Introduction to Hidden Markov Modeling (HMM) Daniel S. Terry Scott Blanchard and Harel Weinstein labs
|
|
- Charla Melton
- 6 years ago
- Views:
Transcription
1 Introduction to Hidden Markov Modeling (HMM) Daniel S. Terry Scott Blanchard and Harel Weinstein labs 1
2 HMM is useful for many, many problems. Speech Recognition and Translation Weather Modeling Sequence Alignment Financial Modeling 2
3
4 So let s say you re riding out nuclear war in a bunker To keep sane, you want to know what the weather outside is like? but all you can observe is if the security guard brings his umbrella. 4
5 Observations Probabilistic reasoning X E Hidden State P(Sunny Umbrella) P(loudy Umbrella) P(Rain Umbrella) P(Sunny No Umbrella) P(loudy No Umbrella) P(Rain No Umbrella) P(X E) = probability of X happening if E is observed. 5
6 Probabilistic reasoning in stochastic processes Time Hidden State X 0 X 1 X 2 X 3 X 4 Observations ( Emissions ) E 0 E 1 E 2 E 3 E 4 Hidden State Observations ( Emissions ) This is called a Markov chain 6
7 Assumptions in Markov modeling Assumption 1: This is a stationary process, specifically a first-order Markov Process: P(X t X t-1,x t-2,x t-3, ) = P(X t X t-1 ) in other words, the current state depends only on the previous state. We call this the transition model. Assumption 2: The current observations depends only on the current state: P(E t X t,x t-1,x t-2,,e t-1,e t-2,e t-3, ) = P(E t X t ) in other words, the current observation depends only on the current state. We call this the observation (or emission) model. Hidden State X 0 X 1 X 2 X 3 X 4 Observations ( Emissions ) E 0 E 1 E 2 E 3 E 4 7
8 The initial and transition probability models: π and A X t-1 P(X t = Sunny) P(X t X t-1 ) P(X t = loudy) P(X t = Raining) P(X) π Sunny 0.7 loudy 0.15 Raining 0.15 Sunny loudy Raining X 0 X 1 E 0 E 1 Encodes prior knowledge about weather trends. 8
9 The observation probability model: B Hidden State X 0 X 1 X 2 X t P(E t =Um.) Sunny 0.05 loudy 0.10 Raining 0.85 Observations ( Emissions ) E 0 E 1 E 2 Encodes prior knowledge about how likely people are to bring their umbrella depending on weather conditions. 9
10 Together these parameters define a Markov model. {, A, B} Initial State Probabilities State Transition Probabilities Observation Distributions a, a R,R a,r π R π R a R, b b R 10
11 Predicting state sequences from observations Observation Sequence (t=1..t) Predicted Hidden State Sequence Markov hain Markov Model a, a R,R X 0 X 1 X 2 X 3 π a,r a R, R π R E 0 E 1 E 2 E 3 b b R 11
12 Finding the optimal state sequence with Viterbi {, A, B} Given a model that describes the system ( the optimal state sequence (idealization) as follows: Time X 0 X 1 X 2 X 3 ), we can determine S S S S States R R R R For each state at time t, calculate probability of the state at time t (X t ) being a particular state x i (sunning, raining, etc), given observations and previous states: P(X t =x i E t,e t-1,e t-2,,x t-1,x t-2,x t-3, ) = P(X t =x i E t, X t-1 =x j ) = P(X t =x i E t ) P(X t =x i X t =x j ) P(X 0 =x i ) = π 12
13 Finding the optimal state sequence with Viterbi Time X 0 X 1 X 2 X 3 S S S S States R R R R Repeat these calculations for all possible transitions recursively. Then at each point in time we have an estimate of how likely we are to be in a particular state at that time given all possible previous paths. We also keep track of the most likely state at each point in time. (This complex looking thing is called a trellis. an you see why?) 13
14 Finding the optimal state sequence with Viterbi Time X 0 X 1 X 2 X 3 S S S S States R R R R Find the most likely end state from the probabilities. We can then backtrack to find the most likely state sequence. You have seen a similar procedure with sequence alignment. 14
15 Predicting state sequences from observations Observation Sequence (t=1..t) Predicted Hidden State Sequence Markov hain Markov Model a, a R,R X 0 X 1 X 2 X 3 π a,r a R, R π R E 0 E 1 E 2 E 3 b b R 15
16 FRET Fluorescence Ok, so I m bored of talking about the weather Time (min) A practical example of Markov modeling: Analysis of single-molecule fluorescence trajectories 16
17 Neurotransmitter release and reuptake is central to neuronal signaling and proper functioning of the brain. NSS Reuptake public domain.
