Visualizing high-dimensional data:
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1 Visualizing high-dimensional data: Applying graph theory to data visualization Wayne Oldford based on joint work with Catherine Hurley (Maynooth, Ireland) Adrian Waddell (Waterloo, Canada)
2 Challenge p values on each of n individuals modern data: n, or p, or both, can be very large
3 Challenge p values on each of n individuals modern data: n, or p, or both, can be very large
4 Challenge p values on each of n individuals modern data: n, or p, or both, can be very large
5 Challenge p values on each of n individuals modern data: n, or p, or both, can be very large
6 Challenge p values on each of n individuals modern data: n, or p, or both, can be very large
7 Challenge p values on each of n individuals modern data: n, or p, or both, can be very large can have non-obvious variables, complex, unanticipated structure,...
8 Data Visualization powerful human visual system use a variety of cues: proximity, movement, shape, colour, texture,... patterns, relations, like and unlike,... recognition and discovery structure need not be anticipated
9 Data Visualization powerful human visual system use a variety of cues: proximity, movement, shape, colour, texture,... patterns, relations, like and unlike,... recognition and discovery structure need not be anticipated
10 Data Visualization powerful human visual system use a variety of cues: proximity, movement, shape, colour, texture,... patterns, relations, like and unlike,... recognition and discovery structure need not be anticipated
11 Data Visualization powerful human visual system use a variety of cues: proximity, movement, shape, colour, texture,... patterns, relations, like and unlike,... recognition and discovery structure need not be anticipated
12 Challenge Large p visually, we re constrained to small p locations: p < 4 use colour, shape, texture, movement,... comprehension depends on only a few dimensions... at a time
13 Challenge Large p visually, we re constrained to small p locations: p < 4 use colour, shape, texture, movement,... comprehension depends on only a few dimensions... at a time Approach: large number of low dimensional views
14 Challenge Large p visually, we re constrained to small p locations: p < 4 use colour, shape, texture, movement,... comprehension depends on only a few dimensions... at a time Approach: large number of low dimensional views p d d-dimensional views, preferably highly interactive
15 Challenge Large p visually, we re constrained to small p locations: p < 4 use colour, shape, texture, movement,... comprehension depends on only a few dimensions... at a time Approach: large number of low dimensional views p d d-dimensional views, preferably highly interactive Which dimensions? How connected? How explored?
16 Axis systems Choice of coordinate axis layout Radial (PairViz R package) Parallel (PairViz R package) Orthogonal (RnavGraph R package) Punchline graph theory framework for exploratory data analysis looks very promising
17 7 dim: A, B, C, D, E, F, G Radial axes
18 Radial axes 7 dim: A, B, C, D, E, F, G C B Equi-angular D radial axes A E G F
19 Radial axes 7 dim: A, B, C, D, E, F, G Equi-angular D C B A radial axes E G F - Length of each radius is proportional to value of variate for that case. - High dimensional data, each case represented by a star shaped glyph
20 Radial axes: B D C A E G F
21 Radial axes: Compare cases by shape of glyph, here 9 cases in 7 dimensions - Visually cluster high dimensional data by shape: {7,8,9,1} {2,3} {4} {5,6}?
22 Radial axes: Compare cases by shape of glyph, here 9 cases in 7 dimensions - Visually cluster high dimensional data by shape: {7,8,9,1} {2,3} {4} {5,6}? - What if the variables were assigned in a different order?
23 Radial axes: order effect Dataset order H0 {7,8,9,1} {2,3} {4} {5,6}? Order H {7,8,9,1} {2,3} {4} {5} {6}? 7 8 9
24 Radial axes: order effect Dataset order H0 {7,8,9,1} {2,3} {4} {5,6}? Order H {7,8,9,1} {2,3} {4} {5} {6}? Order H2 {1,4} {2,3} {5,6} {7,8,9}?
25 Radial axes: order effect Dataset order H0 {7,8,9,1} {2,3} {4} {5,6}? Order H {7,8,9,1} {2,3} {4} {5} {6}? Order H2 {1,4} {2,3} {5,6} {7,8,9}? Order H {1} {2} {3} {4} {5} {6} {7,8,9}? 7 8 9
26 Radial axes: reduced order effect Instead, have all pairs of variables appear together A G B F C E D - Default was an arbitrary selection of pairs such that all nodes were visited once. If via a path (cycle), it is a Hamiltonian path (cycle). - Visiting all edges would give all pairs in some order.
