Formal Grammars and Abstract Machines. Sahar Al Seesi

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1 Formal Grammars and Abstract Machines Sahar Al Seesi

2 What are Formal Languages Describing the sentence structure of a language in a formal way Used in Natural Language Processing Applications (translators, grammar checking tools, etc..) Language: English, French, Spanish, Chinese, etc.. RNA/Protein Structure Analysis RNA in general, ribosomal RNA, protein, etc.. Compilers for programming languages C, Java, Python, Linux shell script, Assembly, etc.. To build a program for any of the above applications, the language rules must be described in a formal inclusive way.

3 Formal Languages and Grammars G={ Σ, R, S } Σ : Non-terminals (NT) Terminals (T) {S, VERB, SUBJECT, OBJECT} {S, A, A 2 } R : Production rules {S SUBJECT VERB OBJECT} S : Starting symbol {children, sam, play, eat, ball} {a, c, g, t} {a,c,g,u} L(G) : The language defined by G; a finite or infinite set of strings (words/sentences) L(G) T*

4 Power of expression Rule complexity Parsing time complexity Chomsky Hierarchy Unrestricted Grammars Recursively Enumerable Languages Context-sensitive Context-free Regular

5 Parsing/Accepting Abstract Machines Grammar Regular grammars Context free grammars Context sensitive grammars Unrestricted grammars Parsing Automaton Finite State Machine (FSM) Push-Down Automaton (PDA) Linear-Bounded Automaton (LBA) Turing Machine (TM)

6 Regular Languages & Regular Expressions A regular language can be represented by a regular expression Let Σ = {a,b} Let L r be the language defined by regular expression r. r L r Σ* the set of all strings over Σ of length or more (includes the empty string, ) Σ + the set of all strings over Σ of length or more (does not include ) a+ the set of all strings of or more a s {a, aa, aaa, } b* the set of all strings of or more b s {, b, bb, bbb, }

7 Combining Regular Languages Concatenation Let r and s be 2 regular expressions, rs corresponds to the language L r L s Example: r = a*, s = b + L r L s : the set of strings consisting of or more a s followed by or more b s {b, bb, ab, aabbbb} L r L s

8 Combining Regular Languages Union Let r and s be 2 regular expressions, r+s corresponds to the language L r L s Example: r = a*, s = b + L r L s : the set of strings consisting of or more a s and strings of or more b s {b, bb, a, aa, bbbb} L r L s

9 Combining Regular Languages Closure Let r be a regular expression, r* corresponds to the language L r * Example: r = ab L r * : the set of strings consisting of or more ab s (ab)* {, ab, abab, abab, ababab} L r *

10 Example R = (a+c+t)ykk(p+q)*vdt(l+z+ )pq Strings that belong to the language defined by R ayykppvdtlpq cyykpqppqvdtpq tyykqvdtzpq

11 Regular Grammars Can be represented by a regular expression Grammar rules are of the form NT T NT NT T Example: The set of all DNA strings Regular Expression: {a,c,g,t} + G= { Σ, {S}, R, S } Σ = {S, a, c, g, t} R = {S as cs gs ts a c g t}

12 Finite State Machine M={Q, Σ,, q, F} Q: Finite set of states Σ: Language alphabet : Transition function (Qx Σ Q) q : Starting state F : Set of final states

13 Finite State Machine Example M={Q, Σ,, q, F} A FSM for R = {S as cs gs ts a c g t} a,c,g,t a,c,g,t 2 Q = {,2} Σ = {a, c, g, t} q = F = {2} (,a) = 2 (,c) = 2 (,g) = 2 (,t) = 2 (2,a) = 2 (2,c) = 2 (2,g) = 2 (2,t) = 2

14 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input:

15 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input:

16 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input:

17 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input:

18 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input:

19 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input:

20 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input2:

21 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input2:

22 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input2:

23 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input2:

24 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input2:

25 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input2:

26 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input3:

27 Another Example L = The set of all strings in {,}*that either begin or end (or both) with R = ((+)*)+((+)*) S C A D B E, Input3:

28 Context Free Grammars (CFG) and Languages CFGs Can represent nested pair-wise correlation between terminal symbols in the string Famous example: palindrome language (ww r ) a b a a a a b a Can you write a regular grammar for ww r? Grammar rules are of the form NT (T+NT) +

