Modern Information Retrieval

Chapter 9
Indexing and Searching
with Gonzalo Navarro
Introduction
Inverted Indexes
Signature Files
Suffix Trees and Suffix Arrays
Sequential Searching
Multi-dimensional Indexing
Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 1
Introduction
Although efficiency might seem a secondary issue
compared to effectiveness, it can rarely be neglected
in the design of an IR system
Efficiency in IR systems: to process user queries with
minimal requirements of computational resources
As we move to larger-scale applications, efficiency
becomes more and more important
For example, in Web search engines that index terabytes of data
and serve hundreds or thousands of queries per second

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 2

Introduction
Index: a data structure built from the text to speed up
the searches
In the context of an IR system that uses an index, the
efficiency of the system can be measured by:
Indexing time: Time needed to build the index
Indexing space: Space used during the generation of the index
Index storage: Space required to store the index
Query latency: Time interval between the arrival of the query
and the generation of the answer
Query throughput: Average number of queries processed per
second

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 3

Introduction
When a text is updated, any index built on it must be
updated as well
Current indexing technology is not well prepared to
support very frequent changes to the text collection
Semi-static collections: collections which are updated
at reasonable regular intervals (say, daily)
Most real text collections, including the Web, are indeed
semi-static
For example, although the Web changes very fast, the crawls of a
search engine are relatively slow

For maintaining freshness, incremental indexing is used

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 4

Inverted Indexes

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 5

Basic Concepts
Inverted index: a word-oriented mechanism for
indexing a text collection to speed up the searching task
The inverted index structure is composed of two
elements: the vocabulary and the occurrences
The vocabulary is the set of all different words in the text
For each word in the vocabulary the index stores the
documents which contain that word (inverted index)

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 6

Basic Concepts
Term-document matrix: the simplest way to represent
the documents that contain each word of the vocabulary

Vocabulary ni d1 d2 d3 d4
to 2 4 2 - -
do 3 2 - 3 3
is 1 2 - - -
be 4 2 2 2 2
or 1 - 1 - -
To do is to be.
not 1 - 1 - - To be is to do. To be or not to be.
I 2 - 2 2 - I am what I am.
am 2 - 2 1 -
what 1 - 1 - -
d1
d2
think 1 - - 1 -
I think therefore I am.
therefore 1 - - 1 - Do be do be do. Do do do, da da da.
da 1 - - - 3 Let it be, let it be.
let 1 - - - 2
it 1 - - - 2
d3
d4

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 7

Basic Concepts
The main problem of this simple solution is that it
requires too much space
As this is a sparse matrix, the solution is to associate a
list of documents with each word
The set of all those lists is called the occurrences

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 8

Basic Concepts
Basic inverted index

Vocabulary ni Occurrences as inverted lists

to 2 [1,4],[2,2]
do 3 [1,2],[3,3],[4,3]
is 1 [1,2]
be 4 [1,2],[2,2],[3,2],[4,2]
or 1 [2,1]
To do is to be.
not 1 [2,1] To be is to do. To be or not to be.
I 2 [2,2],[3,2] I am what I am.
am 2 [2,2],[3,1]
what 1 [2,1]
d1
d2
think 1 [3,1]
I think therefore I am.
therefore 1 [3,1] Do be do be do. Do do do, da da da.
da 1 [4,3] Let it be, let it be.
let 1 [4,2]
it 1 [4,2]
d3
d4

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 9

Inverted Indexes
Full Inverted Indexes

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 10

Full Inverted Indexes
The basic index is not suitable for answering phrase or
proximity queries
Hence, we need to add the positions of each word in
each document to the index (full inverted index)

1 4 12 18 21 24 35 43 50 54 64 67 77 83
In theory, there is no difference between theory and practice. In practice, there is.

Text

between 35
difference 24
practice 54 67
theory 4 43

Vocabulary Occurrences

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 11

Full Inverted Indexes
In the case of multiple documents, we need to store one
occurrence list per term-document pair
Vocabulary ni Occurrences as full inverted lists
to 2 [1,4,[1,4,6,9]],[2,2,[1,5]]
do 3 [1,2,[2,10]],[3,3,[6,8,10]],[4,3,[1,2,3]]
is 1 [1,2,[3,8]]
be 4 [1,2,[5,7]],[2,2,[2,6]],[3,2,[7,9]],[4,2,[9,12]]
or 1 [2,1,[3]]
not 1 [2,1,[4]] To do is to be.
I 2 [2,2,[7,10]],[3,2,[1,4]] To be is to do. To be or not to be.
I am what I am.
am 2 [2,2,[8,11]],[3,1,[5]]
what 1 [2,1,[9]] d1
think 1 [3,1,[2]]
d2
therefore 1 [3,1,[3]] I think therefore I am.
Do be do be do. Do do do, da da da.
da 1 [4,3,[4,5,6]] Let it be, let it be.
let 1 [4,2,[7,10]]
it 1 [4,2,[8,11]]
d3
d4

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 12

Full Inverted Indexes
The space required for the vocabulary is rather small
Heaps’ law: the vocabulary grows as O(nβ ), where
n is the collection size
β is a collection-dependent constant between 0.4 and 0.6

For instance, in the TREC-3 collection, the vocabulary

of 1 gigabyte of text occupies only 5 megabytes
This may be further reduced by stemming and other
normalization techniques

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 13

Full Inverted Indexes
The occurrences demand much more space
The extra space will be O(n) and is around
40% of the text size if stopwords are omitted
80% when stopwords are indexed

Document-addressing indexes are smaller, because

only one occurrence per file must be recorded, for a
given word
Depending on the document (file) size,
document-addressing indexes typically require 20% to
40% of the text size

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 14

Full Inverted Indexes
To reduce space requirements, a technique called
block addressing is used
The documents are divided into blocks, and the
occurrences point to the blocks where the word appears
Block 1 Block 2 Block 3 Block 4

This is a text. A text has many words. Words are made from letters.

Text
Vocabulary Occurrences

letters 4...
made 4...
many 2...
Inverted Index
text 1, 2...
words 3...

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 15

Full Inverted Indexes
The Table below presents the projected space taken by
inverted indexes for texts of different sizes

Index Single document Small collection Medium collection

granularity (1 MB) (200 MB) (2 GB)
Addressing
words 45% 73% 36% 64% 35% 63%

Addressing
documents 19% 26% 18% 32% 26% 47%

Addressing
64K blocks 27% 41% 18% 32% 5% 9%

Addressing
256 blocks 18% 25% 1.7% 2.4% 0.5% 0.7%

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 16

Full Inverted Indexes
The blocks can be of fixed size or they can be defined
using the division of the text collection into documents
The division into blocks of fixed size improves efficiency
at retrieval time
This is because larger blocks match queries more frequently and
are more expensive to traverse

This technique also profits from locality of reference

That is, the same word will be used many times in the same
context and all the references to that word will be collapsed in just
one reference

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 17

Single Word Queries
The simplest type of search is that for the occurrences
of a single word
The vocabulary search can be carried out using any
suitable data structure
Ex: hashing, tries, or B-trees

