( ).666 Information Extraction from Speech and Text

Size: px
Start display at page:

Download "( ).666 Information Extraction from Speech and Text"

Transcription

1 ( ).666 Information Extraction from Speech and Text HMM Parameters Estimation for Gaussian Output Densities April 27, 205. Generalization of the Results of Section 9.4. It is suggested in Section that the results of Section 9.4. for 2-dimensional observations extend easily to d-dimensions. We will work through the details in this note. Specifically, we will consider an HMM with output densities attached to arcs. Let S denote the set of states; the arcs be indexed by t T ; the outputs or emissions take values in IR d for some finite d > 0; L(t) and R(t) respectively denote the origin- and destination-states of the arc t; and p t denote the probability of the arc t when the underlying Markov chain is in L(t). Clearly, t : L(t)s p t, s S. () For each non-null arc t, let the corresponding output density be a multivariate Gaussian, { N t (y) (2π) d 2 Ut exp } y 2 (y m t) T U t (y m t ), y IR d, (2) where m t is the mean vector and U t the covariance matrix of the emitted random vector. Note that y and m t are column vectors here, while they are row-vectors in the textbook, and the arc-dependence of m t and U t is denoted via a subscript here instead of writing m(t) and U(t). The free parameters of the HMM are θ {θ t, t T }, where θ t {p t, m t, U t }, the p t s satisfy the sum-to-one condition (), and the U t s are symmetric and positive-definite. y d

2 Given an n-length observation Y y, y 2,..., y n from this HMM, the EM auxiliary function may be constructed as Q(θ, θ) P θ (t Y) log P θ (t, Y) P θ (t Y) log p tl N tl (y l ), (3) where t t, t 2,..., t denotes any valid path through the HMM, and denotes its length. While it is not made precise in the textbook, it is to be understood in (3) that P θ (t Y) > 0 only for paths t of length n that contain exactly n non-null arcs and n null arcs, and hence other paths need not be considered in the sum over all t; the reference to the l-th output symbol y l is valid only after reindexing Y y, y 2,..., y n and (re)assigning y to the first non-null arc of t, y 2 to the second non-null arc of t, and so on, until y n to the last non-null arc of t, while no symbols are assigned to its null arcs; N tl (y l ) is computed via (2) for non-null arcs t l in t, but N tl ( ) for all null arcs in t. Next, given a θ, we try to maximize Q(θ, θ) as a function of θ. To this end, we form the Lagrangian Q(θ, θ) λ s p t. (4) s S t : L( t)s Updating the Transition Probabilities p t Note that for every arc t T, P θ (t Y) log P θ (t, Y) λ s p t p t p t p t s S t : L( t)s P θ (t Y) log p tl N tl (y l ) λ L(t) p t P θ (t Y) log p tl + log N tl (y l ) λ L(t) p t ] P θ (t Y) log p t + 0 λ L(t) p t P θ (t Y) λ L(t). p t For each arc t T, equating the derivative to 0 yields 0 P θ (t Y) p t p t λ L(t) 2

3 P θ (Y) λ L(t) P θ (Y) P θ (t, Y) p t λ L(t) P θ (t, Y) } {{ } ψ t The brute-force way to compute the double sum ψ t is to. exhaustively enumerate all paths t, 2. traverse each path t t,..., t, and p t, 3. every time t l t, i.e. the arc t is traversed, add P θ (t, Y) to an accumulator for ψ t. Once the ψ t are accumulated for all t T, the role of λ s, for every state s S, is to ensure that the probabilities of arcs leaving s sum to unity. Therefore t : L(t)s p t t : L(t)s ψ t λ s P θ (Y) λ s P θ (Y) t : L(t)s ψ t K s. Now, a n-stage trellis captures all paths t capable of producing Y: all paths t with P θ (t, Y) > 0. Furthermore, if t is a non-null arc, then it appears exactly n times in the trellis, once in each trellis stage, and every time a path t traverses the l-th copy of t, l,..., n, an output y l is produced. Therefore, the contribution of the l-th copy of t to ψ t is the sum of the probabilities of all the paths t that pass through t in the l-th stage of the trellis, namely P θ (y,..., y l, s L(t)) p t N t (y }{{} l ) P θ (y l+,..., y n s R(t)) }{{} α l (L(t)) β l (R(t)). Therefore the total contribution from all stages of the trellis for a non-null arc t is ψ t P θ (t, Y) n α l (L(t)) p t N t (y l ) β l(r(t)). Similarly, a null arc t may appear on a path t within in each column of a vertically aligned set of states. If the l-th copy of t in the trellis is designated as the one traversed before producing y l (i.e. between producing y l and y l ), l,..., n, then its contribution to ψ t from all paths t is P θ (y,..., y l, s L(t)) p t P }{{} θ(y l,..., y n s R(t)), l,..., n. }{{} α l (L(t)) β l (R(t)) Therefore, for a null arc t, the total contribution from all stages of the trellis is ψ t P θ (t, Y) 3 n α l (L(t)) p t β l (R(t)).

4 As noted above, for every state s, K s n ψ t α l (s)p t N t (y l )β l(r(t)) + α l (s)p tβ l (R(t)) t : L(t)s non null t : L(t)s n α l (s) null arcs t : L(t)s p t N t (y l )β l(r(t)) + non null t : L(t)s null arcs t : L(t)s n α l (s)β l (s). p tβ l (R(t)) Updating the Mean Vectors m t Next, note that for every non-null arc t T, if we let m t m t,... m t,d ] T, then m t,i 2 P θ (t Y) log P θ (t, Y) λ s m t,i m t,i s S P θ (t Y) log p tl N tl (y l ) 0 m t,i P θ (t Y) m t,i t : L( t)s log p tl + log N tl (y l ) P θ (t Y) 0 + ] log N t (y l ) m t,i P θ (t Y) { } 2 (y l m t ) T U t (y l m t ) log (2π) d 2 Ut m t,i P θ (t Y) { (yl m t ) T U t (y l m t ) + 0 }. m t,i The partial derivatives of with respect to the components of the mean vector m t may therefore be compactly written as the vector { m t, P θ (t Y) (yl m t, m t ) T U t (y l m t ) } 2. { m t,d (yl m t,d m t ) T U t (y l m t ) }. (5) Next, note that x T b d m x mb m, and thus x i x T b x i 4 d x m b m b i, m p t

