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CS 277, Data Mining Exploratory Data Analysis Padhraic Smyth Department of Computer Science Bren School of Information and Computer Sciences University of California, Irvine

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Padhraic Smyth, UC Irvine: CS 277, Winter Outline of Today’s Lecture Assignment 1: Questions? Overview of Exploratory Data Analysis –Analyzing single variables –Analyzing pairs of variables –Higher-dimensional visualization techniques –Dimension reduction methods –Clustering methods

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Padhraic Smyth, UC Irvine: CS 277, Winter Exploratory Data Analysis: Single Variables

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Padhraic Smyth, UC Irvine: CS 277, Winter Summary Statistics Mean: “center of data” Mode: location of highest data density Variance: “spread of data” Skew: indication of non-symmetry Range: max - min Median: 50% of values below, 50% above Quantiles: e.g., values such that 25%, 50%, 75% are smaller Note that some of these statistics can be misleading E.g., mean for data with 2 clusters may be in a region with zero data

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Padhraic Smyth, UC Irvine: CS 277, Winter Histogram of Unimodal Data 1000 data points simulated from a Normal distribution, mean 10, variance 1, 30 bins

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Padhraic Smyth, UC Irvine: CS 277, Winter Histograms: Unimodal Data 100 data points from a Normal, mean 10, variance 1, with 5, 10, 30 bins

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Padhraic Smyth, UC Irvine: CS 277, Winter Histogram of Multimodal Data data points simulated from a mixture of 3 Normal distributions, 300 bins

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Padhraic Smyth, UC Irvine: CS 277, Winter Histogram of Multimodal Data data points simulated from a mixture of 3 Normal distributions, 300 bins

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Padhraic Smyth, UC Irvine: CS 277, Winter Skewed Data 5000 data points simulated from an exponential distribution, 100 bins

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Padhraic Smyth, UC Irvine: CS 277, Winter Another Skewed Data Set data points simulated from a mixture of 2 exponentials, 100 bins

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Padhraic Smyth, UC Irvine: CS 277, Winter Same Skewed Data after taking Logs (base 10) data points simulated from a mixture of 2 exponentials, 100 bins

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Padhraic Smyth, UC Irvine: CS 277, Winter What will the mean or median tell us about this data?

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Padhraic Smyth, UC Irvine: CS 277, Winter Histogram Most common form: split data range into equal-sized bins For each bin, count the number of points from the data set that fall into the bin. –Vertical axis: frequency or counts –Horizontal axis: variable values

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Padhraic Smyth, UC Irvine: CS 277, Winter Issues with Histograms For small data sets, histograms can be misleading. Small changes in the data or to the bucket boundaries can result in very different histograms. For large data sets, histograms can be quite effective at illustrating general properties of the distribution. Can smooth histogram using a variety of techniques –E.g., kernel density estimation Histograms effectively only work with 1 variable at a time –Difficult to extend to 2 dimensions, not possible for >2 –So histograms tell us nothing about the relationships among variables

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Padhraic Smyth, UC Irvine: CS 277, Winter US Zipcode Data: Population by Zipcode K = 50 K = 500 K = 50

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Padhraic Smyth, UC Irvine: CS 277, Winter Histogram with Outliers X values Number of Individuals Pima Indians Diabetes Data, From UC Irvine Machine Learning Repository

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Padhraic Smyth, UC Irvine: CS 277, Winter Histogram with Outliers blood pressure = 0 ? Diastolic Blood Pressure Number of Individuals Pima Indians Diabetes Data, From UC Irvine Machine Learning Repository

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Padhraic Smyth, UC Irvine: CS 277, Winter Box Plots: Pima Indians Diabetes Data Body Mass Index Healthy Individuals Diabetic Individuals Two side-by-side box-plots of individuals from the Pima Indians Diabetes Data Set

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Padhraic Smyth, UC Irvine: CS 277, Winter Box Plots: Pima Indians Diabetes Data Body Mass Index Healthy Individuals Diabetic Individuals Box = middle 50% of data Plots all data points outside “whiskers” 1.5 x Q3-Q1 Q2 (median) Q3 Q1 Upper Whisker Lower Whisker Two side-by-side box-plots of individuals from the Pima Indians Diabetes Data Set