The first two provide O(m) search cost, where m is the

length of the query
We note that the vocabulary is in most cases sufficiently
small so as to stay in main memory
The occurrence lists, on the other hand, are usually
fetched from disk

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 18

Multiple Word Queries
If the query has more than one word, we have to
consider two cases:
conjunctive (AND operator) queries
disjunctive (OR operator) queries

Conjunctive queries imply to search for all the words

in the query, obtaining one inverted list for each word
Following, we have to intersect all the inverted lists to
obtain the documents that contain all these words
For disjunctive queries the lists must be merged
The first case is popular in the Web due to the size of
the document collection

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 19

List Intersection
The most time-demanding operation on inverted
indexes is the merging of the lists of occurrences
Thus, it is important to optimize it

Consider one pair of lists of sizes m and n respectively,

stored in consecutive memory, that needs to be
intersected
If m is much smaller than n, it is better to do m binary
searches in the larger list to do the intersection
If m and n are comparable, Baeza-Yates devised a
double binary search algorithm
It is O(log n) if the intersection is trivially empty
It requires less than m + n comparisons on average

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 20

List Intersection
When there are more than two lists, there are several
possible heuristics depending on the list sizes
If intersecting the two shortest lists gives a very small
answer, might be better to intersect that to the next
shortest list, and so on
The algorithms are more complicated if lists are stored
non-contiguously and/or compressed

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 21

Phrase and Proximity Queries
Context queries are more difficult to solve with inverted
indexes
The lists of all elements must be traversed to find
places where
all the words appear in sequence (for a phrase), or
appear close enough (for proximity)
these algorithms are similar to a list intersection algorithm

Another solution for phrase queries is based on

indexing two-word phrases and using similar algorithms
over pairs of words
however the index will be much larger as the number of word
pairs is not linear

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 22

More Complex Queries
Prefix and range queries are basically (larger)
disjunctive queries
In these queries there are usually several words that
match the pattern
Thus, we end up again with several inverted lists and we can use
the algorithms for list intersection

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 23

More Complex Queries
To search for regular expressions the data structures
built over the vocabulary are rarely useful
The solution is then to sequentially traverse the
vocabulary, to spot all the words that match the pattern
Such a sequential traversal is not prohibitively costly
because it is carried out only on the vocabulary

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 24

Boolean Queries
In boolean queries, a query syntax tree is naturally
defined AND

translation OR

syntax syntactic

Normally, for boolean queries, the search proceeds in

three phases:
the first phase determines which documents to match
the second determines the likelihood of relevance of the
documents matched
the final phase retrieves the exact positions of the matches to
allow highlighting them during browsing, if required
Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 25
Boolean Queries
Once the leaves of the query syntax tree find the
classifying sets of documents, these sets are further
operated by the internal nodes of the tree
Under this scheme, it is possible to evaluate the syntax
tree in full or lazy form
In the full evaluation form, both operands are first completely
obtained and then the complete result is generated
In lazy evaluation, the partial results from operands are delivered
only when required, and then the final result is recursively
generated

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 26

 Boolean Queries
Processing the internal nodes of the query syntax tree
In (a) full evaluation is used
In (b) we show lazy evaluation in more detail

AND AND 46
a)
146 OR 146 23467

246 237

b)
AND 4 AND 6
AND AND AND AND

1 OR 2 4 OR 2 4 OR 3 4 OR 4 6 OR 6 OR 7

4 3 4 3 4 7 6 7 7

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 27

Inverted Indexes
Searching

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 28

Ranking
How to find the top-k documents and return them to the
user when we have weight-sorted inverted lists?
If we have a single word query, the answer is trivial as
the list can be already sorted by the desired ranking
For other queries, we need to merge the lists

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 29

Ranking
Suppose that we are searching the disjunctive query
“to do” on the collection below
To do is to be.
To be is to do. To be or not to be.
I am what I am.

d1
d2
I think therefore I am.
Do be do be do. Do do do, da da da.
Let it be, let it be.

d3
d4
As our collection is very small, let us assume that we
are interested in the top-2 ranked documents
We can use the following heuristic:
we process terms in idf order (shorter lists first), and
each term is processed in tf order (simple ranking order)

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 30

Ranking
Ranking-in-the-vector-model( query terms t )
01 Create P as C-candidate similarities initialized to (P d , Pw ) = (0, 0)
02 Sort the query terms t by decreasing weight
03 c←1
04 for each sorted term t in the query do
05 Compute the value of the threshold t add
06 Retrieve the inverted list for t, L t
07 for each document d in L t do This is a variant of
08 if wd,t < tadd then break Persin’s algorithm
09 psim ← wd,t × wq,t /Wd
10 if d ∈ Pd (i) then We use a priority queue P of
11 Pw (i) ← Pw (i) + psim C document candidates
11 elif psim > minj (Pw (j)) then
where we will compute partial
11 n ← minj (Pw (j))
12 elif c ≤ C then
similarities
13 n←c
14 c ←c+1
15 if n ≤ C then P (n) ← (d, psim)
16 return the top-k documents according to P w

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 31

Internal Algorithms
Building an index in internal memory is a relatively
simple and low-cost task
A dynamic data structure to hold the vocabulary (B-tree,
hash table, etc.) is created empty
Then, the text is scanned and each consecutive word is
searched for in the vocabulary
If it is a new word, it is inserted in the vocabulary before
proceeding

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 32

Internal Algorithms
A large array is allocated where the identifier of each
consecutive text word is stored
A full-text inverted index for a sample text with the
incremental algorithm:
1 6 9 11 17 19 24 28 33 40 46 50 55 60
This is a text. A text has many words. Words are made from letters.

Text
letters: 60
"l"
"d" made: 50
"m" "a"

many: 28 Vocabulary trie

"t" "n"
text: 11, 19
"w"
words: 33, 40

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 33

Internal Algorithms
A full-text inverted index for a sample text with a sorting
algorithm:
1 4 12 18 21 24 35 43 50 54 64 67 77 83
In theory, there is no difference between theory and practice. In practice, there is.
Text
collect identifiers

1 between
4:4 2:24 1:35 4:43 3:54 3:67
2 difference
3 practice sort

4 theory
1:35 2:24 3:54 3:67 4:4 4:43
Vocabulary
identify headers

Occurrences 35 24 54 67 4 43

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 34

Internal Algorithms
An alternative to avoid this sorting is to separate the
lists from the beginning
In this case, each vocabulary word will hold a pointer to its own
array (list) of occurrences, initially empty

A non trivial issue is how the memory for the many lists
of occurrences should be allocated
A classical list in which each element is allocated individually
wastes too much space
Instead, a scheme where a list of blocks is allocated, each block
holding several entries, is preferable

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 35

Internal Algorithms
Once the process is completed, the vocabulary and the
lists of occurrences are written on two distinct disk files
The vocabulary contains, for each word, a pointer to the
position of the inverted list of the word
This allows the vocabulary to be kept in main memory
at search time in most cases

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 36

External Algorithms
All the previous algorithms can be extended by using
them until the main memory is exhausted
At this point, the partial index Ii obtained up to now is
written to disk and erased from main memory
These indexes are then merged in a hierarchical
fashion

