of the previously mentioned techniques. LB = 25.41
Q A

Tutorial | Time-Series with Matlab

Lower Bounding the Dynamic Time Warping

An even tighter lower bound can be achieved by warping the MBE approximation against any other compressed signal. LB_Warp = 29.05

Time Comparisons
We will use DTW (and the corresponding LBs) for recognition of hand-written digits/shapes.

Lower Bounding approaches for DTW, will typically yield at least an order of magnitude speed improvement compared to the nave approach. Lets compare the 3 LB approaches:

Accuracy: Using DTW we can achieve recognition above 90%. Running Time: runTime LB_Warp < runTime LB_Zhu < runTime LB-Keogh Pruning Power: For some queries LB_Warp can examine up to 65 time fewer sequences

Tutorial | Time-Series with Matlab

Upper Bounding the LCSS

Since LCSS measures similarity and similarity is the inverse of distance, to speed up LCSS we need to upper bound it.

LCSS Application Image Handwriting

Library of Congress has 54 million manuscripts (20TB of text) Increasing interest for automatic transcribing

Word annotation:
1. 1.Extract Extractwords wordsfrom fromdocument document 2. 2.Extract Extractimage imagefeatures features 3. 3.Annotate Annotateaasubset subsetof ofwords words 4. 4.Classify Classifyremaining remainingwords words

LCSS(MBE ,A) >= LCSS(Q,A) Q LCSS(MBE Q,A) >= LCSS(Q,A)

Indexed Sequence Query

1 0.8

Sim.=50/77 = 0.64

Feature Value

0.6 0.4 0.2 0

100

150

200 Column

250

300

350

400

Features:

44 points

6 points

George Washington Manuscript

- Black pixels / column - Ink-paper transitions/ col , etc

Tutorial | Time-Series with Matlab

LCSS Application Image Handwriting

Utilized 2D time-series (2 features) Returned 3-Nearest Neighbors of following words Classification accuracy > 70%

PART II: Time Series Analysis Test Case and Structural Similarity Measures

Tutorial | Time-Series with Matlab

Analyzing Time-Series Weblogs

PKDD 2005

Weblog Data Representation

Record We can aggregate information, eg, number of requests per day for each keyword
Query: Spiderman
Requests

May 2002. Spiderman 1 was released in theaters

Porto

Jan

Feb Mar

Apr May Jun

Jul

Aug Sep Okt

Nov Dec

Weblog of user requests over time

Capture trends and periodicities Privacy preserving

Google Zeitgeist

Priceline

Tutorial | Time-Series with Matlab

Finding similar patterns in query logs

We can find useful patterns and correlation in the user demand patterns which can be useful for: Search engine optimization Recommendations Advertisement pricing (e.g. keyword more expensive at the popular months)

Finding similar patterns in query logs

Requests

Query: ps2
Jan Feb Mar Apr May Jun Jul Aug Sep Okt Nov Dec

Requests

Query: xbox

Query: elvis
Jan Feb Mar Apr May Jun Jul Aug Sep Okt Nov Dec

Game consoles are more popular closer to Christmas

th Burst on Aug. 16 Death Anniversary of Elvis

Tutorial | Time-Series with Matlab

Matching of Weblog data

Use Euclidean distance to match time-series. But which dimensionality reduction technique to use? Lets look at the data:

First Fourier Coefficients vs Best Fourier Coefficients

Query Bach 1 year span

The data is smooth and highly periodic, so we can use Fourier decomposition. Instead of using the first Fourier coefficients we can use the best ones instead. Lets see how the approximation will look:

Using the best coefficients, provides a very high quality approximation of the original time-series

Query stock market

Tutorial | Time-Series with Matlab

Matching results I
Query = Lance Armstrong

Matching results II
Query = Christmas

2000

2001

2002

2000

2001

2002

LeTour
0 2000 2001 2002

Knn4: Christmas coloring books Knn8: Christmas baking Knn12: Christmas clipart

Tour De France Knn20: Santa Letters

0 2000 2001 2002

Tutorial | Time-Series with Matlab

Finding Structural Matches

The Euclidean distance cannot distill all the potentially useful information in the weblog data. Some data are periodic, while other are bursty. We will attempt to provide similarity measures that are based on periodicity and burstiness.
Query cinema. Weakly periodicity. Peak of period every Friday.