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Padhraic Smyth, UC Irvine: CS 277, Winter Box Plots: Pima Indians Diabetes Data healthydiabetichealthydiabetic Diastolic Blood Pressure 24-hour Serum Insulin Plasma Glucose Concentration Body Mass Index

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Padhraic Smyth, UC Irvine: CS 277, Winter Exploratory Data Analysis Tools for Displaying Pairs of Variables

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Padhraic Smyth, UC Irvine: CS 277, Winter Relationships between Pairs of Variables Say we have a variable Y we want to predict and many variables X that we could use to predict Y In exploratory data analysis we may be interested in quickly finding out if a particular X variable is potentially useful at predicting Y Options? –Linear correlation (X, Y) = E [ (X – X ) (Y – Y ) ], between -1 and +1 –Scatter plot: plot Y versus X

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Padhraic Smyth, UC Irvine: CS 277, Winter Examples of X-Y plots and linear correlation values

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Padhraic Smyth, UC Irvine: CS 277, Winter Examples of X-Y plots and linear correlation values

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Padhraic Smyth, UC Irvine: CS 277, Winter Examples of X-Y plots and linear correlation values Linear Dependence Non-Linear Dependence Lack if linear correlation does not imply lack of dependence

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Padhraic Smyth, UC Irvine: CS 277, Winter Anscombe, Francis (1973), Graphs in Statistical Analysis, The American Statistician, pp

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Padhraic Smyth, UC Irvine: CS 277, Winter Guess the Linear Correlation Values for each Data Set Anscombe, Francis (1973), Graphs in Statistical Analysis, The American Statistician, pp

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Padhraic Smyth, UC Irvine: CS 277, Winter Correlation = 0.82 Actual Correlation Values Anscombe, Francis (1973), Graphs in Statistical Analysis, The American Statistician, pp

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Padhraic Smyth, UC Irvine: CS 277, Winter Summary Statistics for each Data Set Summary Statistics of Data Set 1 N = 11 Mean of X = 9.0 Mean of Y = 7.5 Intercept = 3 Slope = 0.5 Correlation = 0.82 Summary Statistics of Data Set 3 N = 11 Mean of X = 9.0 Mean of Y = 7.5 Intercept = 3 Slope = 0.5 Correlation = 0.82 Summary Statistics of Data Set 4 N = 11 Mean of X = 9.0 Mean of Y = 7.5 Intercept = 3 Slope = 0.5 Correlation = 0.82 Summary Statistics of Data Set 2 N = 11 Mean of X = 9.0 Mean of Y = 7.5 Intercept = 3 Slope = 0.5 Correlation = 0.82 Anscombe, Francis (1973), Graphs in Statistical Analysis, The American Statistician, pp

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Padhraic Smyth, UC Irvine: CS 277, Winter Conclusions so far? Summary statistics are useful…..up to a point Linear correlation measures can be misleading There really is no substitute for plotting/visualizing the data

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Padhraic Smyth, UC Irvine: CS 277, Winter Scatter Plot: No apparent relationship

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Padhraic Smyth, UC Irvine: CS 277, Winter Scatter Plot: Linear relationship

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Padhraic Smyth, UC Irvine: CS 277, Winter Scatter Plot: Quadratic relationship

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Padhraic Smyth, UC Irvine: CS 277, Winter Constant Variance Relationship Variation of Y Does Not Depend on X

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Padhraic Smyth, UC Irvine: CS 277, Winter Increasing Variance variation in Y differs depending on the value of X e.g., Y = annual tax paid, X = income

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Padhraic Smyth, UC Irvine: CS 277, Winter (from US Zip code data: each point = 1 Zip code) units = dollars

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Padhraic Smyth, UC Irvine: CS 277, Winter Problems with Scatter Plots of Large Data 96,000 bank loan applicants appears: later apps older; reality: downward slope (more apps, more variance) scatter plot degrades into black smudge...

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Padhraic Smyth, UC Irvine: CS 277, Winter Problems with Scatter Plots of Large Data 96,000 bank loan applicants appears: later apps older; reality: downward slope (more apps, more variance) scatter plot degrades into black smudge...