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 37

External Algorithms
Merging the partial indexes in a binary fashion
Rectangles represent partial indexes, while rounded rectangles
represent merging operations

Level 4
Iï1..8 (final index)

Iï1..4 Iï5..8 Level 3

3 6

Iï1..2 Iï3..4 Iï5..6 Iï7..8 Level 2

1 2 4 5

Level 1
Iï1 Iï2 Iï3 Iï4 Iï5 Iï6 Iï7 Iï8 (initial dumps

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 38

External Algorithms
In general, maintaining an inverted index can be done
in three different ways:
Rebuild
If the text is not that large, rebuilding the index is the simplest
solution
Incremental updates
We can amortize the cost of updates while we search
That is, we only modify an inverted list when needed
Intermittent merge
New documents are indexed and the resultant partial index is
merged with the large index
This in general is the best solution

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 39

 Inverted Indexes
Compressed Inverted Indexes

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 40

Compressed Inverted Indexes
It is possible to combine index compression and text
compression without any complication
In fact, in all the construction algorithms mentioned, compression
can be added as a final step

In a full-text inverted index, the lists of text positions or

file identifiers are in ascending order
Therefore, they can be represented as sequences of
gaps between consecutive numbers
Notice that these gaps are small for frequent words and large for
infrequent words
Thus, compression can be obtained by encoding small values
with shorter codes

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 41

Compressed Inverted Indexes
A coding scheme for this case is the unary code
In this method, each integer x > 0 is coded as (x − 1) 1-bits
followed by a 0-bit

A better scheme is the Elias-γ code, which represents a

number x > 0 by a concatenation of two parts:
1. a unary code for 1 + "log2 x#
2. a code of "log2 x# bits that represents the number x − 2!log2 x" in
binary

Another coding scheme is the Elias-δ code

Elias-δ concatenates parts (1) and (2) as above, yet part
(1) is not represented in unary but using Elias-γ instead

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 42

Compressed Inverted Indexes
Example codes for integers

Gap x Unary Elias-γ Elias-δ Golomb

(b = 3)
1 0 0 0 00
2 10 100 1000 010
3 110 101 1001 011
4 1110 11000 10100 100
5 11110 11001 10101 1010
6 111110 11010 10110 1011
7 1111110 11011 10111 1100
8 11111110 1110000 11000000 11010
9 111111110 1110001 11000001 11011
10 1111111110 1110010 11000010 11100

Note: Golomb codes will be explainedIndexing

later and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 43
Compressed Inverted Indexes
In general,
Elias-γ for an arbitrary integer x > 0 requires 1 + 2"log2 x# bits
Elias-δ requires 1 + 2"log2 log2 2x# + "log2 x# bits

For small values of x Elias-γ codes are shorter than

Elias-δ codes, and the situation is reversed as x grows
Thus the choice depends on which values we expect to
encode

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 44

Compressed Inverted Indexes
Golomb presented another coding method that can be
parametrized to fit smaller or larger gaps
For some parameter b, let q and r be the quotient and
remainder, respectively, of dividing x − 1 by b
I.e., q = "(x − 1)/b# and r = (x − 1) − q · b

Then x is coded by concatenating

the unary representation of q + 1
the binary representation of r, using either "log2 b# or $log2 b% bits

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 45

Compressed Inverted Indexes
If r < 2!log2 b"−1 then r uses "log2 b# bits, and the
representation always starts with a 0-bit
Otherwise it uses $log2 b% bits where the first bit is 1 and
the remaining bits encode the value r − 2!log2 b"−1 in
"log2 b# binary digits
For example,
For b = 3 there are three possible remainders, and those are
coded as 0, 10, and 11, for r = 0, r = 1, and r = 2, respectively
For b = 5 there are five possible remainders r, 0 through 4, and
these are assigned the codes 00, 01, 100, 101, and 110

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 46

Compressed Inverted Indexes
To encode the lists of occurrences using Golomb
codes, we must define the parameter b for each list
Golomb codes usually give better compression than
either Elias-γ or Elias-δ
However they need two passes to be generated as well as
information on terms statistics over the whole document collection
For example, in the TREC-3 collection, the average
number of bits per list entry for each method is
Golomb = 5.73
Elias-δ = 6.19
Elias-γ = 6.43

This represents a five-fold reduction in space compared

to a plain inverted index representation
Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 47
Compressed Inverted Indexes
Let us now consider inverted indexes for ranked search
In this case the documents are sorted by decreasing frequency of
the term or other similar type of weight

Documents that share the same frequency can be

sorted in increasing order of identifiers
This will permit the use of gap encoding to compress
most of each list

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 48

Inverted Indexes
Structural Queries

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 49

Structural Queries
Let us assume that the structure is marked in the text
using tags
The idea is to make the index take the tags as if they
were words
After this process, the inverted index contains all the
information to answer structural queries

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 50

Structural Queries
Consider the query:
select structural elements of type A that contain a structure of
type B

The query can be translated into finding <A> followed

by <B> without </A> in between
The positions of those tags are obtained with the
full-text index
Many queries can be translated into a search for tags
plus validation of the sequence of occurrences
In many cases this technique is efficient and its
integration into an existing text database is simpler

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 51

Signature Files

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 52

Signature Files
Signature files are word-oriented index structures
based on hashing
They pose a low overhead, at the cost of forcing a
sequential search over the index
Since their search complexity is linear, it is suitable only
for not very large texts
Nevertheless, inverted indexes outperform signature
files for most applications

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 53

Structure
A signature divides the text in blocks of b words each,
and maps words to bit masks of B bits
This mask is obtained by bit-wise ORing the signatures
of all the words in the text block
Block 1 Block 2 Block 3 Block 4
This is a text. A text has many words. Words are made from letters.

Text

000101 110101 100100 101101 Text signature

h(text) = 000101
h(many) = 110000
h(words) = 100100 Signature function
h(made) = 001100
h(letters) = 100001

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 54

Structure
If a word is present in a text block, then its signature is
also set in the bit mask of the text block
Hence, if a query signature is not in the mask of the text
block, then the word is not present in the text block
However, it is possible that all the corresponding bits
are set even though the word is not there
This is called a false drop

A delicate part of the design of a signature file is:

to ensure the probability of a false drop is low, and
to keep the signature file as short as possible

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 55

Structure
The hash function is forced to deliver bit masks which
have at least # bits set
A good model assumes that # bits are randomly set in
the mask (with possible repetition)

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 56

Inverted Indexes
Searching

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 57

Searching
Searching a single word is made by comparing its bit
mask W with the bit masks Bi of all the text blocks
Whenever (W & Bi = W ), where & is the bit-wise AND,
the text block may contain the word
Hence, an online traversal must be performed to verify if
the word is actually there
This traversal cannot be avoided as in inverted indexes
(except if the risk of a false match is accepted)

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 58

Searching
This scheme is more efficient to search phrases and
reasonable proximity queries
This is because all the words must be present in a block in order
for that block to hold the phrase or the proximity query

Hence, the bit-wise OR of all the query masks is

searched, so that all their bits must be present
This reduces the probability of false drops