Periodic Matching
Frequency Ignore Phase/ Keep important components Calculate Distance

F ( x), F ( y )
cinema

arg max || F ( x) ||, F ( x + ) k arg max || F ( y ) ||, F ( y + )

Periodogram

D1 =|| F ( x + ) F ( y + ) || D2 =|| F ( x + ) F ( y + ) ||

stock

easter

Query Elvis. Burst in demand on 16th August. Death anniversary of Elvis Presley

christmas

Tutorial | Time-Series with Matlab

Matching Results with Periodic Measure

Now we can discover more flexible matches. We observe a clear separation between seasonal and periodic sequences.

Matching Results with Periodic Measure

Compute pairwise periodic distances and do a mapping of the sequences on 2D using Multi-dimensional scaling (MDS).

Tutorial | Time-Series with Matlab

Matching Based on Bursts

Another method of performing structural matching can be achieved using burst features of sequences. Burst feature detection can be useful for: Identification of important events Query-by-burst
Harry Potter 2 (November 15 2002)

Burst Detection
Burst detection is similar to anomaly detection. Create distribution of values (eg gaussian model) Any value that deviates from the observed distribution (eg more than 3 std) can be considered as burst.

Valentines Day Mothers Day

Harry Potter 1 (Movie)

Harry Potter 1 (DVD)

2002: Harry Potter demand

100

150

200

250

300

350

Tutorial | Time-Series with Matlab

Query-by-burst
To perform query-by-burst we can perform the following steps: 1. 2. 3. Find burst regions in given query Represent query bursts as time segments Find which sequences in DB have overlapping burst regions.

Query-by-burst Results

Queries

Pentagon attack

www.nhc.noaa.gov

Cheap gifts

Matches

Nostradamus prediction

Tropical Storm

Scarfs

Tutorial | Time-Series with Matlab

Structural Similarity Measures

Periodic similarity achieves high clustering/classification accuracy in ECG data
DTW
34 33 30 35 27 26 36 31 28 32 29 25 24 21 17 13 23 20 22 19 15 18 16 14 11 7 9 6 3 2 10 4 12 8 5 1 36 35 33 28 27 26 32 34 30 31 29 25 18 23 20 19 17 24 22 16 14 15 21 13 12 8 2 7 11 5 9 3 10 6 4 1

Structural Similarity Measures

Periodic similarity is a very powerful visualization tool.
Random Walk Random Walk Sunspots: 1869 to 1990 Sunspots: 1749 to 1869 Great Lakes (Ontario) Great Lakes (Erie) Power Demand: April-June (Dutch) Power Demand: Jan-March (Dutch) Power Demand: April-June (Italian) Power Demand: Jan-March (Italian) Random Random Video Surveillance: Eamonn, no gun Video Surveillance: Eamonn, gun Video Surveillance: Ann, no gun Video Surveillance: Ann, gun Koski ECG: fast 2 Koski ECG: fast 1 Koski ECG: slow 2 Koski ECG: slow 1 MotorCurrent: healthy 2 MotorCurrent: healthy 1 MotorCurrent: broken bars 2 MotorCurrent: broken bars 1

Periodic Measure

Incorrect Grouping

Tutorial | Time-Series with Matlab

Structural Similarity Measures

Burst correlation can provide useful insights for understanding which sequences are related/connected. Applications for: Gene Expression Data Stock market data (identification of causal chains of events)
Query: Which stocks exhibited trading bursts during 9/11 attacks?

Conclusion
The traditional shape matching measures cannot address all timeseries matching problems and applications. Structural distance measures can provide more flexibility. There are many other exciting time-series problems that havent been covered in this tutorial: Anomaly Detection

PRICELINE: Stock value dropped

Idont dontwant wantto to I achieveimmortality immortality achieve throughmy myworkI workI through wantto toachieve achieveit it want through not dying. through not dying.

Frequent pattern Discovery

NICE SYSTEMS: Stock value increased (provider of air traffic control systems)

Rule Discovery etc

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