Hidden Markov Models. x 1 x 2 x 3 x N
|
|
- Vanessa Turner
- 6 years ago
- Views:
Transcription
1 Hidden Markov Models K K K K x 1 x x 3 x N
2 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) = 1/10 P(6) = 1/ Casino player switches between fair and loaded die with probability 1/0 at each turn Game: 1. You bet $1. You roll (always with a fair die) 3. Casino player rolls (maybe with fair die, maybe with loaded die) 4. Highest number wins $
3 Question # 1 Evaluation GIVEN A sequence of rolls by the casino player QUESTION Prob = 1.3 x How likely is this sequence, given our model of how the casino works? This is the EVALUATION problem in HMMs
4 Question # Decoding GIVEN A sequence of rolls by the casino player FAIR LOADED FAIR QUESTION What portion of the sequence was generated with the fair die, and what portion with the loaded die? This is the DECODING question in HMMs
5 Question # 3 Learning GIVEN A sequence of rolls by the casino player QUESTION Prob(6) = 64% How loaded is the loaded die? How fair is the fair die? How often does the casino player change from fair to loaded, and back? This is the LEARNING question in HMMs
6 The dishonest casino model P(1 F) = 1/6 P( F) = 1/6 P(3 F) = 1/6 P(4 F) = 1/6 P(5 F) = 1/6 P(6 F) = 1/6 FAIR 0.05 LOADED A Hidden Markov Model: we never observe the state, only observe output dependent (probabilistically) on state P(1 L) = 1/10 P( L) = 1/10 P(3 L) = 1/10 P(4 L) = 1/10 P(5 L) = 1/10 P(6 L) = 1/
7 A parse of a sequence Observation sequence x = x 1 x N, State sequence = 1,, N 1 K 1 K 1 K 1 K x 1 x x 3 x N 1 K
8 An HMM is memoryless At each time step t, the only thing that affects future states is the current state t 1 P( t+1 = k whatever happened so far ) = P( t+1 = k 1,,, t, x 1, x,, x t ) = P( t+1 = k t ) K
9 An HMM is memoryless At each time step t, the only thing that affects x t is the current state t P(x t = b whatever happened so far ) = P(x t = b 1,,, t, x 1, x,, x t-1 ) = P(x t = b t ) 1 K
10 Definition of a hidden Markov model Definition: A hidden Markov model (HMM) Alphabet = { b 1, b,, b M } = Val(x t ) Set of states Q = { 1,..., K }.= Val( t ) Transition probabilities between any two states a ij = transition prob from state i to state j a i1 + + a ik = 1, for all states i = 1K 1 Start probabilities a 0i a a 0K = 1 Emission probabilities within each state e k (b) = P( x t = b t = k) e k (b 1 ) + + e k (b M ) = 1, for all states k = 1K K
11 Hidden Markov Models as Bayes Nets i i+1 i+ i+3 States unobserved x i x i+1 x i+ x i+3 Observations Transition probabilities between any two states a jk = transition prob from state j to state k = P( i+1 = k i = j) Emission probabilities within each state e k (b) = P( x i = b i = k)
12 How special of a case are HMM BNs? Template-based representation All hidden nodes have same CPTs, as do all output nodes Limited connectivity Junction tree has clique nodes of size <= Special-purpose algorithms are simple and efficient
13 HMMs are good for Speech Recognition Gene Sequence Matching Text Processing Part of speech tagging Information extraction Handwriting recognition
14 Generating a sequence by the model Given a HMM, we can generate a sequence of length n as follows: 1. Start at state 1 according to prob a 0 1. Emit letter x 1 according to prob e 1 (x 1 ) 3. Go to state according to prob a 1 4. until emitting x n 1 K 1 K 1 What did we call this earlier, for general Bayes Nets? 0 a 0 e (x 1 ) K 1 x 1 x x 3 x n K
15 A parse of a sequence Given a sequence x = x 1 x N, A parse of x is a sequence of states = 1,, N 1 K 1 K 1 K 1 K x 1 x x 3 x N 1 K
16 Likelihood of a parse Given a sequence x = x 1 x N and a parse = 1,, N, K K K K To find how likely this scenario is: (given our HMM) x 1 x x 3 x K P(x, ) = P(x 1,, x N, 1,, N ) = P(x N N ) P( N N-1 ) P(x ) P( 1 ) P(x 1 1 ) P( 1 ) = a 0 1 a 1 a N-1 N e 1 (x 1 )e N (x N )
