Hidden Markov Models
|
|
- Ashley Williamson
- 6 years ago
- Views:
Transcription
1 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 to calculate this probability for an HMM as well? We must add the probabilities for all possible paths = π P( x) P( x,π ) Bioinformática
2 Forward Algorithm Define f k,i (forward probability) ) as the probability of emitting the prefix x 1 x i and eventually reaching the state π i = k. k f k,i = P(x 1 x i,π i = k) The recurrence for the forward algorithm: f l,i+1 l,i+1 = e l (x i+1 ). Σ f k,i. a kl k Є Q Bioinformática - 55 Forward algorithm Initialization: f begin,0 = 1 f k,0 = 0 for k begin. For each i =0,...,L calculate: f l,i = e l (x i ) Σ k f k,i-1 a kl Termination P(x) ) = Σ k f k,l. a k,end Bioinformática
3 Forward-Backward Problem Given: a sequence of coin tosses generated by an HMM. Goal: find the probability that the dealer was using a biased coin at a particular time. Backward Algorithm However, forward probability is not the only factor affecting P(π i = k x). The sequence of transitions and emissions that the HMM undergoes between π i+1 and π n also affect P(π i = k x). forward x i backward 3
4 Backward Algorithm (cont d) Define backward probability b k,i as the probability of being in state π i = k and emitting the suffix x i+1 x n. The recurrence for the backward algorithm: b k,i (x i+1,i = Σ e l(x i+1 ). b l,i+1. a kl l Є Q Backward-Forward Algorithm The probability that the dealer used a biased coin at any moment i: P(x, π i = k) k f k (i). b k (i) P(π i = k x) ) = P(x) P(x) = P(x) is the sum of P(x, π i = k) over all k 4
5 HMM Parameter Estimation So far, we have assumed that the transition and emission probabilities are known. However, in most HMM applications, the probabilities are not known. It s s very hard to estimate the probabilities. HMM Parameter Estimation Problem Given HMM with states and alphabet (emission characters) Independent training sequences x 1, x m Find HMM parameters Θ (that is, a kl, e k (b)) that maximize P(x 1,, x m Θ) the joint probability of the training sequences. 5
6 Maximize the likelihood P(x 1,, x m Θ) as a function of Θ is called the likelihood of the model. The training sequences are assumed independent, therefore P(x 1,, x m Θ) = Π i P(x i Θ) The parameter estimation problem seeks Θ that realizes max P ( x i Θ) Θ i In practice the log likelihood is computed to avoid underflow errors Two situations Known paths for training sequences CpG islands marked on training sequences One evening the casino dealer allows us to see when he changes dice Unknown paths CpG islands are not marked Do not see when the casino dealer changes dice 6
7 Known paths A kl = # of times each k l is taken in the training sequences E k (b) = # of times b is emitted from state k in the training sequences Compute a kl and e k (b) as maximum likelihood estimators: a = A / A kl k kl e ( b) = E l' k kl' ( b)/ b' E ( b') k Pseudocounts Some state k may not appear in any of the training sequences. This means A kl = 0 for every state l and a kl cannot be computed with the given equation. To avoid this overfitting use predetermined pseudocounts r kl and r k (b). A kl = # of transitions k l + r kl E k (b) = # of emissions of b from k + r k (b) The pseudocounts reflect our prior biases about the probability values. 7
8 Unknown paths: Viterbi training Idea: use Viterbi decoding to compute the most probable path for training sequence x Start with some guess for initial parameters and compute π* the most probable path for x using initial parameters. Iterate until no change in π* : 1. Determine A kl and E k (b) as before 2. Compute new parameters a kl and e k (b) using the same formulas as before 3. Compute new π* for x and the current parameters Viterbi training analysis The algorithm converges precisely There are finitely many possible paths. New parameters are uniquely determined by the current π*. There may be several paths for x with the same probability, hence must compare the new π* with all previous paths having highest probability. Does not maximize the likelihood Π x P(x Θ) but the contribution to the likelihood of the most probable path Π x P(x Θ, π*) In general performs less well than Baum-Welch 8