Some care has to be exercised at block boundaries, to

avoid missing a phrase which crosses a block limit
To search phrases of j words or proximities of up to j
words, consecutive blocks must overlap in j − 1 words
This is the only indexing scheme which improves in
phrase searching
Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 59
Inverted Indexes
Construction

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 60

Construction
The construction of a signature file is rather easy:
The text is simply cut in blocks, and for each block an entry of the
signature file is generated

Adding text is also easy, since it is only necessary to

keep adding records to the signature file
Text deletion is carried out by deleting the appropriate
bit masks

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 61

Compression
There are many alternative ways to compress signature
files
All of them are based on the fact that only a few bits are
set in the whole file
Compression ratios near 70% are reported

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 62

Suffix Trees and Suffix Arrays

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 63

Suffix Trees and Suffix Arrays
Inverted indexes are by far the preferred choice to
implement IR systems
However, they work if the vocabulary is not too large,
otherwise their efficiency would drastically drop
This condition holds in many languages (particularly
Western languages), but not in all
For example, Finnish and German are languages that
concatenate short particles to form long words

Usually, there is no point in querying for those long

words, but by the particles that form them

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 64

Suffix Trees and Suffix Arrays
Suffix trees and suffix arrays enable indexed searching
for any text substring matching a query string
These indexes regard the text as one long string, and
each position in the text is considered as a text suffix
For example, if the text is missing mississippi, the
suffixes are
missing mississippi
issing mississippi
ssing mississippi
..
ppi
pi
i

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 65

Suffix Trees and Suffix Arrays
Structure

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 66

Structure
A trie over a set of strings P = {P1 , . . . , Pr } is a
tree-shaped DFA that recognizes P1 | . . . | Pr
Hence looking for a string in P is equivalent to
determining whether the DFA recognizes the string
A suffix trie is, in essence, a trie data structure built
over all the suffixes of a text T = t1 t2 . . . tn , tn , ‘$’
The pointers to the suffixes ti . . . tn are stored at the
final states

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 67

Structure
To reduce the number of nodes in such a trie, the suffix
trie removes all unary paths that finish at a leaf.
The suffix trie for the text missing mississippi is
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

m i s s i n g m i s s i s s i p p i $

$ g i m n p s

20 8 7 6
i p
18 17 i s
$ n p s i

19 5 16
s s n p s i
4 15 12
s n p s
i
3 14 11
n p s i
2 13 10
n s
1 9

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 68

Structure
Suffix tree: to further reduce the space requirement, all
the remaining unary paths can be compressed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

m i s s i n g m i s s i s s i p p i $

$ g i m n p s

20 8 7 6
i p
18 17 i s
$ n p s i

19 5 16
s s n p s i
4 15 12
s n p s
i
3 14 11
n p s i
2 13 10
n s
1 9

$ g i missi n p s

20 8 7 6
n s i p
1 9 i si
$ n p ssi 18 17

19 5 16
n p s n p s n p s
2 13 10 4 15 12 3 14 11

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 69

Structure
The problem with suffix trees is their space
Depending on the implementation, a suffix tree takes 10
to 20 times the space of the text itself
For example, the suffix tree of a text of 1 gigabyte would need at
least 10 gigabytes of space

In addition, suffix trees do not perform well in secondary

memory

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 70

 Structure
Suffix arrays provide essentially the same functionality
of suffix trees with much lower space requirements
A suffix array of T is defined as an array pointing to all
the suffixes of T , where suffixes have been
lexicographically sorted (that is, the leaves of the suffix
trie from left to right)
The suffix array for the text missing mississippi:

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

m i s s i n g m i s s i s s i p p i $

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
20 8 7 19 5 16 2 13 10 1 9 6 18 17 4 15 12 3 14 11

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 71

Structure
A suffix array takes typically 4 times the text size, which
makes it appealing for longer texts
In exchange, suffix arrays are slightly slower than suffix
trees
In some papers suffix trees and arrays are called PAT
trees and arrays

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 72

Suffix Trees and Suffix Arrays
Searching for Simple Strings

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 73

Searching for Simple Strings
The main property that permits finding substrings equal
to a given pattern string P = p1 p2 . . . pm is as follows:
Every text substring is a prefix of a text suffix

The main idea is then to descend in the trie by following

the characters of P
There are three possible outcomes:
There might be no path in the trie spelling out P : then P does not
occur in T
We find P before reaching a leaf: then P appears in all the
positions stored in the leaves under that path
Maybe we arrive at a leaf before reading P completely: in this
case we have to keep comparing in the text pointed by the leaf to
know if P is in the text or not

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 74

Searching for Simple Strings
If the search is carried out on a suffix tree instead, then
the edges are labeled by strings
Yet, all the strings labeling edges that depart from a
given node differ in their first character
Therefore, at each node, there is at most one edge to
follow

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 75

Searching for Simple Strings
Pseudocode for a suffix tree search

Suffix-Tree-Search (S, P = p1 p2 . . . pm )
(1) i ← 1
(2) while true do
(3) if S is a leaf pointing to j then
(4) if pi . . . pm = tj+i−1 . . . tj+m−1
(5) then return S
(6) else return null
p!1 ...p!s
(7) if there is an edge S −→ S # ∧ p#1 = pi then
(8) j←0
(9) while j < s ∧ i + j ≤ m ∧ p#j+1 = pi+j do j ← j + 1
(10) i←i+j
(11) if i > m then return S #
(12) if j < s then return null
(13) S ← S#
(14) else return null

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 76

 Searching for Simple Strings
Searching in a suffix array is slightly different
We perform a binary search with indirect comparisons
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

m i s s i n g m i s s i s s i p p i $

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
20 8 7 19 5 16 2 13 10 1 9 6 18 17 4 15 12 3 14 11

Note that each step in this binary search requires

comparing P against a text suffix

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 77

Suffix Trees and Suffix Arrays
Searching for Complex Patterns

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 78

Searching for Complex Patterns
Searching for a complex pattern using a suffix trie it is
not a trivial task
Assume for example we wish to search for a certain regular
expression
We build the corresponding non-deterministic finite automaton
without adding the initial self-loop
We will detect all the text suffixes that start with a string matching
the regular expression

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 79

Searching for Complex Patterns
For this sake, the algorithm begins at the trie root
For each child of a node c, the automaton is fed with c
and the algorithm recursively enters the subtree
When the recursion returns from the subtree, the original
automaton state before feeding it with c is restored

The process is repeated for each children of c

The search stops in three possible forms:
The automaton runs out of active states
The automaton arrives at a final state
We arrive at a trie leaf and we keep searching in the suffix
referenced there

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 80

Searching for Complex Patterns
Indexed approximate string matching with tolerance k is
also possible using the same idea
Approximate searching on a trie cannot exceed depth
m + k , and thus the time is independent on the text size
for short enough patterns
For longer patterns the exponential dependence on m becomes
apparent in the search time

Suffix trees are able to perform other complex searches

that we have not considered
Some examples are:
Find the longest substring in the text that appears more than once
Find the most common substring of a fixed length

