OCR-B

OCR-B

OCR-B is a monospace font developed in 1968 by Adrian Frutiger for Monotype by following the European Computer Manufacturer's Association standard. Its function was to facilitate the optical character recognition operations by specific electronic devices, originally for financial and bank-oriented uses. It was accepted as the world standard in 1973. It follows the ISO 1073-2:1976 (E) standard, refined in 1979 ("letterpress" design, size I). It includes all ASCII symbols, and other symbols needed in the bank environment. It is widely used for the human readable digits in UPC/EAN barcodes. It is also used for machine-readable passports. It shares that purpose with OCR-A, but it is easier for the human eye and brain to read and it has a less technical look than OCR-A. == History == In June 1961, the European Computer Manufacturers Association (ECMA) started standardization activities related to Optical Character Recognition (OCR). After evaluating existing OCR designs, it was decided to develop two new fonts: A stylized design with just digits, called “Class A”; and a more conventional type design with broader character coverage, called “Class B”. In February 1965, ECMA proposed a design for the “Class B” font to ISO, who adopted it as international standard ISO 1073-2 in October 1965. The first revision contained three font sizes: I, II and III. The specification included a Letterpress design, intended for high-quality printing equipment; and a rounded-edge Constant Strokewidth design for impact printers with reduced typographic quality. In September 1969, ECMA started work to revise its published standard. To make OCR-B more widely accepted, the shapes of some characters were slightly modified. The new revision removed font size II, which had been rarely used in practice; it deleted five character shapes; and it added a new font size IV. ECMA published the second edition of OCR-B in October 1971. In March 1976, ECMA published a third revision of its ECMA-11 specification. It added the symbols § and ¥ to OCR-B; two types of erasure marks (█) for blackening out mis-printed characters were added; and the length of the Vertical bar was changed to match ISO 1073-2. In 1993, Turkey proposed extending ISO 1073-2 to include the Turkish letters Ğğ, İı, and Şş. The request was generalized to extend OCR-B with a number of Latin and Greek letters used in European languages. A revision of the ISO 1073-2:1976 standard was therefore started, producing three successive draft documents. The final draft would have extended OCR-B with 40 Latin and 10 Greek letters; for six Latin letters, the draft gave new alternate shapes. A request to extend OCR-B with Vietnamese accents was rejected. Other than previous versions of the standard, which specified glyph shapes via reference drawings, the new revision would have included the shapes in machine-readable form. However, industry support for testing the new font could not be secured at the time, so the revision effort was halted in 1997. The working group described their findings in a technical report. In June 1998, the European Committee for Standardization published a report for adding the Euro sign to OCR-B. The report proposed both a single-stroked and a double-stroked variant of the Euro sign, leaving the decision to further testing of OCR performance. Testing was difficult: the theoretical design methods used when the OCR-B glyphs were originally developed could no longer be reproduced, and the technological constraints of the 1960s were also not entirely relevant anymore in the OCR environments of the 1990s. A new test method was devised, using present-time OCR technology. The tests found no difference in OCR performance between the two Euro variants, and recommended the adoption of the double-stroked variant as it matches the conventional glyph shape. The project did not have funds to thoroughly test the glyph extensions of the 1993 proposal; initial results were inconclusive. == Availability == Microsoft Office ships a version of Letterpress OCR-B produced by Monotype. It covers Windows-1252. Many vendors, including Adobe, still sell their versions of OCR-A and OCR-B. The TeX typesetting system has a public domain Constant Strokewidth OCR-B font in METAFONT definition form. It was created by Norbert Swartz in 1995 and updated in 2010. It has a setting for square stroke ends. The definition has also been translated to METATYPE1, so the rounded version is available in TrueType and OpenType too. A version of Constant Strokewidth OCR-B by Matthew Anderson has extended character coverage. It is available under CC-BY 4.0.

Baum–Welch algorithm

In electrical engineering, statistical computing and bioinformatics, the Baum–Welch algorithm is a special case of the expectation–maximization algorithm used to find the unknown parameters of a hidden Markov model (HMM). It makes use of the forward-backward algorithm to compute the statistics for the expectation step. The Baum–Welch algorithm, the primary method for inference in hidden Markov models, is numerically unstable due to its recursive calculation of joint probabilities. As the number of variables grows, these joint probabilities become increasingly small, leading to the forward recursions rapidly approaching values below machine precision. == History == The Baum–Welch algorithm was named after its inventors Leonard E. Baum and Lloyd R. Welch. The algorithm and the Hidden Markov models were first described in a series of articles by Baum and his peers at the IDA Center for Communications Research, Princeton in the late 1960s and early 1970s. One of the first major applications of HMMs was to the field of speech processing. In the 1980s, HMMs were emerging as a useful tool in the analysis of biological systems and information, and in particular genetic information. They have since become an important tool in the probabilistic modeling of genomic sequences. == Description == A hidden Markov model describes the joint probability of a collection of "hidden" and observed discrete random variables. It relies on the assumption that the i-th hidden variable given the (i − 1)-th hidden variable is independent of previous hidden variables, and the current observation variables depend only on the current hidden state. The Baum–Welch algorithm uses the well known EM algorithm to find the maximum likelihood estimate of the parameters of a hidden Markov model given a set of observed feature vectors. Let X t {\displaystyle X_{t}} be a discrete hidden random variable with N {\displaystyle N} possible values (i.e. We assume there are N {\displaystyle N} states in total). We assume the P ( X t ∣ X t − 1 ) {\displaystyle P(X_{t}\mid X_{t-1})} is independent of time t {\displaystyle t} , which leads to the definition of the time-independent stochastic transition matrix A = { a i j } = P ( X t = j ∣ X t − 1 = i ) . {\displaystyle A=\{a_{ij}\}=P(X_{t}=j\mid X_{t-1}=i).} The initial state distribution (i.e. when t = 1 {\displaystyle t=1} ) is given by π i = P ( X 1 = i ) . {\displaystyle \pi _{i}=P(X_{1}=i).} The observation variables Y t {\displaystyle Y_{t}} can take one of K {\displaystyle K} possible values. We also assume the observation given the "hidden" state is time independent. The probability of a certain observation y i {\displaystyle y_{i}} at time t {\displaystyle t} for state X t = j {\displaystyle X_{t}=j} is given by b j ( y i ) = P ( Y t = y i ∣ X t = j ) . {\displaystyle b_{j}(y_{i})=P(Y_{t}=y_{i}\mid X_{t}=j).