9 Unknown paths: Baum-Welch Idea: 1. Guess initial values for parameters. art and experience, not science 2. Estimate new (better) values for parameters. how? 3. Repeat until stopping criteria is met. what criteria? Better values for parameters Would need the A kl and E k (b) values but cannot count (the path is unknown) and do not want to use a most probable path. For all states k,l, symbol b and training sequence x Compute A kl and E k (b) as expected values, given the current parameters 9
10 Notation For any sequence of characters x emitted along some unknown pathπ, denote by π i = k the assumption that the state at position i (in which x i is emitted) is k. Probabilistic setting for A k,l Given x 1,,x m consider a discrete probability space with elementary events ε k,l, = k l is taken in x 1,, x m For each x in {x 1,,x m } and each position i in x let Y x,i be a random variable defined by Y x, i ( ε k, l 1, if π i = k and π i + 1 = l ) = 0, otherwise Define Y = Σ x Σ i Y x,i random var that counts # of times the event ε k,l happens in x 1,,x m. 10
11 The meaning of A kl Let A kl be the expectation of Y E(Y) = Σ x Σ i E(Y x,i ) = Σ x Σ i P(Y x,i = 1) = Σ x Σ i P({ε k,l π i = k and π i+1 = l}) = Σ x Σ i P(π i = k, π i+1 = l x) Need to compute P(π i = k, π i+1 = l x) Probabilistic setting for E k (b) Given x 1,,x m consider a discrete probability space with elementary events ε k,b = b is emitted in state k in x 1,,x m For each x in {x 1,,x m } and each position i in x let Y x,i be a random variable defined by Y x, i( εk, b 1, if xi = b and πi = k ) = 0, otherwise Define Y = Σ x Σ i Y x,i random var that counts # of times the event ε k,b happens in x 1,,x m. 11
12 The meaning of E k (b) Let E k (b) be the expectation of Y E(Y) = Σ x Σ i E(Y x,i ) = Σ x Σ i P(Y x,i = 1) = Σ x Σ i P({ε k,b x i = b and π i = k}) x { i x = b} i Need to compute P(π i = k x) P({ ε π k, b xi = b, π i = k}) = P( i = k x) x { i x = b} i Computing new parameters Consider x = x 1 x n training sequence Concentrate on positions i and i+1 Use the forward-backward values: f ki = P(x 1 x i, π i = k) b ki = P(x i+1 x n π i = k) 12
13 Compute A kl (1) Prob k l is taken at position i of x P(π i = k, π i+1 = l x 1 x n ) = P(x, π i = k, π i+1 = l) / P(x) Compute P(x) using either forward or backward values We ll show that P(x, π i = k, π i+1 = l) = b li+1 e l (x i+1 ) a kl f ki Expected # times k l is used in training sequences A kl = Σ x Σ i (b li+1 e l (x i+1 ) a kl f ki ) / P(x) Compute A kl (2) P(x, π i = k, π i+1 = l) = P(x 1 x i, π i = k, π i+1 = l, x i+1 x n ) = P(π i+1 = l, x i+1 x n x 1 x i, π i = k) P(x 1 x i,π i =k)= P(π i+1 = l, x i+1 x n π i = k) f ki = P(x i+1 x n π i = k, π i+1 = l) P(π i+1 = l π i = k) f ki = P(x i+1 x n π i+1 = l) a kl f ki = P(x i+2 x n x i+1, π i+1 = l) P(x i+1 π i+1 = l) a kl f ki = P(x i+2 x n π i+1 = l) e l (x i+1 ) a kl f ki = b li+1 e l (x i+1 ) a kl f ki 13
14 Compute E k (b) Prob x i of x is emitted in state k P(π i = k x 1 x n ) = P(π i = k, x 1 x n )/P(x) P(π i = k, x 1 x n ) = P(x 1 x i,π i = k,x i+1 x n ) = P(x i+1 x n x 1 x i,π i = k) P(x 1 x i,π i = k) = P(x i+1 x n π i = k) f ki = b ki f ki Expected # times b is emitted in state k E k ( b) = ( fki bki ) x i: x = b i P( x) a e kl = ( b) Finally, new parameters A kl = / E l' A kl' ( b)/ E k k k b' Can add pseudocounts as before. ( b' ) 14
15 Stopping criteria Cannot actually reach maximum (optimization of continuous functions) Therefore need stopping criteria Compute the log likelihood of the model for current Θ Compare with previous log likelihood Stop if small difference Stop after a certain number of iterations x log P ( x Θ ) The Baum-Welch algorithm Initialization: Pick the best-guess for model parameters (or arbitrary) Iteration: 1. Forward for each x 2. Backward for each x 3. Calculate A kl, E k (b) 4. Calculate new a kl, e k (b) 5. Calculate new log-likelihood Until log-likelihood does not change much 15
