Genome 373: Hidden Markov Models II. Doug Fowler
|
|
- Barrie Dominic McLaughlin
- 5 years ago
- Views:
Transcription
1 Genome 373: Hidden Markov Models II Doug Fowler
2 Review From Hidden Markov Models I What does a Markov model describe?
3 Review From Hidden Markov Models I A T A Markov model describes a random process of transitions from one state to another in a state space.
4 Review From Hidden Markov Models I A T A Markov model describes a random process of transitions from one state to another in a state space. What does a Markov model produce, if used generatively?
5 Review From Hidden Markov Models I A T Sequence: AAAATTTT A Markov model describes a random process of transitions from one state to another in a state space. A sequence of states/symbols And what governs the sequence?
6 Review From Hidden Markov Models I A T Sequence: AAAATTTT A Markov model describes a random process of transitions from one state to another in a state space. A sequence of states/symbols And what governs the sequence? The transition probabilities
7 Review From Hidden Markov Models I Sequence: AAAATTTT We learned that a Markov model describes a random process of transitions from one state to another in a state space. What is hidden in a hidden Markov model and how does this relate to emission probabilities?
8 Review From Hidden Markov Models I A T rich rich A: 0.8 A: 0.2 T: 0.2 T: 0.8 Sequence: AAAATTTT State path:??????? We learned that a Markov model describes a random process of transitions from one state to another in a state space. In a HMM, states are unknown to us and associated with a set of emission probabilities so that many different state paths can generate a given sequence
9 Review From Hidden Markov Models I This image cannot currently be displayed. AAAATTTT Sequence: State path #1: aaaat t t State path #2: t t t t aaaa L Y P (x, ) =a 0 1 i=1 e i (x i )a i i+1 Finally, recall that we can calculate the probability of any particular (hidden) state path giving rise to a sequence! P(initial state) P(emitting symbol x i in state π i ) L Y P(transition from state π i to state π i+1 ) P (x, ) =a 0 1 i=1 e i (x i )a i i+1
10 Review From Hidden Markov Models I A T rich rich A: 0.8 A: 0.2 T: 0.2 T: 0.8 AAAATTTT Sequence: State path #1: aaaat t t State path #2: t t t t aaaa P (x, ) =a 0 1 L Y i=1 e i (x i )a i i+1 This is the crux of a HMM and illustrates how we can use HMMs to calculate the probability of a particular state path if we have a model and emission/transition probabilities P(initial state) P(emitting symbol x i in state π i ) L Y P(transition from state π i to state π i+1 ) P (x, ) =a 0 1 i=1 e i (x i )a i i+1
11 Outline The Viterbi Algorithm (or, how can we find the most probable state path?) The Forward-Backward Algorithm (or, how can we find the probability of a state at a particular time) What is an algorithm, anyhow? A procedure for solving a problem