} Taking into account all the possible values of Y t {\displaystyle Y_{t}} and X t {\displaystyle X_{t}} , we obtain the N × K {\displaystyle N\times K} matrix B = { b j ( y i ) } {\displaystyle B=\{b_{j}(y_{i})\}} where b j {\displaystyle b_{j}} belongs to all the possible states and y i {\displaystyle y_{i}} belongs to all the observations. An observation sequence is given by Y = ( Y 1 = y 1 , Y 2 = y 2 , … , Y T = y T ) {\displaystyle Y=(Y_{1}=y_{1},Y_{2}=y_{2},\ldots ,Y_{T}=y_{T})} . Thus we can describe a hidden Markov chain by θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} . The Baum–Welch algorithm finds a local maximum for θ ∗ = a r g m a x θ ⁡ P ( Y ∣ θ ) {\displaystyle \theta ^{}=\operatorname {arg\,max} _{\theta }P(Y\mid \theta )} (i.e. the HMM parameters θ {\displaystyle \theta } that maximize the probability of the observation). === Algorithm === Set θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} with random initial conditions. They can also be set using prior information about the parameters if it is available; this can speed up the algorithm and also steer it toward the desired local maximum. ==== Forward procedure ==== Let α i ( t ) = P ( Y 1 = y 1 , … , Y t = y t , X t = i ∣ θ ) {\displaystyle \alpha _{i}(t)=P(Y_{1}=y_{1},\ldots ,Y_{t}=y_{t},X_{t}=i\mid \theta )} , the probability of seeing the observations y 1 , y 2 , … , y t {\displaystyle y_{1},y_{2},\ldots ,y_{t}} and being in state i {\displaystyle i} at time t {\displaystyle t} . This is found recursively: α i ( 1 ) = π i b i ( y 1 ) , {\displaystyle \alpha _{i}(1)=\pi _{i}b_{i}(y_{1}),} α i ( t + 1 ) = b i ( y t + 1 ) ∑ j = 1 N α j ( t ) a j i . {\displaystyle \alpha _{i}(t+1)=b_{i}(y_{t+1})\sum _{j=1}^{N}\alpha _{j}(t)a_{ji}.} Since this series converges exponentially to zero, the algorithm will numerically underflow for longer sequences. However, this can be avoided in a slightly modified algorithm by scaling α {\displaystyle \alpha } in the forward and β {\displaystyle \beta } in the backward procedure below. ==== Backward procedure ==== Let β i ( t ) = P ( Y t + 1 = y t + 1 , … , Y T = y T ∣ X t = i , θ ) {\displaystyle \beta _{i}(t)=P(Y_{t+1}=y_{t+1},\ldots ,Y_{T}=y_{T}\mid X_{t}=i,\theta )} that is the probability of the ending partial sequence y t + 1 , … , y T {\displaystyle y_{t+1},\ldots ,y_{T}} given starting state i {\displaystyle i} at time t {\displaystyle t} . We calculate β i ( t ) {\displaystyle \beta _{i}(t)} as, β i ( T ) = 1 , {\displaystyle \beta _{i}(T)=1,} β i ( t ) = ∑ j = 1 N β j ( t + 1 ) a i j b j ( y t + 1 ) . {\displaystyle \beta _{i}(t)=\sum _{j=1}^{N}\beta _{j}(t+1)a_{ij}b_{j}(y_{t+1}).} ==== Update ==== We can now calculate the temporary variables, according to Bayes' theorem: γ i ( t ) = P ( X t = i ∣ Y , θ ) = P ( X t = i , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) β i ( t ) ∑ j = 1 N α j ( t ) β j ( t ) , {\displaystyle \gamma _{i}(t)=P(X_{t}=i\mid Y,\theta )={\frac {P(X_{t}=i,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)\beta _{i}(t)}{\sum _{j=1}^{N}\alpha _{j}(t)\beta _{j}(t)}},} which is the probability of being in state i {\displaystyle i} at time t {\displaystyle t} given the observed sequence Y {\displaystyle Y} and the parameters θ {\displaystyle \theta } ξ i j ( t ) = P ( X t = i , X t + 1 = j ∣ Y , θ ) = P ( X t = i , X t + 1 = j , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) a i j β j ( t + 1 ) b j ( y t + 1 ) ∑ k = 1 N ∑ w = 1 N α k ( t ) a k w β w ( t + 1 ) b w ( y t + 1 ) , {\displaystyle \xi _{ij}(t)=P(X_{t}=i,X_{t+1}=j\mid Y,\theta )={\frac {P(X_{t}=i,X_{t+1}=j,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)a_{ij}\beta _{j}(t+1)b_{j}(y_{t+1})}{\sum _{k=1}^{N}\sum _{w=1}^{N}\alpha _{k}(t)a_{kw}\beta _{w}(t+1)b_{w}(y_{t+1})}},} which is the probability of being in state i {\displaystyle i} and j {\displaystyle j} at times t {\displaystyle t} and t + 1 {\displaystyle t+1} respectively given the observed sequence Y {\displaystyle Y} and parameters θ {\displaystyle \theta } . The denominators of γ i ( t ) {\displaystyle \gamma _{i}(t)} and ξ i j ( t ) {\displaystyle \xi _{ij}(t)} are the same ; they represent the probability of making the observation Y {\displaystyle Y} given the parameters θ {\displaystyle \theta } . The parameters of the hidden Markov model θ {\displaystyle \theta } can now be updated: π i ∗ = γ i ( 1 ) , {\displaystyle \pi _{i}^{}=\gamma _{i}(1),} which is the expected frequency spent in state i {\displaystyle i} at time 1 {\displaystyle 1} . a i j ∗ = ∑ t = 1 T − 1 ξ i j ( t ) ∑ t = 1 T − 1 γ i ( t ) , {\displaystyle a_{ij}^{}={\frac {\sum _{t=1}^{T-1}\xi _{ij}(t)}{\sum _{t=1}^{T-1}\gamma _{i}(t)}},} which is the expected number of transitions from state i to state j compared to the expected total number of transitions starting in state i, including from state i to itself. The number of transitions starting in state i is equivalent to the number of times state i is observed in the sequence from t = 1 to t = T − 1. b i ∗ ( v k ) = ∑ t = 1 T 1 y t = v k γ i ( t ) ∑ t = 1 T γ i ( t ) , {\displaystyle b_{i}^{}(v_{k})={\frac {\sum _{t=1}^{T}1_{y_{t}=v_{k}}\gamma _{i}(t)}{\sum _{t=1}^{T}\gamma _{i}(t)}},} where 1 y t = v k = { 1 if y t = v k , 0 otherwise {\displaystyle 1_{y_{t}=v_{k}}={\begin{cases}1&{\text{if }}y_{t}=v_{k},\\0&{\text{otherwise}}\end{cases}}} is an indicator function, and b i ∗ ( v k ) {\displaystyle b_{i}^{}(v_{k})} is the expected number of times the output observations have been equal to v k {\displaystyle v_{k}} while in state i {\displaystyle i} over the expected total number of times in state i {\displaystyle i} . These steps are now repeated iteratively until a desired level of convergence. Note: It is possible to over-fit a particular data set. That is, P ( Y ∣ θ final ) > P ( Y ∣ θ true ) {\displaystyle P(Y\mid \theta _{\text{final}})>P(Y\mid \theta _{\text{true}})} . The algorithm also does not guarantee a global maximum. ==== Multiple sequences ==== The algorithm described thus far assumes a single observed sequence Y = y 1 , … , y T {\displaystyle Y=y_{1},\ldots ,y_{T}} . However, in many situations, there are several sequences observed: Y 1 ,

Baum–Welch algorithm