5 from which it follows that for any d vectors x x... x d ] T and b b... b d ] T x x T b b. x d x T b Similarly x T Ax d m d n x ma mn x n, and therefore x i x T Ax x i d d d d x m a mn x n x m a mi + a in x n + 2a ii x i m n m, m i n, n i d a mi +a im ]x m. m Therefore, for a symmetric d d matrix A, x x T Ax A T x + Ax 2Ax. x d x T Ax Set A U t and x (y t m t ) and note that m t, (y l m t ) T U t (y l m t ). (y (y l, m t, ) l m t ) T U t (y l m t )., m t,d (y l m t ) T U t (y l m t ) (y (y l,d m t,d ) l m t ) T U t (y l m t ) where the negative sign is due to the fact that m t, (y l, m t, ).. m t,d (y l,d m t,d ) This easily provides the partial derivatives (5) of with respect to the components of m t. To obtain the update equation for m t we must set it to zero. i.e. Set m t, 0 P θ (t Y) 2U t (y l m t ) 0 m t,d P θ (t Y)(y l m t ) 0 2U t P θ (t Y)y l P θ (t, Y) 5 P θ (t Y)m t P θ (t, Y)y l m t

6 n n α l (L(t)) p t N t (y l ) β l (R(t))] y l α l (L(t)) p t N t (y l ) β l (R(t))] m t, (6) where the last step, once again, follows from the argument that the overall double sum, similar to ψ t above, may be obtained by separately computing the contribution of all paths t to the arc t in a particular (l-th) stage of the trellis, and accumulating such contributions for l,..., n. To interpret the mean update equation (6) qualitatively, recall that α l (L(t)) p t N t (y l ) β l (R(t)) P θ (Y) P θ (t l t Y) P θ (y l was emitted by arc t Y). The value of m t in (6) that maximizes may thus be seen as a sample mean, where each observation y l in the sample has a fractional count the probability that it came from arc t and the sample size is the expected number of times the arc t was traversed, or as a weighted mean, where the weight of the sample y l is the probability that it was emitted from t. Updating the Covariance Matrices U t To find the U t that maximizes, let V t U t, and v t,ij denote the ij-th element of V t. v t,ij 2 2 P θ (t Y) log P θ (t, Y) v t,ij λ s v t,ij s S P θ (t Y) log p tl N tl (y l ) 0 v t,ij P θ (t Y) P θ (t Y) v t,ij P θ (t Y) t : L( t)s log p tl + log N tl (y l ) 0 + v t,ij ] log N t (y l ) v t,ij { 2 (y l m t ) T U t (y l m t ) log (2π) d 2 Ut P θ (t Y) { (yl m t ) T U t (y l m t ) + log U t } v t,ij P θ (t Y) { (yl m t ) T V t (y l m t ) log V t }. (7) v t,ij V t, the inverse of the covariance matrix, is sometimes called the precision matrix, and is often of interest in multivariate statistics and factor analysis. p t } 6

7 Next, for any d vector x ] T x... x d and symmetric positive-definite d d matrix A, the partial derivatives of the scalar x T Ax with respect to the components of the matrix A are a x T Ax a d x T Ax a ij x T Ax. xx T, a d x T Ax a dd x T Ax and the partial derivatives of the scalar log A with respect to the components of A are a log A a d log A a ij log A. A. a d log A a dd log A The derivatives v ij are obtained by setting x (y l m t ) and A U t in the formulae above: v t, v t,d v t,ij. P θ (t Y) { } (yl m t )(y l m t ) T Vt, 2 v t,d v t,dd and the choice of V t (equivalently U t ) that makes 2 P θ (t Y) P θ (t, Y) v t,ij 0 for all i and j is P θ (t Y) { } (yl m t )(y l m t ) T V 0 P θ (t Y) (y l m t )(y l m t ) T V t P θ (t, Y) (y l m t )(y l m t ) T U t, (8) where, once again, the parameters p t and N t correspond to θ, and α ( ) and β ( ) are the forward- and backward-probabilities computed using θ on a n-stage trellis, with the null arcs going between vertically aligned states and only non-null arcs traversing left-to-right. Finally, the covariance update equation (9) once again follows by observing that, similar to ψ t, the double sum may be obtained by first accumulating the contribution of all paths t in the trellis to the l-th copy of an arc t, and then summing these contributions for l,..., n. t U t n α l (L(t)) p t N t (y l ) β l (R(t))] (y l m t )(y l m t ) T. (9) α l (L(t)) p t N t (y l ) β l (R(t))] n It remains to verify that the updated matrix U t of (9) is symmetric and positive-(semi)definite, thereby justifying why the Lagrangian of (4) did not impose any constraints on the components of the parameter set θ corresponding to the U t s. 7

8 It is straightforward to see that the updated U t of (9) satisfies U T t n P θ (t ] l t, Y) (y l m t )(y l m t ) T T n P θ (t l t, Y) n P θ (t l t, Y) (y l m t )(y l m t ) T] T n P θ (t l t, Y) and that for any vector x, U t, x T U t x n P θ (t l t, Y) x T (y l m t )(y l m t ) T x n P θ (t l t, Y) n P θ (t l t, Y) ( x T (y l m t ) ) 2 n P θ (t l t, Y) 0. This guarantees that U t will always be a bona fide covariance matrix. 8

p(d θ ) l(θ ) 1.2 x x x

p(d θ ) l(θ ) 1.2 x x x p(d θ ).2 x 0-7 0.8 x 0-7 0.4 x 0-7 l(θ ) -20-40 -60-80 -00 2 3 4 5 6 7 θ ˆ 2 3 4 5 6 7 θ ˆ 2 3 4 5 6 7 θ θ x FIGURE 3.. The top graph shows several training points in one dimension, known or assumed to