12 Recalling Our Motivation Given a sequence, we want to be able to predict the major features of genes in the sequence (e.g. create gene models) Start TGAATCAAGTTAGAAGTTATGGAGCATAATAACATG TGGATGGCCAGTGGTCGGTTGCTACACCCCTGCCGC AACGTTGAAGGTCCCGGATTAGACTGGCTGGATCTA TGCCGTGACACCCGTTATACTCCATTACCGTCTGTG GGTCACAGCTTGTTGTGGACTGGATTGCCATTCTCT CAGTGTATTACGCAGGCCGGCGCACGGGTCCCATAT AAACCTGTCATAGCTTACCTGACTCTACTTGGAAAT GTGGCTAGGCCTTTGCCCACGCACCTGATCGGTCCT CGTTTGCTTTTTAGGACCGGATGAACTACAGAGCAT TGCAAGAATCTCTACCTGCTTTACAAAGTGCTGGAT CCTATTCCAGCGGGATGTTTTATCTAAACACGATGA GAGGAGTATTCGTCAGGCCACATGGCTTTCTTGTTC TGGTCGGATCCATCGTTGGCGCCCGACCCCCCCATT CCATAGTGAGTTCTTCGTCCGAGCCATTGTATGCCA GATCGACAGACAGATAGCGGATCCAGTATATCCCTG GAAACTATAGACGCACAGGTTGGAATCTTAAGTGAA GTCGCGCGTCCAAACCCAGCTCTATTTTAGTGGTCA TGGGTTCTGGTCCCCCCGAGCCGCGGAACCGATTAG GACCATGTACAACAATACTTATTAGTCATCTTTTAG ACACAATCTCCCTGCTCAGTGGTATATGGTTTTTGC TATAATTAGCCACCCTCATAAGTTGCACTACTTCTG CGACCCAAATGCACCCTTACCACGAAGACAGGATTG TCCGATCCTATATTACGACTTT Exon 1 Intron 1 Exon 2 Stop TGAATCAAGTTAGAAGTTATGGAGCATAATAACATG TGGATGGCCAGTGGTCGGTTGCTACACCCCTGCCGC AACGTTGAAGGTCCCGGATTATGCTGGCTGGATCTA TGCCGTGACACCCGTTATACTCCATTACCGTCTGTG GGTCACAGCTTGTTGTGGACTGGATTGCCATTCTCT CAGTGTATTACGCAGGCCGGCGCACGGGTCCCATAT AAACCTGTCATAGCTTACCTGACTCTACTTGGAAAT GTGGCTAGGCCTTTGCCCACGCACCTGATCGGTCCT CGTTTGCTTTTTAGGACCGGATGAACTACAGAGCAT TGCAAGAATCTCTACCTGCTTTACAAAGTGCTGGAT CCTATTCCAGCGGGATGTTTTATCTAAACACGATAG AGGGAGTATTCGTCAGGCCACATGGCTTTCTTGTTC TGGTCGGATCCATCGTTGGCGCCCGACCCCCCCATT CCATAGTGAGTTCTTCGTCCGAGCCATTGTATGCCA GATCGACAGACAGATAGCGGATCCAGTATATCCCTG GAAACTATAGACGCACAGGTTGGAATCTTAAGTGAA GTCGCGCGTCCAAACCCAGCTCTATTTTAGTGGTCA TGGGTTCTGGTCCCCCCGAGCCGCGGAACCGATTAG GACCATGTACAACAATACTTATTAGTCATCTTTTAG ACACAATCTCCCTGCTCAGTGGTATATGGTTTTTGC TATAATTAGCCACCCTCATAAGTTGCACTACTTCTG CGACCCAAATGCACCCTTACCACGAAGACAGGATTG TCCGATCCTATATTACGACTTT
13 Recalling Our Motivation We want a model that can predict whether each base in a sequence is in one of a known set of states (intergenic, start exon, intron, stop) Start TGAATCAAGTTAGAAGTTATGGAGCATAATAACATG TGGATGGCCAGTGGTCGGTTGCTACACCCCTGCCGC AACGTTGAAGGTCCCGGATTAGACTGGCTGGATCTA TGCCGTGACACCCGTTATACTCCATTACCGTCTGTG GGTCACAGCTTGTTGTGGACTGGATTGCCATTCTCT CAGTGTATTACGCAGGCCGGCGCACGGGTCCCATAT AAACCTGTCATAGCTTACCTGACTCTACTTGGAAAT GTGGCTAGGCCTTTGCCCACGCACCTGATCGGTCCT CGTTTGCTTTTTAGGACCGGATGAACTACAGAGCAT TGCAAGAATCTCTACCTGCTTTACAAAGTGCTGGAT CCTATTCCAGCGGGATGTTTTATCTAAACACGATGA GAGGAGTATTCGTCAGGCCACATGGCTTTCTTGTTC TGGTCGGATCCATCGTTGGCGCCCGACCCCCCCATT CCATAGTGAGTTCTTCGTCCGAGCCATTGTATGCCA GATCGACAGACAGATAGCGGATCCAGTATATCCCTG GAAACTATAGACGCACAGGTTGGAATCTTAAGTGAA GTCGCGCGTCCAAACCCAGCTCTATTTTAGTGGTCA TGGGTTCTGGTCCCCCCGAGCCGCGGAACCGATTAG GACCATGTACAACAATACTTATTAGTCATCTTTTAG ACACAATCTCCCTGCTCAGTGGTATATGGTTTTTGC TATAATTAGCCACCCTCATAAGTTGCACTACTTCTG CGACCCAAATGCACCCTTACCACGAAGACAGGATTG TCCGATCCTATATTACGACTTT Exon 1 Intron 1 Exon 2 Stop TGAATCAAGTTAGAAGTTATGGAGCATAATAACATG TGGATGGCCAGTGGTCGGTTGCTACACCCCTGCCGC AACGTTGAAGGTCCCGGATTATGCTGGCTGGATCTA TGCCGTGACACCCGTTATACTCCATTACCGTCTGTG GGTCACAGCTTGTTGTGGACTGGATTGCCATTCTCT CAGTGTATTACGCAGGCCGGCGCACGGGTCCCATAT AAACCTGTCATAGCTTACCTGACTCTACTTGGAAAT GTGGCTAGGCCTTTGCCCACGCACCTGATCGGTCCT CGTTTGCTTTTTAGGACCGGATGAACTACAGAGCAT TGCAAGAATCTCTACCTGCTTTACAAAGTGCTGGAT CCTATTCCAGCGGGATGTTTTATCTAAACACGATAG AGGGAGTATTCGTCAGGCCACATGGCTTTCTTGTTC TGGTCGGATCCATCGTTGGCGCCCGACCCCCCCATT CCATAGTGAGTTCTTCGTCCGAGCCATTGTATGCCA GATCGACAGACAGATAGCGGATCCAGTATATCCCTG GAAACTATAGACGCACAGGTTGGAATCTTAAGTGAA GTCGCGCGTCCAAACCCAGCTCTATTTTAGTGGTCA TGGGTTCTGGTCCCCCCGAGCCGCGGAACCGATTAG GACCATGTACAACAATACTTATTAGTCATCTTTTAG ACACAATCTCCCTGCTCAGTGGTATATGGTTTTTGC TATAATTAGCCACCCTCATAAGTTGCACTACTTCTG CGACCCAAATGCACCCTTACCACGAAGACAGGATTG TCCGATCCTATATTACGACTTT
