1 treejuxtaposer side by side comparison of evolutionary trees
TRANSCRIPT
1
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
20
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
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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