27 Radial axes: reduced order effect An Eulerian G A B F C E D
28 Radial axes: reduced order effect An Eulerian A Hamiltonian G A B G A B F C F C E D E D
29 Radial axes: reduced order effect An Eulerian A Hamiltonian G A B G A B G A B F C F C F C E D E D E D
30 Radial axes: reduced order effect An Eulerian A Hamiltonian G A B G A B G A B G A B F C F C F C F C E D E D E D E D
31 Radial axes: reduced order effect A Hamiltonian decomposition G A B G A B G A B G A B F C = F C + F C + F C E D E D E D E D
32 Radial axes: reduced order effect - Which when assembled form an Eulerian cycle composed of Hamiltonians B C D E F G A = B C D E F G A B C D E F G A B C D E F G A A Hamiltonian decomposition
33 Radial axes: reduced order effect - Which when assembled form an Eulerian cycle composed of Hamiltonians - Could build a glyph from these cycles (21 radii instead of 7) B C D E F G A = B C D E F G A B C D E F G A B C D E F G A A Hamiltonian decomposition
34 Radial axes: reduced order effect A Hamiltonian decomposition Hamiltonian decomp, H1:H2:H Could build a glyph from these cycles (21 radii instead of 7)
35 Radial axes glyphs A Hamiltonian decomposition Hamiltonian decomp, H1:H2:H3 {1,4} {2,3} {5,6} {7,8,9} Maserati
36 Radial axes glyphs A Hamiltonian decomposition Hamiltonian decomp, H1:H2:H3 {1,4} {2,3} {5,6} {7,8,9} Clustering dendrogram Height Maserati
37 Radial axes glyphs A Greedy Eulerian (maximizing pairwise correlation) Eulerian order Clustering dendrogram Height Maserati
38 Radial axes glyphs A Greedy Eulerian (maximizing pairwise correlation) 4 First two principal components Clustering dendrogram Height All pairs (Greedy Eulerian or Hamiltonian decomposition) reduce the effect of variable pair patterns, making star glyphs more reliable. Maserati
39 Radial axes glyphs A Greedy Eulerian (maximizing pairwise correlation) Maserati 4 First two principal components Duster 360 Ferrari Dino Clustering dendrogram 5 1 Mercedes 450SE Mercedes 450SL 6 Mazda RX4 Porsche Height Lotus Europa Mercedes 450SLC All pairs (Greedy Eulerian or Hamiltonian decomposition) reduce the effect of variable pair patterns, making star glyphs more reliable. Maserati
40 Parallel Axes X Y
41 Parallel Axes X Y Each point is a curve in two dimensions
42 Parallel Coordinates W X Y Z Each point is a curve in two dimensions Have as many dimensions as the display permits
43 Parallel Coordinates Virginica Versicolor Sepal.Length Sepal.Width Petal.Length Petal.Width Gaspé Irises: Each flower is a curve in two dimensions positioned by that flower s measurement on all variables. Setosa
44 Parallel Coordinates Virginica Versicolor Setosa Sepal.Length Sepal.Width Petal.Length Petal.Width Sepal.Length.1 Petal.Length.1 Sepal.Width.1 Petal.Width.1 By following an Eulerian Tour on the complete graph, every pair of variables will appear side by side.
45 Parallel Coordinates Greedy Eulerian: Focus on most positively correlated Sleep1 data (alr3 R package): 10 variables on 62 mammals Br = log brain weight, Bd = log body weight, SW = Slow wave non-dreaming sleep, PS = Paradoxical dreaming sleep, TS = Total sleep, D = Danger index, P = Predation index, L = Max life span, SE = Sleep exposure index, GP = Gestation time SW TS PS SW P D SE Bd Br GP Bd L Br SE P SE GP L GP D Bd P G
46 Scagnostics Cognostics (Computer aided diagnostics) Scagnostics Scatterplot cognostics Wilkinson et al (2006) (from idea proposed by Tukey & Tukey (1985))
47 Scagnostics Cognostics (Computer aided diagnostics) Scagnostics Scatterplot cognostics Wilkinson et al (2006) (from idea proposed by Tukey & Tukey (1985))
48 Scagnostics
49 Scagnostics
50 Parallel Coordinates Eulerian on scagnostics: Outlying GP L Bd SW L Br GP Bd Br SW Focus on features of interest (Wilkinson et al 2006, from Tukey & Tukey 1985 Cognostics scagnostics ) Eulerian may pick up a subset of the variables
51 Parallel Coordinates Best Hamiltonian on scagnostics: Striated Sparse Bd D PS SE SW GP P L Br TS Focus on features of interest (Wilkinson et al 2006, from Tukey & Tukey 1985 Cognostics scagnostics ) Hamiltonian ensures all variables appear
52 Parallel Coordinates Eulerian on scagnostics: Outlying Same data GP L Bd SW L Br GP Bd Br SW Best Hamiltonian on scagnostics: Striated Sparse Different measures Bd D PS SE SW GP P L Br TS