In electrical engineering, statistical computing and bioinformatics, the Baum–Welch algorithm is a special case of the expectation–maximization algorithm used to find the unknown parameters of a hidden Markov model (HMM). It makes use of the forward-backward algorithm to compute the statistics for the expectation step. The Baum–Welch algorithm, the primary method for inference in hidden Markov models, is numerically unstable due to its recursive calculation of joint probabilities. As the number of variables grows, these joint probabilities become increasingly small, leading to the forward recursions rapidly approaching values below machine precision. == History == The Baum–Welch algorithm was named after its inventors Leonard E. Baum and Lloyd R. Welch. The algorithm and the Hidden Markov models were first described in a series of articles by Baum and his peers at the IDA Center for Communications Research, Princeton in the late 1960s and early 1970s. One of the first major applications of HMMs was to the field of speech processing. In the 1980s, HMMs were emerging as a useful tool in the analysis of biological systems and information, and in particular genetic information. They have since become an important tool in the probabilistic modeling of genomic sequences. == Description == A hidden Markov model describes the joint probability of a collection of "hidden" and observed discrete random variables. It relies on the assumption that the i-th hidden variable given the (i − 1)-th hidden variable is independent of previous hidden variables, and the current observation variables depend only on the current hidden state. The Baum–Welch algorithm uses the well known EM algorithm to find the maximum likelihood estimate of the parameters of a hidden Markov model given a set of observed feature vectors. Let X t {\displaystyle X_{t}} be a discrete hidden random variable with N {\displaystyle N} possible values (i.e. We assume there are N {\displaystyle N} states in total). We assume the P ( X t ∣ X t − 1 ) {\displaystyle P(X_{t}\mid X_{t-1})} is independent of time t {\displaystyle t} , which leads to the definition of the time-independent stochastic transition matrix A = { a i j } = P ( X t = j ∣ X t − 1 = i ) . {\displaystyle A=\{a_{ij}\}=P(X_{t}=j\mid X_{t-1}=i).} The initial state distribution (i.e. when t = 1 {\displaystyle t=1} ) is given by π i = P ( X 1 = i ) . {\displaystyle \pi _{i}=P(X_{1}=i).} The observation variables Y t {\displaystyle Y_{t}} can take one of K {\displaystyle K} possible values. We also assume the observation given the "hidden" state is time independent. The probability of a certain observation y i {\displaystyle y_{i}} at time t {\displaystyle t} for state X t = j {\displaystyle X_{t}=j} is given by b j ( y i ) = P ( Y t = y i ∣ X t = j ) . {\displaystyle b_{j}(y_{i})=P(Y_{t}=y_{i}\mid X_{t}=j).} Taking into account all the possible values of Y t {\displaystyle Y_{t}} and X t {\displaystyle X_{t}} , we obtain the N × K {\displaystyle N\times K} matrix B = { b j ( y i ) } {\displaystyle B=\{b_{j}(y_{i})\}} where b j {\displaystyle b_{j}} belongs to all the possible states and y i {\displaystyle y_{i}} belongs to all the observations. An observation sequence is given by Y = ( Y 1 = y 1 , Y 2 = y 2 , … , Y T = y T ) {\displaystyle Y=(Y_{1}=y_{1},Y_{2}=y_{2},\ldots ,Y_{T}=y_{T})} . Thus we can describe a hidden Markov chain by θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} . The Baum–Welch algorithm finds a local maximum for θ ∗ = a r g m a x θ ⁡ P ( Y ∣ θ ) {\displaystyle \theta ^{}=\operatorname {arg\,max} _{\theta }P(Y\mid \theta )} (i.e. the HMM parameters θ {\displaystyle \theta } that maximize the probability of the observation). === Algorithm === Set θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} with random initial conditions. They can also be set using prior information about the parameters if it is available; this can speed up the algorithm and also steer it toward the desired local maximum. ==== Forward procedure ==== Let α i ( t ) = P ( Y 1 = y 1 , … , Y t = y t , X t = i ∣ θ ) {\displaystyle \alpha _{i}(t)=P(Y_{1}=y_{1},\ldots ,Y_{t}=y_{t},X_{t}=i\mid \theta )} , the probability of seeing the observations y 1 , y 2 , … , y t {\displaystyle y_{1},y_{2},\ldots ,y_{t}} and being in state i {\displaystyle i} at time t {\displaystyle t} . This is found recursively: α i ( 1 ) = π i b i ( y 1 ) , {\displaystyle \alpha _{i}(1)=\pi _{i}b_{i}(y_{1}),} α i ( t + 1 ) = b i ( y t + 1 ) ∑ j = 1 N α j ( t ) a j i . {\displaystyle \alpha _{i}(t+1)=b_{i}(y_{t+1})\sum _{j=1}^{N}\alpha _{j}(t)a_{ji}.} Since this series converges exponentially to zero, the algorithm will numerically underflow for longer sequences. However, this can be avoided in a slightly modified algorithm by scaling α {\displaystyle \alpha } in the forward and β {\displaystyle \beta } in the backward procedure below. ==== Backward procedure ==== Let β i ( t ) = P ( Y t + 1 = y t + 1 , … , Y T = y T ∣ X t = i , θ ) {\displaystyle \beta _{i}(t)=P(Y_{t+1}=y_{t+1},\ldots ,Y_{T}=y_{T}\mid X_{t}=i,\theta )} that is the probability of the ending partial sequence y t + 1 , … , y T {\displaystyle y_{t+1},\ldots ,y_{T}} given starting state i {\displaystyle i} at time t {\displaystyle t} . We calculate β i ( t ) {\displaystyle \beta _{i}(t)} as, β i ( T ) = 1 , {\displaystyle \beta _{i}(T)=1,} β i ( t ) = ∑ j = 1 N β j ( t + 1 ) a i j b j ( y t + 1 ) . {\displaystyle \beta _{i}(t)=\sum _{j=1}^{N}\beta _{j}(t+1)a_{ij}b_{j}(y_{t+1}).} ==== Update ==== We can now calculate the temporary variables, according to Bayes' theorem: γ i ( t ) = P ( X t = i ∣ Y , θ ) = P ( X t = i , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) β i ( t ) ∑ j = 1 N α j ( t ) β j ( t ) , {\displaystyle \gamma _{i}(t)=P(X_{t}=i\mid Y,\theta )={\frac {P(X_{t}=i,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)\beta _{i}(t)}{\sum _{j=1}^{N}\alpha _{j}(t)\beta _{j}(t)}},} which is the probability of being in state i {\displaystyle i} at time t {\displaystyle t} given the observed sequence Y {\displaystyle Y} and the parameters θ {\displaystyle \theta } ξ i j ( t ) = P ( X t = i , X t + 1 = j ∣ Y , θ ) = P ( X t = i , X t + 1 = j , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) a i j β j ( t + 1 ) b j ( y t + 1 ) ∑ k = 1 N ∑ w = 1 N α k ( t ) a k w β w ( t + 1 ) b w ( y t + 1 ) , {\displaystyle \xi _{ij}(t)=P(X_{t}=i,X_{t+1}=j\mid Y,\theta )={\frac {P(X_{t}=i,X_{t+1}=j,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)a_{ij}\beta _{j}(t+1)b_{j}(y_{t+1})}{\sum _{k=1}^{N}\sum _{w=1}^{N}\alpha _{k}(t)a_{kw}\beta _{w}(t+1)b_{w}(y_{t+1})}},} which is the probability of being in state i {\displaystyle i} and j {\displaystyle j} at times t {\displaystyle t} and t + 1 {\displaystyle t+1} respectively given the observed sequence Y {\displaystyle Y} and parameters θ {\displaystyle \theta } . The denominators of γ i ( t ) {\displaystyle \gamma _{i}(t)} and ξ i j ( t ) {\displaystyle \xi _{ij}(t)} are the same ; they represent the probability of making the observation Y {\displaystyle Y} given the parameters θ {\displaystyle \theta } . The parameters of the hidden Markov model θ {\displaystyle \theta } can now be updated: π i ∗ = γ i ( 1 ) , {\displaystyle \pi _{i}^{}=\gamma _{i}(1),} which is the expected frequency spent in state i {\displaystyle i} at time 1 {\displaystyle 1} . a i j ∗ = ∑ t = 1 T − 1 ξ i j ( t ) ∑ t = 1 T − 1 γ i ( t ) , {\displaystyle a_{ij}^{}={\frac {\sum _{t=1}^{T-1}\xi _{ij}(t)}{\sum _{t=1}^{T-1}\gamma _{i}(t)}},} which is the expected number of transitions from state i to state j compared to the expected total number of transitions starting in state i, including from state i to itself. The number of transitions starting in state i is equivalent to the number of times state i is observed in the sequence from t = 1 to t = T − 1. b i ∗ ( v k ) = ∑ t = 1 T 1 y t = v k γ i ( t ) ∑ t = 1 T γ i ( t ) , {\displaystyle b_{i}^{}(v_{k})={\frac {\sum _{t=1}^{T}1_{y_{t}=v_{k}}\gamma _{i}(t)}{\sum _{t=1}^{T}\gamma _{i}(t)}},} where 1 y t = v k = { 1 if y t = v k , 0 otherwise {\displaystyle 1_{y_{t}=v_{k}}={\begin{cases}1&{\text{if }}y_{t}=v_{k},\\0&{\text{otherwise}}\end{cases}}} is an indicator function, and b i ∗ ( v k ) {\displaystyle b_{i}^{}(v_{k})} is the expected number of times the output observations have been equal to v k {\displaystyle v_{k}} while in state i {\displaystyle i} over the expected total number of times in state i {\displaystyle i} . These steps are now repeated iteratively until a desired level of convergence. Note: It is possible to over-fit a particular data set. That is, P ( Y ∣ θ final ) > P ( Y ∣ θ true ) {\displaystyle P(Y\mid \theta _{\text{final}})>P(Y\mid \theta _{\text{true}})} . The algorithm also does not guarantee a global maximum. ==== Multiple sequences ==== The algorithm described thus far assumes a single observed sequence Y = y 1 , … , y T {\displaystyle Y=y_{1},\ldots ,y_{T}} . However, in many situations, there are several sequences observed: Y 1 ,