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Padhraic Smyth, UC Irvine: CS 277, Winter Contour Plots Can Help (same 96,000 bank loan apps as before) recall: unimodal skewed shows variance(y) with x is indeed due to horizontal skew in density skewed

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Padhraic Smyth, UC Irvine: CS 277, Winter Summary on Exploration/Visualization Always useful and worthwhile to visualize data –human visual system is excellent at pattern recognition –gives us a general idea of how data is distributed, e.g., extreme skew –detect “obvious outliers” and errors in the data –gain a general understanding of low-dimensional properties Many different visualization techniques Limitations –generally only useful up to 3 or 4 dimensions –massive data: only so many pixels on a screen - but subsampling is useful

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Padhraic Smyth, UC Irvine: CS 277, Winter Exploratory Data Analysis Tools for Displaying More than 2 Variables

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Padhraic Smyth, UC Irvine: CS 277, Winter Multivariate Visualization Multivariate -> multiple variables 2 variables: scatter plots, etc 3 variables: –3-dimensional plots –Look impressive, but often not used –Can be cognitively challenging to interpret –Alternatives: overlay color-coding (e.g., categorical data) on 2d scatter plot 4 variables: –3d with color or time –Can be effective in certain situations, but tricky Higher dimensions –Generally difficult –Scatter plots, icon plots, parallel coordinates: all have weaknesses –Alternative: “map” data to lower dimensions, e.g., PCA or multidimensional scaling –Main problem: high-dimensional structure may not be apparent in low-dimensional views

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Padhraic Smyth, UC Irvine: CS 277, Winter Scatter Plot Matrix For interactive visualization the concept of “linked plots” is generally useful

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Padhraic Smyth, UC Irvine: CS 277, Winter Using Icons to Encode Information, e.g., Star Plots Each star represents a single observation. Star plots are used to examine the relative values for a single data point The star plot consists of a sequence of equi-angular spokes, called radii, with each spoke representing one of the variables. Useful for small data sets with up to 10 or so variables Limitations? –Small data sets, small dimensions –Ordering of variables may affect perception 1 Price 2 Mileage (MPG) Repair Record (1 = Worst, 5 = Best) Repair Record (1 = Worst, 5 = Best) 5 Headroom 6 Rear Seat Room 7 Trunk Space 8 Weight 9 Length

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Padhraic Smyth, UC Irvine: CS 277, Winter Chernoff Faces Described by ten facial characteristic parameters: head eccentricity, eye eccentricity, pupil size, eyebrow slant, nose size, mouth shape, eye spacing, eye size, mouth length and degree of mouth opening Limitations? –Only up to 10 or so dimensions –Overemphasizes certain variables because of our perceptual biases

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Padhraic Smyth, UC Irvine: CS 277, Winter Parallel Coordinates Method Interactive “brushing” is useful for seeing distinctions Epileptic Seizure Data 1 (of n) cases (this case is a “brushed” one, with a darker line, to standout from the n-1 other cases)

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Padhraic Smyth, UC Irvine: CS 277, Winter More elaborate parallel coordinates example (from E. Wegman, 1999). 12,000 bank customers with 8 variables Additional “dependent” variable is profit (green for positive, red for negative)

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Padhraic Smyth, UC Irvine: CS 277, Winter Interactive “Grand Tour” Techniques “Grand Tour” idea –Cycle continuously through multiple projections of the data –Cycles through all possible projections (depending on time constraints) –Projects can be 1, 2, or 3d typically (often 2d) –Can link with scatter plot matrices (see following example) – Asimov (1985) Example on following 2 slides –7 dimensional physics data, color-coded by group, shown with (a)Standard scatter matrix (b)2 static snapshots of grand tour

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Padhraic Smyth, UC Irvine: CS 277, Winter

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Padhraic Smyth, UC Irvine: CS 277, Winter

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Padhraic Smyth, UC Irvine: CS 277, Winter Exploratory Data Analysis Visualizing Time-Series Data

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Padhraic Smyth, UC Irvine: CS 277, Winter Time-Series Data: Example 1 steady growth trend New Year bumps Summer peaks Summer “double peaks” (favor early or late) Historical data on millions of miles flown by UK airline passengers …..note a number of different systematic effects