18 Neurotransmitter:Sodium Symporter (NSS) proteins are the targets of many clinically-important drugs. Therapeutic Inhibitors NSS Reuptake Drugs of Abuse public domain.
19 A practical example of Markov modeling: Analysis of single-molecule fluorescence trajectories High Na + Outside Neurotransmitter Extracellular Intracellular Low Na + Inside Key Question: What are the specific conformational changes required for such a mechanism and how do they mediate transport?
20 FRET Single molecule FRET: A tool for examining conformational dynamics Acceptor Donor 0.2 R Distance (nm) 20
21 FRET Fluorescence FRET imaging of single-molecules can be achieved using a few tricks, including total internal reflection excitation Time (min) Acceptor Donor Surface 532 nm TIR Excitation 21
22 FRET Fluorescence onformation HMM is a statistical framework for modeling a hidden system using a sequence of observations generated by that system. Sequence of Hidden States X 0 X 1 X 2 Sequence of Observations E 0 E 1 E Time (sec) We want to know: 1) How many distinct states are there? 2) What are their FRET values? 3) What are the rates? 4) Most likely state at each point in time? Unlike with the weather, we have to learn the model form the data itself!! 22
23 Hidden Markov models have three components: 1) Initial state probabilities: O, a O,O {, A, B} a, a O, 2) Transition probabilities: A { a i, j} a a O, O, O a a O,, π O O b O a,o b π 3) Observation probability distribution (OPD): 1 ( Et i ) B bi ( Et ) exp i i 2 μ i σ i FRET FRET distribution for state i. 23
24 Goal: best model to explain the experimental data. In other words, we want to maximize the probability of the model giving the data. ˆ argmax P( E) (where λ is the model, E is the observed FRET trajectory) But we don t know how to calculate P( λ E )! Instead, turn it around using Bayes theorem: P( E) P( E ) P( ) P( E) The prior probability P(E) is independent of the model choice and will not affect model ranking. If we assume all models are equally likely, then: ˆ argmax P( E) argmax P( E ) P( E λ ) is easy to calculate it is the observation distribution. Why is X not here? We have to do this over all possible state sequences! 24
25 FRET Segmental k-means (SKM): optimization on the cheap λ 0 State assignment (Viterbi) Parameter reestimation Time (min) λ i To get B, simply calculate the mean and std for each state from the current assignment. To get A, count the number of transitions of each type and normalize. To get π, count the number of times each dwell starts with each state x i and normalize. Works only if the starting model that is close to final. F. Qin (2004), Biophys J 86:
26 Model optimization: expectation maximization (EM). Expectation: alculate the probability of data given the model (expectation). P( E ) Initial (π) Transition (A) Observation (B) P( X ) t0.. T P( X t X t1 ) P( X t Et ) LL log[ P( X )] t0.. T log[ P( X t X ) P( X t1 t t E )] Maximization: Adjust model parameters to better fit the calculated probabilities. Termination: Iterate until log-likelihood converges (e.g., ΔLL<10-4 ). Restarts: if the likelihood landscape is very frustrated, restarting from a random initial model can help get out of local minima. 26
27 The forward-backward algorithm (Baum Welch) The past The future X 0 X 1 X 2 X 3 X 96 X 97 X 98 X 99 E 0 E 1 E 2 E 3 E 96 E 97 E 98 E 99 alculating the probabilities at a particular point in time (t): P( X t E.. T ) P( X t E1.. t, Et T ) α P( X t E.. t ) P( X t Et T Forward Backward ) We can do this because of Bayes rule and conditional independence of observations over time We calculate these much like we did with Viterbi 27
28 The forward algorithm Time X 0 X 1 X 2 X 3 O O O O States Partial probabilities (α) are calculated recursively as: α t (j) = P(observation hidden state is j) P(all paths to state j at time t) Initial condition: α 0 (j) = π( j ) B(j,E t ) Iterate: n t1 ( j ) B ), i1 j, E t t ( i ai j Then the total probability of the sequence is the sum of these α s 28
29 Maximization using forward-backward probabilities Probability of transitioning from state i to j at time t: (from the Forward-Backward algorithm) Probability of being in state i at time t: Model parameters adjusted to maximize log-likelihood: This very much like SKM, except we use explicit probabilities instead of just counting. 29