Baum–Welch algorithm

In electrical engineering, statistical computing and bioinformatics, the Baum–Welch algorithm is a special case of the expectation–maximization algorithm used to find the unknown parameters of a hidden Markov model (HMM). It makes use of the forward-backward algorithm to compute the statistics for the expectation step. The Baum–Welch algorithm, the primary method for inference in hidden Markov models, is numerically unstable due to its recursive calculation of joint probabilities. As the number of variables grows, these joint probabilities become increasingly small, leading to the forward recursions rapidly approaching values below machine precision. == History == The Baum–Welch algorithm was named after its inventors Leonard E. Baum and Lloyd R. Welch. The algorithm and the Hidden Markov models were first described in a series of articles by Baum and his peers at the IDA Center for Communications Research, Princeton in the late 1960s and early 1970s. One of the first major applications of HMMs was to the field of speech processing. In the 1980s, HMMs were emerging as a useful tool in the analysis of biological systems and information, and in particular genetic information. They have since become an important tool in the probabilistic modeling of genomic sequences. == Description == A hidden Markov model describes the joint probability of a collection of "hidden" and observed discrete random variables. It relies on the assumption that the i-th hidden variable given the (i − 1)-th hidden variable is independent of previous hidden variables, and the current observation variables depend only on the current hidden state. The Baum–Welch algorithm uses the well known EM algorithm to find the maximum likelihood estimate of the parameters of a hidden Markov model given a set of observed feature vectors. Let X t {\displaystyle X_{t}} be a discrete hidden random variable with N {\displaystyle N} possible values (i.e. We assume there are N {\displaystyle N} states in total). We assume the P ( X t ∣ X t − 1 ) {\displaystyle P(X_{t}\mid X_{t-1})} is independent of time t {\displaystyle t} , which leads to the definition of the time-independent stochastic transition matrix A = { a i j } = P ( X t = j ∣ X t − 1 = i ) . {\displaystyle A=\{a_{ij}\}=P(X_{t}=j\mid X_{t-1}=i).} The initial state distribution (i.e. when t = 1 {\displaystyle t=1} ) is given by π i = P ( X 1 = i ) . {\displaystyle \pi _{i}=P(X_{1}=i).} The observation variables Y t {\displaystyle Y_{t}} can take one of K {\displaystyle K} possible values. We also assume the observation given the "hidden" state is time independent. The probability of a certain observation y i {\displaystyle y_{i}} at time t {\displaystyle t} for state X t = j {\displaystyle X_{t}=j} is given by b j ( y i ) = P ( Y t = y i ∣ X t = j ) . {\displaystyle b_{j}(y_{i})=P(Y_{t}=y_{i}\mid X_{t}=j).} Taking into account all the possible values of Y t {\displaystyle Y_{t}} and X t {\displaystyle X_{t}} , we obtain the N × K {\displaystyle N\times K} matrix B = { b j ( y i ) } {\displaystyle B=\{b_{j}(y_{i})\}} where b j {\displaystyle b_{j}} belongs to all the possible states and y i {\displaystyle y_{i}} belongs to all the observations. An observation sequence is given by Y = ( Y 1 = y 1 , Y 2 = y 2 , … , Y T = y T ) {\displaystyle Y=(Y_{1}=y_{1},Y_{2}=y_{2},\ldots ,Y_{T}=y_{T})} . Thus we can describe a hidden Markov chain by θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} . The Baum–Welch algorithm finds a local maximum for θ ∗ = a r g m a x θ ⁡ P ( Y ∣ θ ) {\displaystyle \theta ^{}=\operatorname {arg\,max} _{\theta }P(Y\mid \theta )} (i.e. the HMM parameters θ {\displaystyle \theta } that maximize the probability of the observation). === Algorithm === Set θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} with random initial conditions. They can also be set using prior information about the parameters if it is available; this can speed up the algorithm and also steer it toward the desired local maximum. ==== Forward procedure ==== Let α i ( t ) = P ( Y 1 = y 1 , … , Y t = y t , X t = i ∣ θ ) {\displaystyle \alpha _{i}(t)=P(Y_{1}=y_{1},\ldots ,Y_{t}=y_{t},X_{t}=i\mid \theta )} , the probability of seeing the observations y 1 , y 2 , … , y t {\displaystyle y_{1},y_{2},\ldots ,y_{t}} and being in state i {\displaystyle i} at time t {\displaystyle t} . This is found recursively: α i ( 1 ) = π i b i ( y 1 ) , {\displaystyle \alpha _{i}(1)=\pi _{i}b_{i}(y_{1}),} α i ( t + 1 ) = b i ( y t + 1 ) ∑ j = 1 N α j ( t ) a j i . {\displaystyle \alpha _{i}(t+1)=b_{i}(y_{t+1})\sum _{j=1}^{N}\alpha _{j}(t)a_{ji}.} Since this series converges exponentially to zero, the algorithm will numerically underflow for longer sequences. However, this can be avoided in a slightly modified algorithm by scaling α {\displaystyle \alpha } in the forward and β {\displaystyle \beta } in the backward procedure below. ==== Backward procedure ==== Let β i ( t ) = P ( Y t + 1 = y t + 1 , … , Y T = y T ∣ X t = i , θ ) {\displaystyle \beta _{i}(t)=P(Y_{t+1}=y_{t+1},\ldots ,Y_{T}=y_{T}\mid X_{t}=i,\theta )} that is the probability of the ending partial sequence y t + 1 , … , y T {\displaystyle y_{t+1},\ldots ,y_{T}} given starting state i {\displaystyle i} at time t {\displaystyle t} . We calculate β i ( t ) {\displaystyle \beta _{i}(t)} as, β i ( T ) = 1 , {\displaystyle \beta _{i}(T)=1,} β i ( t ) = ∑ j = 1 N β j ( t + 1 ) a i j b j ( y t + 1 ) . {\displaystyle \beta _{i}(t)=\sum _{j=1}^{N}\beta _{j}(t+1)a_{ij}b_{j}(y_{t+1}).} ==== Update ==== We can now calculate the temporary variables, according to Bayes' theorem: γ i ( t ) = P ( X t = i ∣ Y , θ ) = P ( X t = i , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) β i ( t ) ∑ j = 1 N α j ( t ) β j ( t ) , {\displaystyle \gamma _{i}(t)=P(X_{t}=i\mid Y,\theta )={\frac {P(X_{t}=i,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)\beta _{i}(t)}{\sum _{j=1}^{N}\alpha _{j}(t)\beta _{j}(t)}},} which is the probability of being in state i {\displaystyle i} at time t {\displaystyle t} given the observed sequence Y {\displaystyle Y} and the parameters θ {\displaystyle \theta } ξ i j ( t ) = P ( X t = i , X t + 1 = j ∣ Y , θ ) = P ( X t = i , X t + 1 = j , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) a i j β j ( t + 1 ) b j ( y t + 1 ) ∑ k = 1 N ∑ w = 1 N α k ( t ) a k w β w ( t + 1 ) b w ( y t + 1 ) , {\displaystyle \xi _{ij}(t)=P(X_{t}=i,X_{t+1}=j\mid Y,\theta )={\frac {P(X_{t}=i,X_{t+1}=j,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)a_{ij}\beta _{j}(t+1)b_{j}(y_{t+1})}{\sum _{k=1}^{N}\sum _{w=1}^{N}\alpha _{k}(t)a_{kw}\beta _{w}(t+1)b_{w}(y_{t+1})}},} which is the probability of being in state i {\displaystyle i} and