14 How Can We Find the Most Probable Path? Can anyone tell me a way to find the most probable state path? Hint: we talked about a way to calculate the probability of any individual state path given a sequence: P(initial state) P(emitting symbol x i in state π i ) L Y P(transition from state π i to state π i+1 ) P (x, ) =a 0 1 i=1 e i (x i )a i i+1
15 Could We Work Out Every Possibility? Simplest answer: calculate all possible state path probabilities and choose the largest However, there is a big problem with this way of doing things
16 Could We Work Out Every Possibility? Simplest answer: calculate all possible state path probabilities and choose the largest However, there is a big problem with this way of doing things which is that there are a very large number of possible state paths! In fact, there are S^N possibilities for S states and N symbols
17 Could We Work Out Every Possibility? No. Simplest answer: calculate all possible state path probabilities and choose the largest However, there is a big problem with this way of doing things which is that there are a very large number of possible state paths! In fact, there are S^N possibilities for S states and N symbols A T rich rich A: 0.8 A: 0.2 T: 0.2 T: 0.8 Two states, 100 positions = Even a fast computer won t help you much
18 Sound Like A Familiar Problem? You all have seen something very similar to this already the goal is to find the optimal path without having to explicitly test every possibility
19 Sound Like A Familiar Problem? You all have seen something very similar to this already sequence alignment There, you learned about dynamic programming approaches to find the best alignment between two sequences without examining all the possibilities
20 Sound Like A Familiar Problem? You all have seen something very similar to this already sequence alignment There, you learned about dynamic programming approaches to find the best alignment between two sequences without examining all the possibilities The Viterbi algorithm is similar, finding the most probable state path given a sequence and a model without examining all the possible state paths
21 The Viterbi Algorithm A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 Let s go back to our AT example, with one small change (note A-rich emission probabilities). Can someone talk through the parts of this model?
22 Begin 0.5 The Viterbi Algorithm A We can write down a graph of all possible state paths for an example sequence (AAT) T rich rich A: 0.7 A: 0.2 T: 0.3 T: a-rich a-rich a-rich A A T
23 The Viterbi Algorithm Begin A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T 0.5*0.7 = *0.2 = We calculate the probability of each transition/emission step
24 Begin The Viterbi Algorithm 0.5*0.7 = *0.2 = A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T What calculation should we do here, to get P(A,A a-rich, a-rich)?