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Padhraic Smyth, UC Irvine: CS 277, Winter Time-Series Data: Example 2 Experimental Study: More milk -> better health? 20,000 children: 5k raw, 5k pasteurize, 10k control (no supplement) mean weight vs mean age for 10k control group Would expect smooth weight growth plot. Plot shows an unexpected pattern (steps), not apparent from raw data table. Why do the children appear to grow in spurts? Data from study on weight measurements over time of children in Scotland Age Weight

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Padhraic Smyth, UC Irvine: CS 277, Winter Time-Series Data: Example 3 (Google Trends) Search Query = whiskey

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Padhraic Smyth, UC Irvine: CS 277, Winter Time-Series Data: Example 4 (Google Trends) Search Query = NSA

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Padhraic Smyth, UC Irvine: CS 277, Winter Spatial Distribution of the Same Data (Google Trends) Search Query = whiskey

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Padhraic Smyth, UC Irvine: CS 277, Winter Non-Stationarity in Temporal Data Stationarity: –(loose definition) A probability distribution p (x | t) is stationary with respect to t if p (x | t ) = p (x) for all t, where x is the set of variables of interest, and t is some other varying quantity (e.g., usually t = time, but could represent spatial information, group information, etc) Examples: –p(patrient demographics today) = p(patient demographics 10 years ago)? –p(weights in Scotland) = p(weights in US) ? –p(income of customers in Bank 1) = p(income of customers in Bank 2)? Non-stationarity is common in real data sets –Solutions? –Model stationarity (e.g., increasing trend over time) and extrapolate –Build model only on most recent/most similar data

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Padhraic Smyth, UC Irvine: CS 277, Winter Exploratory Data Analysis Cluster Analysis

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Padhraic Smyth, UC Irvine: CS 277, Winter Clustering “automated detection of group structure in data” –Typically: partition N data points into K groups (clusters) such that the points in each group are more similar to each other than to points in other groups –descriptive technique (contrast with predictive) –for real-valued vectors, clusters can be thought of as clouds of points in d-dimensional space

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Padhraic Smyth, UC Irvine: CS 277, Winter Clustering Sometimes easy Sometimes impossible and sometimes in between

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Padhraic Smyth, UC Irvine: CS 277, Winter Why is Clustering Useful? “Discovery” of new knowledge from data –Contrast with supervised classification (where labels are known) –Long history in the sciences of categories, taxonomies, etc –Can be very useful for summarizing large data sets For large n and/or high dimensionality Applications of clustering –Clustering of documents produced by a search engine –Segmentation of patients in a medical stidy –Discovery of new types of galaxies in astronomical data –Clustering of genes with similar expression profiles –Cluster pixels in an image into regions of similar intensity –…. many more

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Padhraic Smyth, UC Irvine: CS 277, Winter General Issues in Clustering Clustering algorithm = Representation + Score + Optimization Cluster Representation: –What “shapes” of clusters are we looking for? What defines a cluster? Score: –A clustering = assignment of n objects to K clusters –Score = quantitative criterion used to evaluate different clusterings Optimization and Search –Finding the optimal (minimal/maximal score) clustering is typically NP-hard –Greedy algorithms to optimize the score are widely used

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Padhraic Smyth, UC Irvine: CS 277, Winter Other Issues in Clustering Distance function, d[x(i),x(j)] critical aspect of clustering, both –distance of individual pairs of objects –distance of individual objects from clusters How is K, number of clusters, selected? Different types of data –Real-valued versus categorical –Input data: N vectors or an N 2 distance matrix?

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Padhraic Smyth, UC Irvine: CS 277, Winter Different Types of Clustering Algorithms partition-based clustering –Represent points as vectors and partition points into clusters based on distance in d- dimensional space probabilistic model-based clustering –e.g. mixture models [both work with measurement data, e.g., feature vectors] hierarchical clustering –Builds a tree (dendrogram) starting from an N x N distance matrix graph-based clustering –represent inter-pointdistances via a graph and apply graph algorithms

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Padhraic Smyth, UC Irvine: CS 277, Winter The K-Means Clustering Algorithm Input: –N vectors x of dimension d –K = number of clusters required (K > 1) Output: –K cluster centers, c(1)…… c(K), each of dimension d –A list of cluster assignments (values 1 to K) for each of the N input vectors

