Conditional Random Fields and beyond D A N I E L K H A S H A B I C S U I U C,

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1 Conditional Random Fields and beyond D A N I E L K H A S H A B I C S U I U C,

2 Outline Modeling Inference Training Applications

3 Outline Modeling Problem definition Discriminative vs. Generative Chain CRF General CRF Inference Training Applications

4 Problem Description X Given (observations), find (predictions) For example, X { temperature, moisture, pressure,...} Y { Sunny, Rainy, Stormy,...} Y Might depend on previous days and each other Might depend on previous days and each other

5 Problem Description The relational connection occurs in many applications, NLP, Computer Vision, Signal Processing,.

6 Problem Description The relational connection occurs in many applications, NLP, Computer Vision, Signal Processing,. Traditionally in graphical models,

7 Problem Description The relational connection occurs in many applications, NLP, Computer Vision, Signal Processing,. Traditionally in graphical models, p( xy, )

8 Problem Description The relational connection occurs in many applications, NLP, Computer Vision, Signal Processing,. Traditionally in graphical models, p( xy, ) p( y x) p( x)

9 Problem Description The relational connection occurs in many applications, NLP, Computer Vision, Signal Processing,. Traditionally in graphical models, p( xy, ) p( y x) p( x) Modeling the joint distribution can lead to difficulties

10 Problem Description The relational connection occurs in many applications, NLP, Computer Vision, Signal Processing,. Traditionally in graphical models, p( xy, ) p( y x) p( x) Modeling the joint distribution can lead to difficulties rich local features occur in relational data,

11 Problem Description The relational connection occurs in many applications, NLP, Computer Vision, Signal Processing,. Traditionally in graphical models, p( xy, ) p( y x) p( x) Modeling the joint distribution can lead to difficulties rich local features occur in relational data, p( x)

12 Problem Description The relational connection occurs in many applications, NLP, Computer Vision, Signal Processing,. Traditionally in graphical models, p( xy, ) p( y x) p( x) Modeling the joint distribution can lead to difficulties rich local features occur in relational data, p( x)

13 Problem Description The relational connection occurs in many applications, NLP, Computer Vision, Signal Processing,. Traditionally in graphical models, p( xy, ) p( y x) p( x) Modeling the joint distribution can lead to difficulties rich local features occur in relational data, p( x) features may have complex dependencies, constructing probability distribution over them is difficult

14 Problem Description The relational connection occurs in many applications, NLP, Computer Vision, Signal Processing,. Traditionally in graphical models, p( xy, ) p( y x) p( x) Modeling the joint distribution can lead to difficulties rich local features occur in relational data, p( x) features may have complex dependencies, constructing probability distribution over them is difficult Solution: directly model the conditional, is sufficient for classification! p( y x)

15 Problem Description The relational connection occurs in many applications, NLP, Computer Vision, Signal Processing,. Traditionally in graphical models, p( xy, ) p( y x) p( x) Modeling the joint distribution can lead to difficulties rich local features occur in relational data, p( x) features may have complex dependencies, constructing probability distribution over them is difficult Solution: directly model the conditional, is sufficient for classification! CRF is simply a conditional distribution associated graphical structure p( y x) p( y x) with an

16 Discriminative Vs. Generative p( yx, ) p( y x)

17 Discriminative Vs. Generative p( yx, ) Generative Model: A model that generate observed data randomly p( y x)

18 Discriminative Vs. Generative p( yx, ) Generative Model: A model that generate observed data randomly Naïve Bayes: once the class label is known, all the features are independent p( y x)

19 Discriminative Vs. Generative p( yx, ) Generative Model: A model that generate observed data randomly Naïve Bayes: once the class label is known, all the features are independent p( y x) Discriminative: Directly estimate the posterior probability; Aim at modeling the discrimination between different outputs

20 Discriminative Vs. Generative p( yx, ) Generative Model: A model that generate observed data randomly Naïve Bayes: once the class label is known, all the features are independent p( y x) Discriminative: Directly estimate the posterior probability; Aim at modeling the discrimination between different outputs