17 Example: the dishonest casino Let the sequence of rolls be: x = 1,, 1, 5, 6,, 1, 5,, 4 Then, what is the likelihood of = Fair, Fair, Fair, Fair, Fair, Fair, Fair, Fair, Fair, Fair? (say initial probs a 0Fair = ½, a 0Loaded = ½) ½ P(1 Fair) P(Fair Fair) P( Fair) P(Fair Fair) P(4 Fair) = ½ (1/6) 10 (0.95) 9 = ~=
18 Example: the dishonest casino So, the likelihood the die is fair in this run is just What is the likelihood of = Loaded, Loaded, Loaded, Loaded, Loaded, Loaded, Loaded, Loaded, Loaded, Loaded? ½ P(1 Loaded) P(Loaded, Loaded) P(4 Loaded) = ½ (1/10) 9 (1/) 1 (0.95) 9 = ~= Therefore, it s somewhat more likely that all the rolls are done with the fair die, than that they are all done with the loaded die
19 Example: the dishonest casino Let the sequence of rolls be: x = 1, 6, 6, 5, 6,, 6, 6, 3, 6 Now, what is the likelihood = F, F,, F? ½ (1/6) 10 (0.95) 9 ~= , same as before What is the likelihood = L, L,, L? ½ (1/10) 4 (1/) 6 (0.95) 9 = ~= So, it is 100 times more likely the die is loaded
20 The three main questions for HMMs 1. Evaluation GIVEN a HMM M, and a sequence x, FIND Prob[ x M ]. Decoding GIVEN a HMM M, and a sequence x, FIND the sequence of states that maximizes P[ x, M ] 3. Learning GIVEN a HMM M, with unspecified transition/emission probs., and a sequence x, FIND parameters = (e i (.), a ij ) that maximize P[ x ]
21 Problem 1: Evaluation Compute the likelihood that a sequence is generated by the model
22 Generating a sequence by the model Given a HMM, we can generate a sequence of length n as follows: 1. Start at state 1 according to prob a 0 1. Emit letter x 1 according to prob e 1 (x 1 ) 3. Go to state according to prob a 1 4. until emitting x n a 0 K K K K e (x 1 ) x 1 x x 3 x n
23 Evaluation We will develop algorithms that allow us to compute: P(x) Probability of x given the model P(x i x j ) Probability of a substring of x given the model P( i = k x) Posterior probability that the i th state is k, given x
24 The Forward Algorithm We want to calculate P(x) = probability of x, given the HMM Sum over all possible ways of generating x: P(x) = P(x, ) = P(x ) P( ) To avoid summing over exponentially many paths, use variable elimination. In HMMs, VE has same form at each i. Define: f k (i) = P(x 1 x i, i = k) (the forward probability) generate i first observations and end up in state k
25 The Forward Algorithm derivation Define the forward probability: f k (i) = P(x 1 x i, i = k) = 1 i-1 P(x 1 x i-1, 1,, i-1, i = k) e k (x i ) = j 1 i- P(x 1 x i-1, 1,, i-, i-1 = j) a jk e k (x i ) = j P(x 1 x i-1, i-1 = j) a jk e k (x i ) = e k (x i ) j f j (i 1) a jk
26 The Forward Algorithm We can compute f k (i) for all k, i, using dynamic programming! Initialization: f 0 (0) = 1 f k (0) = 0, for all k > 0 Iteration: f k (i) = e k (x i ) j f j (i 1) a jk Termination: P(x) = k f k (N)
27 Backward Algorithm Forward algorithm can compute P(x). But we d also like: P( i = k x), the probability distribution on the i th position, given x Again, we ll use variable elimination. We start by computing: P( i = k, x) = P(x 1 x i, i = k, x i+1 x N ) = P(x 1 x i, i = k) P(x i+1 x N x 1 x i, i = k) = P(x 1 x i, i = k) P(x i+1 x N i = k) Forward, f k (i) Backward, b k (i) Then, P( i = k x) = P( i = k, x) / P(x)
28 The Backward Algorithm derivation Define the backward probability: b k (i) = P(x i+1 x N i = k) starting from i th state = k, generate rest of x = i+1 N P(x i+1,x i+,, x N, i+1,, N i = k) = j i+ N P(x i+1,x i+,, x N, i+1 = j, i+,, N i = k) = j e j (x i+1 ) a kj i+ N P(x i+,, x N, i+,, N i+1 = j) = j e l (x i+1 ) a kj b j (i+1)
29 The Backward Algorithm We can compute b k (i) for all k, i, using dynamic programming Initialization: b k (N) = 1, for all k Iteration: b k (i) = l e l (x i+1 ) a kl b l (i+1) Termination: P(x) = l a 0l e l (x 1 ) b l (1)
30 Computational Complexity What is the running time, and space required, for Forward and Backward? Time: O(K N) Space: O(KN) Useful implementation technique to avoid underflows: rescaling at each few positions by multiplying by a constant Assuming we want to save all forward, backward messages. Otherwise space can be O(K)