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Padhraic Smyth, UC Irvine: CS 277, Winter Squared Errors and Cluster Centers Squared error (distance) between a data point x and a cluster center c: d [ x, c ] = j ( x j - c j ) 2 Sum is over the d components/dimensions of the vectors

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Padhraic Smyth, UC Irvine: CS 277, Winter Squared Errors and Cluster Centers Squared error (distance) between a data point x and a cluster center c: d [ x, c ] = j ( x j - c j ) 2 Total squared error between a cluster center c(k) and all N k points assigned to that cluster: S k = i d [ x (i), c(k) ] Sum is over the d components/dimensions of the vectors Sum is over the N k points assigned to cluster k

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Padhraic Smyth, UC Irvine: CS 277, Winter Squared Errors and Cluster Centers Squared error (distance) between a data point x and a cluster center c: d [ x, c ] = j ( x j - c j ) 2 Total squared error between a cluster center c(k) and all N k points assigned to that cluster: S k = i d [ x (i), c(k) ] Total squared error summed across K clusters S = k S k Sum is over the d components/dimensions of the vectors Sum is over the N k points assigned to cluster k Sum is over the K clusters

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Padhraic Smyth, UC Irvine: CS 277, Winter K-means Objective Function K-means: minimize the total squared error, i.e., find the K clusters centers m(k), and assignments, that minimize S = k S k = k ( i d [ x (i), c(k) ] ) K-means seeks to minimize S, i.e., find the cluster centers such that the total squared error is smallest –will place cluster centers strategically to “cover” data –similar to data compression (in fact used in data compression algorithms)

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Padhraic Smyth, UC Irvine: CS 277, Winter Example of Running Kmeans

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Padhraic Smyth, UC Irvine: CS 277, Winter Example MSE Cluster 1 = 1.31 MSE Cluster 2 = 3.21 Overall MSE = 2.57

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Padhraic Smyth, UC Irvine: CS 277, Winter Example MSE Cluster 1 = 1.31 MSE Cluster 2 = 3.21 Overall MSE = 2.57 MSE Cluster 1 = 1.01 MSE Cluster 2 = 1.76 Overall MSE = 1.38

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Padhraic Smyth, UC Irvine: CS 277, Winter Example MSE Cluster 1 = 0.84 MSE Cluster 2 = 1.28 Overall MSE = 1.05

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Padhraic Smyth, UC Irvine: CS 277, Winter Example MSE Cluster 1 = 0.84 MSE Cluster 2 = 1.28 Overall MSE = 1.04

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Padhraic Smyth, UC Irvine: CS 277, Winter K-means Algorithm Select the initial K centers randomly, e.g., pick K out of the N input vectors randomly Iterate: –Assignment Step: Assign each of the N input vectors to their closest mean –Update the K Means Compute updated centers: the average value of the vectors assigned to k New c (k) = 1/N k i x(i) Convergence: –Are all new c(k) = old c(k)? Yes: terminate No: return to Iterate step Sum is over the N k points assigned to cluster k

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Padhraic Smyth, UC Irvine: CS 277, Winter K-means 1.Ask user how many clusters they’d like. (e.g. K=5) (Example is courtesy of Andrew Moore, CMU)

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Padhraic Smyth, UC Irvine: CS 277, Winter K-means 1.Ask user how many clusters they’d like. (e.g. K=5) 2.Randomly guess K cluster Center locations

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Padhraic Smyth, UC Irvine: CS 277, Winter K-means 1.Ask user how many clusters they’d like. (e.g. K=5) 2.Randomly guess K cluster Center locations 3.Each datapoint finds out which Center it’s closest to. 4.Thus each Center “owns” a set of datapoints)

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Padhraic Smyth, UC Irvine: CS 277, Winter K-means 1.Ask user how many clusters they’d like. (e.g. K=5) 2.Randomly guess k cluster Center locations 3.Each datapoint finds out which Center it’s closest to. 4.Each Center finds the centroid of the points it owns

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Padhraic Smyth, UC Irvine: CS 277, Winter K-means 1.Ask user how many clusters they’d like. (e.g. K=5) 2.Randomly guess k cluster Center locations 3.Each datapoint finds out which Center it’s closest to. 4.Each Center finds the centroid of the points it owns 5.New Centers => new boundaries 6.Repeat until no change