j {\displaystyle j} at times t {\displaystyle t} and t + 1 {\displaystyle t+1} respectively given the observed sequence Y {\displaystyle Y} and parameters θ {\displaystyle \theta } . The denominators of γ i ( t ) {\displaystyle \gamma _{i}(t)} and ξ i j ( t ) {\displaystyle \xi _{ij}(t)} are the same ; they represent the probability of making the observation Y {\displaystyle Y} given the parameters θ {\displaystyle \theta } . The parameters of the hidden Markov model θ {\displaystyle \theta } can now be updated: π i ∗ = γ i ( 1 ) , {\displaystyle \pi _{i}^{}=\gamma _{i}(1),} which is the expected frequency spent in state i {\displaystyle i} at time 1 {\displaystyle 1} . a i j ∗ = ∑ t = 1 T − 1 ξ i j ( t ) ∑ t = 1 T − 1 γ i ( t ) , {\displaystyle a_{ij}^{}={\frac {\sum _{t=1}^{T-1}\xi _{ij}(t)}{\sum _{t=1}^{T-1}\gamma _{i}(t)}},} which is the expected number of transitions from state i to state j compared to the expected total number of transitions starting in state i, including from state i to itself. The number of transitions starting in state i is equivalent to the number of times state i is observed in the sequence from t = 1 to t = T − 1. b i ∗ ( v k ) = ∑ t = 1 T 1 y t = v k γ i ( t ) ∑ t = 1 T γ i ( t ) , {\displaystyle b_{i}^{}(v_{k})={\frac {\sum _{t=1}^{T}1_{y_{t}=v_{k}}\gamma _{i}(t)}{\sum _{t=1}^{T}\gamma _{i}(t)}},} where 1 y t = v k = { 1 if y t = v k , 0 otherwise {\displaystyle 1_{y_{t}=v_{k}}={\begin{cases}1&{\text{if }}y_{t}=v_{k},\\0&{\text{otherwise}}\end{cases}}} is an indicator function, and b i ∗ ( v k ) {\displaystyle b_{i}^{}(v_{k})} is the expected number of times the output observations have been equal to v k {\displaystyle v_{k}} while in state i {\displaystyle i} over the expected total number of times in state i {\displaystyle i} . These steps are now repeated iteratively until a desired level of convergence. Note: It is possible to over-fit a particular data set. That is, P ( Y ∣ θ final ) > P ( Y ∣ θ true ) {\displaystyle P(Y\mid \theta _{\text{final}})>P(Y\mid \theta _{\text{true}})} . The algorithm also does not guarantee a global maximum. ==== Multiple sequences ==== The algorithm described thus far assumes a single observed sequence Y = y 1 , … , y T {\displaystyle Y=y_{1},\ldots ,y_{T}} . However, in many situations, there are several sequences observed: Y 1 ,

Baum–Welch algorithm

In electrical engineering, statistical computing and bioinformatics, the Baum–Welch algorithm is a special case of the expectation–maximization algorithm used to find the unknown parameters of a hidden Markov model (HMM). It makes use of the forward-backward algorithm to compute the statistics for the expectation step. The Baum–Welch algorithm, the primary method for inference in hidden Markov models, is numerically unstable due to its recursive calculation of joint probabilities. As the number of variables grows, these joint probabilities become increasingly small, leading to the forward recursions rapidly approaching values below machine precision. == History == The Baum–Welch algorithm was named after its inventors Leonard E. Baum and Lloyd R. Welch. The algorithm and the Hidden Markov models were first described in a series of articles by Baum and his peers at the IDA Center for Communications Research, Princeton in the late 1960s and early 1970s. One of the first major applications of HMMs was to the field of speech processing. In the 1980s, HMMs were emerging as a useful tool in the analysis of biological systems and information, and in particular genetic information. They have since become an important tool in the probabilistic modeling of genomic sequences. == Description == A hidden Markov model describes the joint probability of a collection of "hidden" and observed discrete random variables. It relies on the assumption that the i-th hidden variable given the (i − 1)-th hidden variable is independent of previous hidden variables, and the current observation variables depend only on the current hidden state. The Baum–Welch algorithm uses the well known EM algorithm to find the maximum likelihood estimate of the parameters of a hidden Markov model given a set of observed feature vectors. Let X t {\displaystyle X_{t}} be a discrete hidden random variable with N {\displaystyle N} possible values (i.e. We assume there are N {\displaystyle N} states in total). We assume the P ( X t ∣ X t − 1 ) {\displaystyle P(X_{t}\mid X_{t-1})} is independent of time t {\displaystyle t} , which leads to the definition of the time-independent stochastic transition matrix A = { a i j } = P ( X t = j ∣ X t − 1 = i ) . {\displaystyle A=\{a_{ij}\}=P(X_{t}=j\mid X_{t-1}=i).} The initial state distribution (i.e. when t = 1 {\displaystyle t=1} ) is given by π i = P ( X 1 = i ) . {\displaystyle \pi _{i}=P(X_{1}=i).} The observation variables Y t {\displaystyle Y_{t}} can take one of K {\displaystyle K} possible values. We also assume the observation given the "hidden" state is time independent. The probability of a certain observation y i {\displaystyle y_{i}} at time t {\displaystyle t} for state X t = j {\displaystyle X_{t}=j} is given by b j ( y i ) = P ( Y t = y i ∣ X t = j ) . {\displaystyle b_{j}(y_{i})=P(Y_{t}=y_{i}\mid X_{t}=j).} Taking into account all the possible values of Y t {\displaystyle Y_{t}} and X t {\displaystyle X_{t}} , we obtain the N × K {\displaystyle N\times K} matrix B = { b j ( y i ) } {\displaystyle B=\{b_{j}(y_{i})\}} where b j {\displaystyle b_{j}} belongs to all the possible states and y i {\displaystyle y_{i}} belongs to all the observations. An observation sequence is given by Y = ( Y 1 = y 1 , Y 2 = y 2 , … , Y T = y T ) {\displaystyle Y=(Y_{1}=y_{1},Y_{2}=y_{2},\ldots ,Y_{T}=y_{T})} . Thus we can describe a hidden Markov chain by θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} . The Baum–Welch algorithm finds a local maximum for θ ∗ = a r g m a x θ ⁡ P ( Y ∣ θ ) {\displaystyle \theta ^{}=\operatorname {arg\,max} _{\theta }P(Y\mid \theta )} (i.e. the HMM parameters θ {\displaystyle \theta } that maximize the probability of the observation). === Algorithm === Set θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} with random initial conditions. They can also be set using prior information about the parameters if it is available; this can speed up the algorithm and also steer it toward the desired local maximum. ==== Forward procedure ==== Let α i ( t ) = P ( Y 1 = y 1 , … , Y t = y t , X t = i ∣ θ ) {\displaystyle \alpha _{i}(t)=P(Y_{1}=y_{1},\ldots ,Y_{t}=y_{t},X_{t}=i\mid \theta )} , the probability of seeing the observations y 1 , y 2 , … , y t {\displaystyle y_{1},y_{2},\ldots ,y_{t}} and being in state i {\displaystyle i} at time t {\displaystyle t} . This is found recursively: α i ( 1 ) = π i b i ( y 1 ) , {\displaystyle \alpha _{i}(1)=\pi _{i}b_{i}(y_{1}),} α i ( t + 1 ) = b i ( y t + 1 ) ∑ j = 1 N α j ( t ) a j i . {\displaystyle \alpha _{i}(t+1)=b_{i}(y_{t+1})\sum _{j=1}^{N}\alpha _{j}(t)a_{ji}.