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 81

Suffix Trees and Suffix Arrays
Construction

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 82

Construction
A simple way to generate a suffix array is to
lexicographically sort all the pointed suffixes
To compare two suffix array entries in this sorting, the
corresponding text positions must be accessed
There are several much stronger sorting algorithms for
suffix arrays
The main idea: if we know that ti+1 . . . tn < tj+1 . . . tn and
ti = tj , then we directly infer that ti . . . tn < tj . . . tn

Different algorithms build on this idea in different ways

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 83

Suffix Trees and Suffix Arrays
Construction for Large Texts

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 84

Construction for Large Texts
When the data is not in main memory, algorithms for
secondary memory construction are required
We present an algorithm that splits the text into blocks
that can be sorted in main memory
For each block, it builds the suffix array of the block in
main memory, and merges it with the rest of the suffix
array already built for the preceding text:
(1) build the suffix array for block 1
(2) build the suffix array for block 2
(3) merge the suffix array for block 2 with that of block 1
(4) build the suffix array for block 3
(5) merge the suffix array for block 3 with that of block 1+2
(6) .... etc

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 85

Construction for Large Texts
How to merge a large suffix array LA for blocks
1, 2, . . . , i − 1 with the small suffix array SA for block i?
The solution is to determine how many elements of LA
are to be placed between the elements in SA
The information is stored in a counter array C: C[j] tells how
many suffixes of LA lie between SA[j] and SA[j + 1]

Once C is computed, LA and SA are easily merged:

(1) append the first C[0] elements of LA
(2) append SA[1]
(3) append the next C[1] elements of LA
(4) append SA[2]
(5) append the next C[2] elements of LA
(6) append SA[3]
(7) .... etc

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 86

Construction for Large Texts
The remaining point is how to compute the counter
array C
This is done without accessing LA: the text corresponding to
LA is sequentially read into main memory

Each suffix of that text is searched for in SA (in main

memory)
Once we determine that the text suffix lies between
SA[j] and SA[j + 1], we increment C[j]
Notice that this same algorithm can be used for index
maintenance

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 87

Construction for Large Texts
A step of the suffix array construction for large texts:
(a) the local suffix array SA is built
(b) the counters C are computed
(c) suffix arrays SA and LA are merged

a) small text
b) small text

SA
SA small suffix array long text
small suffix array
C
counters

small text LA
c) SA long suffix array
small suffix array
C
counters final suffix array

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 88

Suffix Trees and Suffix Arrays
Compressed Suffix Arrays

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 89

 Compressed Suffix Arrays
An important problem of suffix arrays is their high space
requirement
Consider again the suffix array of the Figure below, and
call it A[1, n]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

m i s s i n g m i s s i s s i p p i $

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
20 8 7 19 5 16 2 13 10 1 9 6 18 17 4 15 12 3 14 11

The values at A[15..17] are 4, 15, 12

The same sequence is found, displaced by one value,
at A[18..20], and further displaced at A[7..9]

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 90

 Compressed Suffix Arrays
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

m i s s i n g m i s s i s s i p p i $

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
20 8 7 19 5 16 2 13 10 1 9 6 18 17 4 15 12 3 14 11

A compressor can realize that every time it has seen

si, the next character it will see is s and then i
This is related to k-th order compression

By exploiting these regularities, the suffix array of a

compressible text can also be compressed
Manipulating a suffix array in compressed form is
indeed slower than using the uncompressed suffix array
There is not much development on using suffix array
indexes (compressed or not) on disk
Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 91
Using Function Ψ
One way to exhibit the suffix array regularities is by
means of a function called Ψ and defined so that

A[Ψ(i)] = A[i] + 1,

except when A[i] = n, in which case A[Ψ(i)] = 1

That is, Ψ(i) tells where in A is the value that follows the
current one

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 92

 Using Function Ψ
Function Ψ computed for the example suffix array, and
diff(i) = Ψ(i) − Ψ(i − 1)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

T m i s s i n g m i s s i s s i p p i $

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

A 20 8 7 19 5 16 2 13 10 1 9 6 18 17 4 15 12 3 14 11

^ 10 11 2 1 12 14 18 19 20 7 9 3 4 13 5 6 8 15 16 17

diff 10 1 ï9 ï1 11 2 4 1 1 ï 13 2 ï6 1 9 ï8 1 2 7 1 1

$ g i m n p s

We indicate the areas of the arrays where the suffixes

start with the same character

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 93

 Using Function Ψ
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

T m i s s i n g m i s s i s s i p p i $

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

A 20 8 7 19 5 16 2 13 10 1 9 6 18 17 4 15 12 3 14 11

^ 10 11 2 1 12 14 18 19 20 7 9 3 4 13 5 6 8 15 16 17

diff 10 1 ï9 ï1 11 2 4 1 1 ï 13 2 ï6 1 9 ï8 1 2 7 1 1

$ g i m n p s

Several properties of Ψ are apparent from the figure

and not difficult to prove:
First, Ψ is increasing within the areas where the suffixes start with
the same character
Second, in the areas where the regularities we pointed out before
arise, it holds Ψ(i) − Ψ(i − 1) = 1

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 94

Using Function Ψ
What is most interesting is that the characters of T can
be obtained without accessing T
Therefore, T can be actually deleted and any substring
of it can be obtained just from Ψ
However, this is rarely sufficient, as one usually wants
to know the text positions where the pattern P occurs,
not the interval in A
Yet, we do not have A in order to display the positions of
the occurrences, A[i] for sp ≤ i ≤ ep

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 95

Using Function Ψ
To be able to locate those occurrences in T , we sample
A at regular intervals of T :
Every s-th character in T , record the suffix array position pointing
to that text position

That is, for each text position of the form 1 + j · s, let

A[i] = 1 + j · s
Then we store the pair (i, A[i]) in a dictionary
searchable by its first component
Finally, we should also be able to display any text
substring, as we plan to discard T
Note that we already know how to obtain the characters
of T starting at text position A[i], given i

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 96

The Burrows-Wheeler Transform
A radically different method for compressing is by
means of the Burrows-Wheeler Transform (BWT)
The BWT of T can be obtained by just concatenating
the characters that precede each suffix in A
That is, tA[i]−1 or tn if A[i] = 1

For example, the BWT of T = missing

mississippi$ is T bwt = ignpssmsm$ ipisssiii
It turns out that the BWT tends to group equal
characters into runs
Further, there are large zones where few different
characters appear

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 97

Sequential Searching

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 98

Sequential Searching
In general the sequential search problem is:
Given a text T = t1 t2 . . . tn and a pattern denoting a set of strings
P, find all the occurrences of the strings of P in T

Exact string matching: the simplest case, where the

pattern denotes just a single string P = p1 p2 . . . pm
This problem subsumes many of the basic queries,
such as word, prefix, suffix, and substring search
We assume that the strings are sequences of
characters drawn from an alphabet Σ of size σ

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 99

Sequential Searching
Simple Strings

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 100
Simple Strings: Brute Force
The brute force algorithm:
Try out all the possible pattern positions in the text and checks
them one by one

More precisely, the algorithm slides a window of length

m across the text, ti+1 ti+2 . . . ti+m for 0 ≤ i ≤ n − m
Each window denotes a potential pattern occurrence
that must be verified
Once verified, the algorithm slides the window to the
next position