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Padhraic Smyth, UC Irvine: CS 277, Winter Properties of the K-Means Algorithm Time complexity?? –O( N K d ) in time –This is good: linear time in each input parameter Convergence? –Does K-means always converge to the best possible solution? –No: always converges to *some* solution, but not necessarily the best Depends on the starting point

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Padhraic Smyth, UC Irvine: CS 277, Winter Local Search and Local Minima TSE Hard (non-convex) K-means

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Padhraic Smyth, UC Irvine: CS 277, Winter Local Search and Local Minima TSE Hard (non-convex) K-means Global Minimum

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Padhraic Smyth, UC Irvine: CS 277, Winter Local Search and Local Minima TSE Hard (non-convex) K-means Local Minima

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Padhraic Smyth, UC Irvine: CS 277, Winter Local Search and Local Minima TSE Hard (non-convex) K-means TSE K-means

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Padhraic Smyth, UC Irvine: CS 277, Winter Issues with K-means clustering Simple, but useful –tends to select compact “isotropic” cluster shapes –can be useful for initializing more complex methods –many algorithmic variations on the basic theme e.g., in signal processing/data compression is similar to vector-quantization Choice of distance measure –Euclidean distance –Weighted Euclidean distance –Many others possible Selection of K –“screen diagram” - plot SSE versus K, look for “knee” of curve Limitation: may not be any clear K value

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Padhraic Smyth, UC Irvine: CS 277, Winter Issues Representing non-numeric data? –E.g., color = {red, blue, green, ….} –Simplest approach: represent as multiple binary variables, one per value Standardizing the data –Say we have Length of a person’s arm in feet Width of a person’s foot in millimeters In kmeans distance calculations, the measurements in millimeters will dominate the measurements in feet –Solution? Try to place all the variables on a similar scale E.g., z = (x – mean(x) )/ std(x) Or, y = (x – mean(x) ) / interquartile_range(x)

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Padhraic Smyth, UC Irvine: CS 277, Winter Hierarchical Clustering Representation: tree of nested clusters Works from a distance matrix –advantage: x’s can be any type of object –disadvantage: computation two basic approachs: –merge points (agglomerative) –divide superclusters (divisive) visualize both via “dendograms” –shows nesting structure –merges or splits = tree nodes Applications –e.g., clustering of gene expression data –Useful for seeing hierarchical structure, for relatively small data sets

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Padhraic Smyth, UC Irvine: CS 277, Winter Simple example of hierarchical clustering

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Padhraic Smyth, UC Irvine: CS 277, Winter Agglomerative Methods: Bottom-Up algorithm based on distance between clusters: –for i=1 to n let C i = { x(i) }, i.e. start with n singletons –while more than one cluster left let C i and C j be cluster pair with minimum distance, dist[C i, C j ] merge them, via C i = C i C j and remove C j time complexity = O(n 2 ) to O(n 3 ) –n iterations (start: n clusters; end: 1 cluster) –1st iteration: O(n 2 ) to find nearest singleton pair space complexity = O(n 2 ) –accesses all distances between x(i)’s interpreting large n dendrogram difficult anyway (like decision trees) –large n idea: partition-based clusters at leafs

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Padhraic Smyth, UC Irvine: CS 277, Winter Distances Between Clusters single link / nearest neighbor measure: –D(Ci,Cj) = min { d(x,y) | x Ci, y Cj } –can be outlier/noise sensitive

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Padhraic Smyth, UC Irvine: CS 277, Winter Distances Between Clusters single link / nearest neighbor measure: –D(Ci,Cj) = min { d(x,y) | x Ci, y Cj } –can be outlier/noise sensitive complete link / furthest neighbor measure: –D(Ci,Cj) = max { d(x,y) | x Ci, y Cj } –enforces more “compact” clusters