21 Discriminative Vs. Generative p( yx, ) Generative Model: A model that generate observed data randomly Naïve Bayes: once the class label is known, all the features are independent p( y x) Discriminative: Directly estimate the posterior probability; Aim at modeling the discrimination between different outputs MaxEnt classifier: linear combination of feature function in the exponent,

22 Discriminative Vs. Generative p( yx, ) Generative Model: A model that generate observed data randomly Naïve Bayes: once the class label is known, all the features are independent p( y x) Discriminative: Directly estimate the posterior probability; Aim at modeling the discrimination between different outputs MaxEnt classifier: linear combination of feature function in the exponent, Both generative models and discriminative models describe distributions over (y, x), but they work in different directions.

23 Discriminative Vs. Generative p( yx, ) p( y x) =observable =unobservable

24 Discriminative Vs. Generative p( yx, ) p( y x) =observable =unobservable

25 Discriminative Vs. Generative p( yx, ) p( y x) =observable =unobservable

26 Discriminative Vs. Generative p( yx, ) p( y x) =observable =unobservable

27 Discriminative Vs. Generative p( yx, ) p( y x) =observable =unobservable

28 Discriminative Vs. Generative p( yx, ) p( y x) =observable =unobservable

29 Markov Random Field(MRF) and Factor Graphs On an undirected graph, the joint distribution of variables y 1 p( y) C ( yc ), Z C ( yc ) Z C y C C( yc) 0:Potential function Typically : C ( yc ) exp{ E( yc )} Z :Partition function

30 Markov Random Field(MRF) and Factor Graphs On an undirected graph, the joint distribution of variables y 1 p( y) C ( yc ), Z C ( yc ) Z C y C C( yc) 0:Potential function Typically : C ( yc ) exp{ E( yc )} Z :Partition function

31 Markov Random Field(MRF) and Factor Graphs On an undirected graph, the joint distribution of variables y 1 p( y) C ( yc ), Z C ( yc ) Z C y C C( yc) 0:Potential function variable Typically : C ( yc ) exp{ E( yc )} Z :Partition function

32 Markov Random Field(MRF) and Factor Graphs On an undirected graph, the joint distribution of variables y 1 p( y) C ( yc ), Z C ( yc ) Z C y C factor C( yc) 0:Potential function variable Typically : C ( yc ) exp{ E( yc )} Z :Partition function

33 Markov Random Field(MRF) and Factor Graphs On an undirected graph, the joint distribution of variables y 1 p( y) C ( yc ), Z C ( yc ) Z C y C factor C( yc) 0:Potential function variable Typically : C ( yc ) exp{ E( yc )} Z :Partition function Not all distributions satisfy Markovian properties Hammersley-Clifford Theorem The ones which do can be factorized

34 Directed Graphical Models(Bayesian Network) Local conditional distributions If () s indices of the parents of ys

35 Directed Graphical Models(Bayesian Network) Local conditional distributions If () s indices of the parents of ys Generally used as generative models E.g. Naïve Bayes: once the class label is known, all the features are independent

36 Directed Graphical Models(Bayesian Network) Local conditional distributions If () s indices of the parents of ys Generally used as generative models E.g. Naïve Bayes: once the class label is known, all the features are independent

37 Directed Graphical Models(Bayesian Network) Local conditional distributions If () s indices of the parents of ys Generally used as generative models E.g. Naïve Bayes: once the class label is known, all the features are independent

38 Sequence prediction Like NER: identifying and classifying proper names in text, e.g. China as location; George Bush as people; United Nations as organizations Set of observation,

39 Sequence prediction Like NER: identifying and classifying proper names in text, e.g. China as location; George Bush as people; United Nations as organizations Set of observation,

40 Sequence prediction Like NER: identifying and classifying proper names in text, e.g. China as location; George Bush as people; United Nations as organizations Set of observation, Set of underlying sequence of states,