More information

order is number of previous outputs

order is number of previous outputs Markov Models Lecture : Markov and Hidden Markov Models PSfrag Use past replacements as state. Next output depends on previous output(s): y t = f[y t, y t,...] order is number of previous outputs y t y

More information

Hidden Markov Models and Gaussian Mixture Models

Hidden Markov Models and Gaussian Mixture Models Hidden Markov Models and Gaussian Mixture Models Hiroshi Shimodaira and Steve Renals Automatic Speech Recognition ASR Lectures 4&5 23&27 January 2014 ASR Lectures 4&5 Hidden Markov Models and Gaussian

More information

University of Cambridge. MPhil in Computer Speech Text & Internet Technology. Module: Speech Processing II. Lecture 2: Hidden Markov Models I

University of Cambridge. MPhil in Computer Speech Text & Internet Technology. Module: Speech Processing II. Lecture 2: Hidden Markov Models I University of Cambridge MPhil in Computer Speech Text & Internet Technology Module: Speech Processing II Lecture 2: Hidden Markov Models I o o o o o 1 2 3 4 T 1 b 2 () a 12 2 a 3 a 4 5 34 a 23 b () b ()

More information

Statistical Sequence Recognition and Training: An Introduction to HMMs

Statistical Sequence Recognition and Training: An Introduction to HMMs Statistical Sequence Recognition and Training: An Introduction to HMMs EECS 225D Nikki Mirghafori nikki@icsi.berkeley.edu March 7, 2005 Credit: many of the HMM slides have been borrowed and adapted, with

More information

Statistical NLP: Hidden Markov Models. Updated 12/15

Statistical NLP: Hidden Markov Models. Updated 12/15 Statistical NLP: Hidden Markov Models Updated 12/15 Markov Models Markov models are statistical tools that are useful for NLP because they can be used for part-of-speech-tagging applications Their first

More information

Statistical Methods for NLP

Statistical Methods for NLP Statistical Methods for NLP Information Extraction, Hidden Markov Models Sameer Maskey Week 5, Oct 3, 2012 *many slides provided by Bhuvana Ramabhadran, Stanley Chen, Michael Picheny Speech Recognition

More information

A Gentle Tutorial of the EM Algorithm and its Application to Parameter Estimation for Gaussian Mixture and Hidden Markov Models

A Gentle Tutorial of the EM Algorithm and its Application to Parameter Estimation for Gaussian Mixture and Hidden Markov Models A Gentle Tutorial of the EM Algorithm and its Application to Parameter Estimation for Gaussian Mixture and Hidden Markov Models Jeff A. Bilmes (bilmes@cs.berkeley.edu) International Computer Science Institute

More information

Note Set 5: Hidden Markov Models

Note Set 5: Hidden Markov Models Note Set 5: Hidden Markov Models Probabilistic Learning: Theory and Algorithms, CS 274A, Winter 2016 1 Hidden Markov Models (HMMs) 1.1 Introduction Consider observed data vectors x t that are d-dimensional

More information

Basic math for biology

Basic math for biology Basic math for biology Lei Li Florida State University, Feb 6, 2002 The EM algorithm: setup Parametric models: {P θ }. Data: full data (Y, X); partial data Y. Missing data: X. Likelihood and maximum likelihood

More information

CS 136a Lecture 7 Speech Recognition Architecture: Training models with the Forward backward algorithm

CS 136a Lecture 7 Speech Recognition Architecture: Training models with the Forward backward algorithm + September13, 2016 Professor Meteer CS 136a Lecture 7 Speech Recognition Architecture: Training models with the Forward backward algorithm Thanks to Dan Jurafsky for these slides + ASR components n Feature

More information

Hidden Markov Models and Gaussian Mixture Models

Hidden Markov Models and Gaussian Mixture Models Hidden Markov Models and Gaussian Mixture Models Hiroshi Shimodaira and Steve Renals Automatic Speech Recognition ASR Lectures 4&5 25&29 January 2018 ASR Lectures 4&5 Hidden Markov Models and Gaussian

More information

Linear Dynamical Systems

Linear Dynamical Systems Linear Dynamical Systems Sargur N. srihari@cedar.buffalo.edu Machine Learning Course: http://www.cedar.buffalo.edu/~srihari/cse574/index.html Two Models Described by Same Graph Latent variables Observations

More information

Hidden Markov Modelling

Hidden Markov Modelling Hidden Markov Modelling Introduction Problem formulation Forward-Backward algorithm Viterbi search Baum-Welch parameter estimation Other considerations Multiple observation sequences Phone-based models

More information

Basic Text Analysis. Hidden Markov Models. Joakim Nivre. Uppsala University Department of Linguistics and Philology

Basic Text Analysis. Hidden Markov Models. Joakim Nivre. Uppsala University Department of Linguistics and Philology Basic Text Analysis Hidden Markov Models Joakim Nivre Uppsala University Department of Linguistics and Philology joakimnivre@lingfiluuse Basic Text Analysis 1(33) Hidden Markov Models Markov models are

More information

Expectation Maximization (EM)

Expectation Maximization (EM) Expectation Maximization (EM) The Expectation Maximization (EM) algorithm is one approach to unsupervised, semi-supervised, or lightly supervised learning. In this kind of learning either no labels are

More information

Dept. of Linguistics, Indiana University Fall 2009

Dept. of Linguistics, Indiana University Fall 2009 1 / 14 Markov L645 Dept. of Linguistics, Indiana University Fall 2009 2 / 14 Markov (1) (review) Markov A Markov Model consists of: a finite set of statesω={s 1,...,s n }; an signal alphabetσ={σ 1,...,σ

More information

Hidden Markov Models

Hidden Markov Models CS769 Spring 2010 Advanced Natural Language Processing Hidden Markov Models Lecturer: Xiaojin Zhu jerryzhu@cs.wisc.edu 1 Part-of-Speech Tagging The goal of Part-of-Speech (POS) tagging is to label each