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Padhraic Smyth, UC Irvine: CS 277, Winter Distances Between Clusters single link / nearest neighbor measure: –D(Ci,Cj) = min { d(x,y) | x Ci, y Cj } –can be outlier/noise sensitive complete link / furthest neighbor measure: –D(Ci,Cj) = max { d(x,y) | x Ci, y Cj } –enforces more “compact” clusters intermediates between those extremes: –average link: D(Ci,Cj) = avg { d(x,y) | x Ci, y Cj } –centroid: D(Ci,Cj) = d(c i,c j ) where c i, c j are centroids –Wards’s SSE measure (for vector data): Merge clusters than minimize increase in within-cluster sum-of-squared-dists –Note that centroid and Ward require that centroid (vector mean) can be defined Which to choose? Different methods may be used for exploratory purposes, depends on goals and application

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Padhraic Smyth, UC Irvine: CS 277, Winter Dendrogram Using Single-Link Method Old Faithful Eruption Duration vs Wait Data Notice how single-link tends to “chain”. dendrogram y-axis = crossbar’s distance score

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Padhraic Smyth, UC Irvine: CS 277, Winter Add pointer to Nature clustering paper for Text

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Padhraic Smyth, UC Irvine: CS 277, Winter

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Padhraic Smyth, UC Irvine: CS 277, Winter Approach Hierarchical clustering of genes using average linkage method Clustered time-course data of 8600 human genes and 2467 genes in budding yeast This paper was the first to show that clustering of expression data yields significant biological insights into gene function

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Padhraic Smyth, UC Irvine: CS 277, Winter “Heat-Map” Representation (human data)

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Padhraic Smyth, UC Irvine: CS 277, Winter “Heat-Map” Representation (yeast data)

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Padhraic Smyth, UC Irvine: CS 277, Winter Evaluation

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Padhraic Smyth, UC Irvine: CS 277, Winter Clustered display of data from time course of serum stimulation of primary human fibroblasts. Eisen M B et al. PNAS 1998;95: ©1998 by National Academy of Sciences

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Padhraic Smyth, UC Irvine: CS 277, Winter Probabilistic Clustering Hypothesize that the data are being generated by a mixture of K multivariate probability density functions (e.g., Gaussians) –Each density function is a cluster –Data vectors have a probability of belonging to a cluster rather than 0-1 membership Clustering algorithm –Learn the parameters (mean, covariance for Gaussians) of the K densities –Learn the probability memberships for each input vector Can be solved with the Expectation-Maximization algorithm Can be thought of as a probabilistic version of K-means

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Padhraic Smyth, UC Irvine: CS 277, Winter

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Padhraic Smyth, UC Irvine: CS 277, Winter Anemia Group Control Group

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Padhraic Smyth, UC Irvine: CS 277, Winter Summary Many different approaches and algorithms What type of cluster structure are you looking for? Computational complexity may be an issue for large n Data dimensionality can also be an issue Validation/selection of K is often an ill-posed problem

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Padhraic Smyth, UC Irvine: CS 277, Winter References: Data Sets and Case Studies GEO Database –Barrett et al, NCBI GEO: mining tens of millions of expression profiles – database and tools update, Nucl Acids Res. (2007) 35(suppl 1): D , doi: /nar/gkl887 Clustering expression data –Eisen, Spellman, Brown, Botstein, Cluster analysis and display of genome-wide expression patterns, PNAS, Dec 2998, 95(25), –Link:

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Padhraic Smyth, UC Irvine: CS 277, Winter General References on Clustering Cluster Analysis (5 th ed), B. S. Everitt, S. Landau, M. Leese, and D. Stahl, Wiley, 2011 (broad overview of clustering methods and algorithms) Algorithms for Clustering Data, A. K. Jain and R. C. Dubes, 1988, Prentice Hall. (a bit outdated but has many useful ideas and references on clustering) How many clusters? which clustering method? answers via model-based cluster analysis, C. Fraley and A. E. Raftery, the Computer Journal, (good overview article on probabilistic model-based clustering)

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Padhraic Smyth, UC Irvine: CS 277, Winter Exploratory Data Analysis Dimension Reduction Methods

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Padhraic Smyth, UC Irvine: CS 277, Winter Class Projects Project proposal due Wednesday May 2 nd Final project report due Monday May 21 st Details at We will discuss in more detail next week

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Padhraic Smyth, UC Irvine: CS 277, Winter Software Packages Commercial packages –SAS –Statistica –Many others – see kdnuggets.org Free packages –Weka Programming environments –R –MATLAB (commercial) –Python