16 Baum-Welch analysis Log-likelihood is increased by iterations Baum-Welch is a particular case of the EM (expectation maximization) algorithm Convergence to local maximum. Choice of initial parameters determines local maximum to which the algorithm converges Finding Distant Members of a Protein Family A distant cousin of functionally related sequences in a protein family may have weak pairwise similarities with each member of the family and thus fail significance test. However, they may have weak similarities with many members of the family. The goal is to align a sequence to all members of the family at once. Family of related proteins can be represented by their multiple alignment and the corresponding profile. 16
17 Profile Representation of Protein Families Aligned DNA sequences can be represented by a 4 n profile matrix reflecting the frequencies of nucleotides in every aligned position. Protein family can be represented by a 20 n profile representing frequencies of amino acids. Profiles and HMMs HMMs can also be used for aligning a sequence against a profile representing protein family. A 20 n profile P corresponds to n sequentially linked match states M 1,,M n in the profile HMM of P. 17
18 Multiple Alignments and Protein Family Classification Multiple alignment of a protein family shows variations in conservation along the length of a protein Example: after aligning many globin proteins, the biologists recognized that the helices region in globins are more conserved than others. What are Profile HMMs? A Profile HMM is a probabilistic representation of a multiple alignment. A given multiple alignment (of a protein family) is used to build a profile HMM. This model then may be used to find and score less obvious potential matches of new protein sequences. 18
19 Profile HMMs D D D D I I I I I Start M 1 M 2 M 3 M 4 End I Match: Insert: a Delete: conserved an insertion a deletion, position with a general with silent state specialized (background) without emission any emission probability probability L M W K E ILMWKE ILWK Profile HMM A profile HMM 19
20 Building a profile HMM Multiple alignment is used to construct the HMM model. Assign each column to a Match state in HMM. Add Insertion and Deletion state. Estimate the emission probabilities according to amino acid counts in column. Different positions in the protein will have different emission probabilities. Estimate the transition probabilities between Match, Deletion and Insertion states The HMM model gets trained to derive the optimal parameters. States of Profile HMM Match states Insertion states Insertion states I 0 I 1 I n Deletion states Deletion states D 1 D n M 1 M n (plus begin/end states) 20
21 Transition Probabilities in Profile HMM log(a MI )+log(a IM ) = gap initiation penalty log(a II ) = gap extension penalty Emission Probabilities in Profile HMM Probabilty of emitting a symbol a at an insertion state I j : e Ij (a) = p(a) where p(a) is the frequency of the occurrence of the symbol a in all the sequences. 21
22 Profile HMM Alignment Define v M j (i) as the logarithmic likelihood score of the best path for matching x 1..x i to profile HMM ending with x i emitted by the state M j. v I j (i) and v D j (i) are defined similarly. Profile HMM Alignment: Dynamic Programming v M j(i) = log (e( M j (x i)/p( v M j-1(i-1) + log(a M j-1, 1,Mj ) )) + max v I j-1(i-1) + log(a I j-1,m j ) v D j-1(i-1) + log(a D j-1,m j ) )/p(x i )) + max v I j(i) = log (e( I j (x i)/p( v M j(i-1) + log(a M j, I j ) )) + max v I j(i-1) + log(a I j, I j ) v D j(i-1) + log(a D j, I j ) )/p(x i )) + max 22
23 Paths in Edit Graph and Profile HMM A path through an edit graph and the corresponding path through a profile HMM 23
Hidden Markov Models
Hidden Markov Models Outline CG-islands The Fair Bet Casino Hidden Markov Model Decoding Algorithm Forward-Backward Algorithm Profile HMMs HMM Parameter Estimation Viterbi training Baum-Welch algorithm
More informationHidden Markov Models. Three classic HMM problems
An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Hidden Markov Models Slides revised and adapted to Computational Biology IST 2015/2016 Ana Teresa Freitas Three classic HMM problems