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 101
Simple Strings: Brute Force
A sample text and pattern searched for using brute
force

The first text window is T abraca bracadabra T

abracabraca
After verifying that it P abracadabra P
does not match P , the
window is shifted by abracadabra
one position
abracadabra

abracadabra

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 102
Simple Strings: Horspool
Horspool’s algorithm is in the fortunate position of
being very simple to understand and program
It is the fastest algorithm in many situations, especially
when searching natural language texts
Horspool’s algorithm uses the previous idea to shift the
window in a smarter way
A table d indexed by the characters of the alphabet is
precomputed:
d[c] tells how many positions can the window be shifted if the final
character of the window is c
In other words, d[c] is the distance from the end of the
pattern to the last occurrence of c in P , excluding the
occurrence of pm
Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 103
Simple Strings: Horspool
The Figure repeats the previous example, now also
applying Horspool’s shift
T abraca bracadabra T abraca bracadabra

P abracadabra P abracadabra

abracadabra abracadabra

abracadabra

abracadabra

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 104
Simple Strings: Horspool
Pseudocode for Horspool’s string matching algorithm
Horspool (T = t1 t2 . . . tn , P = p1 p2 . . . pm )
(1) for c ∈ Σ do d[c] ← m
(2) for j ← 1 . . . m − 1 do d[pj ] ← m − j
(3) i←0
(4) while i ≤ n − m do
(5) j←1
(6) while j ≤ m ∧ ti+j = pj do j ← j + 1
(7) if j > m then report an occurrence at text position i + 1
(8) i ← i + d[ti+m ]

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 105
Small alphabets and long patterns
When searching for long patterns over small alphabets
Horspool’s algorithm does not perform well
Imagine a computational biology application where strings of 300
nucleotides over the four-letter alphabet {A, C, G, T} are sought

This problem can be alleviated by considering

consecutive pairs of characters to shift the window
On other words, we can align the pattern with the last pair of
window characters, ti+m−1 ti+m

In the previous example, we would shift by 42 = 16

positions on average

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 106
Small alphabets and long patterns
In general we can shift using q characters at the end of
the window: which is the best value for q ?
We cannot shift by more than m, and thus σ q ≤ m seems to be a
natural limit
If we set q = logσ m, the average search time will be
O(n logσ (m)/m)

Actually, this average complexity is optimal, and the

choice for q we derived is close to correct
It can be analytically shown that, by choosing
q = 2 logσ m, the average search time achieves the
optimal O(n logσ (m)/m)

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 107
Small alphabets and long patterns
This technique is used in the agrep software
A hash function is chosen to map q -grams (strings of
length q ) onto an integer range
Then the distance from each q -gram of P to the end of
P is recorded in the hash table
For the q -grams that do not exist in P , distance
m − q + 1 is used

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 108
Small alphabets and long patterns
Pseudocode for the agrep’s algorithm to match long
patterns over small alphabets (simplified)
Agrep (T = t1 t2 . . . tn , P = p1 p2 . . . pm , q, h( ), N )
(1) for i ∈ [1, N ] do d[i] ← m − q + 1
(2) for j ← 0 . . . m − q do d[h(pj+1 pj+2 . . . pj+q )] ← m − q − j
(3) i←0
(4) while i ≤ n − m do
(5) s ← d[h(ti+m−q+1 ti+m−q+2 . . . ti+m )]
(6) if s > 0 then i ← i + s
(7) else
(8) j←1
(9) while j ≤ m ∧ ti+j = pj do j ← j + 1
(10) if j > m then report an occurrence at text position i + 1
(11) i←i+1

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 109
Automata and Bit-Parallelism
Horspool’s algorithm, as well as most classical
algorithms, does not adapt well to complex patterns
We now show how automata and bit-parallelism
permit handling many complex patterns

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 110
Automata
Figure below shows, on top, a NFA to search for the
pattern P = abracadabra
The initial self-loop matches any character
Each table column corresponds to an edge of the automaton

a b r a c a d a b r a

B[a] = 0 1 1 0 1 0 1 0 1 1 0
B[b] = 1 0 1 1 1 1 1 1 0 1 1
B[r] = 1 1 0 1 1 1 1 1 1 0 1
B[c] = 1 1 1 1 0 1 1 1 1 1 1
B[d] = 1 1 1 1 1 1 0 1 1 1 1
B[*] = 1 1 1 1 1 1 1 1 1 1 1

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 111
Automata
It can be seen that the NFA in the previous Figure
accepts any string that finishes with P =
‘abracadabra’
The initial state is always active because of the self-loop
that can be traversed by any character
Note that several states can be simultaneously active
For example, after reading ‘abra’, NFA states 0, 1, and 4 will be
active

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 112
Bit-parallelism and Shift-And
Bit-parallelism takes advantage of the intrinsic
parallelism of bit operations
Bit masks are read right to left, so that the first bit of
bm . . . b1 is b1
Bit masks are handled with operations like:
| to denote the bit-wise or
& to denote the bit-wise and, and
! to denote the bit-wise xor

Unary operation ‘∼’ complements all the bits

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 113
Bit-parallelism and Shift-And
In addition:
mask << i means shifting all the bits in mask by i positions to
the left, entering zero bits from the right
mask >> i is analogous

Finally, it is possible to operate bit masks as numbers,

for example adding or subtracting them

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 114
Bit-parallelism and Shift-And
The simplest bit-parallel algorithm permits matching
single strings, and it is called Shift-And
The algorithm builds a table B which, for each
character, stores a bit mask bm . . . b1
The mask in B[c] has the i-th bit set if and only if pi = c

The state of the search is kept in a machine word

D = dm . . . d1 , where di is set if the state i is active
Therefore, a match is reported whenever dm = 1

Note that state number zero is not represented in D

because it is always active and then can be left implicit

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 115
Bit-parallelism and Shift-And
Pseudocode for the Shift-And algorithm
Shift-And (T = t1 t2 . . . tn , P = p1 p2 . . . pm )

(1) for c ∈ Σ do B[c] ← 0

(2) for j ← 1 . . . m do B[pj ] ← B[pj ] | (1 << (j − 1))
(3) D←0
(4) for i ← 1 . . . n do
(5) D ← ((D << 1) | 1) & B[ti ]
(6) if D & (1 << (m − 1)) += 0
(7) then report an occurrence at text position i − m + 1

There must be sufficient bits in the computer word to

store one bit per pattern position
For longer patterns, in practice we can search for p1 p2 . . . pw , and
directly check the occurrences of this prefix for the complete P
Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 116
Extending Shift-And
Shift-And can deal with much more complex patterns
than Horspool
The simplest case is that of classes of characters:
This is the case, for example, when one wishes to search in
case-insensitive fashion, or one wishes to look for a whole word

Let us now consider a more complicated pattern

Imagine that we search for neighbour, but we wish the u to be
optional (accepting both English and American style)

The Figure below shows an NFA that does the task

using an ε-transition

n e i g h b o u r
0 1 2 3 4 5 6 7 8 9
¡

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 117
Extending Shift-And
Another feature in complex patterns is the use of wild
cards, or more generally repeatable characters
Those are pattern positions that can appear once or more times,
consecutively, in the text