53 Orthogonal axes Y X
54 Orthogonal axes Y X Z
55 Orthogonal axes Petal Width Sepal Length? Petal Length Sepal Width What about more than 3 dimensions?
56 Example: Italian olive oils Different regions of Italy: NORTH (Umbria, East- Liguria, West-Liguria) Liguria SOUTH (Calabria, Sicily, North-Apulia, South-Apulia) SARDINIA (Inland, Coast) Sardinia Umbria Apulia Calabria Sicily
57 Example: Italian olive oils Different regions of Italy: NORTH (Umbria, East- Liguria, West-Liguria) SOUTH (Calabria, Sicily, North-Apulia, South-Apulia) SARDINIA (Inland, Coast) NORTH ALL SOUTH Liguria Umbria Sardinia Sicily SARDINIA Apulia Calabria Liguria Umbria Calabria Apulia Sicily Inland Coast West East South North
58 Example: Italian olive oils Measurements: n = 572 different olive samples concentrations of p=8 fatty acids: arachidic, eicosenoic, linoleic (l1), linolenic (l2), oleic, palmitic (p1), palmitoleic (p2), and stearic. Liguria Sardinia Umbria Sicily Apulia Calabria
59 Connecting low-d spaces Navigation Graphs node = variable pair edges connect nodes that share a variable could display scatterplot at each node edges are 3D transitions high dimensional space is explored by moving from one 2D space to another through 3D (or 4D) transitions track/map exploration suggest routes
60 Connecting low-d spaces Navigation Graphs node = variable pair edges connect nodes that share a variable could display scatterplot at each node edges are 3D transitions high dimensional space is explored by moving from one 2D space to another through 3D (or 4D) transitions track/map exploration suggest routes
61 Connecting low-d spaces Navigation Graphs node = variable pair edges connect nodes that share a variable could display scatterplot at each node edges are 3D transitions high dimensional space is explored by moving from one 2D space to another through 3D (or 4D) transitions track/map exploration suggest routes
62 Connecting low-d spaces Navigation Graphs node = variable pair edges connect nodes that share a variable could display scatterplot at each node edges are 3D transitions high dimensional space is explored by moving from one 2D space to another through 3D (or 4D) transitions track/map exploration suggest routes
63 Navigation Graphs RNavgraph... R implementation
64 Example: Italian olive oils Interactive Interactive scatterplot 3d transition graph
65 Example: Italian olive oils Interactive Interactive scatterplot 3d transition graph
66 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Move back and forth by hand
67 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Move back and forth by hand
68 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Scatterplot control panel offers interactive features
69 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Brushing
70 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Deactivate selected points
71 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Deactivate selected points Return to starting position
72 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Zoom and relocate Note World View changes
73 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot At least 3 groups; Colour two of them.
74 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Could also select a whole path to traverse
75 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Could also select a whole path to traverse
76 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Paths can be saved, annotated, viewed, and walked again.
77 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Paths can be saved, annotated, viewed, and walked again.
78 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Appears to be a third horizontal group... zoom etc.
79 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Appears to be a third horizontal group... zoom etc. And that outlier
80 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Colour group orange, outlier red.
81 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Colour group orange, outlier red. Can switch to glyphs
82 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Colour group orange, outlier red. Focus on a region
83 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Colour group orange, outlier red. Move to compare shapes
84 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Colour group orange, outlier red. Enlarge to compare shapes
85 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Colour group orange, outlier red. Identify possible orange?