25 Begin The Viterbi Algorithm 0.5*0.7 = *0.2 = A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T 0.35**0.7 = 0.22 Multiply P(A a-rich) by the appropriate transition and emission probabilities
26 Begin The Viterbi Algorithm 0.5*0.7 = 0.35 A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T 0.35**0.7 = *0.2 = **0.7 = We calculate the probability of each transition/emission step
27 Begin The Viterbi Algorithm 0.5*0.7 = *0.2 = A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T 0.35**0.7 = 0.22 We calculate the probability of each transition/emission step and discard all but the most likely path leading to each state
28 Begin The Viterbi Algorithm 0.5*0.7 = *0.2 = A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T How about for the state at position 2? Take a minute to do the two probability calculations.
29 Begin The Viterbi Algorithm 0.5*0.7 = 0.35 A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T 0.35**0.2 = *0.2 = **0.2 = And which path should we discard?
30 Begin The Viterbi Algorithm 0.5*0.7 = 0.35 A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T 0.35**0.2 = *0.2 = **0.2 = And which path should we discard?
31 Begin The Viterbi Algorithm 0.5*0.7 = 0.35 A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T 0.35**0.7 = **0.3 = *0.2 = **0.2 = **0.8 = Here is the answer for the third step of the 8 (2 states ^ 3 symbols) possible paths, the Viterbi algorithm leaves us with two
32 Begin The Viterbi Algorithm 0.5*0.7 = 0.35 A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T 0.35**0.7 = **0.3 = *0.2 = **0.2 = **0.8 = Which should we pick?
33 Begin The Viterbi Algorithm 0.5*0.7 = 0.35 A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T 0.35**0.7 = **0.3 = *0.2 = **0.2 = **0.8 = We can pick the most likely
34 Begin The Viterbi Algorithm A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich 0.5*0.7 = 0.35 A A T 0.35**0.7 = **0.3 = *0.2 = **0.2 = **0.8 = Note, we didn t switch to this step what would happen if we the kept getting T s?
35 Begin The Viterbi Algorithm A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich 0.5*0.7 = 0.35 A A T 0.35**0.7 = **0.3 = *0.2 = **0.2 = **0.8 = Eventually, the likeliest state path would become one with a transition to a state!
36 Begin The Viterbi Algorithm A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich 0.5*0.7 = 0.35 A A T 0.35**0.7 = **0.3 = *0.2 = **0.2 = **0.8 = Said another way, if several paths converge on a particular state instead of recalculating them all when we calculate probabilities for the next step we discard the less likely paths
37 Begin The Viterbi Algorithm 0.5*0.7 = 0.35 A T rich rich A: 0.7 A: 0.2 T: 0.3 T: 0.8 a-rich a-rich a-rich A A T 0.35**0.7 = **0.3 = *0.2 = **0.2 = **0.8 = For practical reasons, we typically operate in log space (i.e. take the log of the probabilities), since the probabilities get very small very quickly
38 Outline The Viterbi Algorithm (or, how can we find the most probable state path?) The Forward-Backward Algorithm (or, how can we find the probability of a state at a particular time)
39 A slightly different question P ( i = k x) What if we are interested in the probability that the HMM was in a particular state k at a particular position i?
40 A slightly different question P ( i = k x) Any thoughts about conceptually how to do this?
41 A slightly different question P ( i = k x) = P (x, i = k) P (x) We can obtain this probability by dividing the probability of all state paths with i = k by the sum of the probability of all paths
42 A slightly different question P ( i = k x) = P (x, i = k) P (x) P (x, i = k) = X i=k P ( x) P (x) = X P ( x) We can obtain this probability by dividing the probability of all state paths with i = k by the sum of the probability of all paths
43 A slightly different question P ( i = k x) = P (x, i = k) P (x) P (x, i = k) = X i=k P ( x) P (x) = X P ( x) We can obtain this probability by dividing the probability of all state paths with i = k by the sum of the probability of all paths
44 A slightly different question P ( i = k x) = P (x, i = k) P (x) P (x, i = k) = X i=k P ( x) P (x) = X P ( x) What problem are we doing to run into here, without an algorithm to help?