More informationAn Introduction to Bioinformatics Algorithms Hidden Markov Models
Hidden Markov Models Outline 1. CG-Islands 2. The Fair Bet Casino 3. Hidden Markov Model 4. Decoding Algorithm 5. Forward-Backward Algorithm 6. Profile HMMs 7. HMM Parameter Estimation 8. Viterbi Training
More informationHidden Markov Models
Hidden Markov Models Outline 1. CG-Islands 2. The Fair Bet Casino 3. Hidden Markov Model 4. Decoding Algorithm 5. Forward-Backward Algorithm 6. Profile HMMs 7. HMM Parameter Estimation 8. Viterbi Training
More informationHidden Markov Models. Ivan Gesteira Costa Filho IZKF Research Group Bioinformatics RWTH Aachen Adapted from:
Hidden Markov Models Ivan Gesteira Costa Filho IZKF Research Group Bioinformatics RWTH Aachen Adapted from: www.ioalgorithms.info Outline CG-islands The Fair Bet Casino Hidden Markov Model Decoding Algorithm
More information11.3 Decoding Algorithm
11.3 Decoding Algorithm 393 For convenience, we have introduced π 0 and π n+1 as the fictitious initial and terminal states begin and end. This model defines the probability P(x π) for a given sequence
More informationHIDDEN MARKOV MODELS
HIDDEN MARKOV MODELS Outline CG-islands The Fair Bet Casino Hidden Markov Model Decoding Algorithm Forward-Backward Algorithm Profile HMMs HMM Parameter Estimation Viterbi training Baum-Welch algorithm
More informationAn Introduction to Bioinformatics Algorithms Hidden Markov Models
Hidden Markov Models Hidden Markov Models Outline CG-islands The Fair Bet Casino Hidden Markov Model Decoding Algorithm Forward-Backward Algorithm Profile HMMs HMM Parameter Estimation Viterbi training
More informationHidden Markov Models
Hidden Markov Models Slides revised and adapted to Bioinformática 55 Engª Biomédica/IST 2005 Ana Teresa Freitas CG-Islands Given 4 nucleotides: probability of occurrence is ~ 1/4. Thus, probability of
More informationHidden 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 Viterbi, Forward, Backward VITERBI FORWARD BACKWARD Initialization: V 0 (0) = 1 V k (0) = 0, for all k > 0 Initialization: f 0 (0) = 1 f k (0)
More informationCSCE 471/871 Lecture 3: Markov Chains and
and and 1 / 26 sscott@cse.unl.edu 2 / 26 Outline and chains models (s) Formal definition Finding most probable state path (Viterbi algorithm) Forward and backward algorithms State sequence known State
More informationStephen Scott.
1 / 27 sscott@cse.unl.edu 2 / 27 Useful for modeling/making predictions on sequential data E.g., biological sequences, text, series of sounds/spoken words Will return to graphical models that are generative
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 informationHidden 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 informationHidden Markov Models for biological sequence analysis
Hidden Markov Models for biological sequence analysis Master in Bioinformatics UPF 2017-2018 http://comprna.upf.edu/courses/master_agb/ Eduardo Eyras Computational Genomics Pompeu Fabra University - ICREA
More informationHidden 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 informationExample: The Dishonest Casino. Hidden Markov Models. Question # 1 Evaluation. The dishonest casino model. Question # 3 Learning. Question # 2 Decoding
Example: The Dishonest Casino Hidden Markov Models Durbin and Eddy, chapter 3 Game:. You bet $. You roll 3. Casino player rolls 4. Highest number wins $ The casino has two dice: Fair die P() = P() = P(3)
More informationCSCE 478/878 Lecture 9: Hidden. Markov. Models. Stephen Scott. Introduction. Outline. Markov. Chains. Hidden Markov Models. CSCE 478/878 Lecture 9:
Useful for modeling/making predictions on sequential data E.g., biological sequences, text, series of sounds/spoken words Will return to graphical models that are generative sscott@cse.unl.edu 1 / 27 2
More informationHidden Markov Models for biological sequence analysis I
Hidden Markov Models for biological sequence analysis I Master in Bioinformatics UPF 2014-2015 Eduardo Eyras Computational Genomics Pompeu Fabra University - ICREA Barcelona, Spain Example: CpG Islands
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 informationStephen Scott.