31 Posterior Decoding We can now calculate f k (i) b k (i) P( i = k x) = P(x) Then, we can ask P( i = k x) = P( i = k, x)/p(x) = P(x 1,, x i, i = k, x i+1, x n ) / P(x) = P(x 1,, x i, i = k) P(x i+1, x n i = k) / P(x) = f k (i) b k (i) / P(x) What is the most likely state at position i of sequence x: Define ^ by Posterior Decoding: ^i = argmax k P( i = k x)
32 Posterior Decoding State 1 x 1 x x 3 x N l P( i =j x) k
33 Problem : Decoding Find the most likely parse of a sequence
34 Most likely sequences vs. ind. states Given a sequence x, Most likely sequence of states 1.49*10 very -9 different from sequence of most likely states Example: the dishonest casino P(box: FFFFFFFFFFF) = (1/6) 11 * =.76 * 10-9 * 0.54 = P(box: LLLLLLLLLLL) = [ (1/) 6 * (1/10) 5 ] * * 0.05 = 1.56*10-7 * 1.5 * 10-3 = 0.3 * 10-9 Say x = F F Most likely path: = FFF (too unlikely to transition F L F) However: marked letters more likely to be L than unmarked letters
35 Decoding GIVEN x = x 1 x x N Find = 1,, N, to maximize P[ x, ] K K K K * = argmax P[ x, ] x 1 x x 3 x N Maximizes a 0 1 e 1 (x 1 ) a 1 a N-1 N e N (x N ) Like forward alg, with max instead of sum V k (i) = max { 1 i-1} P[x 1 x i-1, 1,, i-1, x i, i = k] = Prob. of most likely sequence of states ending at state i = k
36 Decoding main idea Induction: Given that for all states k, and for a fixed position i, V k (i) = max { 1 i-1} P[x 1 x i-1, 1,, i-1, x i, i = k] What is V j (i+1)? From definition, V l (i+1) = max { 1 i} P[ x 1 x i, 1,, i, x i+1, i+1 = j ] = max { 1 i} P(x i+1, i+1 = j x 1 x i, 1,, i ) P[x 1 x i, 1,, i ] = max { 1 i} P(x i+1, i+1 = j i ) P[x 1 x i-1, 1,, i-1, x i, i ] = max k [P(x i+1, i+1 = j i =k) max { 1 i-1} P[x 1 x i-1, 1,, i- 1,x i, i =k]] = max k [ P(x i+1 i+1 = j ) P( i+1 = j i =k) V k (i) ] = e j (x i+1 ) max k a kj V k (i)
37 The Viterbi Algorithm Input: x = x 1 x N Initialization: V 0 (0) = 1 V k (0) = 0, for all k > 0 (0 is the imaginary first position) Iteration: V j (i) = e j (x i ) max k a kj V k (i 1) Ptr j (i) = argmax k a kj V k (i 1) Termination: P(x, *) = max k V k (N) Traceback: N * = argmax k V k (N) i-1 * = Ptr i (i)
38 The Viterbi Algorithm x 1 x x 3..x N State 1 V j (i) K Time: Space: O(K N) O(KN)
39 Viterbi Algorithm a practical detail Underflows are a significant problem (like with forward, backward) P[ x 1,., x i, 1,, i ] = a 0 1 a 1 a i e 1 (x 1 )e i (x i ) These numbers become extremely small underflow Solution: Take the logs of all values V l (i) = log e k (x i ) + max k [ V k (i-1) + log a kl ]
40 Example Let x be a long sequence with a portion of ~ 1/6 6 s, followed by a portion of ~ ½ 6 s x = Then, it is not hard to show that optimal parse is: FFF...F LLL...L 6 characters parsed as F, contribute.95 6 (1/6) 6 = parsed as L, contribute.95 6 (1/) 1 (1/10) 5 = parsed as F, contribute.95 6 (1/6) 6 = parsed as L, contribute.95 6 (1/) 3 (1/10) 3 =
41 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) = 0, for all k > 0 Initialization: b k (N) = 1, for all k Iteration: Iteration: Iteration: V l (i) = e l (x i ) max k V k (i-1) a kl f l (i) = e l (x i ) k f k (i-1) a kl b l (i) = k e l (x i +1) a kl b k (i+1) Termination: Termination: Termination: P(x, *) = max k V k (N) P(x) = k f k (N) P(x) = k a 0k e k (x 1 ) b k (1)
42 Problem 3: Learning Find the parameters that maximize the likelihood of the observed sequence
43 Estimating HMM parameters Easy if we know the sequence of hidden states Count # times each transition occurs Count #times each observation occurs in each state Given an HMM and observed sequence, we can compute the distribution over paths, and therefore the expected counts Chicken and egg problem
44 Solution: Use the EM algorithm Guess initial HMM parameters E step: Compute distribution over paths M step: Compute max likelihood parameters But how do we do this efficiently?