} Since this series converges exponentially to zero, the algorithm will numerically underflow for longer sequences. However, this can be avoided in a slightly modified algorithm by scaling α {\displaystyle \alpha } in the forward and β {\displaystyle \beta } in the backward procedure below. ==== Backward procedure ==== Let β i ( t ) = P ( Y t + 1 = y t + 1 , … , Y T = y T ∣ X t = i , θ ) {\displaystyle \beta _{i}(t)=P(Y_{t+1}=y_{t+1},\ldots ,Y_{T}=y_{T}\mid X_{t}=i,\theta )} that is the probability of the ending partial sequence y t + 1 , … , y T {\displaystyle y_{t+1},\ldots ,y_{T}} given starting state i {\displaystyle i} at time t {\displaystyle t} . We calculate β i ( t ) {\displaystyle \beta _{i}(t)} as, β i ( T ) = 1 , {\displaystyle \beta _{i}(T)=1,} β i ( t ) = ∑ j = 1 N β j ( t + 1 ) a i j b j ( y t + 1 ) . {\displaystyle \beta _{i}(t)=\sum _{j=1}^{N}\beta _{j}(t+1)a_{ij}b_{j}(y_{t+1}).} ==== Update ==== We can now calculate the temporary variables, according to Bayes' theorem: γ i ( t ) = P ( X t = i ∣ Y , θ ) = P ( X t = i , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) β i ( t ) ∑ j = 1 N α j ( t ) β j ( t ) , {\displaystyle \gamma _{i}(t)=P(X_{t}=i\mid Y,\theta )={\frac {P(X_{t}=i,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)\beta _{i}(t)}{\sum _{j=1}^{N}\alpha _{j}(t)\beta _{j}(t)}},} which is the probability of being in state i {\displaystyle i} at time t {\displaystyle t} given the observed sequence Y {\displaystyle Y} and the parameters θ {\displaystyle \theta } ξ i j ( t ) = P ( X t = i , X t + 1 = j ∣ Y , θ ) = P ( X t = i , X t + 1 = j , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) a i j β j ( t + 1 ) b j ( y t + 1 ) ∑ k = 1 N ∑ w = 1 N α k ( t ) a k w β w ( t + 1 ) b w ( y t + 1 ) , {\displaystyle \xi _{ij}(t)=P(X_{t}=i,X_{t+1}=j\mid Y,\theta )={\frac {P(X_{t}=i,X_{t+1}=j,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)a_{ij}\beta _{j}(t+1)b_{j}(y_{t+1})}{\sum _{k=1}^{N}\sum _{w=1}^{N}\alpha _{k}(t)a_{kw}\beta _{w}(t+1)b_{w}(y_{t+1})}},} which is the probability of being in state i {\displaystyle i} and j {\displaystyle j} at times t {\displaystyle t} and t + 1 {\displaystyle t+1} respectively given the observed sequence Y {\displaystyle Y} and parameters θ {\displaystyle \theta } . The denominators of γ i ( t ) {\displaystyle \gamma _{i}(t)} and ξ i j ( t ) {\displaystyle \xi _{ij}(t)} are the same ; they represent the probability of making the observation Y {\displaystyle Y} given the parameters θ {\displaystyle \theta } . The parameters of the hidden Markov model θ {\displaystyle \theta } can now be updated: π i ∗ = γ i ( 1 ) , {\displaystyle \pi _{i}^{}=\gamma _{i}(1),} which is the expected frequency spent in state i {\displaystyle i} at time 1 {\displaystyle 1} . a i j ∗ = ∑ t = 1 T − 1 ξ i j ( t ) ∑ t = 1 T − 1 γ i ( t ) , {\displaystyle a_{ij}^{}={\frac {\sum _{t=1}^{T-1}\xi _{ij}(t)}{\sum _{t=1}^{T-1}\gamma _{i}(t)}},} which is the expected number of transitions from state i to state j compared to the expected total number of transitions starting in state i, including from state i to itself. The number of transitions starting in state i is equivalent to the number of times state i is observed in the sequence from t = 1 to t = T − 1. b i ∗ ( v k ) = ∑ t = 1 T 1 y t = v k γ i ( t ) ∑ t = 1 T γ i ( t ) , {\displaystyle b_{i}^{}(v_{k})={\frac {\sum _{t=1}^{T}1_{y_{t}=v_{k}}\gamma _{i}(t)}{\sum _{t=1}^{T}\gamma _{i}(t)}},} where 1 y t = v k = { 1 if y t = v k , 0 otherwise {\displaystyle 1_{y_{t}=v_{k}}={\begin{cases}1&{\text{if }}y_{t}=v_{k},\\0&{\text{otherwise}}\end{cases}}} is an indicator function, and b i ∗ ( v k ) {\displaystyle b_{i}^{}(v_{k})} is the expected number of times the output observations have been equal to v k {\displaystyle v_{k}} while in state i {\displaystyle i} over the expected total number of times in state i {\displaystyle i} . These steps are now repeated iteratively until a desired level of convergence. Note: It is possible to over-fit a particular data set. That is, P ( Y ∣ θ final ) > P ( Y ∣ θ true ) {\displaystyle P(Y\mid \theta _{\text{final}})>P(Y\mid \theta _{\text{true}})} . The algorithm also does not guarantee a global maximum. ==== Multiple sequences ==== The algorithm described thus far assumes a single observed sequence Y = y 1 , … , y T {\displaystyle Y=y_{1},\ldots ,y_{T}} . However, in many situations, there are several sequences observed: Y 1 ,

Baum–Welch algorithm

In electrical engineering, statistical computing and bioinformatics, the Baum–Welch algorithm is a special case of the expectation–maximization algorithm used to find the unknown parameters of a hidden Markov model (HMM). It makes use of the forward-backward algorithm to compute the statistics for the expectation step. The Baum–Welch algorithm, the primary method for inference in hidden Markov models, is numerically unstable due to its recursive calculation of joint probabilities. As the number of variables grows, these joint probabilities become increasingly small, leading to the forward recursions rapidly approaching values below machine precision. == History == The Baum–Welch algorithm was named after its inventors Leonard E. Baum and Lloyd R. Welch. The algorithm and the Hidden Markov models were first described in a series of articles by Baum and his peers at the IDA Center for Communications Research, Princeton in the late 1960s and early 1970s. One of the first major applications of HMMs was to the field of speech processing. In the 1980s, HMMs were emerging as a useful tool in the analysis of biological systems and information, and in particular genetic information. They have since become an important tool in the probabilistic modeling of genomic sequences. == Description == A hidden Markov model describes the joint probability of a collection of "hidden" and observed discrete random variables. It relies on the assumption that the i-th hidden variable given the (i − 1)-th hidden variable is independent of previous hidden variables, and the current observation variables depend only on the current hidden state. The Baum–Welch algorithm uses the well known EM algorithm to find the maximum likelihood estimate of the parameters of a hidden Markov model given a set of observed feature vectors. Let X t {\displaystyle X_{t}} be a discrete hidden random variable with N {\displaystyle N} possible values (i.e. We assume there are N {\displaystyle N} states in total). We assume the P ( X t ∣ X t − 1 ) {\displaystyle P(X_{t}\mid X_{t-1})} is independent of time t {\displaystyle t} , which leads to the definition of the time-independent stochastic transition matrix A = { a i j } = P ( X t = j ∣ X t − 1 = i ) . {\displaystyle A=\{a_{ij}\}=P(X_{t}=j\mid X_{t-1}=i).} The initial state distribution (i.e. when t = 1 {\displaystyle t=1} ) is given by π i = P ( X 1 = i ) . {\displaystyle \pi _{i}=P(X_{1}=i).} The observation variables Y t {\displaystyle Y_{t}} can take one of K {\displaystyle K} possible values. We also assume the observation given the "hidden" state is time independent. The probability of a certain observation y i {\displaystyle y_{i}} at time t {\displaystyle t} for state X t = j {\displaystyle X_{t}=j} is given by b j ( y i ) = P ( Y t = y i ∣ X t = j ) . {\displaystyle b_{j}(y_{i})=P(Y_{t}=y_{i}\mid X_{t}=j).