45 A slightly different question P ( i = k x) = P (x, i = k) P (x) P (x, i = k) = X i=k P ( x) P (x) = X P ( x) As before, the number of possible state paths is too large to brute force
46 The forward-backward algorithm P ( 2 = A, A, T ) Begin a-rich a-rich a-rich A A T Let s revisit our simple example. Our goal is to calculate the probability, given the model and the sequence, that the state at position 2 was
47 The forward-backward algorithm P ( 2 = A, A, T ) Begin a-rich a-rich a-rich A A T What arrows should we remove to illustrate possible paths through state space that correspond to our question?
48 The forward-backward algorithm Begin a-rich a-rich a-rich A A T These are the possible paths through state space where 2 =
49 The forward-backward algorithm Begin a-rich a-rich a-rich A A T Let s first just consider the forward part of the problem: probability of seeing AA and reaching the state
50 The forward-backward algorithm Begin a-rich a-rich a-rich A A T 0.5*0.7 = *0.2 = f (2) = 0.2 ( ) In the forward algorithm, we sum all the joint transition/emission probabilities leading to 2 =
51 The forward-backward algorithm Begin a-rich a-rich a-rich A A T 0.5*0.7 = *0.2 = f (2) = This gives us probability of seeing AA and reaching the state
52 The forward-backward algorithm Begin a-rich a-rich a-rich A A T But, if our goal is to calculate Why? P ( 2 = A, A, T ) we re not done yet.
53 The forward-backward algorithm Begin a-rich a-rich a-rich A A T But, if our goal is to calculate P ( 2 = A, A, T ) we re not done yet. Why? Because we have the rest of the sequence to account for!
54 The forward-backward algorithm Begin a-rich a-rich a-rich A A T So, let s consider the backward part of the problem, which is the probability of getting the rest of the sequence given that 2 =
55 The forward-backward algorithm Begin a-rich a-rich a-rich A A T b (2) = ( ) In the backward algorithm we sum the emission and transition probabilities across all states
56 The forward-backward algorithm Begin a-rich a-rich a-rich A A T P ( 2 = A,A,T) = f (2) b (2) P (x) Now, we can solve our problem. The probability of the model being in a state at position 2 is equal to the product of the forward and backward probabilities divided by probability of all paths P(x). How could we obtain this quantity?
57 The forward-backward algorithm Begin a-rich a-rich a-rich A A T P ( 2 = A,A,T) = f (2) b (2) P (x) One way is to use the forward algorithm, summing over all the possible ending states of the final position
58 General form of the F-B Algorithm f k,i = e k (x i ) X l f l,i 1 a lk P (transitioning from l to k) P (emitting x i i = k) P (sequence from 1 to i i = k) P (sequence from 1 to i-1 i 1 = l) In our simple example with a three symbol sequence, we calculated one step forward and one step backward to the middle position. The forward algorithm is recursive, with each calculation being reused rather than recomputed
59 General form of the F-B Algorithm f k,i = e k (x i ) X l f l,i 1 a lk b k.i = X l e l (x i+1 )b l,i+1 a kl The power of these algorithms is that they eliminate the need to calculate all possible state paths
60 Viterbi vs F-B Algorithms Viterbi start: at the beginning of the sequence of symbols x algorithm: results:
61 Viterbi vs F-B Algorithms Viterbi start: at the beginning of the sequence of symbols x algorithm: moving forward, find the likeliest path for each state in each position and discard all the rest results:
62 Viterbi vs F-B Algorithms Viterbi start: at the beginning of the sequence of symbols x algorithm: moving forward, find the likeliest path for each state in each position and discard all the rest results: the most likely state path
63 Viterbi vs F-B Algorithms Viterbi start: at the beginning of the sequence of symbols x algorithm: moving forward, find the likeliest path for each state in each position and discard all the rest results: the most likely state path This process is often referred to as decoding an HMM, because it reveals the most likely sequence of (hidden, encoded) states Begin a-rich a-rich a-rich A A T
64 Viterbi vs F-B Algorithms F-B Algorithm start: at the i th position algorithm: results:
65 Viterbi vs F-B Algorithms F-B Algorithm start: at the i th position algorithm: moving forward or backward, sum the probabilities of paths leading to a particular state π i = k results:
66 Viterbi vs F-B Algorithms F-B Algorithm start: at the i th position algorithm: moving forward or backward, sum the probabilities of paths leading to a particular state π i = k results: the probability that the model was in state k at position i The F-B algorithm can be used to solve many other decoding problems (e.g. find the most probable state at position i)
CISC 889 Bioinformatics (Spring 2004) Hidden Markov Models (II)
CISC 889 Bioinformatics (Spring 24) Hidden Markov Models (II) a. Likelihood: forward algorithm b. Decoding: Viterbi algorithm c. Model building: Baum-Welch algorithm Viterbi training Hidden Markov models
More 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 informationEvolutionary Models. Evolutionary Models
Edit Operators In standard pairwise alignment, what are the allowed edit operators that transform one sequence into the other? Describe how each of these edit operations are represented on a sequence alignment
More 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 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. 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 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 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 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 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 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 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 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 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 informationLecture 3: Markov chains.