45 The forward-backward algorithm Also known as the Baum-Welch algorithm Compute probability of each state at each position using forward and backward probabilities (Expected) observation counts Compute probability of each pair of states at each pair of consecutive positions i and i+1 using forward(i) and backward(i+1) (Expected) transition counts Count(j k) i f j (i) a jk b k (i+1)
46 Application: HMMs for Information Extraction (IE) IE: Text machine-understandable data Paris, the capital of France, (Paris, France) CapitalOf, p=0.85 Applied to Web: better search engines, semantic Web, step toward human-level AI
47 IE Automatically? Intractable to get human labels for every concept expressed on the Web Idea: extract from semantically tractable sentences Edison invented the light bulb (Edison, light bulb) Invented x V y => (x, y) V Bloomberg, mayor of New York City (Bloomberg, New York City) Mayor x, C of y => (x, y) C
48 But Extraction patterns make errors: Erik Jonsson, CEO of Texas Instruments, mayor of Dallas from , and Empirical fact: Extractions you see over and over tend to be correct The problem is the long tail 48
49 Challenge: the long tail Number of times extraction appears in pattern e.g., (Bloomberg, New York City) Frequency rank of extraction Tend to be correct e.g., (Dave Shaver, Pickerington) (Ronald McDonald, McDonaldland) 49 A mixture of correct and incorrect
50 Mayor McCheese 50
51 Assessing Sparse Extractions Strategy 1) Model how common extractions occur in text ) Rank sparse extractions by fit to model 51
52 The Distributional Hypothesis Terms in the same class tend to appear in similar contexts. Hits with Hits with Context Chicago Twisp cities including 4,000 1 and other cities 37,900 0 hotels,000,000 1,670 mayor of 657,
53 HMM Language Models Precomputed scalable Handle sparsity 53
54 Baseline: context vectors cities such as Chicago, Boston, But Chicago isn t the best cities such as Chicago, Boston, Los Angeles and Chicago. 1 1 Compute dot products between vectors of common and sparse extractions [cf. Ravichandran et al. 005] 54
55 Hidden Markov Model (HMM) t i t i+1 t i+ t i+3 States unobserved w i w i+1 w i+ w i+3 Words observed cities such as Seattle Hidden States t i {1,, N} (N fairly small) Train on unlabeled data P(t i w i = w) is N-dim. distributional summary of w Compare extractions using KL divergence 55
56 HMM Compresses Context Vectors Twisp: < > P(t Twisp): t=1 N Distributional Summary P(t w) Compact (efficient 10-50x less data retrieved) Dense (accurate 3-46% error reduction) 56
57 Example Is Pickerington of the same type as Chicago? Chicago, Illinois Pickerington, Ohio Chicago: Pickerington: => Context vectors say no, dot product is 0! 57
58 Example HMM Generalizes: Chicago, Illinois Pickerington, Ohio 58
59 Experimental Results Task: Ranking sparse TextRunner extractions. Metric: Area under precision-recall curve. Headquartered Merged Average Frequency PL LM Language models reduce missing area by 39% over nearest competitor. 59
60 Example word distributions (1 of ) P(word state 3) unk new more unk few small good large great important other major little P(word state 4), ; ! :
61 Example word distributions ( of ) P(word state 1) unk United+States world U.S University Internet time end unk war country way city US Sun Earth P(word state 3) the a an its our this unk your
62 Correlation between LM and IE accuracy Below: correlation coefficients As LM error decreases, IE accuracy increases
63 Correlation between LM and IE accuracy
64 Correlation between LM and IE accuracy
65 What this suggests Better HMM language models => better information extraction Better HMM language models => => human-level AI? Consider: a good enough LM could do question answering, pass the Turing Test, etc. There are lots of paths to human-level AI, but LMs have: Well-defined progress Ridiculous amounts of training data
66 Also: active learning Today, people train language models by taking what comes Larger corpora => better language models But corpus size limited by # of humans typing What if we asked for the most informative sentences? (active learning)
67 What have we learned? In HMMs, general Bayes Net algorithms have simple & efficient form 1. Evaluation GIVEN a HMM M, and a sequence x, FIND Prob[ x M ] Forward Algorithm and Backward Algorithm (Variable Elimination). Decoding GIVEN a HMM M, and a sequence x, FIND the sequence of states that maximizes P[ x, M ] Viterbi Algorithm (MAP query) 3. Learning GIVEN A sequence x, FIND HMM parameters = (e i (.), a ij ) that maximize P[ x ] Baum-Welch/Forward-Backward algorithm (EM)
68 What have we learned? Unsupervised Learning of HMMs can power more scalable, accurate unsupervised IE Today, unsupervised learning of neural network language models is much more popular Deep networks to be discussed in future weeks
