TreeJuxtaposer
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Transcript of TreeJuxtaposer
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TreeJuxtaposer• side by side comparison of evolutionary trees
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Phylogenetic/Evolutionary Tree
M Meegaskumbura et al., Science 298:379 (2002)
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Common Dataset Size Today
M Meegaskumbura et al., Science 298:379 (2002)
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Future Goal: 10M node Tree of Life
David Hillis, Science 300:1687 (2003)
Plants
Protists
Fungi
Animals
You arehere
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Paper Comparison: Multiple Trees
focus
context
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Accordion Drawing• rubber-sheet navigation
– stretch out part of surface, the rest squishes
– borders nailed down– Focus+Context technique
• integrated overview, details
– old idea• [Sarkar et al 93],
[Robertson et al 91]
• guaranteed visibility– marks always visible– important for scalability – new idea
• [Munzner et al 03]
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Guaranteed Visibility
• marks are always visible• easy with small datasets
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Guaranteed Visibility Challenges
• hard with larger datasets
• reasons a mark could be invisible
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Guaranteed Visibility Challenges
• hard with larger datasets
• reasons a mark could be invisible– outside the window
• AD solution: constrained navigation
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Guaranteed Visibility Challenges
• hard with larger datasets
• reasons a mark could be invisible– outside the window
• AD solution: constrained navigation
– underneath other marks• AD solution: avoid 3D
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Guaranteed Visibility Challenges
• hard with larger datasets
• reasons a mark could be invisible– outside the window
• AD solution: constrained navigation
– underneath other marks• AD solution: avoid 3D
– smaller than a pixel• AD solution: smart culling
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Guaranteed Visibility: Small Items
• Naïve culling may not draw all marked items
GV no GV
Guaranteed visibilityof marks
No guaranteed visibility
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Guaranteed Visibility: Small Items
• Naïve culling may not draw all marked items
GV no GV
Guaranteed visibilityof marks
No guaranteed visibility
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Structural Comparison
rayfinned fish
lungfish
salamander
frog
mammal
turtle
bird
crocodile
lizard
snake
rayfinned fish
bird
lungfish
salamander
frog
mammal
turtle
snake
lizard
crocodile
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Matching Leaf Nodes
rayfinned fish
lungfish
salamander
frog
mammal
turtle
bird
crocodile
lizard
snake
rayfinned fish
bird
lungfish
salamander
frog
mammal
turtle
snake
lizard
crocodile
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Matching Leaf Nodes
rayfinned fish
lungfish
salamander
frog
mammal
turtle
bird
crocodile
lizard
snake
rayfinned fish
bird
lungfish
salamander
frog
mammal
turtle
snake
lizard
crocodile
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Matching Leaf Nodes
rayfinned fish
lungfish
salamander
frog
mammal
turtle
bird
crocodile
lizard
snake
rayfinned fish
bird
lungfish
salamander
frog
mammal
turtle
snake
lizard
crocodile
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Matching Interior Nodes
rayfinned fish
lungfish
salamander
frog
mammal
turtle
bird
crocodile
lizard
snake
rayfinned fish
bird
lungfish
salamander
frog
mammal
turtle
snake
lizard
crocodile
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Matching Interior Nodes
rayfinned fish
lungfish
salamander
frog
mammal
turtle
bird
crocodile
lizard
snake
rayfinned fish
bird
lungfish
salamander
frog
mammal
turtle
snake
lizard
crocodile
![Page 20: TreeJuxtaposer](https://reader035.fdocuments.us/reader035/viewer/2022062422/56812cd8550346895d91957a/html5/thumbnails/20.jpg)
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Matching Interior Nodes
rayfinned fish
lungfish
salamander
frog
mammal
turtle
bird
crocodile
lizard
snake
rayfinned fish
mammal
lungfish
salamander
frog
bird
turtle
snake
lizard
crocodile
![Page 21: TreeJuxtaposer](https://reader035.fdocuments.us/reader035/viewer/2022062422/56812cd8550346895d91957a/html5/thumbnails/21.jpg)
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Matching Interior Nodes
rayfinned fish
lungfish
salamander
frog
mammal
turtle
bird
crocodile
lizard
snake
rayfinned fish
bird
lungfish
salamander
frog
mammal
turtle
snake
lizard
crocodile
?
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Similarity Score: S(m,n)
3
2)()(
)()(),(
FE,D,
FE,
nm
nmnm
LL
LLS
FE,D,n )(L FE,m )(L
T1 T2A
B
C
D
E
F
A
C
B
D
F
Em n
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Best Corresponding Node
• – computable in O(n log2 n)– linked highlighting
T1 T2A
B
C
D
E
F
A
C
B
D
F
Em BCN(m) = n
1/32/3
2/6
00
0
0
0
0
1/2
1/2
)),(( vSv margmax)mBCN(2T
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• – Matches intuition
1))BCN(,( whichfor Nodes vvS
Marking Structural DifferencesT1 T2A
B
C
D
E
F
A
C
B
D
F
Em n
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TreeJuxtaposer• video, software from olduvai.sourceforge.net/tj