More information

Probabilistic Graphical Models

Probabilistic Graphical Models Probabilistic Graphical Models Brown University CSCI 2950-P, Spring 2013 Prof. Erik Sudderth Lecture 12: Gaussian Belief Propagation, State Space Models and Kalman Filters Guest Kalman Filter Lecture by

More information

1. Markov models. 1.1 Markov-chain

1. Markov models. 1.1 Markov-chain 1. Markov models 1.1 Markov-chain Let X be a random variable X = (X 1,..., X t ) taking values in some set S = {s 1,..., s N }. The sequence is Markov chain if it has the following properties: 1. Limited

More information

6.864: Lecture 5 (September 22nd, 2005) The EM Algorithm

6.864: Lecture 5 (September 22nd, 2005) The EM Algorithm 6.864: Lecture 5 (September 22nd, 2005) The EM Algorithm Overview The EM algorithm in general form The EM algorithm for hidden markov models (brute force) The EM algorithm for hidden markov models (dynamic

More information

1 EM algorithm: updating the mixing proportions {π k } ik are the posterior probabilities at the qth iteration of EM.

1 EM algorithm: updating the mixing proportions {π k } ik are the posterior probabilities at the qth iteration of EM. Université du Sud Toulon - Var Master Informatique Probabilistic Learning and Data Analysis TD: Model-based clustering by Faicel CHAMROUKHI Solution The aim of this practical wor is to show how the Classification

More information

Sequence labeling. Taking collective a set of interrelated instances x 1,, x T and jointly labeling them

Sequence labeling. Taking collective a set of interrelated instances x 1,, x T and jointly labeling them HMM, MEMM and CRF 40-957 Special opics in Artificial Intelligence: Probabilistic Graphical Models Sharif University of echnology Soleymani Spring 2014 Sequence labeling aking collective a set of interrelated

More information

Linear Dynamical Systems (Kalman filter)

Linear Dynamical Systems (Kalman filter) Linear Dynamical Systems (Kalman filter) (a) Overview of HMMs (b) From HMMs to Linear Dynamical Systems (LDS) 1 Markov Chains with Discrete Random Variables x 1 x 2 x 3 x T Let s assume we have discrete

More information

Parametric Models Part III: Hidden Markov Models

Parametric Models Part III: Hidden Markov Models Parametric Models Part III: Hidden Markov Models Selim Aksoy Department of Computer Engineering Bilkent University saksoy@cs.bilkent.edu.tr CS 551, Spring 2014 CS 551, Spring 2014 c 2014, Selim Aksoy (Bilkent

More information

Graphical Models Seminar

Graphical Models Seminar Graphical Models Seminar Forward-Backward and Viterbi Algorithm for HMMs Bishop, PRML, Chapters 13.2.2, 13.2.3, 13.2.5 Dinu Kaufmann Departement Mathematik und Informatik Universität Basel April 8, 2013

More information

Hidden Markov Models Part 2: Algorithms

Hidden Markov Models Part 2: Algorithms Hidden Markov Models Part 2: Algorithms CSE 6363 Machine Learning Vassilis Athitsos Computer Science and Engineering Department University of Texas at Arlington 1 Hidden Markov Model An HMM consists of:

More information

CS Lecture 19. Exponential Families & Expectation Propagation

CS Lecture 19. Exponential Families & Expectation Propagation CS 6347 Lecture 19 Exponential Families & Expectation Propagation Discrete State Spaces We have been focusing on the case of MRFs over discrete state spaces Probability distributions over discrete spaces

More information

We Live in Exciting Times. CSCI-567: Machine Learning (Spring 2019) Outline. Outline. ACM (an international computing research society) has named

We Live in Exciting Times. CSCI-567: Machine Learning (Spring 2019) Outline. Outline. ACM (an international computing research society) has named We Live in Exciting Times ACM (an international computing research society) has named CSCI-567: Machine Learning (Spring 2019) Prof. Victor Adamchik U of Southern California Apr. 2, 2019 Yoshua Bengio,

More information

L23: hidden Markov models

L23: hidden Markov models L23: hidden Markov models Discrete Markov processes Hidden Markov models Forward and Backward procedures The Viterbi algorithm This lecture is based on [Rabiner and Juang, 1993] Introduction to Speech

More information

Machine Learning 4771

Machine Learning 4771 Machine Learning 4771 Instructor: ony Jebara Kalman Filtering Linear Dynamical Systems and Kalman Filtering Structure from Motion Linear Dynamical Systems Audio: x=pitch y=acoustic waveform Vision: x=object

More information

HIDDEN MARKOV MODELS IN SPEECH RECOGNITION

HIDDEN MARKOV MODELS IN SPEECH RECOGNITION HIDDEN MARKOV MODELS IN SPEECH RECOGNITION Wayne Ward Carnegie Mellon University Pittsburgh, PA 1 Acknowledgements Much of this talk is derived from the paper "An Introduction to Hidden Markov Models",

More information

Hidden Markov Models. Representing sequence data. Markov Models. A dice-y example 4/26/2018. CISC 5800 Professor Daniel Leeds Π A = 0.3, Π B = 0.