30 The problem of bias You can always get a better fit using more parameters! But it may not be a good model. Bayesian information criterion (BI): -2 ln* P(E k) + BI = -2 ln(ll) + k ln(n) k is the number of free parameters, LL is log-likelihood of the optimal fit, and n is the number of data points. Akike information (AI) AI = -2 k - 2 ln(ll) Maximum evidence methods (vbfret), etc. 30
31 FRET Fluorescence onformation HMM is a statistical framework for modeling a hidden system using a sequence of observations generated by that system. Sequence of Hidden States X 0 X 1 X 2 E 0 E 1 E 2 Sequence of Observations We want to know: 1) How many distinct states are there? 2) What are their FRET values? 3) What are the rates? 4) Most likely state at each point in time? Time (sec) 31
32 Occupancy (%) FRET Dwell Time (s) Quantifying kinetics is then useful for understanding how outside factors (ligands) influence dynamics mm Na + : +2 mm Ala Time (min) Open State losed State log [Ala] (M) log [Ala] (M) Zhao and Terry, et al (2011), Nature 474
33 Other important examples of Markov modeling: Single-channel recordings (patch clamp) O Sequence analysis ardiac electrical modeling Systems modeling of metabolic networks 33
34 We can do non-equilibrium Markov modeling, too Geggier et al (2010), JMB 399:
35 HMM is useful for many, many problems. Speech Recognition and Translation Weather Modeling Sequence Alignment Financial Modeling 35
36 Some useful references Artificial Intelligence: A Modern Approach html_dev/main.html Rabiner (1989), Proc. of the IEEE 77: 257. Qin F. Principles of single-channel kinetic analysis. Methods Mol Biol. 2007; 403. Bronson et al (2009), Biophys J 97: QuB software suite: 36
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 informationCS 343: Artificial Intelligence
CS 343: Artificial Intelligence Particle Filters and Applications of HMMs Prof. Scott Niekum The University of Texas at Austin [These slides based on those of Dan Klein and Pieter Abbeel for CS188 Intro
More informationHidden 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 informationSTA 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 informationL23: 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 informationHidden 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 informationHidden 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 informationHidden 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 informationCS 343: Artificial Intelligence
CS 343: Artificial Intelligence Particle Filters and Applications of HMMs Prof. Scott Niekum The University of Texas at Austin [These slides based on those of Dan Klein and Pieter Abbeel for CS188 Intro
More informationLecture 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 informationStatistical 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 informationHidden Markov Models
Hidden Markov Models Slides mostly from Mitch Marcus and Eric Fosler (with lots of modifications). Have you seen HMMs? Have you seen Kalman filters? Have you seen dynamic programming? HMMs are dynamic
More informationCS 5522: Artificial Intelligence II
CS 5522: Artificial Intelligence II Particle Filters and Applications of HMMs Instructor: Wei Xu Ohio State University [These slides were adapted from CS188 Intro to AI at UC Berkeley.] Recap: Reasoning
More informationCS 5522: Artificial Intelligence II
CS 5522: Artificial Intelligence II Particle Filters and Applications of HMMs Instructor: Alan Ritter Ohio State University [These slides were adapted from CS188 Intro to AI at UC Berkeley. All materials
More informationHidden 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 informationCS 188: Artificial Intelligence Fall 2011
CS 188: Artificial Intelligence Fall 2011 Lecture 20: HMMs / Speech / ML 11/8/2011 Dan Klein UC Berkeley Today HMMs Demo bonanza! Most likely explanation queries Speech recognition A massive HMM! Details
More informationIntroduction 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 informationBrief Introduction of Machine Learning Techniques for Content Analysis