41 Sequence prediction Like NER: identifying and classifying proper names in text, e.g. China as location; George Bush as people; United Nations as organizations Set of observation, Set of underlying sequence of states,

42 Sequence prediction Like NER: identifying and classifying proper names in text, e.g. China as location; George Bush as people; United Nations as organizations Set of observation, Set of underlying sequence of states, HMM is generative:

43 Sequence prediction Like NER: identifying and classifying proper names in text, e.g. China as location; George Bush as people; United Nations as organizations Set of observation, Set of underlying sequence of states, HMM is generative: Transition probability

44 Sequence prediction Like NER: identifying and classifying proper names in text, e.g. China as location; George Bush as people; United Nations as organizations Set of observation, Set of underlying sequence of states, HMM is generative: Transition probability Observation probability

45 Sequence prediction Like NER: identifying and classifying proper names in text, e.g. China as location; George Bush as people; United Nations as organizations Set of observation, Set of underlying sequence of states, HMM is generative: Transition probability Doesn t model long-range dependencies Not practical to represent multiple interacting features (hard to model p(x)) Observation probability

46 Sequence prediction Like NER: identifying and classifying proper names in text, e.g. China as location; George Bush as people; United Nations as organizations Set of observation, Set of underlying sequence of states, HMM is generative: Transition probability Observation probability Doesn t model long-range dependencies Not practical to represent multiple interacting features (hard to model p(x)) The primary advantage of CRFs over hidden Markov models is their conditional nature, resulting in the relaxation of the independence assumption And it can handle overlapping features

47 Chain CRFs Each potential function will operate on pairs of adjacent label variables =unobservable =observable

48 Chain CRFs Each potential function will operate on pairs of adjacent label variables =unobservable =observable

49 Chain CRFs Each potential function will operate on pairs of adjacent label variables Feature functions =unobservable =observable

50 Chain CRFs Each potential function will operate on pairs of adjacent label variables Parameters to be estimated, Feature functions =unobservable =observable

51 Chain CRF We can change it so that each state depends on more observations =unobservable =observable

52 Chain CRF We can change it so that each state depends on more observations =unobservable =observable Or inputs at previous steps

53 Chain CRF We can change it so that each state depends on more observations =unobservable =observable Or inputs at previous steps Or all inputs

54 Chain CRF We can change it so that each state depends on more observations =unobservable =observable Or inputs at previous steps Or all inputs

55 General CRF: visualization If, and, ; is a CRF, if Y and are neighbors the MRF the CRF X fixed, observable, variables X (not in the MRF)

56 General CRF: visualization If, and, ; is a CRF, if Y and are neighbors the MRF the CRF X fixed, observable, variables X (not in the MRF) Note that in a CRF we do not explicitly model any direct relationships between the observables (i.e., among the X) (Lafferty et al., 2001).

57 General CRF: visualization If, and, ; is a CRF, if Y and are neighbors the MRF the CRF X fixed, observable, variables X (not in the MRF) Note that in a CRF we do not explicitly model any direct relationships between the observables (i.e., among the X) (Lafferty et al., 2001). Hammersley-Clifford does not apply to X!

58 General CRF: visualization Y CRF cliques (include only the unobservables, Y) X observables, X (not included in the cliques) Divide y MRF into cliques. The parameters inside each template are tied ( y, x) --potential functions; functions for the template c c

59 General CRF: visualization Y CRF cliques (include only the unobservables, Y) X observables, X (not included in the cliques) Divide y MRF into cliques. The parameters inside each template are tied ( y, x) --potential functions; functions for the template c c 1 Q( y, x) 1 Q( y, x) p( y x) e e, Q(, ) Z( ) y x x e y Q(y,x) cc c (y c,x)