Hidden Markov Models. Representing sequence data. Markov Models. A dice-y example 4/26/2018. CISC 5800 Professor Daniel Leeds Π A = 0.3, Π B = 0. Representing sequence data Hidden Markov Models CISC 5800 Professor Daniel Leeds Spoken language DNA sequences Daily stock values Example: spoken language F?r plu? fi?e is nine Between F and r expect a

More information

STA 4273H: Statistical Machine Learning

STA 4273H: Statistical Machine Learning STA 4273H: Statistical Machine Learning Russ Salakhutdinov Department of Statistics! rsalakhu@utstat.toronto.edu! http://www.utstat.utoronto.ca/~rsalakhu/ Sidney Smith Hall, Room 6002 Lecture 11 Project

More information

Hidden Markov Models The three basic HMM problems (note: change in notation) Mitch Marcus CSE 391

Hidden Markov Models The three basic HMM problems (note: change in notation) Mitch Marcus CSE 391 Hidden Markov Models The three basic HMM problems (note: change in notation) Mitch Marcus CSE 391 Parameters of an HMM States: A set of states S=s 1, s n Transition probabilities: A= a 1,1, a 1,2,, a n,n

More information

Hidden Markov Models

Hidden Markov Models Hidden Markov Models CI/CI(CS) UE, SS 2015 Christian Knoll Signal Processing and Speech Communication Laboratory Graz University of Technology June 23, 2015 CI/CI(CS) SS 2015 June 23, 2015 Slide 1/26 Content

More information

Page 1. References. Hidden Markov models and multiple sequence alignment. Markov chains. Probability review. Example. Markovian sequence

Page 1. References. Hidden Markov models and multiple sequence alignment. Markov chains. Probability review. Example. Markovian sequence Page Hidden Markov models and multiple sequence alignment Russ B Altman BMI 4 CS 74 Some slides borrowed from Scott C Schmidler (BMI graduate student) References Bioinformatics Classic: Krogh et al (994)

More information

CS 188: Artificial Intelligence

CS 188: Artificial Intelligence CS 188: Artificial Intelligence Hidden Markov Models Instructor: Anca Dragan --- University of California, Berkeley [These slides were created by Dan Klein, Pieter Abbeel, and Anca. http://ai.berkeley.edu.]

More information

Chapter 4 Dynamic Bayesian Networks Fall Jin Gu, Michael Zhang

Chapter 4 Dynamic Bayesian Networks Fall Jin Gu, Michael Zhang Chapter 4 Dynamic Bayesian Networks 2016 Fall Jin Gu, Michael Zhang Reviews: BN Representation Basic steps for BN representations Define variables Define the preliminary relations between variables Check

More information

O 3 O 4 O 5. q 3. q 4. Transition

O 3 O 4 O 5. q 3. q 4. Transition Hidden Markov Models Hidden Markov models (HMM) were developed in the early part of the 1970 s and at that time mostly applied in the area of computerized speech recognition. They are first described in

More information

Hidden Markov Models Hamid R. Rabiee

Hidden Markov Models Hamid R. Rabiee Hidden Markov Models Hamid R. Rabiee 1 Hidden Markov Models (HMMs) In the previous slides, we have seen that in many cases the underlying behavior of nature could be modeled as a Markov process. However

More information

CS838-1 Advanced NLP: Hidden Markov Models

CS838-1 Advanced NLP: Hidden Markov Models CS838-1 Advanced NLP: Hidden Markov Models Xiaojin Zhu 2007 Send comments to jerryzhu@cs.wisc.edu 1 Part of Speech Tagging Tag each word in a sentence with its part-of-speech, e.g., The/AT representative/nn

More information

Hidden Markov Models

Hidden Markov Models Hidden Markov Models Lecture Notes Speech Communication 2, SS 2004 Erhard Rank/Franz Pernkopf Signal Processing and Speech Communication Laboratory Graz University of Technology Inffeldgasse 16c, A-8010

More information

Further details of the Baum-Welch algorithm

Further details of the Baum-Welch algorithm Further details of the Baum-Welch algorithm Martin Emms November 15, 2018 real Baum-Welch: summing the clock-tick probs brute-force EM would for each o d calculate responsibility γ d (s) = p(s o d ) for

More information

Lecture 8 Learning Sequence Motif Models Using Expectation Maximization (EM) Colin Dewey February 14, 2008

Lecture 8 Learning Sequence Motif Models Using Expectation Maximization (EM) Colin Dewey February 14, 2008 Lecture 8 Learning Sequence Motif Models Using Expectation Maximization (EM) Colin Dewey February 14, 2008 1 Sequence Motifs what is a sequence motif? a sequence pattern of biological significance typically

More information

Lecture 4: Hidden Markov Models: An Introduction to Dynamic Decision Making. November 11, 2010

Lecture 4: Hidden Markov Models: An Introduction to Dynamic Decision Making. November 11, 2010 Hidden Lecture 4: Hidden : An Introduction to Dynamic Decision Making November 11, 2010 Special Meeting 1/26 Markov Model Hidden When a dynamical system is probabilistic it may be determined by the transition

More information

Hidden Markov Models. By Parisa Abedi. Slides courtesy: Eric Xing

Hidden Markov Models. By Parisa Abedi. Slides courtesy: Eric Xing Hidden Markov Models By Parisa Abedi Slides courtesy: Eric Xing i.i.d to sequential data So far we assumed independent, identically distributed data Sequential (non i.i.d.) data Time-series data E.g. Speech

More information

STA 414/2104: Machine Learning

STA 414/2104: Machine Learning STA 414/2104: Machine Learning Russ Salakhutdinov Department of Computer Science! Department of Statistics! rsalakhu@cs.toronto.edu! http://www.cs.toronto.edu/~rsalakhu/ Lecture 9 Sequential Data So far

More information

Speech Recognition HMM

Speech Recognition HMM Speech Recognition HMM Jan Černocký, Valentina Hubeika {cernocky ihubeika}@fit.vutbr.cz FIT BUT Brno Speech Recognition HMM Jan Černocký, Valentina Hubeika, DCGM FIT BUT Brno 1/38 Agenda Recap variability

More information

Hidden Markov Models. Representing sequence data. Markov Models. A dice-y example 4/5/2017. CISC 5800 Professor Daniel Leeds Π A = 0.3, Π B = 0.