1 BIOINFORMATIK II PROBABILITY & STATISTICS Summer semester 2008 The University of Zürich and ETH Zürich Lecture 3: Markov chains. Prof. Andrew Barbour Dr. Nicolas Pétrélis Adapted from a course by Dr.
More informationAlignment Algorithms. Alignment Algorithms
Midterm Results Big improvement over scores from the previous two years. Since this class grade is based on the previous years curve, that means this class will get higher grades than the previous years.
More informationBMI/CS 576 Fall 2016 Final Exam
BMI/CS 576 all 2016 inal Exam Prof. Colin Dewey Saturday, December 17th, 2016 10:05am-12:05pm Name: KEY Write your answers on these pages and show your work. You may use the back sides of pages as necessary.
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 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 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 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 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 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 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 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 informationHidden Markov Models. Terminology and Basic Algorithms
Hidden Markov Models Terminology and Basic Algorithms The next two weeks Hidden Markov models (HMMs): Wed 9/11: Terminology and basic algorithms Mon 14/11: Implementing the basic algorithms Wed 16/11:
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 information6.047 / Computational Biology: Genomes, Networks, Evolution Fall 2008
MIT OpenCourseWare http://ocw.mit.edu 6.047 / 6.878 Computational Biology: Genomes, etworks, Evolution Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms.
More 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 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
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 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 (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 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. Terminology and Basic Algorithms
Hidden Markov Models Terminology and Basic Algorithms What is machine learning? From http://en.wikipedia.org/wiki/machine_learning Machine learning, a branch of artificial intelligence, is about the construction
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 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 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 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 informationHidden Markov Models. Implementing the forward-, backward- and Viterbi-algorithms
Hidden Markov Models Implementing the forward-, backward- and Viterbi-algorithms Viterbi Forward Backward Viterbi Problem: The values in the ω-, α-, and β-tables can come very close to zero, by multiplying
More informationHMM for modeling aligned multiple sequences: phylo-hmm & multivariate HMM
I529: Machine Learning in Bioinformatics (Spring 2017) HMM for modeling aligned multiple sequences: phylo-hmm & multivariate HMM Yuzhen Ye School of Informatics and Computing Indiana University, Bloomington
More 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 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 information3/1/17. Content. TWINSCAN model. Example. TWINSCAN algorithm. HMM for modeling aligned multiple sequences: phylo-hmm & multivariate HMM
I529: Machine Learning in Bioinformatics (Spring 2017) Content HMM for modeling aligned multiple sequences: phylo-hmm & multivariate HMM Yuzhen Ye School of Informatics and Computing Indiana University,
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 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 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 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 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 informationNatural Language Processing Prof. Pushpak Bhattacharyya Department of Computer Science & Engineering, Indian Institute of Technology, Bombay
Natural Language Processing Prof. Pushpak Bhattacharyya Department of Computer Science & Engineering, Indian Institute of Technology, Bombay Lecture - 21 HMM, Forward and Backward Algorithms, Baum Welch
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: All the Glorious Gory Details
Hidden Markov Models: All the Glorious Gory Details Noah A. Smith Department of Computer Science Johns Hopkins University nasmith@cs.jhu.edu 18 October 2004 1 Introduction Hidden Markov models (HMMs, hereafter)
More 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 informationCSC321 Lecture 7 Neural language models
CSC321 Lecture 7 Neural language models Roger Grosse and Nitish Srivastava February 1, 2015 Roger Grosse and Nitish Srivastava CSC321 Lecture 7 Neural language models February 1, 2015 1 / 19 Overview We
More informationLinear Dynamical Systems
Linear Dynamical Systems Sargur N. srihari@cedar.buffalo.edu Machine Learning Course: http://www.cedar.buffalo.edu/~srihari/cse574/index.html Two Models Described by Same Graph Latent variables Observations