For example, we might want to catch all the transfer

records in a banking log

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 118
Extending Shift-And
As another example, we might look for well known,
yet there might be a hyphen or one or more spaces
For instance ‘well known’, ‘well known’, ‘well-known’,
‘well - known’, ‘well \n known’, and so on

sep

w e l l sep k n o w n
0 1 2 3 4 5 6 7 8 9 10

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 119
Extending Shift-And
Figure below shows pseudocode for a Shift-And
extension that handles all these cases
Shift-And-Extended (T = t1 t2 . . . tn , m, B[ ], A, S)

(1) I ← (A >> 1) & (A ! (A >> 1))

(2) F ← A & (A ! (A >> 1))
(3) D←0
(4) for i ← 1 . . . n do
(5) D ← (((D << 1) | 1) | (D & S)) & B[ti ]
(6) Df ← D | F
(7) D ← D | (A & ((∼ (Df − I)) ! Df ))
(8) if D & (1 << (m − 1)) += 0
(9) then report an occurrence at text position i − m + 1

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 120
Faster Bit-Parallel Algorithms
There exist some algorithms that can handle complex
patterns and still skip text characters (like Horspool)
For instance, Suffix Automata and Interlaced Shift-And algorithms

Those algorithms run progressively slower as the

pattern gets more complex

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 121
Suffix Automata
The suffix automaton of a pattern P is an automaton
that recognizes all the suffixes of P
Below we present a non-deterministic suffix automaton
for P = ‘abracadabra’

¡
I
a b r a c a d a b r a
0 1 2 3 4 5 6 7 8 9 10 11

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 122
Suffix Automata
To search for pattern P , the suffix automaton of P rev
(the reversed pattern) is built
The algorithm scans the text window backwards and
feeds the characters into the suffix automaton of P rev
If the automaton runs out of active states after scanning
ti+m ti+m−1 . . . ti+j , this means that ti+j ti+j+1 . . . ti+m is
not a substring of P
Thus, no occurrence of P can contain this substring,
and the window can be safely shifted past ti+j
If, instead, we reach the beginning of the window and
the automaton still has active states, this means that
the window is equal to the pattern

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 123
Suffix Automata
The need to implement the suffix automaton and make
it deterministic makes the algorithm more complex
An attractive variant, called BNDM, implements the
suffix automaton using bit-parallelism
It achieves improved performance when the pattern is
not very long
say, at most twice the number of bits in the computer word

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 124
Suffix Automata
Pseudocode for BNDM algorithm:
BNDM (T = t1 t2 . . . tn , P = p1 p2 . . . pm )

(1) for c ∈ Σ do B[c] ← 0

(2) for j ← 1 . . . m do B[pj ] ← B[pj ] | (1 << (m − j))
(3) i←0
(4) while i ≤ n − m do
(5) j ←m−1
(6) D ← B[ti+m ]
(7) while j > 0 ∧ D += 0 do
(8) D ← (D << 1) & B[ti+j ]
(9) j ←j−1
(10) if D += 0 then report an occurrence at text position i + 1
(11) i←i+j+1

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 125
Interlaced Shift-And
Another idea to achieve optimal average search time is
to read one text character out of q
To fix ideas, assume P = neighborhood and q = 3
If we read one text position out of 3, and P occurs at
some text window ti+1 ti+2 . . . ti+m then we will read
either ‘ngoo’, ‘ehro’, or ‘ibhd’ at the window
Therefore, it is sufficient to search simultaneously for
the three subsequences of P

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 126
Interlaced Shift-And
Now the initial state can activate the first q positions of
P , and the bit-parallel shifts are by q positions
A non-deterministic suffix automaton for interlaced
searching of P = ‘neighborhood’ with q = 3 is:

n
0 1 2 3 4 5 6 7 8 9 10 11 12
e

i g h b o r h o o d

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 127
Interlaced Shift-And
Pseudocode for Interlaced Shift-And algorithm with
sampling step q (simplified):
Interlaced-Shift-And (T = t1 t2 . . . tn , P = p1 p2 . . . pm , q)

(1) for c ∈ Σ do B[c] ← 0

(2) for j ← 1 . . . m do B[pj ] ← B[pj ] | (1 << (j − 1))
(3) S ← (1 << q) − 1
(4) D←0
(5) for i ← 1 . . . "n/q# do
(6) D ← ((D << q) | S) & B[tq·i ]
(7) if D & (S << ("m/q# · q − q)) += 0
(8) then run Shift-And over tq·i−m+1 . . . tq·i+q−1

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 128
Regular Expressions
The first part in processing a regular expression is to
build an NFA from it
There are different NFA construction methods

We present the more traditional Thompson’s technique

as it is simpler to explain

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 129
Regular Expressions
Recursive Thompson’s construction of an NFA from a
regular expression
¡ a
Th ( ¡ ) = Th ( a ) =

Th ( E . E’) = Th ( E ) Th ( E’)

Th ( E ) ¡
¡

Th ( E | E’) =
¡
¡
Th ( E’)

¡ ¡
Th ( E * ) = Th ( E )

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 130
Regular Expressions
Once the NFA is built we add a self-loop (traversable by
any character) at the initial state
Another alternative is to make the NFA deterministic,
converting it into a DFA
However the number of states can grow non linearly,
even exponentially in the worst case

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 131
Multiple Patterns
Several of the algorithms for single string matching can
be extended to handle multiple strings
P = {P1 , P2 , . . . , Pr }
For example, we can extend Horspool so that d[c] is the minimum
over the di [c] values of the individual patterns Pi

To compute each di we must truncate Pi to the length of

the shortest pattern in P , and that length will be m
Other variants that perform well are extensions of
BNDM
Yet, bit-parallel algorithms are not useful for this case

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 132
Approximate Searching
A simple string matching problem where not only a
string P must be reported, but also text positions where
P occurs with at most k ‘errors’
Different definitions of what is an error can be adopted
The simplest definition is the Hamming distance that allows just
substitutions of characters
A very popular one corresponds to the so-called
Levenshtein or edit distance:
A error is the deletion, insertion, or substitution of a single
character

This model is simple enough to permit fast searching,

being useful for most IR scenarios
This can be extended to approximate pattern matching
Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 133
Dynamic Programming
The classical solution to approximate string matching is
based on dynamic programming
A matrix C[0..m, 0..n] is filled column by column, where
C[i, j] represents the minimum number of errors needed
to match p1 p2 . . . pi to some suffix of t1 t2 . . . tj
This is computed as follows:

C[0, j] = 0,
C[i, 0] = i,
C[i, j] = if (pi = tj ) then C[i − 1, j − 1]
else 1 + min(C[i − 1, j], C[i, j − 1], C[i − 1, j − 1]),

where a match is reported at text positions j such that

C[m, j] ≤ k
Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 134
Dynamic Programming
The dynamic programming algorithm to search for
‘colour’ in the text kolorama with k = 2 errors

k o l o r a m a
0 0 0 0 0 0 0 0 0
c 1 1 1 1 1 1 1 1 1
o 2 2 1 2 1 2 2 2 2
l 3 3 2 1 2 2 3 3 3
o 4 4 3 2 1 2 3 4 4
u 5 5 4 3 2 2 3 4 5
r 6 6 5 4 3 2* 3 4 5