} Taking into account all the possible values of Y t {\displaystyle Y_{t}} and X t {\displaystyle X_{t}} , we obtain the N × K {\displaystyle N\times K} matrix B = { b j ( y i ) } {\displaystyle B=\{b_{j}(y_{i})\}} where b j {\displaystyle b_{j}} belongs to all the possible states and y i {\displaystyle y_{i}} belongs to all the observations. An observation sequence is given by Y = ( Y 1 = y 1 , Y 2 = y 2 , … , Y T = y T ) {\displaystyle Y=(Y_{1}=y_{1},Y_{2}=y_{2},\ldots ,Y_{T}=y_{T})} . Thus we can describe a hidden Markov chain by θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} . The Baum–Welch algorithm finds a local maximum for θ ∗ = a r g m a x θ ⁡ P ( Y ∣ θ ) {\displaystyle \theta ^{}=\operatorname {arg\,max} _{\theta }P(Y\mid \theta )} (i.e. the HMM parameters θ {\displaystyle \theta } that maximize the probability of the observation). === Algorithm === Set θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} with random initial conditions. They can also be set using prior information about the parameters if it is available; this can speed up the algorithm and also steer it toward the desired local maximum. ==== Forward procedure ==== Let α i ( t ) = P ( Y 1 = y 1 , … , Y t = y t , X t = i ∣ θ ) {\displaystyle \alpha _{i}(t)=P(Y_{1}=y_{1},\ldots ,Y_{t}=y_{t},X_{t}=i\mid \theta )} , the probability of seeing the observations y 1 , y 2 , … , y t {\displaystyle y_{1},y_{2},\ldots ,y_{t}} and being in state i {\displaystyle i} at time t {\displaystyle t} . This is found recursively: α i ( 1 ) = π i b i ( y 1 ) , {\displaystyle \alpha _{i}(1)=\pi _{i}b_{i}(y_{1}),} α i ( t + 1 ) = b i ( y t + 1 ) ∑ j = 1 N α j ( t ) a j i . {\displaystyle \alpha _{i}(t+1)=b_{i}(y_{t+1})\sum _{j=1}^{N}\alpha _{j}(t)a_{ji}.} Since this series converges exponentially to zero, the algorithm will numerically underflow for longer sequences. However, this can be avoided in a slightly modified algorithm by scaling α {\displaystyle \alpha } in the forward and β {\displaystyle \beta } in the backward procedure below. ==== Backward procedure ==== Let β i ( t ) = P ( Y t + 1 = y t + 1 , … , Y T = y T ∣ X t = i , θ ) {\displaystyle \beta _{i}(t)=P(Y_{t+1}=y_{t+1},\ldots ,Y_{T}=y_{T}\mid X_{t}=i,\theta )} that is the probability of the ending partial sequence y t + 1 , … , y T {\displaystyle y_{t+1},\ldots ,y_{T}} given starting state i {\displaystyle i} at time t {\displaystyle t} . We calculate β i ( t ) {\displaystyle \beta _{i}(t)} as, β i ( T ) = 1 , {\displaystyle \beta _{i}(T)=1,} β i ( t ) = ∑ j = 1 N β j ( t + 1 ) a i j b j ( y t + 1 ) . {\displaystyle \beta _{i}(t)=\sum _{j=1}^{N}\beta _{j}(t+1)a_{ij}b_{j}(y_{t+1}).} ==== Update ==== We can now calculate the temporary variables, according to Bayes' theorem: γ i ( t ) = P ( X t = i ∣ Y , θ ) = P ( X t = i , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) β i ( t ) ∑ j = 1 N α j ( t ) β j ( t ) , {\displaystyle \gamma _{i}(t)=P(X_{t}=i\mid Y,\theta )={\frac {P(X_{t}=i,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)\beta _{i}(t)}{\sum _{j=1}^{N}\alpha _{j}(t)\beta _{j}(t)}},} which is the probability of being in state i {\displaystyle i} at time t {\displaystyle t} given the observed sequence Y {\displaystyle Y} and the parameters θ {\displaystyle \theta } ξ i j ( t ) = P ( X t = i , X t + 1 = j ∣ Y , θ ) = P ( X t = i , X t + 1 = j , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) a i j β j ( t + 1 ) b j ( y t + 1 ) ∑ k = 1 N ∑ w = 1 N α k ( t ) a k w β w ( t + 1 ) b w ( y t + 1 ) , {\displaystyle \xi _{ij}(t)=P(X_{t}=i,X_{t+1}=j\mid Y,\theta )={\frac {P(X_{t}=i,X_{t+1}=j,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)a_{ij}\beta _{j}(t+1)b_{j}(y_{t+1})}{\sum _{k=1}^{N}\sum _{w=1}^{N}\alpha _{k}(t)a_{kw}\beta _{w}(t+1)b_{w}(y_{t+1})}},} which is the probability of being in state i {\displaystyle i} and j {\displaystyle j} at times t {\displaystyle t} and t + 1 {\displaystyle t+1} respectively given the observed sequence Y {\displaystyle Y} and parameters θ {\displaystyle \theta } . The denominators of γ i ( t ) {\displaystyle \gamma _{i}(t)} and ξ i j ( t ) {\displaystyle \xi _{ij}(t)} are the same ; they represent the probability of making the observation Y {\displaystyle Y} given the parameters θ {\displaystyle \theta } . The parameters of the hidden Markov model θ {\displaystyle \theta } can now be updated: π i ∗ = γ i ( 1 ) , {\displaystyle \pi _{i}^{}=\gamma _{i}(1),} which is the expected frequency spent in state i {\displaystyle i} at time 1 {\displaystyle 1} . a i j ∗ = ∑ t = 1 T − 1 ξ i j ( t ) ∑ t = 1 T − 1 γ i ( t ) , {\displaystyle a_{ij}^{}={\frac {\sum _{t=1}^{T-1}\xi _{ij}(t)}{\sum _{t=1}^{T-1}\gamma _{i}(t)}},} which is the expected number of transitions from state i to state j compared to the expected total number of transitions starting in state i, including from state i to itself. The number of transitions starting in state i is equivalent to the number of times state i is observed in the sequence from t = 1 to t = T − 1. b i ∗ ( v k ) = ∑ t = 1 T 1 y t = v k γ i ( t ) ∑ t = 1 T γ i ( t ) , {\displaystyle b_{i}^{}(v_{k})={\frac {\sum _{t=1}^{T}1_{y_{t}=v_{k}}\gamma _{i}(t)}{\sum _{t=1}^{T}\gamma _{i}(t)}},} where 1 y t = v k = { 1 if y t = v k , 0 otherwise {\displaystyle 1_{y_{t}=v_{k}}={\begin{cases}1&{\text{if }}y_{t}=v_{k},\\0&{\text{otherwise}}\end{cases}}} is an indicator function, and b i ∗ ( v k ) {\displaystyle b_{i}^{}(v_{k})} is the expected number of times the output observations have been equal to v k {\displaystyle v_{k}} while in state i {\displaystyle i} over the expected total number of times in state i {\displaystyle i} . These steps are now repeated iteratively until a desired level of convergence. Note: It is possible to over-fit a particular data set. That is, P ( Y ∣ θ final ) > P ( Y ∣ θ true ) {\displaystyle P(Y\mid \theta _{\text{final}})>P(Y\mid \theta _{\text{true}})} . The algorithm also does not guarantee a global maximum. ==== Multiple sequences ==== The algorithm described thus far assumes a single observed sequence Y = y 1 , … , y T {\displaystyle Y=y_{1},\ldots ,y_{T}} . However, in many situations, there are several sequences observed: Y 1 ,

Baum–Welch algorithm

In electrical engineering, statistical computing and bioinformatics, the Baum–Welch algorithm is a special case of the expectation–maximization algorithm used to find the unknown parameters of a hidden Markov model (HMM). It makes use of the forward-backward algorithm to compute the statistics for the expectation step. The Baum–Welch algorithm, the primary method for inference in hidden Markov models, is numerically unstable due to its recursive calculation of joint probabilities. As the number of variables grows, these joint probabilities become increasingly small, leading to the forward recursions rapidly approaching values below machine precision. == History == The Baum–Welch algorithm was named after its inventors Leonard E. Baum and Lloyd R. Welch. The algorithm and the Hidden Markov models were first described in a series of articles by Baum and his peers at the IDA Center for Communications Research, Princeton in the late 1960s and early 1970s. One of the first major applications of HMMs was to the field of speech processing. In the 1980s, HMMs were emerging as a useful tool in the analysis of biological systems and information, and in particular genetic information. They have since become an important tool in the probabilistic modeling of genomic sequences. == Description == A hidden Markov model describes the joint probability of a collection of "hidden" and observed discrete random variables. It relies on the assumption that the i-th hidden variable given the (i − 1)-th hidden variable is independent of previous hidden variables, and the current observation variables depend only on the current hidden state. The Baum–Welch algorithm uses the well known EM algorithm to find the maximum likelihood estimate of the parameters of a hidden Markov model given a set of observed feature vectors. Let X t {\displaystyle X_{t}} be a discrete hidden random variable with N {\displaystyle N} possible values (i.e. We assume there are N {\displaystyle N} states in total). We assume the P ( X t ∣ X t − 1 ) {\displaystyle P(X_{t}\mid X_{t-1})} is independent of time t {\displaystyle t} , which leads to the definition of the time-independent stochastic transition matrix A = { a i j } = P ( X t = j ∣ X t − 1 = i ) . {\displaystyle A=\{a_{ij}\}=P(X_{t}=j\mid X_{t-1}=i).