Hidden Markov Models. Representing sequence data. Markov Models. A dice-y example 4/5/2017. CISC 5800 Professor Daniel Leeds Π A = 0.3, Π B = 0. Representing sequence data Hidden Markov Models CISC 5800 Professor Daniel Leeds Spoken language DNA sequences Daily stock values Example: spoken language F?r plu? fi?e is nine Between F and r expect a

More information

. D CR Nomenclature D 1

. D CR Nomenclature D 1 . D CR Nomenclature D 1 Appendix D: CR NOMENCLATURE D 2 The notation used by different investigators working in CR formulations has not coalesced, since the topic is in flux. This Appendix identifies the

More information

Machine Learning for natural language processing

Machine Learning for natural language processing Machine Learning for natural language processing Hidden Markov Models Laura Kallmeyer Heinrich-Heine-Universität Düsseldorf Summer 2016 1 / 33 Introduction So far, we have classified texts/observations

More information

Hidden Markov Models. Aarti Singh Slides courtesy: Eric Xing. Machine Learning / Nov 8, 2010

Hidden Markov Models. Aarti Singh Slides courtesy: Eric Xing. Machine Learning / Nov 8, 2010 Hidden Markov Models Aarti Singh Slides courtesy: Eric Xing Machine Learning 10-701/15-781 Nov 8, 2010 i.i.d to sequential data So far we assumed independent, identically distributed data Sequential data

More information

CMSC 723: Computational Linguistics I Session #5 Hidden Markov Models. The ischool University of Maryland. Wednesday, September 30, 2009

CMSC 723: Computational Linguistics I Session #5 Hidden Markov Models. The ischool University of Maryland. Wednesday, September 30, 2009 CMSC 723: Computational Linguistics I Session #5 Hidden Markov Models Jimmy Lin The ischool University of Maryland Wednesday, September 30, 2009 Today s Agenda The great leap forward in NLP Hidden Markov

More information

Principal Component Analysis (PCA) Our starting point consists of T observations from N variables, which will be arranged in an T N matrix R,

Principal Component Analysis (PCA) Our starting point consists of T observations from N variables, which will be arranged in an T N matrix R, Principal Component Analysis (PCA) PCA is a widely used statistical tool for dimension reduction. The objective of PCA is to find common factors, the so called principal components, in form of linear combinations

More information

CS1820 Notes. hgupta1, kjline, smechery. April 3-April 5. output: plausible Ancestral Recombination Graph (ARG)

CS1820 Notes. hgupta1, kjline, smechery. April 3-April 5. output: plausible Ancestral Recombination Graph (ARG) CS1820 Notes hgupta1, kjline, smechery April 3-April 5 April 3 Notes 1 Minichiello-Durbin Algorithm input: set of sequences output: plausible Ancestral Recombination Graph (ARG) note: the optimal ARG is

More information

Part of Speech Tagging: Viterbi, Forward, Backward, Forward- Backward, Baum-Welch. COMP-599 Oct 1, 2015

Part of Speech Tagging: Viterbi, Forward, Backward, Forward- Backward, Baum-Welch. COMP-599 Oct 1, 2015 Part of Speech Tagging: Viterbi, Forward, Backward, Forward- Backward, Baum-Welch COMP-599 Oct 1, 2015 Announcements Research skills workshop today 3pm-4:30pm Schulich Library room 313 Start thinking about

More information

Expectation Maximization (EM)

Expectation Maximization (EM) Expectation Maximization (EM) The EM algorithm is used to train models involving latent variables using training data in which the latent variables are not observed (unlabeled data). This is to be contrasted

More information

min 4x 1 5x 2 + 3x 3 s.t. x 1 + 2x 2 + x 3 = 10 x 1 x 2 6 x 1 + 3x 2 + x 3 14

min 4x 1 5x 2 + 3x 3 s.t. x 1 + 2x 2 + x 3 = 10 x 1 x 2 6 x 1 + 3x 2 + x 3 14 The exam is three hours long and consists of 4 exercises. The exam is graded on a scale 0-25 points, and the points assigned to each question are indicated in parenthesis within the text. If necessary,

More information

Massachusetts Institute of Technology

Massachusetts Institute of Technology Massachusetts Institute of Technology 6.867 Machine Learning, Fall 2006 Problem Set 5 Due Date: Thursday, Nov 30, 12:00 noon You may submit your solutions in class or in the box. 1. Wilhelm and Klaus are

More information

A gentle introduction to Hidden Markov Models

A gentle introduction to Hidden Markov Models A gentle introduction to Hidden Markov Models Mark Johnson Brown University November 2009 1 / 27 Outline What is sequence labeling? Markov models Hidden Markov models Finding the most likely state sequence

More information

Introduction to Machine Learning CMU-10701

Introduction to Machine Learning CMU-10701 Introduction to Machine Learning CMU-10701 Hidden Markov Models Barnabás Póczos & Aarti Singh Slides courtesy: Eric Xing i.i.d to sequential data So far we assumed independent, identically distributed

More information

Sequential Supervised Learning

Sequential Supervised Learning Sequential Supervised Learning Many Application Problems Require Sequential Learning Part-of of-speech Tagging Information Extraction from the Web Text-to to-speech Mapping Part-of of-speech Tagging Given

More information

Conditional Random Field

Conditional Random Field Introduction Linear-Chain General Specific Implementations Conclusions Corso di Elaborazione del Linguaggio Naturale Pisa, May, 2011 Introduction Linear-Chain General Specific Implementations Conclusions

More information

Hidden Markov Model. Ying Wu. Electrical Engineering and Computer Science Northwestern University Evanston, IL 60208

Hidden Markov Model. Ying Wu. Electrical Engineering and Computer Science Northwestern University Evanston, IL 60208 Hidden Markov Model Ying Wu Electrical Engineering and Computer Science Northwestern University Evanston, IL 60208 http://www.eecs.northwestern.edu/~yingwu 1/19 Outline Example: Hidden Coin Tossing Hidden

More information

Hidden Markov Models. x 1 x 2 x 3 x K

Hidden Markov Models. x 1 x 2 x 3 x K Hidden Markov Models 1 1 1 1 2 2 2 2 K K K K x 1 x 2 x 3 x K HiSeq X & NextSeq Viterbi, Forward, Backward VITERBI FORWARD BACKWARD Initialization: V 0 (0) = 1 V k (0) = 0, for all k > 0 Initialization:

More information

Today s Lecture: HMMs

Today s Lecture: HMMs Today s Lecture: HMMs Definitions Examples Probability calculations WDAG Dynamic programming algorithms: Forward Viterbi Parameter estimation Viterbi training 1 Hidden Markov Models Probability models

More information

Lecture 11: Hidden Markov Models

Lecture 11: Hidden Markov Models Lecture 11: Hidden Markov Models Cognitive Systems - Machine Learning Cognitive Systems, Applied Computer Science, Bamberg University slides by Dr. Philip Jackson Centre for Vision, Speech & Signal Processing

More information

Applications of Hidden Markov Models

Applications of Hidden Markov Models 18.417 Introduction to Computational Molecular Biology Lecture 18: November 9, 2004 Scribe: Chris Peikert Lecturer: Ross Lippert Editor: Chris Peikert Applications of Hidden Markov Models Review of Notation

More information

Modeling conditional distributions with mixture models: Theory and Inference

Modeling conditional distributions with mixture models: Theory and Inference Modeling conditional distributions with mixture models: Theory and Inference John Geweke University of Iowa, USA Journal of Applied Econometrics Invited Lecture Università di Venezia Italia June 2, 2005

More information

Hidden Markov Models. Main source: Durbin et al., Biological Sequence Alignment (Cambridge, 98)

Hidden Markov Models. Main source: Durbin et al., Biological Sequence Alignment (Cambridge, 98) Hidden Markov Models Main source: Durbin et al., Biological Sequence Alignment (Cambridge, 98) 1 The occasionally dishonest casino A P A (1) = P A (2) = = 1/6 P A->B = P B->A = 1/10 B P B (1)=0.1... P

More information

Pivoting. Reading: GV96 Section 3.4, Stew98 Chapter 3: 1.3

Pivoting. Reading: GV96 Section 3.4, Stew98 Chapter 3: 1.3 Pivoting Reading: GV96 Section 3.4, Stew98 Chapter 3: 1.3 In the previous discussions we have assumed that the LU factorization of A existed and the various versions could compute it in a stable manner.

More information

Hidden Markov Models: All the Glorious Gory Details

Hidden Markov Models: All the Glorious Gory Details Hidden Markov Models: All the Glorious Gory Details Noah A. Smith Department of Computer Science Johns Hopkins University nasmith@cs.jhu.edu 18 October 2004 1 Introduction Hidden Markov models (HMMs, hereafter)

More information

Adaptive Localization: Proposals for a high-resolution multivariate system Ross Bannister, HRAA, December 2008, January 2009 Version 3.

Adaptive Localization: Proposals for a high-resolution multivariate system Ross Bannister, HRAA, December 2008, January 2009 Version 3. Adaptive Localization: Proposals for a high-resolution multivariate system Ross Bannister, HRAA, December 2008, January 2009 Version 3.. The implicit Schur product 2. The Bishop method for adaptive localization

More information

Data-Intensive Computing with MapReduce

Data-Intensive Computing with MapReduce Data-Intensive Computing with MapReduce Session 8: Sequence Labeling Jimmy Lin University of Maryland Thursday, March 14, 2013 This work is licensed under a Creative Commons Attribution-Noncommercial-Share

More information

ELE539A: Optimization of Communication Systems Lecture 15: Semidefinite Programming, Detection and Estimation Applications

ELE539A: Optimization of Communication Systems Lecture 15: Semidefinite Programming, Detection and Estimation Applications ELE539A: Optimization of Communication Systems Lecture 15: Semidefinite Programming, Detection and Estimation Applications Professor M. Chiang Electrical Engineering Department, Princeton University March

More information

Sequence Modelling with Features: Linear-Chain Conditional Random Fields. COMP-599 Oct 6, 2015

Sequence Modelling with Features: Linear-Chain Conditional Random Fields. COMP-599 Oct 6, 2015 Sequence Modelling with Features: Linear-Chain Conditional Random Fields COMP-599 Oct 6, 2015 Announcement A2 is out. Due Oct 20 at 1pm. 2 Outline Hidden Markov models: shortcomings Generative vs. discriminative

More information

Computational Genomics and Molecular Biology, Fall

Computational Genomics and Molecular Biology, Fall Computational Genomics and Molecular Biology, Fall 2011 1 HMM Lecture Notes Dannie Durand and Rose Hoberman October 11th 1 Hidden Markov Models In the last few lectures, we have focussed on three problems

More information

CS839: Probabilistic Graphical Models. Lecture 7: Learning Fully Observed BNs. Theo Rekatsinas

CS839: Probabilistic Graphical Models. Lecture 7: Learning Fully Observed BNs. Theo Rekatsinas CS839: Probabilistic Graphical Models Lecture 7: Learning Fully Observed BNs Theo Rekatsinas 1 Exponential family: a basic building block For a numeric random variable X p(x ) =h(x)exp T T (x) A( ) = 1

More information

Hidden Markov Models

Hidden Markov Models Hidden Markov Models Slides revised and adapted to Bioinformática 55 Engª Biomédica/IST 2005 Ana Teresa Freitas Forward Algorithm For Markov chains we calculate the probability of a sequence, P(x) How

More information

CISC 889 Bioinformatics (Spring 2004) Hidden Markov Models (II)

CISC 889 Bioinformatics (Spring 2004) Hidden Markov Models (II) CISC 889 Bioinformatics (Spring 24) Hidden Markov Models (II) a. Likelihood: forward algorithm b. Decoding: Viterbi algorithm c. Model building: Baum-Welch algorithm Viterbi training Hidden Markov models

More information

Machine Learning. Gaussian Mixture Models. Zhiyao Duan & Bryan Pardo, Machine Learning: EECS 349 Fall

Machine Learning. Gaussian Mixture Models. Zhiyao Duan & Bryan Pardo, Machine Learning: EECS 349 Fall Machine Learning Gaussian Mixture Models Zhiyao Duan & Bryan Pardo, Machine Learning: EECS 349 Fall 2012 1 The Generative Model POV We think of the data as being generated from some process. We assume