1 / 21 sscott@cse.unl.edu 2 / 21 Introduction Designed to model (profile) a multiple alignment of a protein family (e.g., Fig. 5.1) Gives a probabilistic model of the proteins in the family Useful for
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 informationHidden Markov Models. Hosein Mohimani GHC7717
Hidden Markov Models Hosein Mohimani GHC7717 hoseinm@andrew.cmu.edu Fair et Casino Problem Dealer flips a coin and player bets on outcome Dealer use either a fair coin (head and tail equally likely) or
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 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 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 informationGrundlagen der Bioinformatik, SS 09, D. Huson, June 16, S. Durbin, S. Eddy, A. Krogh and G. Mitchison, Biological Sequence
rundlagen der Bioinformatik, SS 09,. Huson, June 16, 2009 81 7 Markov chains and Hidden Markov Models We will discuss: Markov chains Hidden Markov Models (HMMs) Profile HMMs his chapter is based on: nalysis,
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 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 informationEECS730: Introduction to Bioinformatics
EECS730: Introduction to Bioinformatics Lecture 07: profile Hidden Markov Model http://bibiserv.techfak.uni-bielefeld.de/sadr2/databasesearch/hmmer/profilehmm.gif Slides adapted from Dr. Shaojie Zhang
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 informationPairwise alignment using HMMs
Pairwise alignment using HMMs The states of an HMM fulfill the Markov property: probability of transition depends only on the last state. CpG islands and casino example: HMMs emit sequence of symbols (nucleotides
More informationGrundlagen der Bioinformatik, SS 08, D. Huson, June 16, S. Durbin, S. Eddy, A. Krogh and G. Mitchison, Biological Sequence
rundlagen der Bioinformatik, SS 08,. Huson, June 16, 2008 89 8 Markov chains and Hidden Markov Models We will discuss: Markov chains Hidden Markov Models (HMMs) Profile HMMs his chapter is based on: nalysis,
More informationHidden Markov Models (I)
GLOBEX Bioinformatics (Summer 2015) Hidden Markov Models (I) a. The model b. The decoding: Viterbi algorithm Hidden Markov models A Markov chain of states At each state, there are a set of possible observables
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 informationToday 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 informationHMMs and biological sequence analysis
HMMs and biological sequence analysis Hidden Markov Model A Markov chain is a sequence of random variables X 1, X 2, X 3,... That has the property that the value of the current state depends only on the
More informationLecture 7 Sequence analysis. Hidden Markov Models
Lecture 7 Sequence analysis. Hidden Markov Models Nicolas Lartillot may 2012 Nicolas Lartillot (Universite de Montréal) BIN6009 may 2012 1 / 60 1 Motivation 2 Examples of Hidden Markov models 3 Hidden
More informationLecture 5: December 13, 2001
Algorithms for Molecular Biology Fall Semester, 2001 Lecture 5: December 13, 2001 Lecturer: Ron Shamir Scribe: Roi Yehoshua and Oren Danewitz 1 5.1 Hidden Markov Models 5.1.1 Preface: CpG islands CpG is
More informationHidden Markov Models. based on chapters from the book Durbin, Eddy, Krogh and Mitchison Biological Sequence Analysis via Shamir s lecture notes
Hidden Markov Models based on chapters from the book Durbin, Eddy, Krogh and Mitchison Biological Sequence Analysis via Shamir s lecture notes music recognition deal with variations in - actual sound -
More informationHidden Markov Models 1
Hidden Markov Models Dinucleotide Frequency Consider all 2-mers in a sequence {AA,AC,AG,AT,CA,CC,CG,CT,GA,GC,GG,GT,TA,TC,TG,TT} Given 4 nucleotides: each with a probability of occurrence of. 4 Thus, one
More information6.047/6.878/HST.507 Computational Biology: Genomes, Networks, Evolution. Lecture 05. Hidden Markov Models Part II
6.047/6.878/HST.507 Computational Biology: Genomes, Networks, Evolution Lecture 05 Hidden Markov Models Part II 1 2 Module 1: Aligning and modeling genomes Module 1: Computational foundations Dynamic programming:
More informationMarkov Chains and Hidden Markov Models. = stochastic, generative models
Markov Chains and Hidden Markov Models = stochastic, generative models (Drawing heavily from Durbin et al., Biological Sequence Analysis) BCH339N Systems Biology / Bioinformatics Spring 2016 Edward Marcotte,
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 informationHMM applications. Applications of HMMs. Gene finding with HMMs. Using the gene finder
HMM applications Applications of HMMs Gene finding Pairwise alignment (pair HMMs) Characterizing protein families (profile HMMs) Predicting membrane proteins, and membrane protein topology Gene finding
More informationGiri Narasimhan. CAP 5510: Introduction to Bioinformatics. ECS 254; Phone: x3748
CAP 5510: Introduction to Bioinformatics Giri Narasimhan ECS 254; Phone: x3748 giri@cis.fiu.edu www.cis.fiu.edu/~giri/teach/bioinfs07.html 2/14/07 CAP5510 1 CpG Islands Regions in DNA sequences with increased
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 informationIntroduction to Hidden Markov Models for Gene Prediction ECE-S690
Introduction to Hidden Markov Models for Gene Prediction ECE-S690 Outline Markov Models The Hidden Part How can we use this for gene prediction? Learning Models Want to recognize patterns (e.g. sequence
More informationBioinformatics: Biology X
Bud Mishra Room 1002, 715 Broadway, Courant Institute, NYU, New York, USA Model Building/Checking, Reverse Engineering, Causality Outline 1 Where (or of what) one cannot speak, one must pass over in silence.