60 General CRF: visualization Y CRF cliques (include only the unobservables, Y) X observables, X (not included in the cliques) Divide y MRF into cliques. The parameters inside each template are tied ( y, x) --potential functions; functions for the template c c 1 Q( y, x) 1 Q( y, x) p( y x) e e, Q(, ) Z( ) y x x e y Q(y,x) cc c (y c,x) Note that we are not summing over x in the denominator

61 General CRF: visualization Y CRF cliques (include only the unobservables, Y) X observables, X (not included in the cliques) Divide y MRF into cliques. The parameters inside each template are tied ( y, x) --potential functions; functions for the template c c 1 Q( y, x) 1 Q( y, x) p( y x) e e, Q(, ) Z( ) y x x e y Q(y,x) cc c (y c,x) Note that we are not summing over x in the denominator The cliques contain only unobservables (y); though, x is an argument to c

62 General CRF: visualization Y CRF cliques (include only the unobservables, Y) X observables, X (not included in the cliques) Divide y MRF into cliques. The parameters inside each template are tied ( y, x) --potential functions; functions for the template c c 1 Q( y, x) 1 Q( y, x) p( y x) e e, Q(, ) Z( ) y x x e y Q(y,x) cc c (y c,x) Note that we are not summing over x in the denominator The cliques contain only unobservables (y); though, x is an argument to c The probability P M (y x) is a joint distribution over the unobservables Y

63 General CRF: visualization A number of ad hoc modeling decisions are typically made with regard to the form of the potential functions. c is typically decomposed into a weighted sum of feature sensors f i, producing: p( y x) Q(y,x) 1 Z cc e Q( yx, ) c (y c,x)

64 General CRF: visualization A number of ad hoc modeling decisions are typically made with regard to the form of the potential functions. c is typically decomposed into a weighted sum of feature sensors f i, producing: p( y x) Q(y,x) 1 Z cc e Q( yx, ) c (y c,x) ( y, x) f ( y, x) c c i i c if

65 General CRF: visualization A number of ad hoc modeling decisions are typically made with regard to the form of the potential functions. c is typically decomposed into a weighted sum of feature sensors f i, producing: p( y x) Q(y,x) 1 Z cc e Q( yx, ) c (y c,x) ( y, x) f ( y, x) c c i i c if P( y x) 1 Z cc if e f ( y, x) i i c

66 General CRF: visualization A number of ad hoc modeling decisions are typically made with regard to the form of the potential functions. c is typically decomposed into a weighted sum of feature sensors f i, producing: p( y x) Q(y,x) 1 Z cc e Q( yx, ) c (y c,x) ( y, x) f ( y, x) c c i i c if P( y x) Back to the chain-crf! Cliques can be identified as pairs of adjacent Ys: 1 Z cc if e f ( y, x) i i c

67 General CRF: visualization A number of ad hoc modeling decisions are typically made with regard to the form of the potential functions. c is typically decomposed into a weighted sum of feature sensors f i, producing: p( y x) Q(y,x) 1 Z cc e Q( yx, ) c (y c,x) ( y, x) f ( y, x) c c i i c if P( y x) Back to the chain-crf! Cliques can be identified as pairs of adjacent Ys: 1 Z cc if e f ( y, x) i i c

68 Chain CRFs vs. MEMM Linear-chain CRFs were originally introduced as an improvement to MEMM Maximum Entropy Markov Models (MEMM) Transition probabilities are given by logistic regression Notice the per-state normalization Only dependent on the previous inputs; no dependence on the future states. Label-bias problem

69 CRFs vs. MEMM vs. HMM HMM MEMM CRF

70 CRFs vs. MEMM vs. HMM HMM MEMM CRF

71 CRFs vs. MEMM vs. HMM HMM MEMM CRF

72 Outline Modeling Inference General CRF Chain CRF Training Applications

73 Inference

74 Inference Given the observations,{xi})and parameters, we target to find the best state sequence

75 Inference Given the observations,{xi})and parameters, we target to find the best state sequence For the general CRF: (, ) * 1 c yc x cc y arg max P( y x) arg max e arg max c( yc, x) y y Z y cc