More information

Probabilistic Graphical Models Homework 2: Due February 24, 2014 at 4 pm

Probabilistic Graphical Models Homework 2: Due February 24, 2014 at 4 pm Probabilistic Graphical Models 10-708 Homework 2: Due February 24, 2014 at 4 pm Directions. This homework assignment covers the material presented in Lectures 4-8. You must complete all four problems to

More information

Factor Analysis and Kalman Filtering (11/2/04)

Factor Analysis and Kalman Filtering (11/2/04) CS281A/Stat241A: Statistical Learning Theory Factor Analysis and Kalman Filtering (11/2/04) Lecturer: Michael I. Jordan Scribes: Byung-Gon Chun and Sunghoon Kim 1 Factor Analysis Factor analysis is used

More information

Master 2 Informatique Probabilistic Learning and Data Analysis

Master 2 Informatique Probabilistic Learning and Data Analysis Master 2 Informatique Probabilistic Learning and Data Analysis Faicel Chamroukhi Maître de Conférences USTV, LSIS UMR CNRS 7296 email: chamroukhi@univ-tln.fr web: chamroukhi.univ-tln.fr 2013/2014 Faicel

More information

CS229 Lecture notes. Andrew Ng

CS229 Lecture notes. Andrew Ng CS229 Lecture notes Andrew Ng Part X Factor analysis When we have data x (i) R n that comes from a mixture of several Gaussians, the EM algorithm can be applied to fit a mixture model. In this setting,

More information

Evolutionary Models. Evolutionary Models

Evolutionary Models. Evolutionary Models Edit Operators In standard pairwise alignment, what are the allowed edit operators that transform one sequence into the other? Describe how each of these edit operations are represented on a sequence alignment

More information

Hidden Markov models for time series of counts with excess zeros

Hidden Markov models for time series of counts with excess zeros Hidden Markov models for time series of counts with excess zeros Madalina Olteanu and James Ridgway University Paris 1 Pantheon-Sorbonne - SAMM, EA4543 90 Rue de Tolbiac, 75013 Paris - France Abstract.

More information

Hidden Markov Models (HMMs) November 14, 2017

Hidden Markov Models (HMMs) November 14, 2017 Hidden Markov Models (HMMs) November 14, 2017 inferring a hidden truth 1) You hear a static-filled radio transmission. how can you determine what did the sender intended to say? 2) You know that genes

More information

HMM for modeling aligned multiple sequences: phylo-hmm & multivariate HMM

HMM for modeling aligned multiple sequences: phylo-hmm & multivariate HMM I529: Machine Learning in Bioinformatics (Spring 2017) HMM for modeling aligned multiple sequences: phylo-hmm & multivariate HMM Yuzhen Ye School of Informatics and Computing Indiana University, Bloomington

More information

12. Cholesky factorization

12. Cholesky factorization L. Vandenberghe ECE133A (Winter 2018) 12. Cholesky factorization positive definite matrices examples Cholesky factorization complex positive definite matrices kernel methods 12-1 Definitions a symmetric

More information

The Expectation-Maximization Algorithm

The Expectation-Maximization Algorithm 1/29 EM & Latent Variable Models Gaussian Mixture Models EM Theory The Expectation-Maximization Algorithm Mihaela van der Schaar Department of Engineering Science University of Oxford MLE for Latent Variable

More information

Hidden Markov Models for precipitation

Hidden Markov Models for precipitation Hidden Markov Models for precipitation Pierre Ailliot Université de Brest Joint work with Peter Thomson Statistics Research Associates (NZ) Page 1 Context Part of the project Climate-related risks for

More information

1 What is a hidden Markov model?

1 What is a hidden Markov model? 1 What is a hidden Markov model? Consider a Markov chain {X k }, where k is a non-negative integer. Suppose {X k } embedded in signals corrupted by some noise. Indeed, {X k } is hidden due to noise and

More information

6.047 / Computational Biology: Genomes, Networks, Evolution Fall 2008

6.047 / Computational Biology: Genomes, Networks, Evolution Fall 2008 MIT OpenCourseWare http://ocw.mit.edu 6.047 / 6.878 Computational Biology: Genomes, etworks, Evolution Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms.

More information

10. Hidden Markov Models (HMM) for Speech Processing. (some slides taken from Glass and Zue course)

10. Hidden Markov Models (HMM) for Speech Processing. (some slides taken from Glass and Zue course) 10. Hidden Markov Models (HMM) for Speech Processing (some slides taken from Glass and Zue course) Definition of an HMM The HMM are powerful statistical methods to characterize the observed samples of

More information

Markov Chains and Hidden Markov Models

Markov Chains and Hidden Markov Models Chapter 1 Markov Chains and Hidden Markov Models In this chapter, we will introduce the concept of Markov chains, and show how Markov chains can be used to model signals using structures such as hidden

More information

Supplemental Information Likelihood-based inference in isolation-by-distance models using the spatial distribution of low-frequency alleles

Supplemental Information Likelihood-based inference in isolation-by-distance models using the spatial distribution of low-frequency alleles Supplemental Information Likelihood-based inference in isolation-by-distance models using the spatial distribution of low-frequency alleles John Novembre and Montgomery Slatkin Supplementary Methods To

More information

COM336: Neural Computing

COM336: Neural Computing COM336: Neural Computing http://www.dcs.shef.ac.uk/ sjr/com336/ Lecture 2: Density Estimation Steve Renals Department of Computer Science University of Sheffield Sheffield S1 4DP UK email: s.renals@dcs.shef.ac.uk

More information

. Also, in this case, p i = N1 ) T, (2) where. I γ C N(N 2 2 F + N1 2 Q)

. Also, in this case, p i = N1 ) T, (2) where. I γ C N(N 2 2 F + N1 2 Q) Supplementary information S7 Testing for association at imputed SPs puted SPs Score tests A Score Test needs calculations of the observed data score and information matrix only under the null hypothesis,

More information