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 informationMultiple Sequence Alignment using Profile HMM
Multiple Sequence Alignment using Profile HMM. based on Chapter 5 and Section 6.5 from Biological Sequence Analysis by R. Durbin et al., 1998 Acknowledgements: M.Sc. students Beatrice Miron, Oana Răţoi,
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 informationComputational Biology Lecture #3: Probability and Statistics. Bud Mishra Professor of Computer Science, Mathematics, & Cell Biology Sept
Computational Biology Lecture #3: Probability and Statistics Bud Mishra Professor of Computer Science, Mathematics, & Cell Biology Sept 26 2005 L2-1 Basic Probabilities L2-2 1 Random Variables L2-3 Examples
More informationStatistical 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 informationHidden Markov Models. music recognition. deal with variations in - pitch - timing - timbre 2
Hidden Markov Models based on chapters from the book Durbin, Eddy, Krogh and Mitchison Biological Sequence Analysis Shamir s lecture notes and Rabiner s tutorial on HMM 1 music recognition deal with variations
More informationPair Hidden Markov Models
Pair Hidden Markov Models Scribe: Rishi Bedi Lecturer: Serafim Batzoglou January 29, 2015 1 Recap of HMMs alphabet: Σ = {b 1,...b M } set of states: Q = {1,..., K} transition probabilities: A = [a ij ]
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 informationCAP 5510: Introduction to Bioinformatics CGS 5166: Bioinformatics Tools. Giri Narasimhan
CAP 5510: Introduction to Bioinformatics CGS 5166: Bioinformatics Tools Giri Narasimhan ECS 254; Phone: x3748 giri@cis.fiu.edu www.cis.fiu.edu/~giri/teach/bioinfs15.html Describing & Modeling Patterns
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 informationComparative Gene Finding. BMI/CS 776 Spring 2015 Colin Dewey
Comparative Gene Finding BMI/CS 776 www.biostat.wisc.edu/bmi776/ Spring 2015 Colin Dewey cdewey@biostat.wisc.edu Goals for Lecture the key concepts to understand are the following: using related genomes
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 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 information6 Markov Chains and Hidden Markov Models
6 Markov Chains and Hidden Markov Models (This chapter 1 is primarily based on Durbin et al., chapter 3, [DEKM98] and the overview article by Rabiner [Rab89] on HMMs.) Why probabilistic models? In problems
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 information6.864: 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 informationHidden Markov Models. Ron Shamir, CG 08
Hidden Markov Models 1 Dr Richard Durbin is a graduate in mathematics from Cambridge University and one of the founder members of the Sanger Institute. He has also held carried out research at the Laboratory
More informationR. Durbin, S. Eddy, A. Krogh, G. Mitchison: Biological sequence analysis. Cambridge University Press, ISBN (Chapter 3)
9 Markov chains and Hidden Markov Models We will discuss: Markov chains Hidden Markov Models (HMMs) lgorithms: Viterbi, forward, backward, posterior decoding Profile HMMs Baum-Welch algorithm This chapter
More informationMarkov chains and Hidden Markov Models
Discrete Math for Bioinformatics WS 10/11:, b A. Bockmar/K. Reinert, 7. November 2011, 10:24 2001 Markov chains and Hidden Markov Models We will discuss: Hidden Markov Models (HMMs) Algorithms: Viterbi,
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 informationStatistical Machine Learning Methods for Bioinformatics II. Hidden Markov Model for Biological Sequences
Statistical Machine Learning Methods for Bioinformatics II. Hidden Markov Model for Biological Sequences Jianlin Cheng, PhD Department of Computer Science University of Missouri 2008 Free for Academic
More informationDynamic Approaches: The Hidden Markov Model
Dynamic Approaches: The Hidden Markov Model Davide Bacciu Dipartimento di Informatica Università di Pisa bacciu@di.unipi.it Machine Learning: Neural Networks and Advanced Models (AA2) Inference as Message
More informationROBI POLIKAR. ECE 402/504 Lecture Hidden Markov Models IGNAL PROCESSING & PATTERN RECOGNITION ROWAN UNIVERSITY
BIOINFORMATICS Lecture 11-12 Hidden Markov Models ROBI POLIKAR 2011, All Rights Reserved, Robi Polikar. IGNAL PROCESSING & PATTERN RECOGNITION LABORATORY @ ROWAN UNIVERSITY These lecture notes are prepared