76 Inference Given the observations,{xi})and parameters, we target to find the best state sequence For the general CRF: (, ) * 1 c yc x cc y arg max P( y x) arg max e arg max c( yc, x) y y Z y cc For general graphs, the problem of exact inference in CRFs is intractable Approximate methods! A large literature

77 Inference in HMM Dynamic Programming: K K K K x1 x2 x 3 xk

78 Inference in HMM Dynamic Programming: Forward K K K K x1 x2 x 3 xk

79 Inference in HMM Dynamic Programming: Forward Backward K K K K x1 x2 x 3 xk

80 Inference in HMM Dynamic Programming: Forward Backward Viterbi K K K K x1 x2 x 3 xk

81 Parameter Learning: Chain CRF Chain CRF could be done using dynamic programming

82 Parameter Learning: Chain CRF Chain CRF could be done using dynamic programming Assume Naively doing could be intractable: y n

83 Parameter Learning: Chain CRF Chain CRF could be done using dynamic programming Assume y Naively doing could be intractable: Define a matrix n with size

84 Parameter Learning: Chain CRF Chain CRF could be done using dynamic programming Assume y Naively doing could be intractable: Define a matrix n with size

85 Parameter Learning: Chain CRF By defining the following forward and backward parameters,

86 Parameter Learning: Chain CRF By defining the following forward and backward parameters,

87 Parameter Learning: Chain CRF By defining the following forward and backward parameters,

88 Parameter Learning: Chain CRF By defining the following forward and backward parameters,

89 Inference: Chain-CRF The inference of linear-chain CRF is very similar to that of HMM We can write the marginal distribution: Solve Chain-CRF using Dynamic Programming (Similar to Viterbi)!

90 Inference: Chain-CRF The inference of linear-chain CRF is very similar to that of HMM We can write the marginal distribution: Solve Chain-CRF using Dynamic Programming (Similar to Viterbi)! 1. First computing α for all t (forward), then compute β for all t (backward). 2. Return the marginal distributions computed. 3. Run viterbi to find the optimal sequence 2 n.

91 Outline Modeling Inference Training General CRF Some notes on approximate learning Applications

92 Parameter Learning Given the training data, model. we wish to learn parameters of the

93 Parameter Learning Given the training data, model. we wish to learn parameters of the For chain or tree structured CRFs, they can be trained by maximum likelihood

94 Parameter Learning Given the training data, model. we wish to learn parameters of the For chain or tree structured CRFs, they can be trained by maximum likelihood The objective function for chain-crf is convex(see Lafferty et al(2001) ).

95 Parameter Learning Given the training data, model. we wish to learn parameters of the For chain or tree structured CRFs, they can be trained by maximum likelihood The objective function for chain-crf is convex(see Lafferty et al(2001) ). General CRFs are intractable hence approximation solutions are necessary

96 Parameter Learning Given the training data, we wish to learn parameters of the mode.

97 Parameter Learning Given the training data, we wish to learn parameters of the mode. Conditional log-likelihood for a general CRF:

98 Parameter Learning Given the training data, we wish to learn parameters of the mode. Conditional log-likelihood for a general CRF: Empirical Distribution

99 Parameter Learning Given the training data, we wish to learn parameters of the mode. Conditional log-likelihood for a general CRF: Empirical Distribution

100 Parameter Learning Given the training data, we wish to learn parameters of the mode. Conditional log-likelihood for a general CRF: Empirical Distribution Hard to calculate!