1 Brief Introduction of Machine Learning Techniques for Content Analysis Wei-Ta Chu 2008/11/20 Outline 2 Overview Gaussian Mixture Model (GMM) Hidden Markov Model (HMM) Support Vector Machine (SVM) Overview
More informationHidden Markov Models. AIMA Chapter 15, Sections 1 5. AIMA Chapter 15, Sections 1 5 1
Hidden Markov Models AIMA Chapter 15, Sections 1 5 AIMA Chapter 15, Sections 1 5 1 Consider a target tracking problem Time and uncertainty X t = set of unobservable state variables at time t e.g., Position
More informationHidden 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 informationPage 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 informationWe 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 informationCS532, Winter 2010 Hidden Markov Models
CS532, Winter 2010 Hidden Markov Models Dr. Alan Fern, afern@eecs.oregonstate.edu March 8, 2010 1 Hidden Markov Models The world is dynamic and evolves over time. An intelligent agent in such a world needs
More informationCISC 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 informationHidden 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 informationAdvanced Data Science
Advanced Data Science Dr. Kira Radinsky Slides Adapted from Tom M. Mitchell Agenda Topics Covered: Time series data Markov Models Hidden Markov Models Dynamic Bayes Nets Additional Reading: Bishop: Chapter
More informationParametric 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 informationCSE 473: Artificial Intelligence
CSE 473: Artificial Intelligence Hidden Markov Models Dieter Fox --- University of Washington [Most slides were created by Dan Klein and Pieter Abbeel for CS188 Intro to AI at UC Berkeley. All CS188 materials
More informationChapter 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 informationHidden Markov models 1
Hidden Markov models 1 Outline Time and uncertainty Markov process Hidden Markov models Inference: filtering, prediction, smoothing Most likely explanation: Viterbi 2 Time and uncertainty The world changes;
More informationMath 350: An exploration of HMMs through doodles.
Math 350: An exploration of HMMs through doodles. Joshua Little (407673) 19 December 2012 1 Background 1.1 Hidden Markov models. Markov chains (MCs) work well for modelling discrete-time processes, or
More informationA 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 informationNote 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 informationGraphical 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 informationSequence 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 informationCSEP 573: Artificial Intelligence
CSEP 573: Artificial Intelligence Hidden Markov Models Luke Zettlemoyer Many slides over the course adapted from either Dan Klein, Stuart Russell, Andrew Moore, Ali Farhadi, or Dan Weld 1 Outline Probabilistic
More informationCheng Soon Ong & Christian Walder. Canberra February June 2018
Cheng Soon Ong & Christian Walder Research Group and College of Engineering and Computer Science Canberra February June 2018 Outlines Overview Introduction Linear Algebra Probability Linear Regression
More informationHuman-Oriented Robotics. Temporal Reasoning. Kai Arras Social Robotics Lab, University of Freiburg
Temporal Reasoning Kai Arras, University of Freiburg 1 Temporal Reasoning Contents Introduction Temporal Reasoning Hidden Markov Models Linear Dynamical Systems (LDS) Kalman Filter 2 Temporal Reasoning
More informationA Higher-Order Interactive Hidden Markov Model and Its Applications Wai-Ki Ching Department of Mathematics The University of Hong Kong
A Higher-Order Interactive Hidden Markov Model and Its Applications Wai-Ki Ching Department of Mathematics The University of Hong Kong Abstract: In this talk, a higher-order Interactive Hidden Markov Model
More informationGraphical models for part of speech tagging
Indian Institute of Technology, Bombay and Research Division, India Research Lab Graphical models for part of speech tagging Different Models for POS tagging HMM Maximum Entropy Markov Models Conditional
More informationCS 343: Artificial Intelligence
CS 343: Artificial Intelligence Hidden Markov Models Prof. Scott Niekum The University of Texas at Austin [These slides based on those of Dan Klein and Pieter Abbeel for CS188 Intro to AI at UC Berkeley.
