indexed search tree (trie)
DESCRIPTION
Indexed Search Tree (Trie). Fawzi Emad Chau-Wen Tseng Department of Computer Science University of Maryland, College Park. Indexed Search Tree ( Trie). Special case of tree Applicable when Key C can be decomposed into a sequence of subkeys C 1 , C 2 , … C n - PowerPoint PPT PresentationTRANSCRIPT
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Indexed Search Tree (Trie)
Fawzi EmadChau-Wen Tseng
Department of Computer ScienceUniversity of Maryland, College Park
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Indexed Search Tree (Trie)
Special case of treeApplicable when
Key C can be decomposed into a sequence of subkeys C1, C2, … Cn
Redundancy exists between subkeys
ApproachStore subkey at each nodePath through trie yields full key
ExampleHuffman tree
C3
C1
C2
C4C3
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Tries
Useful for searching strings String decomposes into sequence of lettersExample
“ART” “A” “R” “T”
Can be very fastLess overhead than hashing
May reduce memoryExploiting redundancy
May require more memoryExplicitly storing substrings
S
A
R
TE
“ART”
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Types of Tries
StandardSingle character per node
CompressedEliminating chains of nodes
CompactStores indices into original string(s)
SuffixStores all suffixes of string
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Standard Tries
ApproachEach node (except root) is labeled with a characterChildren of node are ordered (alphabetically)Paths from root to leaves yield all input strings
Trie for Morse Code
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Standard Trie Example
For strings{ a, an, and, any, at }
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Standard Trie Example
For strings{ bear, bell, bid, bull, buy, sell, stock, stop }
a
e
b
r
l
l
s
u
l
l
y
e t
l
l
o
c
k
p
i
d
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Standard Tries
Node structureValue between 1…mReference to m children
Array or linked list
ExampleClass Node {
Letter value; // Letter V = { V1, V2, … Vm }Node child[ m ];
}
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Standard Tries
EfficiencyUses O(n) space Supports search / insert / delete in O(dm) timeFor
n total size of strings indexed by tried length of the parameter stringm size of the alphabet
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Word Matching Trie
Insert words into trieEach leaf stores occurrences of word in the text
s e e b e a r ? s e l l s t o c k !
s e e b u l l ? b u y s t o c k !
b i d s t o c k !
a
a
h e t h e b e l l ? s t o p !
b i d s t o c k !
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46
47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68
69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86a r
87 88
a
e
b
l
s
u
l
e t
e
0, 24
o
c
i
l
r
6
l
78
d
47, 58l
30
y
36l
12 k
17, 40,51, 62
p
84
h
e
r
69
a
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Compressed Trie
ObservationInternal node v of T is redundant if v has one child and is not the root
ApproachA chain of redundant nodes can be compressed
Replace chain with single node Include concatenation of labels from chain
ResultInternal nodes have at least 2 childrenSome nodes have multiple characters
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Compressed Trie
e
b
ar ll
s
u
ll y
ell to
ck p
id
a
e
b
r
l
l
s
u
l
l
y
e t
l
l
o
c
k
p
i
d
Example
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Compact Tries
Compact representation of a compressed trieApproach
For an array of strings S = S[0], … S[s-1]Store ranges of indices at each node
Instead of substringRepresent as a triplet of integers (i, j, k)
Such that X = s[i][j..k]Example: S[0] = “abcd”, (0,1,2) = “bc”
PropertiesUses O(s) space, where s = # of strings in the arrayServes as an auxiliary index structure
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Compact Representation
Example
s e eb e a rs e l ls t o c k
b u l lb u yb i d
h eb e l ls t o p
0 1 2 3 4a rS[0] =
S[1] =
S[2] =
S[3] =
S[4] =
S[5] =
S[6] =
S[7] =
S[8] =
S[9] =
0 1 2 3 0 1 2 3
1, 1, 1
1, 0, 0 0, 0, 0
4, 1, 1
0, 2, 2
3, 1, 2
1, 2, 3 8, 2, 3
6, 1, 2
4, 2, 3 5, 2, 2 2, 2, 3 3, 3, 4 9, 3, 3
7, 0, 3
0, 1, 1
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Suffix Trie
Compressed trie of all suffixes of textExample: “IPDPS”
SuffixesIPDPSPDPSDPSPSS
Useful for finding pattern in any part of textOccurrence prefix of some suffixExample: find PDP in IPDPS
DP
S
P
IP
D
S
P
S
DP
SS
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Suffix Trie
PropertiesFor
String X with length nAlphabet of size mPattern P with length d
Uses O(n) spaceCan be constructed in O(n) timeFind pattern P in X in O(dm) time
Proportional to length of pattern, not text
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Suffix Trie Example
e nimize
nimize ze
zei mi
mize nimize ze
m i n i z em i0 1 2 3 4 5 6 7
7, 7 2, 7
2, 7 6, 7
6, 7
4, 7 2, 7 6, 7
1, 1 0, 1
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Tries and Web Search Engines
Search engine indexCollection of all searchable wordsStored in compressed trie
Each leaf of trie Associated with a word List of pages (URLs) containing that word
Called occurrence list
Trie is kept in memory (fast)Occurrence lists kept in external memory
Ranked by relevance
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Computational Biology
DNASequence of 4 different nucleotides (ATCG)Portions of DNA sequence produce proteins (genes)
GenomeMaster DNA sequence for organismFor Human
46 chromosomes3 billion nucleotides
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Tries and Computational Biology
ESTsFragments of expressed DNA Indicator for genes (& location)5.5 million sequences at NIH
ESTmapperBuild suffix trie of genome
8 hours, 60 GbytesSearch for ESTs in suffix trie
11 hours w/ 8 processor Sun
Search genome w/ BLAST 5+ years (predicted)
Genome
ESTsSuffix tree
Mapping
Gene