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 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 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 informationComputational Genomics and Molecular Biology, Fall
Computational Genomics and Molecular Biology, Fall 2014 1 HMM Lecture Notes Dannie Durand and Rose Hoberman November 6th Introduction In the last few lectures, we have focused on three problems related
More informationWhat s an HMM? Extraction with Finite State Machines e.g. Hidden Markov Models (HMMs) Hidden Markov Models (HMMs) for Information Extraction
Hidden Markov Models (HMMs) for Information Extraction Daniel S. Weld CSE 454 Extraction with Finite State Machines e.g. Hidden Markov Models (HMMs) standard sequence model in genomics, speech, NLP, What
More informationSequences and Information
Sequences and Information Rahul Siddharthan The Institute of Mathematical Sciences, Chennai, India http://www.imsc.res.in/ rsidd/ Facets 16, 04/07/2016 This box says something By looking at the symbols
More informationCS711008Z Algorithm Design and Analysis
.. Lecture 6. Hidden Markov model and Viterbi s decoding algorithm Institute of Computing Technology Chinese Academy of Sciences, Beijing, China . Outline The occasionally dishonest casino: an example
More informationList of Code Challenges. About the Textbook Meet the Authors... xix Meet the Development Team... xx Acknowledgments... xxi
Contents List of Code Challenges xvii About the Textbook xix Meet the Authors................................... xix Meet the Development Team............................ xx Acknowledgments..................................
More informationp(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 informationChapter 4: Hidden Markov Models
Chapter 4: Hidden Markov Models 4.1 Introduction to HMM Prof. Yechiam Yemini (YY) Computer Science Department Columbia University Overview Markov models of sequence structures Introduction to Hidden Markov
More informationHidden 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 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 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 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 informationStatistical Machine Learning from Data
Samy Bengio Statistical Machine Learning from Data Statistical Machine Learning from Data Samy Bengio IDIAP Research Institute, Martigny, Switzerland, and Ecole Polytechnique Fédérale de Lausanne (EPFL),
More informationCS1820 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 informationBio nformatics. Lecture 3. Saad Mneimneh
Bio nformatics Lecture 3 Sequencing As before, DNA is cut into small ( 0.4KB) fragments and a clone library is formed. Biological experiments allow to read a certain number of these short fragments per
More informationGenome 373: Hidden Markov Models II. Doug Fowler
Genome 373: Hidden Markov Models II Doug Fowler Review From Hidden Markov Models I What does a Markov model describe? Review From Hidden Markov Models I A T A Markov model describes a random process of
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 informationDesign and Implementation of Speech Recognition Systems
Design and Implementation of Speech Recognition Systems Spring 2013 Class 7: Templates to HMMs 13 Feb 2013 1 Recap Thus far, we have looked at dynamic programming for string matching, And derived DTW from
More informationStatistical 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 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 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 informationHidden Markov Models. Terminology, Representation and Basic Problems
Hidden Markov Models Terminology, Representation and Basic Problems Data analysis? Machine learning? In bioinformatics, we analyze a lot of (sequential) data (biological sequences) to learn unknown parameters
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 informationHidden Markov Models (HMMs) and Profiles
Hidden Markov Models (HMMs) and Profiles Swiss Institute of Bioinformatics (SIB) 26-30 November 2001 Markov Chain Models A Markov Chain Model is a succession of states S i (i = 0, 1,...) connected by transitions.
More informationMACHINE LEARNING 2 UGM,HMMS Lecture 7
LOREM I P S U M Royal Institute of Technology MACHINE LEARNING 2 UGM,HMMS Lecture 7 THIS LECTURE DGM semantics UGM De-noising HMMs Applications (interesting probabilities) DP for generation probability
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 information