7. Sequence Mining

7/03 Data Mining – SequencesH. Liu (ASU) & G Dong (WSU)

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7. Sequence Mining

Sequences and StringsRecognition with Strings

MM & HMMSequence Association Rules


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Sequences and Strings

• A sequence x is an ordered list of discrete items, such as a sequence of letters or a gene sequence– Sequences and strings are often used as synonyms– String elements (characters, letters, or symbols) are nominal– A type of particularly long string text

• |x| denotes the length of sequence x– |AGCTTC| is 6

• Any contiguous string that is part of x is called a substring, segment, or factor of x– GCT is a factor of AGCTTC


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Recognition with Strings

• String matching– Given x and text, determine whether x is a factor of text

• Edit distance (for inexact string matching)– Given two strings x and y, compute the minimum

number of basic operations (character insertions, deletions and exchanges) needed to transform x into y


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String Matching

• Given |text| >> |x|, with characters taken from an alphabet A– A can be {0, 1}, {0, 1, 2,…, 9}, {A,G,C,T}, or {A, B,…}

• A shift s is an offset needed to align the first character of x with character number s+1 in text

• Find if there exists a valid shift where there is a perfect match between characters in x and the corresponding ones in text


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Naïve (Brute-Force) String Matching

• Given A, x, text, n = |text|, m = |x|s = 0while s ≤ n-m

if x[1 …m] = text [s+1 … s+m] then print “pattern occurs at shift” ss = s + 1

• Time complexity (worst case): O((n-m+1)m)• One character shift at a time is not necessary


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Boyer-Moore and KMP• See StringMatching.ppt and do not use the following alg• Given Given AA, , xx, , texttext, , nn = | = |texttext|, |, mm = | = |xx||

F(x) = last-occurrence functionF(x) = last-occurrence functionG(x) = good-suffix function; G(x) = good-suffix function; ss = 0 = 0whilewhile s s ≤ n-m≤ n-m

j = mj = mwhile while j>0j>0 and and xx[j] = [j] = texttext [s+j] [s+j] j = j-1j = j-1ifif j = 0 j = 0 thenthen print “pattern occurs at shift” s print “pattern occurs at shift” s

s = s + G(0)s = s + G(0) else s = s + max[G(j), j-F(text[s+j0])]else s = s + max[G(j), j-F(text[s+j0])]


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Edit Distance

• ED between x and y describes how many fundamental operations are required to transform x to y.

• Fundamental operations (x=‘excused’, y=‘exhausted’)

– Substitutions e.g. ‘c’ is replaced by ‘h’– Insertions e.g. ‘a’ is inserted into x after ‘h’– Deletions e.g. a character in x is deleted

• ED is one way of measuring similarity between two strings


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Classification using ED

• Nearest-neighbor algorithm can be applied for pattern recognition.– Training: data of strings with their class labels stored– Classification (testing): a test string is compared to

each stored string and an ED is computed; the nearest stored string’s label is assigned to the test string.

• The key is how to calculate ED.• An example of calculating ED


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Hidden Markov Model

• Markov Model: transitional states• Hidden Markov Model: additional visible states• Evaluation• Decoding• Learning


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Markov Model• The Markov property:

– given the current state, the transition probability is independent of any previous states.

• A simple Markov Model – State ω(t) at time t– Sequence of length T:

• ωT = {ω(1), ω(2), …, ω(T)}– Transition probability

• P(ω j(t+1)| ω i(t)) = aij

– It’s not required that aij = aji


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Hidden Markov Model• Visible states

– VT = {v(1), v(2), …, v(T)}• Emitting a visible state vk(t)

– P(v k(t)| ω j(t)) = bjk

• Only visible states vk (t) are accessible and states ωi (t) are unobservable.

• A Markov model is ergodic if every state has a nonzero prob of occuring give some starting state.


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Three Key Issues with HMM• Evaluation

– Given an HMM, complete with transition probabilities aij and bjk. Determine the probability that a particular sequence of visible states VT was generated by that model

• Decoding– Given an HMM and a set of observations VT. Determine

the most likely sequence of hidden states ωT that led to VT.• Learning

– Given the number of states and visible states and a set of training observations of visible symbols, determine the probabilities aij and bjk.


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Other Sequential Patterns Mining Problems

• Sequence alignment (homology) and sequence assembly (genome sequencing)

• Trend analysis– Trend movement vs. cyclic variations, seasonal variations

and random fluctuations• Sequential pattern mining

– Various kinds of sequences (weblogs)– Various methods: From GSP to PrefixSpan

• Periodicity analysis– Full periodicity, partial periodicity, cyclic association rules


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Periodic Pattern• Full periodic pattern

– ABC ABC ABC• Partial periodic pattern

– ABC ADC ACC ABC• Pattern hierarchy

– ABC ABC ABC DE DE DE DE ABC ABC ABC DE DE DE DE ABC ABC ABC DE DE DE DE

Sequences of transactions

[ABC:3|DE:4]

Guozhu Dong

Full periodic patterns: too restrictive for data mining.Pattern hierarchy: Overall pattern is made from two more detailed patterns, each with a duration


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Sequence Association Rule Mining

• SPADE (Sequential Pattern Discovery using Equivalence classes)

• Constrained sequence mining (SPIRIT)


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Bibliography

• R.O. Duda, P.E. Hart, and D.G. Stork, 2001. Pattern Classification. 2nd Edition. Wiley Interscience.


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7. Sequence Mining

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