The starred entry indicates a position finishing an

approximate occurrence
Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 135
Dynamic Programming
The previous algorithm requires O(mn) time
Several extensions of it have been presented that
achieve O(kn) time
A simple O(kn) algorithm is obtained by computing each column
only up to the point where one knows that all the subsequent cell
values will exceed k
The memory needed can also be reduced to O(kn)

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 136
Dynamic Programming
Figure below gives the pseudocode for this variant
Approximate-DP (T = t1 t2 . . . tn , P = p1 p2 . . . pm , k)
(1) for i ← 0 . . . m do C[i] ← i
(2) last ← k + 1
(3) for j ← 1 . . . n do
(4) pC, nC ← 0
(5) for i ← 1 . . . last do
(6) if pi = tj then nC ← pC
(7) else
(8) if pC < nC then nC ← pC
(9) if C[i] < nC then nC ← C[i]
(10) nC ← nC + 1
(11) pC ← C[i]
(12) C[i] ← nC
(13) if nC ≤ k
(14) then if last = m then report an occurrence ending at position i
(15) else last ← last + 1
(16) else while C[last − 1] > k do last ← last − 1

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 137
Automata and Bit-parallelism
Approximate string matching can also be expressed as
an NFA search
Figure below depicts an NFA for approximate string
matching for the pattern ‘colour’ with two errors
c o l o u r no errors

¡ ¡ ¡ ¡ ¡ ¡

c o l o u r 1 error

¡ ¡ ¡ ¡ ¡ ¡

c o l o u r 2 errors

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 138
Automata and Bit-parallelism
Although the search phase is O(n), the NFA tends to be
large (O(kn))
A better solution, based on bit-parallelism, is an
extension of Shift-And
We can simulate k + 1 Shift-And processes while taking
care of vertical and diagonal arrows as well

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 139
Automata and Bit-parallelism
Pseudocode for approximate string matching using the
Shift-And algorithm
Approximate-Shift-And (T = t1 t2 . . . tn , P = p1 p2 . . . pm , k)
(1) for c ∈ Σ do B[c] ← 0
(2) for j ← 1 . . . m do B[pj ] ← B[pj ] | (1 << (j − 1))
(3) for i ← 0 . . . k do Di ← (1 << i) − 1
(4) for j ← 1 . . . n do
(5) pD ← D0
(6) nD, D0 ← ((D0 << 1) | 1) & B[ti ]
(7) for i ← 1 . . . k do
(8) nD ← ((Di << 1) & B[ti ]) | pD | ((pD | nD) << 1) | 1
(9) pD ← Di , Di ← nD
(10) if nD & (1 << (m − 1)) += 0
(11) then report an occurrence ending at position i

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 140
Filtration
Frequently it is easier to tell that a text position cannot
match than to ensure that it matches with k errors
Filtration is based on applying a fast filter over the text,
which hopefully discards most of the text positions
Then we can apply an approximate search algorithm
over the areas that could not be discarded
A simple and fast filter:
Split the pattern into k + 1 pieces of about the same length
Then we can run a multi-pattern search algorithm for the pieces
If piece pj . . . pj ! appears in ti . . . ti! , then we run an approximate
string matching algorithm over ti−j+1−k . . . ti−j+m+k

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 141
Searching Compressed Text
An extension of traditional compression mechanisms
gives a very powerful way of matching much more
complex patterns
Let us start with phrase queries that can be searched
for by
compressing each of its words and
searching the compressed text for the concatenated string of
target symbols

This is true as long as

the phrase is made up of simple words, each of which can be
translated into one codeword, and
we want the separators to appear exactly as in the query

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 142
Searching Compressed Text
A more robust search mechanism is based in word
patterns
For example, we may wish to search for:
Any word matching ‘United’ in case-insensitive form and
permitting two errors
Then a separator
And then any word matching ‘States’ in case-insensitive form
and permitting two errors

This search problem can be modeled by means of an

automaton over codewords

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 143
Searching Compressed Text
Let C be the set of different codewords created by the
compressor
We can take C as an alphabet and see the compressed
text as a sequence of atomic symbols over C
Our pattern has three positions, each denoting a class
of characters:
The first is the set of codewords corresponding to words that
match ‘United’ in case-insensitive form and allowing two errors
The second is the set of codewords for separators and is an
optional class
The third is like the first but for the word ‘States’

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 144
Searching Compressed Text
The Figure below illustrates the previous example
, \n 010
\n 010

States 001

any
UNITED 100

 United separator  States

United 100
Unnited 100 ¡

state 001

unates 101
unite 100

Vocabulary B[ ] table
(alphabet)

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 145
Searching Compressed Text
This process can be used to search for much more
complex patterns
Assume that we wish to search for ‘the number of
elements successfully classified’, or
something alike
Many other phrases can actually mean more or less the
same, for example:
the number of elements classified with success
the elements successfully classified
the number of elements we successfully classified
the number of elements that were successfully classified
the number of elements correctly classified
the number of elements we could correctly classify
...

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 146
Searching Compressed Text
To recover from linguistic variants as shown above we
must resort to word-level approximate string matching
In this model, we permit a limited number of missing,
extra, or substituted words
For example, with 3 word-level errors we can recover from all the
variants in the example above

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 147
Multi-dimensional Indexing

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 148
Multi-dimensional Indexing
In multimedia data, we can represent every object by
several numerical features
For example, imagine an image from where we can
extract a color histogram, edge positions, etc
One way to search in this case is to map these object
features into points in a multi-dimensional space
Another approach is to have a distance function for
objects and then use a distance based index
The main mapping methods form three main classes:
R∗ -trees and the rest of the R-tree family,
linear quadtrees,
grid-files

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 149
Multi-dimensional Indexing
The R-tree-based methods seem to be most robust for
higher dimensions
The R-tree represents a spatial object by its minimum
bounding rectangle (MBR)
Data rectangles are grouped to form parent nodes,
which are recursively grouped, to form grandparent
nodes and, eventually, a tree hierarchy
Disk pages are consecutive byte positions on the
surface of the disk that are fetched with one disk access
The goal of the insertion, split, and deletion routines is
to give trees that will have good clustering

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 150
Multi-dimensional Indexing
Figure below illustrates data rectangles (in black),
organized in an R-tree with fanout 3

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 151
Multi-dimensional Search
A range query specifies a region of interest, requiring all
the data regions that intersect it
To answer this query, we first retrieve a superset of the
qualifying data regions:
We compute the MBR of the query region, and then we
recursively descend the R-tree, excluding the branches whose
MBRs do not intersect the query MBR
Thus, the R-tree will give us quickly the data regions whose MBR
intersects the MBR of the query region

The retrieved data regions will be further examined for

intersection with the query region

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 152
Multi-dimensional Search
The data structure of the R-tree for the previous figure
is (fanout = 3)

Indexing and Searching, Modern Information Retrieval, Addison Wesley, 2010 – p. 153