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Padhraic Smyth, UC Irvine: CS 277, Winter Concepts in Multivariate Data Analysis

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Padhraic Smyth, UC Irvine: CS 277, Winter An Example of a Data Set Patient IDZipcodeAge….Test ScoreDiagnosis … Notation: Columns may be called “measurements”, “variables”, “features”, “attributes”, “fields”, etc Rows may be individuals, entities, objects, samples, etc

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Padhraic Smyth, UC Irvine: CS 277, Winter Vectors and Data Beyond 3 dimensions we cannot manually see our data Consider a data set of 10 measurements on 100 patients –We can think of each patient’s data as a “tuple” with 10 elements –If the variable values are numbers, we can represent this as a 10-dimensional vector e.g., x = ( x 1, x 2, x 3, ……., x 9, x 10 ) -Our data set is now a set of such vectors -We can imagine our data as “living” in a 10-dimensional space -Each patient is represented as a vector, with a 10-dimensional location -Sets of patients can be viewed as clouds of points in this 10d space

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Padhraic Smyth, UC Irvine: CS 277, Winter Hypersphere in d dimensions Hypercube in d dimensions High-dimensional data Volume of sphere relative to cube in d dimensions? Rel. Volume0.79????? Dimension (David Scott, Multivariate Density Estimation, Wiley, 1992)

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Padhraic Smyth, UC Irvine: CS 277, Winter Hypersphere in d dimensions Hypercube in d dimensions High-dimensional data Volume of sphere relative to cube in d dimensions? Rel. Volume Dimension (David Scott, Multivariate Density Estimation, Wiley, 1992)

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Padhraic Smyth, UC Irvine: CS 277, Winter The Geometry of Data Geometric view: data set = set of vectors in a d-dimensional space This allows us to think of geometric constructs for data analysis, e.g., –Distance between data points = distance between vectors –Centroid = center of mass of a cloud of data points –Density = relative density of points in a particular region of space –Decision boundaries -> partition the space into regions (Note that not all types of data can be naturally represented geometrically)

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Padhraic Smyth, UC Irvine: CS 277, Winter Basic Concepts: Distance D(x, y) = distance between 2 vectors x and y How should we define this? –E.g., Euclidean distance –Manhattan distance –Jaccard distance –And more….

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Padhraic Smyth, UC Irvine: CS 277, Winter Basic Concepts: Center of Mass What is the “center” of a set of data points Multidimensional mean Defined as: What happens if there is a “hole” in the center of the data?

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Padhraic Smyth, UC Irvine: CS 277, Winter Geometry of Data Analysis

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Padhraic Smyth, UC Irvine: CS 277, Winter Basic Concepts: Decision Boundaries In 2 dimensions we can partition the 2d space into 2 regions using a line or a curve, e.g., In d-dimensions, we can defined a (d-1)dimensional hyperplane or hypersurface to partition the space into 2 pieces

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Padhraic Smyth, UC Irvine: CS 277, Winter Geometry of Data Analysis Good boundary? Better boundary?

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Padhraic Smyth, UC Irvine: CS 277, Winter Example: Assigning Data Points to Two Exemplars Say we have 2 exemplars, e.g., –1 data point that is the prototype of healthy patients –1 data point that is the prototype of non-healthy patients Now we want to assign all individuals to the closest prototype –Lets use Euclidean distance as our measure of distance This is equivalent to –having a decision boundary that lies exactly halfway between the two exemplar points –The decision boundary is at right angles to the line between the two exemplars (see next slide for a 2-dimensional example)

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Padhraic Smyth, UC Irvine: CS 277, Winter Geometry of Data Analysis

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Padhraic Smyth, UC Irvine: CS 277, Winter Geometry of Data Analysis

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Padhraic Smyth, UC Irvine: CS 277, Winter High Dimensional Data Example: 100 dimensional data –Visualization is of limited value –Although can still useful to look at variables 1 or 2 at a time “Curse of dimensionality” –Hypercube/hypersphere example (Scott) –Number of samples need for accurate density estimate in high-d Question –How would you find outliers (if any) with 1000 data points in a 100 dimensional data space?

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Padhraic Smyth, UC Irvine: CS 277, Winter Clustering: Finding Group Structure

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