101 Parameter Learning Given the training data, we wish to learn parameters of the mode. Conditional log-likelihood for a general CRF: Empirical Distribution Hard to calculate! It is not possible to analytically determine the parameter values that maximize the log-likelihood setting the gradient to zero and solving for λ does not always yield a closed form solution. (Almost always)

102 Parameter Learning

103 Parameter Learning This could be done using gradient descent max ( ; y x) max log p( y x; ) N i1

104 Parameter Learning This could be done using gradient descent max ( ; y x) max log p( y x; ) N i1 i 1 i. ( ; y x)

105 Parameter Learning This could be done using gradient descent Until we reach convergence max ( ; y x) max log p( y x; ) N i1 i 1 i. ( ; y x)

106 Parameter Learning This could be done using gradient descent Until we reach convergence max ( ; y x) max log p( y x; ) N i1 i 1 i. ( ; y x) ( ; ) ( ; ) i1 y x i y x

107 Parameter Learning This could be done using gradient descent Until we reach convergence Or any other optimization: max ( ; y x) max log p( y x; ) Quasi-Newton methods: BFGS [Bertsekas,1999] or L-BFGS [Byrd, 1994] N i1 i 1 i. ( ; y x) ( ; ) ( ; ) i1 y x i y x

108 Parameter Learning This could be done using gradient descent Until we reach convergence Or any other optimization: max ( ; y x) max log p( y x; ) Quasi-Newton methods: BFGS [Bertsekas,1999] or L-BFGS [Byrd, 1994] General CRFs are intractable hence approximation solutions are necessary N i1 i 1 i. ( ; y x) ( ; ) ( ; ) i1 y x i y x

109 Parameter Learning This could be done using gradient descent Until we reach convergence Or any other optimization: Quasi-Newton methods: BFGS [Bertsekas,1999] or L-BFGS [Byrd, 1994] General CRFs are intractable hence approximation solutions are necessary max ( ; y x) max log p( y x; ) N i1 i 1 i. ( ; y x) ( ; ) ( ; ) i1 y x i y x Compared with Markov chains, CRF s should be more discriminative, much slower to train and possibly more susceptible to over-training.

110 Parameter Learning This could be done using gradient descent Until we reach convergence Or any other optimization: max ( ; y x) max log p( y x; ) Quasi-Newton methods: BFGS [Bertsekas,1999] or L-BFGS [Byrd, 1994] General CRFs are intractable hence approximation solutions are necessary Compared with Markov chains, CRF s should be more discriminative, much slower to train and possibly more susceptible to over-training. Regularization: 2 is a regularization parameter f objective () P (y x) N i1 i 1 i. ( ; y x) ( ; ) ( ; ) i1 y x i y x 2 2

111 Training ( and Inference): General Case Approximate solution, to get faster inference.

112 Training ( and Inference): General Case Approximate solution, to get faster inference. Treat inference as shortest path problem in the network consisting of paths(with costs) Max Flow-Min Cut (Ford-Fulkerson, 1956 )

113 Training ( and Inference): General Case Approximate solution, to get faster inference. Treat inference as shortest path problem in the network consisting of paths(with costs) Max Flow-Min Cut (Ford-Fulkerson, 1956 ) Pseudo-likelihood approximation: Convert a CRF into separate patches; each consists of a hidden node and true values of neighbors; Run ML on separate patches Efficient but may over-estimate inter-dependencies

114 Training ( and Inference): General Case Approximate solution, to get faster inference. Treat inference as shortest path problem in the network consisting of paths(with costs) Max Flow-Min Cut (Ford-Fulkerson, 1956 ) Pseudo-likelihood approximation: Convert a CRF into separate patches; each consists of a hidden node and true values of neighbors; Run ML on separate patches Efficient but may over-estimate inter-dependencies Belief propagation?! variational inference algorithm it is a direct generalization of the exact inference algorithms for linear-chain CRFs

115 Training ( and Inference): General Case Approximate solution, to get faster inference. Treat inference as shortest path problem in the network consisting of paths(with costs) Max Flow-Min Cut (Ford-Fulkerson, 1956 ) Pseudo-likelihood approximation: Convert a CRF into separate patches; each consists of a hidden node and true values of neighbors; Run ML on separate patches Efficient but may over-estimate inter-dependencies Belief propagation?! variational inference algorithm it is a direct generalization of the exact inference algorithms for linear-chain CRFs Sampling based method(mcmc)