} The initial state distribution (i.e. when t = 1 {\displaystyle t=1} ) is given by π i = P ( X 1 = i ) . {\displaystyle \pi _{i}=P(X_{1}=i).} The observation variables Y t {\displaystyle Y_{t}} can take one of K {\displaystyle K} possible values. We also assume the observation given the "hidden" state is time independent. The probability of a certain observation y i {\displaystyle y_{i}} at time t {\displaystyle t} for state X t = j {\displaystyle X_{t}=j} is given by b j ( y i ) = P ( Y t = y i ∣ X t = j ) . {\displaystyle b_{j}(y_{i})=P(Y_{t}=y_{i}\mid X_{t}=j).} Taking into account all the possible values of Y t {\displaystyle Y_{t}} and X t {\displaystyle X_{t}} , we obtain the N × K {\displaystyle N\times K} matrix B = { b j ( y i ) } {\displaystyle B=\{b_{j}(y_{i})\}} where b j {\displaystyle b_{j}} belongs to all the possible states and y i {\displaystyle y_{i}} belongs to all the observations. An observation sequence is given by Y = ( Y 1 = y 1 , Y 2 = y 2 , … , Y T = y T ) {\displaystyle Y=(Y_{1}=y_{1},Y_{2}=y_{2},\ldots ,Y_{T}=y_{T})} . Thus we can describe a hidden Markov chain by θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} . The Baum–Welch algorithm finds a local maximum for θ ∗ = a r g m a x θ ⁡ P ( Y ∣ θ ) {\displaystyle \theta ^{}=\operatorname {arg\,max} _{\theta }P(Y\mid \theta )} (i.e. the HMM parameters θ {\displaystyle \theta } that maximize the probability of the observation). === Algorithm === Set θ = ( A , B , π ) {\displaystyle \theta =(A,B,\pi )} with random initial conditions. They can also be set using prior information about the parameters if it is available; this can speed up the algorithm and also steer it toward the desired local maximum. ==== Forward procedure ==== Let α i ( t ) = P ( Y 1 = y 1 , … , Y t = y t , X t = i ∣ θ ) {\displaystyle \alpha _{i}(t)=P(Y_{1}=y_{1},\ldots ,Y_{t}=y_{t},X_{t}=i\mid \theta )} , the probability of seeing the observations y 1 , y 2 , … , y t {\displaystyle y_{1},y_{2},\ldots ,y_{t}} and being in state i {\displaystyle i} at time t {\displaystyle t} . This is found recursively: α i ( 1 ) = π i b i ( y 1 ) , {\displaystyle \alpha _{i}(1)=\pi _{i}b_{i}(y_{1}),} α i ( t + 1 ) = b i ( y t + 1 ) ∑ j = 1 N α j ( t ) a j i . {\displaystyle \alpha _{i}(t+1)=b_{i}(y_{t+1})\sum _{j=1}^{N}\alpha _{j}(t)a_{ji}.} Since this series converges exponentially to zero, the algorithm will numerically underflow for longer sequences. However, this can be avoided in a slightly modified algorithm by scaling α {\displaystyle \alpha } in the forward and β {\displaystyle \beta } in the backward procedure below. ==== Backward procedure ==== Let β i ( t ) = P ( Y t + 1 = y t + 1 , … , Y T = y T ∣ X t = i , θ ) {\displaystyle \beta _{i}(t)=P(Y_{t+1}=y_{t+1},\ldots ,Y_{T}=y_{T}\mid X_{t}=i,\theta )} that is the probability of the ending partial sequence y t + 1 , … , y T {\displaystyle y_{t+1},\ldots ,y_{T}} given starting state i {\displaystyle i} at time t {\displaystyle t} . We calculate β i ( t ) {\displaystyle \beta _{i}(t)} as, β i ( T ) = 1 , {\displaystyle \beta _{i}(T)=1,} β i ( t ) = ∑ j = 1 N β j ( t + 1 ) a i j b j ( y t + 1 ) . {\displaystyle \beta _{i}(t)=\sum _{j=1}^{N}\beta _{j}(t+1)a_{ij}b_{j}(y_{t+1}).} ==== Update ==== We can now calculate the temporary variables, according to Bayes' theorem: γ i ( t ) = P ( X t = i ∣ Y , θ ) = P ( X t = i , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) β i ( t ) ∑ j = 1 N α j ( t ) β j ( t ) , {\displaystyle \gamma _{i}(t)=P(X_{t}=i\mid Y,\theta )={\frac {P(X_{t}=i,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)\beta _{i}(t)}{\sum _{j=1}^{N}\alpha _{j}(t)\beta _{j}(t)}},} which is the probability of being in state i {\displaystyle i} at time t {\displaystyle t} given the observed sequence Y {\displaystyle Y} and the parameters θ {\displaystyle \theta } ξ i j ( t ) = P ( X t = i , X t + 1 = j ∣ Y , θ ) = P ( X t = i , X t + 1 = j , Y ∣ θ ) P ( Y ∣ θ ) = α i ( t ) a i j β j ( t + 1 ) b j ( y t + 1 ) ∑ k = 1 N ∑ w = 1 N α k ( t ) a k w β w ( t + 1 ) b w ( y t + 1 ) , {\displaystyle \xi _{ij}(t)=P(X_{t}=i,X_{t+1}=j\mid Y,\theta )={\frac {P(X_{t}=i,X_{t+1}=j,Y\mid \theta )}{P(Y\mid \theta )}}={\frac {\alpha _{i}(t)a_{ij}\beta _{j}(t+1)b_{j}(y_{t+1})}{\sum _{k=1}^{N}\sum _{w=1}^{N}\alpha _{k}(t)a_{kw}\beta _{w}(t+1)b_{w}(y_{t+1})}},} which is the probability of being in state i {\displaystyle i} and j {\displaystyle j} at times t {\displaystyle t} and t + 1 {\displaystyle t+1} respectively given the observed sequence Y {\displaystyle Y} and parameters θ {\displaystyle \theta } . The denominators of γ i ( t ) {\displaystyle \gamma _{i}(t)} and ξ i j ( t ) {\displaystyle \xi _{ij}(t)} are the same ; they represent the probability of making the observation Y {\displaystyle Y} given the parameters θ {\displaystyle \theta } . The parameters of the hidden Markov model θ {\displaystyle \theta } can now be updated: π i ∗ = γ i ( 1 ) , {\displaystyle \pi _{i}^{}=\gamma _{i}(1),} which is the expected frequency spent in state i {\displaystyle i} at time 1 {\displaystyle 1} . a i j ∗ = ∑ t = 1 T − 1 ξ i j ( t ) ∑ t = 1 T − 1 γ i ( t ) , {\displaystyle a_{ij}^{}={\frac {\sum _{t=1}^{T-1}\xi _{ij}(t)}{\sum _{t=1}^{T-1}\gamma _{i}(t)}},} which is the expected number of transitions from state i to state j compared to the expected total number of transitions starting in state i, including from state i to itself. The number of transitions starting in state i is equivalent to the number of times state i is observed in the sequence from t = 1 to t = T − 1. b i ∗ ( v k ) = ∑ t = 1 T 1 y t = v k γ i ( t ) ∑ t = 1 T γ i ( t ) , {\displaystyle b_{i}^{}(v_{k})={\frac {\sum _{t=1}^{T}1_{y_{t}=v_{k}}\gamma _{i}(t)}{\sum _{t=1}^{T}\gamma _{i}(t)}},} where 1 y t = v k = { 1 if y t = v k , 0 otherwise {\displaystyle 1_{y_{t}=v_{k}}={\begin{cases}1&{\text{if }}y_{t}=v_{k},\\0&{\text{otherwise}}\end{cases}}} is an indicator function, and b i ∗ ( v k ) {\displaystyle b_{i}^{}(v_{k})} is the expected number of times the output observations have been equal to v k {\displaystyle v_{k}} while in state i {\displaystyle i} over the expected total number of times in state i {\displaystyle i} . These steps are now repeated iteratively until a desired level of convergence. Note: It is possible to over-fit a particular data set. That is, P ( Y ∣ θ final ) > P ( Y ∣ θ true ) {\displaystyle P(Y\mid \theta _{\text{final}})>P(Y\mid \theta _{\text{true}})} . The algorithm also does not guarantee a global maximum. ==== Multiple sequences ==== The algorithm described thus far assumes a single observed sequence Y = y 1 , … , y T {\displaystyle Y=y_{1},\ldots ,y_{T}} . However, in many situations, there are several sequences observed: Y 1 ,