More informationBasic 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 informationCS 7180: Behavioral Modeling and Decision- making in AI
CS 7180: Behavioral Modeling and Decision- making in AI Learning Probabilistic Graphical Models Prof. Amy Sliva October 31, 2012 Hidden Markov model Stochastic system represented by three matrices N =
More informationHMM part 1. Dr Philip Jackson
Centre for Vision Speech & Signal Processing University of Surrey, Guildford GU2 7XH. HMM part 1 Dr Philip Jackson Probability fundamentals Markov models State topology diagrams Hidden Markov models -
More informationStatistical Processing of Natural Language
Statistical Processing of Natural Language and DMKM - Universitat Politècnica de Catalunya and 1 2 and 3 1. Observation Probability 2. Best State Sequence 3. Parameter Estimation 4 Graphical and Generative
More informationCS 7180: Behavioral Modeling and Decision- making in AI
CS 7180: Behavioral Modeling and Decision- making in AI Hidden Markov Models Prof. Amy Sliva October 26, 2012 Par?ally observable temporal domains POMDPs represented uncertainty about the state Belief
More informationMarkov Chains and Hidden Markov Models
Markov Chains and Hidden Markov Models CE417: Introduction to Artificial Intelligence Sharif University of Technology Spring 2018 Soleymani Slides are based on Klein and Abdeel, CS188, UC Berkeley. Reasoning
More informationLecture 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 informationMachine Learning & Data Mining Caltech CS/CNS/EE 155 Hidden Markov Models Last Updated: Feb 7th, 2017
1 Introduction Let x = (x 1,..., x M ) denote a sequence (e.g. a sequence of words), and let y = (y 1,..., y M ) denote a corresponding hidden sequence that we believe explains or influences x somehow
More informationMultiscale Systems Engineering Research Group
Hidden Markov Model Prof. Yan Wang Woodruff School of Mechanical Engineering Georgia Institute of echnology Atlanta, GA 30332, U.S.A. yan.wang@me.gatech.edu Learning Objectives o familiarize the hidden
More informationLecture 3: ASR: HMMs, Forward, Viterbi
Original slides by Dan Jurafsky CS 224S / LINGUIST 285 Spoken Language Processing Andrew Maas Stanford University Spring 2017 Lecture 3: ASR: HMMs, Forward, Viterbi Fun informative read on phonetics The
More informationHidden Markov Models. Hal Daumé III. Computer Science University of Maryland CS 421: Introduction to Artificial Intelligence 19 Apr 2012
Hidden Markov Models Hal Daumé III Computer Science University of Maryland me@hal3.name CS 421: Introduction to Artificial Intelligence 19 Apr 2012 Many slides courtesy of Dan Klein, Stuart Russell, or
More informationHidden 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 informationLEARNING DYNAMIC SYSTEMS: MARKOV MODELS
LEARNING DYNAMIC SYSTEMS: MARKOV MODELS Markov Process and Markov Chains Hidden Markov Models Kalman Filters Types of dynamic systems Problem of future state prediction Predictability Observability Easily
More information10. 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 informationAnnouncements. CS 188: Artificial Intelligence Fall Markov Models. Example: Markov Chain. Mini-Forward Algorithm. Example
CS 88: Artificial Intelligence Fall 29 Lecture 9: Hidden Markov Models /3/29 Announcements Written 3 is up! Due on /2 (i.e. under two weeks) Project 4 up very soon! Due on /9 (i.e. a little over two weeks)
More informationCS 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 informationHidden Markov Models. Vibhav Gogate The University of Texas at Dallas
Hidden Markov Models Vibhav Gogate The University of Texas at Dallas Intro to AI (CS 4365) Many slides over the course adapted from either Dan Klein, Luke Zettlemoyer, Stuart Russell or Andrew Moore 1
More informationHidden Markov Models NIKOLAY YAKOVETS
Hidden Markov Models NIKOLAY YAKOVETS A Markov System N states s 1,..,s N S 2 S 1 S 3 A Markov System N states s 1,..,s N S 2 S 1 S 3 modeling weather A Markov System state changes over time.. S 1 S 2
More informationorder 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 informationPart 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 informationCS 188: Artificial Intelligence Spring 2009