116 Training ( and Inference): General Case Approximate solution, to get faster inference. Treat inference as shortest path problem in the network consisting of paths(with costs) Max Flow-Min Cut (Ford-Fulkerson, 1956 ) Pseudo-likelihood approximation: Convert a CRF into separate patches; each consists of a hidden node and true values of neighbors; Run ML on separate patches Efficient but may over-estimate inter-dependencies Belief propagation?! variational inference algorithm it is a direct generalization of the exact inference algorithms for linear-chain CRFs Sampling based method(mcmc) sorry about that, man!

117 CRF frontiers Bayesian CRF: Because of the large number of parameters in typical applications of CRFs

118 CRF frontiers Bayesian CRF: Because of the large number of parameters in typical applications of CRFs prone to overfitting.

119 CRF frontiers Bayesian CRF: Because of the large number of parameters in typical applications of CRFs prone to overfitting. Regularization?

120 CRF frontiers Bayesian CRF: Because of the large number of parameters in typical applications of CRFs prone to overfitting. Regularization? Instead of Too complicated! How can we approximate this?

121 CRF frontiers Bayesian CRF: Because of the large number of parameters in typical applications of CRFs prone to overfitting. Regularization? Instead of Too complicated! How can we approximate this? Semi-supervised CRF: The need to have big labeled data! Unlike in generative models, it is less obvious how to incorporate unlabelled data into a conditional criterion, because the unlabelled data is a sample from the distribution p( x)

122 Outline Modeling Inference Training Some Applications

123 Some applications: Part-of-Speech-Tagging POS(part of speech) tagging; the identification of words as nouns, verbs, adjectives, adverbs, etc. Students need another break CRF features: noun verb article noun Feature Type Transition Description k,k y i = k and y i+1 =k Word k,w y i = k and x i =w k,w y i = k and x i-1 =w k,w y i = k and x i+1 =w k,w,w y i = k and x i =w and x i-1 =w k,w,w y i = k and x i =w and x i+1 =w Orthography: Suffix Orthography: Punctuation s in { ing, ed, ogy, s, ly, ion, tion, ity, } and k y i =k and x i ends with s k y i = k and x i is capitalized k y i = k and x i is hyphenated

124 Is HMM(Gen.) better or CRF(Disc.) If your application gives you good structural information such that could be easily modeled by dependent distributions, and could be learnt tractably, go the generative way!

125 Is HMM(Gen.) better or CRF(Disc.) If your application gives you good structural information such that could be easily modeled by dependent distributions, and could be learnt tractably, go the generative way! Ex. Higher-order emissions from individual states unobservables observables A A T C G

126 Is HMM(Gen.) better or CRF(Disc.) If your application gives you good structural information such that could be easily modeled by dependent distributions, and could be learnt tractably, go the generative way! Ex. Higher-order emissions from individual states unobservables observables A A T C G Incorporating evolutionary conservation from an alignment: PhyloHMM, for which efficient decoding methods exist: states target genome informant genomes

127 References J. Lafferty, A. McCallum, and F. Pereira. Conditional random fields: Probabilistic models for segmenting and labeling sequence data. In Proc. ICML01, Charles Elkan, Log-linear Models and Conditional Random Field, Notes for a tutorial at CIKM, Charles Sutton and Andrew McCallum, An Introduction to Conditional Random Fields for Relational Learning, MIT Press, 2006 Slides: An Introduction to Conditional Random Field, Ching-Chun Hsiao Hanna M. Wallach, Conditional Random Fields: An Introduction, 2004 Sutton, Charles, and Andrew McCallum. An introduction to conditional random fields for relational learning. Introduction to statistical relational learning. MIT Press, Sutton, Charles, and Andrew McCallum. "An introduction to conditional random fields." arxiv preprint arxiv: (2010). B. Majoros, Conditional Random Fields, for eukaryotic gene prediction

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