29 CFG and Push Down Automata M={Q, Σ,,, q, F} Q: Finite set of states Σ: Language alphabet : Stack alphabet : Transition function (Q x Σ x Q x *) q : Starting state F : Set of final states

30 Grammar ww r G={ Σ, V, R, S } Σ = {a, b}, V = {S} R = {S asa bsb aa bb} Parse tree for string: abbbba S a S a b S b b b

31 Context Free Grammar for an RNA stem loop Language : wvw cr G={ Σ, R, S } Σ = {S, L, a, c, g, u} R = {S asu usa gsc csg L, L al cl gl ul a c g u} Durbin et. al., Biological Sequence Analysis, adapted

32 Context Sensitive Grammars and Languages Can represent crossing pair-wise correlation between terminal symbols in the string Famous example: copy language (ww) a a b b a a b b Grammar rules are of the form: (T+NT) * NT (T+NT) * (T+NT) + LHS <= RHS (generated RHS cannot shrink from one production step to the next)

33 CSG and Linear Bounded Automata SKIP FOR NOW

34 Non-deterministic and stochastic models A stochastic grammar has a probability associated with each rule in the grammar Similarly, in automata, a probability would be associated with each transition

35 Unrestricted Grammars and Recursively Enumerable Languages Grammar rules are of the form: - (T+NT) * NT (T+NT) * (T+NT) * - The only rule is that the left hand side must contain at least one variable A recursively enumerable language is one that can be represented by an unrestricted grammar

36 Turing Machines M={Q, Σ,,, q, B, F} Q: Finite set of states Σ: Language alphabet : tape alphabet (Σ ) : Transition function (Q x Σ Q x x {L,R}) q : Starting state B: The blank symbol F : Set of final states

37 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r

38 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # a a b b # # # # # # #

39 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X a b b # # # # # # #

40 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X a b b # # # # # # #

41 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X a Y b # # # # # # #

42 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X a Y b # # # # # # #

43 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X a Y b # # # # # # #

44 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X X Y b # # # # # # #

45 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X X Y b # # # # # # #

46 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X X Y Y # # # # # # #

47 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X X Y Y # # # # # # #

48 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X X Y Y # # # # # # #

49 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X X Y Y # # # # # # #

50 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X X Y Y # # # # # # #

51 Example a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X X Y Y # # # # # # #

52 What is the language this TM accepts? a/x,r b/y,l a/a,l Y/Y,L q q q2 q3 q4 a/a,r

53 Example -cont. (input 2) a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # a b a b # # # # # # #

54 Example -cont. (input 2) a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X b a b # # # # # # #

55 Example -cont. (input 2) a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X Y a b # # # # # # #

56 Example -cont. (input 2) a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X Y a b # # # # # # #

57 Example -cont. (input 2) a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r # # # # X Y a b # # # # # # #

58 a/x,r a/a,l Y/Y,L b/y,l q q q2 q3 q4 a/a,r Language: a n b n

59 Computing with Turing Machines Examples: A TM that accepts a number x divisible by 3 in unary format and outputs the results of the computation x/3 q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8

60 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # # # # # # # #

61 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # X # # # # # # #

62 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XX # # # # # # #

63 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXX # # # # # # #

64 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXX # # # # # # #

65 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXX # # # # # # #

66 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXX # # # # # # #

67 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXX # # # # # # #

68 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXX # # # # # #

69 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXX # # # # # #

70 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXX # # # # # #

71 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXX # # # # # #

72 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXX # # # # # #

73 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXX # # # # # #

74 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXXX # # # # # #

75 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXXXX # # # # # #

76 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXXXXX # # # # # #

77 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXXXXX # # # # # #

78 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXXXXX # # # # # #

79 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXXXXX # # # # #

80 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXXXXX # # # # #

81 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXXXXX # # # # #

82 Divide by 3 TM q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8 # # # # XXXXXX # # # # #

83 Divide by 3 TM Try to parse q7 #/,L q q q2 q3 q4 q5 #/#,L q6 /,R /,R q8

84 More complex TM models Several tapes Several read/write heads A Turing machine can simulate a computer.

85 Back to Linear Bounded Automata state $ $ boundary boundary LBA is a TM whose read/write head never moves off the portion of the tape occupied by the input string

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