Example: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 informationSoundex distance metric
Text Algorithms (4AP) Lecture: Time warping and sound Jaak Vilo 008 fall Jaak Vilo MTAT.03.90 Text Algorithms Soundex distance metric Soundex is a coarse phonetic indexing scheme, widely used in genealogy.
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. 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 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 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. 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 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 informationSTA 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 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 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 information1 : Introduction. 1 Course Overview. 2 Notation. 3 Representing Multivariate Distributions : Probabilistic Graphical Models , Spring 2014
10-708: Probabilistic Graphical Models 10-708, Spring 2014 1 : Introduction Lecturer: Eric P. Xing Scribes: Daniel Silva and Calvin McCarter 1 Course Overview In this lecture we introduce the concept of
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 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 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 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 informationLecture 15. Probabilistic Models on Graph
Lecture 15. Probabilistic Models on Graph Prof. Alan Yuille Spring 2014 1 Introduction We discuss how to define probabilistic models that use richly structured probability distributions and describe how
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 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 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 informationAdministrivia. What is Information Extraction. Finite State Models. Graphical Models. Hidden Markov Models (HMMs) for Information Extraction
Administrivia Hidden Markov Models (HMMs) for Information Extraction Group meetings next week Feel free to rev proposals thru weekend Daniel S. Weld CSE 454 What is Information Extraction Landscape of
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 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 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 informationHidden 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 information2 : Directed GMs: Bayesian Networks
10-708: Probabilistic Graphical Models, Spring 2015 2 : Directed GMs: Bayesian Networks Lecturer: Eric P. Xing Scribes: Yi Cheng, Cong Lu 1 Notation Here the notations used in this course are defined:
More informationExpectation 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 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 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 in Language Processing
Hidden Markov Models in Language Processing Dustin Hillard Lecture notes courtesy of Prof. Mari Ostendorf Outline Review of Markov models What is an HMM? Examples General idea of hidden variables: implications
More information2 : Directed GMs: Bayesian Networks
10-708: Probabilistic Graphical Models 10-708, Spring 2017 2 : Directed GMs: Bayesian Networks Lecturer: Eric P. Xing Scribes: Jayanth Koushik, Hiroaki Hayashi, Christian Perez Topic: Directed GMs 1 Types
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 informationBasic 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 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 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 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 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 information8: Hidden Markov Models
8: Hidden Markov Models Machine Learning and Real-world Data Helen Yannakoudakis 1 Computer Laboratory University of Cambridge Lent 2018 1 Based on slides created by Simone Teufel So far we ve looked at
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 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 information8: Hidden Markov Models
8: Hidden Markov Models Machine Learning and Real-world Data Simone Teufel and Ann Copestake Computer Laboratory University of Cambridge Lent 2017 Last session: catchup 1 Research ideas from sentiment
More informationRecap: HMM. ANLP Lecture 9: Algorithms for HMMs. More general notation. Recap: HMM. Elements of HMM: Sharon Goldwater 4 Oct 2018.
Recap: HMM ANLP Lecture 9: Algorithms for HMMs Sharon Goldwater 4 Oct 2018 Elements of HMM: Set of states (tags) Output alphabet (word types) Start state (beginning of sentence) State transition probabilities
More informationLecture 12: Algorithms for HMMs
Lecture 12: Algorithms for HMMs Nathan Schneider (some slides from Sharon Goldwater; thanks to Jonathan May for bug fixes) ENLP 26 February 2018 Recap: tagging POS tagging is a sequence labelling task.