CS 188: Artificial Intelligence Spring 2009 Lecture 21: Hidden Markov Models 4/7/2009 John DeNero UC Berkeley Slides adapted from Dan Klein Announcements Written 3 deadline extended! Posted last Friday
More informationPlan for today. ! Part 1: (Hidden) Markov models. ! Part 2: String matching and read mapping
Plan for today! Part 1: (Hidden) Markov models! Part 2: String matching and read mapping! 2.1 Exact algorithms! 2.2 Heuristic methods for approximate search (Hidden) Markov models Why consider probabilistics
More informationHidden 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 informationApproximate Inference
Approximate Inference Simulation has a name: sampling Sampling is a hot topic in machine learning, and it s really simple Basic idea: Draw N samples from a sampling distribution S Compute an approximate
More informationLecture 9. Intro to Hidden Markov Models (finish up)
Lecture 9 Intro to Hidden Markov Models (finish up) Review Structure Number of states Q 1.. Q N M output symbols Parameters: Transition probability matrix a ij Emission probabilities b i (a), which is
More informationData Mining in Bioinformatics HMM
Data Mining in Bioinformatics HMM Microarray Problem: Major Objective n Major Objective: Discover a comprehensive theory of life s organization at the molecular level 2 1 Data Mining in Bioinformatics
More informationRobert Collins CSE586 CSE 586, Spring 2015 Computer Vision II
CSE 586, Spring 2015 Computer Vision II Hidden Markov Model and Kalman Filter Recall: Modeling Time Series State-Space Model: You have a Markov chain of latent (unobserved) states Each state generates
More informationRecall: Modeling Time Series. CSE 586, Spring 2015 Computer Vision II. Hidden Markov Model and Kalman Filter. Modeling Time Series
Recall: Modeling Time Series CSE 586, Spring 2015 Computer Vision II Hidden Markov Model and Kalman Filter State-Space Model: You have a Markov chain of latent (unobserved) states Each state generates
More informationCOMS 4771 Probabilistic Reasoning via Graphical Models. Nakul Verma
COMS 4771 Probabilistic Reasoning via Graphical Models Nakul Verma Last time Dimensionality Reduction Linear vs non-linear Dimensionality Reduction Principal Component Analysis (PCA) Non-linear methods
More informationCS 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 informationO 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 informationStatistical Methods for NLP
Statistical Methods for NLP Sequence Models Joakim Nivre Uppsala University Department of Linguistics and Philology joakim.nivre@lingfil.uu.se Statistical Methods for NLP 1(21) Introduction Structured
More informationHidden 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 informationVL Algorithmen und Datenstrukturen für Bioinformatik ( ) WS15/2016 Woche 16
VL Algorithmen und Datenstrukturen für Bioinformatik (19400001) WS15/2016 Woche 16 Tim Conrad AG Medical Bioinformatics Institut für Mathematik & Informatik, Freie Universität Berlin Based on slides by
More informationCS 188: Artificial Intelligence Spring Announcements
CS 188: Artificial Intelligence Spring 2011 Lecture 18: HMMs and Particle Filtering 4/4/2011 Pieter Abbeel --- UC Berkeley Many slides over this course adapted from Dan Klein, Stuart Russell, Andrew Moore
More informationThe main algorithms used in the seqhmm package
The main algorithms used in the seqhmm package Jouni Helske University of Jyväskylä, Finland May 9, 2018 1 Introduction This vignette contains the descriptions of the main algorithms used in the seqhmm
More informationCS 5522: Artificial Intelligence II
CS 5522: Artificial Intelligence II Hidden Markov Models Instructor: Wei Xu Ohio State University [These slides were adapted from CS188 Intro to AI at UC Berkeley.] Pacman Sonar (P4) [Demo: Pacman Sonar
More informationCS 5522: Artificial Intelligence II
CS 5522: Artificial Intelligence II Hidden Markov Models Instructor: Alan Ritter Ohio State University [These slides were adapted from CS188 Intro to AI at UC Berkeley. All materials available at http://ai.berkeley.edu.]