More 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 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 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 68: BIOINFORMATICS. Prof. Sara Mathieson Swarthmore College Spring 2018
CS 68: BIOINFORMTICS Prof. Sara Mathieson Swarthmore College Spring 2018 Outline: pr 4 Lab 5 Examples HMM example in population genetics Recap Viterbi lgorithm Forward-Backward lgorithm Posterior Decoding
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 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 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 Methods. Algorithms and Implementation
Hidden Markov Methods. Algorithms and Implementation Final Project Report. MATH 127. Nasser M. Abbasi Course taken during Fall 2002 page compiled on July 2, 2015 at 12:08am Contents 1 Example HMM 5 2 Forward
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 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 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 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 informationFactor Graphs and Message Passing Algorithms Part 1: Introduction
Factor Graphs and Message Passing Algorithms Part 1: Introduction Hans-Andrea Loeliger December 2007 1 The Two Basic Problems 1. Marginalization: Compute f k (x k ) f(x 1,..., x n ) x 1,..., x n except
More informationGraphical Models Another Approach to Generalize the Viterbi Algorithm
Exact Marginalization Another Approach to Generalize the Viterbi Algorithm Oberseminar Bioinformatik am 20. Mai 2010 Institut für Mikrobiologie und Genetik Universität Göttingen mario@gobics.de 1.1 Undirected
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 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 information1/22/13. Example: CpG Island. Question 2: Finding CpG Islands
I529: Machine Learning in Bioinformatics (Spring 203 Hidden Markov Models Yuzhen Ye School of Informatics and Computing Indiana Univerty, Bloomington Spring 203 Outline Review of Markov chain & CpG island
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 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 informationIntroduction to Hidden Markov Models (HMMs)
Introduction to Hidden Markov Models (HMMs) But first, some probability and statistics background Important Topics 1.! Random Variables and Probability 2.! Probability Distributions 3.! Parameter Estimation
More informationPhysics Motion Math. (Read objectives on screen.)
Physics 302 - Motion Math (Read objectives on screen.) Welcome back. When we ended the last program, your teacher gave you some motion graphs to interpret. For each section, you were to describe the motion
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 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 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 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 informationBayesian Networks Introduction to Machine Learning. Matt Gormley Lecture 24 April 9, 2018
10-601 Introduction to Machine Learning Machine Learning Department School of Computer Science Carnegie Mellon University Bayesian Networks Matt Gormley Lecture 24 April 9, 2018 1 Homework 7: HMMs Reminders
More informationHidden Markov Models, I. Examples. Steven R. Dunbar. Toy Models. Standard Mathematical Models. Realistic Hidden Markov Models.
, I. Toy Markov, I. February 17, 2017 1 / 39 Outline, I. Toy Markov 1 Toy 2 3 Markov 2 / 39 , I. Toy Markov A good stack of examples, as large as possible, is indispensable for a thorough understanding
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 informationMachine Learning, Fall 2011: Homework 5
10-601 Machine Learning, Fall 2011: Homework 5 Machine Learning Department Carnegie Mellon University Due:???????????, 5pm Instructions There are???? questions on this assignment. The?????? question involves
More informationProbability. CS 3793/5233 Artificial Intelligence Probability 1
CS 3793/5233 Artificial Intelligence 1 Motivation Motivation Random Variables Semantics Dice Example Joint Dist. Ex. Axioms Agents don t have complete knowledge about the world. Agents need to make decisions
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 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 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 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 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 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 informationChapter 1 Review of Equations and Inequalities
Chapter 1 Review of Equations and Inequalities Part I Review of Basic Equations Recall that an equation is an expression with an equal sign in the middle. Also recall that, if a question asks you to solve
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 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 (Part 1)
Hidden Marov Models (Part ) BMI/CS 576 www.biostat.wisc.edu/bmi576.html Mar Craven craven@biostat.wisc.edu Fall 0 A simple HMM A G A G C T C T! given say a T in our input sequence, which state emitted
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 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 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 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 information