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 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 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 informationStatistical Pattern Recognition
Statistical Pattern Recognition Expectation Maximization (EM) and Mixture Models Hamid R. Rabiee Jafar Muhammadi, Mohammad J. Hosseini Spring 2014 http://ce.sharif.edu/courses/92-93/2/ce725-2 Agenda Expectation-maximization
More informationSTATS 306B: Unsupervised Learning Spring Lecture 5 April 14
STATS 306B: Unsupervised Learning Spring 2014 Lecture 5 April 14 Lecturer: Lester Mackey Scribe: Brian Do and Robin Jia 5.1 Discrete Hidden Markov Models 5.1.1 Recap In the last lecture, we introduced
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 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 informationMachine 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 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 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 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 informationCSCI 5832 Natural Language Processing. Today 2/19. Statistical Sequence Classification. Lecture 9
CSCI 5832 Natural Language Processing Jim Martin Lecture 9 1 Today 2/19 Review HMMs for POS tagging Entropy intuition Statistical Sequence classifiers HMMs MaxEnt MEMMs 2 Statistical Sequence Classification
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 informationHidden Markov models
Hidden Markov models Charles Elkan November 26, 2012 Important: These lecture notes are based on notes written by Lawrence Saul. Also, these typeset notes lack illustrations. See the classroom lectures
More informationLecture 12: Algorithms for HMMs
Lecture 12: Algorithms for HMMs Nathan Schneider (some slides from Sharon Goldwater; thanks to Jonathan May for bug fixes) ENLP 17 October 2016 updated 9 September 2017 Recap: tagging POS tagging is a
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 information1. 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 informationBayesian Networks: Construction, Inference, Learning and Causal Interpretation. Volker Tresp Summer 2016
Bayesian Networks: Construction, Inference, Learning and Causal Interpretation Volker Tresp Summer 2016 1 Introduction So far we were mostly concerned with supervised learning: we predicted one or several
More informationBayesian Networks: Construction, Inference, Learning and Causal Interpretation. Volker Tresp Summer 2014
Bayesian Networks: Construction, Inference, Learning and Causal Interpretation Volker Tresp Summer 2014 1 Introduction So far we were mostly concerned with supervised learning: we predicted one or several
More informationCS839: Probabilistic Graphical Models. Lecture 2: Directed Graphical Models. Theo Rekatsinas
CS839: Probabilistic Graphical Models Lecture 2: Directed Graphical Models Theo Rekatsinas 1 Questions Questions? Waiting list Questions on other logistics 2 Section 1 1. Intro to Bayes Nets 3 Section
More informationCMSC 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 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 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 informationData-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 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 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 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 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 information10 : HMM and CRF. 1 Case Study: Supervised Part-of-Speech Tagging
10-708: Probabilistic Graphical Models 10-708, Spring 2018 10 : HMM and CRF Lecturer: Kayhan Batmanghelich Scribes: Ben Lengerich, Michael Kleyman 1 Case Study: Supervised Part-of-Speech Tagging We will
More informationHidden Markov Models and Applica2ons. Spring 2017 February 21,23, 2017
Hidden Markov Models and Applica2ons Spring 2017 February 21,23, 2017 Gene finding in prokaryotes Reading frames A protein is coded by groups of three nucleo2des (codons): ACGTACGTACGTACGT ACG-TAC-GTA-CGT-ACG-T
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 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 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 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 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 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 informationDynamic Programming: Hidden Markov Models
University of Oslo : Department of Informatics Dynamic Programming: Hidden Markov Models Rebecca Dridan 16 October 2013 INF4820: Algorithms for AI and NLP Topics Recap n-grams Parts-of-speech Hidden Markov
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 informationDirected Probabilistic Graphical Models CMSC 678 UMBC
Directed Probabilistic Graphical Models CMSC 678 UMBC Announcement 1: Assignment 3 Due Wednesday April 11 th, 11:59 AM Any questions? Announcement 2: Progress Report on Project Due Monday April 16 th,
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 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 informationTemporal Modeling and Basic Speech Recognition
UNIVERSITY ILLINOIS @ URBANA-CHAMPAIGN OF CS 498PS Audio Computing Lab Temporal Modeling and Basic Speech Recognition Paris Smaragdis paris@illinois.edu paris.cs.illinois.edu Today s lecture Recognizing
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 information