More informationCourse 495: Advanced Statistical Machine Learning/Pattern Recognition
Course 495: Advanced Statistical Machine Learning/Pattern Recognition Lecturer: Stefanos Zafeiriou Goal (Lectures): To present discrete and continuous valued probabilistic linear dynamical systems (HMMs
More informationHidden Markov Models. x 1 x 2 x 3 x N
Hidden Markov Models 1 1 1 1 K K K K x 1 x x 3 x N Example: The dishonest casino A casino has two dice: Fair die P(1) = P() = P(3) = P(4) = P(5) = P(6) = 1/6 Loaded die P(1) = P() = P(3) = P(4) = P(5)
More informationIntroduction to Artificial Intelligence (AI)
Introduction to Artificial Intelligence (AI) Computer Science cpsc502, Lecture 10 Oct, 13, 2011 CPSC 502, Lecture 10 Slide 1 Today Oct 13 Inference in HMMs More on Robot Localization CPSC 502, Lecture
More informationHidden 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 informationLinear 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 informationSpeech 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 informationHidden Markov Models (HMMs)
Hidden Markov Models (HMMs) Reading Assignments R. Duda, P. Hart, and D. Stork, Pattern Classification, John-Wiley, 2nd edition, 2001 (section 3.10, hard-copy). L. Rabiner, "A tutorial on HMMs and selected
More informationMarkov Chains and Hidden Markov Models. COMP 571 Luay Nakhleh, Rice University
Markov Chains and Hidden Markov Models COMP 571 Luay Nakhleh, Rice University Markov Chains and Hidden Markov Models Modeling the statistical properties of biological sequences and distinguishing regions
More informationMore on HMMs and other sequence models. Intro to NLP - ETHZ - 18/03/2013
More on HMMs and other sequence models Intro to NLP - ETHZ - 18/03/2013 Summary Parts of speech tagging HMMs: Unsupervised parameter estimation Forward Backward algorithm Bayesian variants Discriminative
More informationComputational 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 informationHMM: Parameter Estimation
I529: Machine Learning in Bioinformatics (Spring 2017) HMM: Parameter Estimation Yuzhen Ye School of Informatics and Computing Indiana University, Bloomington Spring 2017 Content Review HMM: three problems
More informationMarkov Models. CS 188: Artificial Intelligence Fall Example. Mini-Forward Algorithm. Stationary Distributions.
CS 88: Artificial Intelligence Fall 27 Lecture 2: HMMs /6/27 Markov Models A Markov model is a chain-structured BN Each node is identically distributed (stationarity) Value of X at a given time is called
More informationHidden Markov Models
Andrea Passerini passerini@disi.unitn.it Statistical relational learning The aim Modeling temporal sequences Model signals which vary over time (e.g. speech) Two alternatives: deterministic models directly
More informationData Analyzing and Daily Activity Learning with Hidden Markov Model
Data Analyzing and Daily Activity Learning with Hidden Markov Model GuoQing Yin and Dietmar Bruckner Institute of Computer Technology Vienna University of Technology, Austria, Europe {yin, bruckner}@ict.tuwien.ac.at
More informationA.I. in health informatics lecture 8 structured learning. kevin small & byron wallace
A.I. in health informatics lecture 8 structured learning kevin small & byron wallace today models for structured learning: HMMs and CRFs structured learning is particularly useful in biomedical applications:
More informationA 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 informationHidden Markov Models
Hidden Markov Models Dr Philip Jackson Centre for Vision, Speech & Signal Processing University of Surrey, UK 1 3 2 http://www.ee.surrey.ac.uk/personal/p.jackson/isspr/ Outline 1. Recognizing patterns
More informationBioinformatics Introduction to Hidden Markov Models Hidden Markov Models and Multiple Sequence Alignment
Bioinformatics Introduction to Hidden Markov Models Hidden Markov Models and Multiple Sequence Alignment Slides borrowed from Scott C. Schmidler (MIS graduated student) Outline! Probability Review! Markov
More informationAnnouncements. CS 188: Artificial Intelligence Fall VPI Example. VPI Properties. Reasoning over Time. Markov Models. Lecture 19: HMMs 11/4/2008
CS 88: Artificial Intelligence Fall 28 Lecture 9: HMMs /4/28 Announcements Midterm solutions up, submit regrade requests within a week Midterm course evaluation up on web, please fill out! Dan Klein UC
More informationCOMP90051 Statistical Machine Learning
COMP90051 Statistical Machine Learning Semester 2, 2017 Lecturer: Trevor Cohn 24. Hidden Markov Models & message passing Looking back Representation of joint distributions Conditional/marginal independence
More informationHidden 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