86 Example: Italian olive oils Interactive 3d transition graph Interactive scatterplot Colour group orange, outlier red. Can actually check here
87 Example: Italian olive oils Continue in this way: bring back deactivated points identify groups, reassign points note natural hierarchical clustering save grouping by colour in R
88 Challenge Large p => large graphs p... overall dimensionality (olive, p=8) p 2 p... potential 2d nodes (28) 3... potential 3d edges (56) p p 2 p
89 Challenge Large p => large graphs p... overall dimensionality (olive, p=8) p 2 p... potential 2d nodes (28) 3... potential 3d edges (56) p p 2 p Need to start with small, but interesting, graphs
90 Interesting node pairs For each scagnostic, calculate the value for every pair. View only those pairs with high scores (e.g. top fraction of scores).
91 Scagnostics: Italian olive oils 3D Monotonic Groups coloured by regions
92 Scagnostics: Italian olive oils 3D Monotonic Groups coloured by regions
93 Scagnostics: Italian olive oils Switch to 3D Striated Groups coloured by regions
94 Scagnostics: Italian olive oils 3D Striated Groups coloured by regions
95 Scagnostics: Italian olive oils 3D Non-Convex Groups coloured by regions
96 Challenge Large p => large graphs scagnostics work well, but when p is very large, so is p 2 dimensionality reduction methods could be employed.
97 Example: images Frey: 1,965 movie frames
98 Example: images Frey: 1,965 movie frames 28 x 20 array
99 Example: images Frey: 1,965 movie frames 28 x 20 array 560 dimensions
100 Example: images Frey: 1,965 movie frames 28 x 20 array 560 dimensions explore via low dimensional spaces
101 Example: images Frey: 1,965 movie frames 560 dimensions
102 Example: images Frey: 1,965 movie frames 560 dimensions Using LLE: local linear embedding k=12 neighbours
103 Example: images Frey: 1,965 movie frames 560 dimensions Using LLE: local linear embedding k=12 neighbours reduce to 5
104 Example: images Frey: 1,965 movie frames 560 dimensions reduce to 5 interactive low-d view
105 Example: images Frey: 1,965 movie frames 560 dimensions reduce to 5 interactive low-d view connect low-d views
106 Example: images
107 Example: images Interactive panel
108 Example: images Switch to images
109 Example: images Back to dots
110 Example: images Lots of structure... explored in 5d
111 Example: images Lots of structure... explored in 5d
112 Example: images Lots of structure... explored in 5d
113 Can link across NavGraph Sessions Here LLE and ISOMAP embeddings
114 Can link across NavGraph Sessions Here LLE and ISOMAP embeddings
115 Can link across NavGraph Sessions Here LLE and ISOMAP embeddings
116 Multiple visualizations Kernel density contours and 3D surface
117 Multiple visualizations Kernel density contours and 3D surface
118 Multiple visualizations Kernel density contours and 3D surface
119 Multiple visualizations Kernel density contours and 3D surface
120 Summary Graph theory structure organizes order of axes (e.g. radial, parallel, orthog.) use interesting orders (correlations, scagnostics, etc.) organizes ANY display order (e.g. multiple comparisons) graphs become maps to navigate high-dimensional space graph walks are low dimensional trajectories can focus on interesting trajectories capitalizes on visual ability graphs easily constructed; graph theory/algorithms exist
121 Summary Try it yourself R packages: PairViz Hurley & Oldford RnavGraph Waddell & Oldford
122 Thank you
123 Thank you Questions?
124 Papers Hurley & Oldford: Graphs as navigational infrastructure for high dimensional data spaces (Comp Stats 2011) Pairwise display of high dimensional information via Eulerian tours and Hamiltonian decompositions (JCGS, 2010) Eulerian tour algorithms for data visualization and the PairViz package (Comp Stats 2011) PairViz R package available on CRAN. Oldford & Waddell: Visual clustering of high-dimensional data by navigating low-dimensional spaces (ISI Dublin, 2011) RnavGraph: A visualization tool for navigating through high dimensional data (ISI Dublin, 2011) RnavGraph R package available on CRAN Oldford & Zhou: Tree Ensemble Reduced Clustering via a Graph Algebraic Framework. submitted
125 Aside: 4d transitions 3d and 4d transition graphs 3d transition graph
126 Aside: 4d transitions 3d and 4d transition graphs 3d transition graph
127 Aside: 4d transitions 3d and 4d transition graphs 3d transition graph its complement a 4d transition graph
128 Aside: 4d transitions 3d and 4d transition graphs a 4d transition graph
129 Aside: 4d transitions 3d and 4d transition graphs
130 Aside: 4d transitions 3d and 4d transition graphs 4d navgraph Observe the 4d transition NOT a rigid rotation
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