2,693 research outputs found
A linear memory algorithm for Baum-Welch training
Background: Baum-Welch training is an expectation-maximisation algorithm for
training the emission and transition probabilities of hidden Markov models in a
fully automated way.
Methods and results: We introduce a linear space algorithm for Baum-Welch
training. For a hidden Markov model with M states, T free transition and E free
emission parameters, and an input sequence of length L, our new algorithm
requires O(M) memory and O(L M T_max (T + E)) time for one Baum-Welch
iteration, where T_max is the maximum number of states that any state is
connected to. The most memory efficient algorithm until now was the
checkpointing algorithm with O(log(L) M) memory and O(log(L) L M T_max) time
requirement. Our novel algorithm thus renders the memory requirement completely
independent of the length of the training sequences. More generally, for an
n-hidden Markov model and n input sequences of length L, the memory requirement
of O(log(L) L^(n-1) M) is reduced to O(L^(n-1) M) memory while the running time
is changed from O(log(L) L^n M T_max + L^n (T + E)) to O(L^n M T_max (T + E)).
Conclusions: For the large class of hidden Markov models used for example in
gene prediction, whose number of states does not scale with the length of the
input sequence, our novel algorithm can thus be both faster and more
memory-efficient than any of the existing algorithms.Comment: 14 pages, 1 figure version 2: fixed some errors, final version of
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Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory
<p>Abstract</p> <p>Background</p> <p>The Baum-Welch learning procedure for Hidden Markov Models (HMMs) provides a powerful tool for tailoring HMM topologies to data for use in knowledge discovery and clustering. A linear memory procedure recently proposed by <it>Miklós, I. and Meyer, I.M. </it>describes a memory sparse version of the Baum-Welch algorithm with modifications to the original probabilistic table topologies to make memory use independent of sequence length (and linearly dependent on state number). The original description of the technique has some errors that we amend. We then compare the corrected implementation on a variety of data sets with conventional and checkpointing implementations.</p> <p>Results</p> <p>We provide a correct recurrence relation for the emission parameter estimate and extend it to parameter estimates of the Normal distribution. To accelerate estimation of the prior state probabilities, and decrease memory use, we reverse the originally proposed forward sweep. We describe different scaling strategies necessary in all real implementations of the algorithm to prevent underflow. In this paper we also describe our approach to a linear memory implementation of the Viterbi decoding algorithm (with linearity in the sequence length, while memory use is approximately independent of state number). We demonstrate the use of the linear memory implementation on an extended Duration Hidden Markov Model (DHMM) and on an HMM with a spike detection topology. Comparing the various implementations of the Baum-Welch procedure we find that the checkpointing algorithm produces the best overall tradeoff between memory use and speed. In cases where sequence length is very large (for Baum-Welch), or state number is very large (for Viterbi), the linear memory methods outlined may offer some utility.</p> <p>Conclusion</p> <p>Our performance-optimized Java implementations of Baum-Welch algorithm are available at <url>http://logos.cs.uno.edu/~achurban</url>. The described method and implementations will aid sequence alignment, gene structure prediction, HMM profile training, nanopore ionic flow blockades analysis and many other domains that require efficient HMM training with EM.</p
Unsupervised Neural Hidden Markov Models
In this work, we present the first results for neuralizing an Unsupervised
Hidden Markov Model. We evaluate our approach on tag in- duction. Our approach
outperforms existing generative models and is competitive with the
state-of-the-art though with a simpler model easily extended to include
additional context.Comment: accepted at EMNLP 2016, Workshop on Structured Prediction for NLP.
Oral presentatio
Duration modeling with expanded HMM applied to speech recognition
The occupancy of the HMM states is modeled by means of a Markov chain. A linear estimator is introduced to compute the probabilities of the Markov chain. The distribution function (DF) represents accurately the observed data. Representing the DF as a Markov chain allows the use of standard HMM recognizers. The increase of complexity is negligible in training and strongly limited during recognition. Experiments performed on acoustic-phonetic decoding shows how the phone recognition rate increases from 60.6 to 61.1. Furthermore, on a task of database inquires, where phones are used as subword units, the correct word rate increases from 88.2 to 88.4.Peer ReviewedPostprint (published version
Hierarchical Decomposition of Nonlinear Dynamics and Control for System Identification and Policy Distillation
The control of nonlinear dynamical systems remains a major challenge for
autonomous agents. Current trends in reinforcement learning (RL) focus on
complex representations of dynamics and policies, which have yielded impressive
results in solving a variety of hard control tasks. However, this new
sophistication and extremely over-parameterized models have come with the cost
of an overall reduction in our ability to interpret the resulting policies. In
this paper, we take inspiration from the control community and apply the
principles of hybrid switching systems in order to break down complex dynamics
into simpler components. We exploit the rich representational power of
probabilistic graphical models and derive an expectation-maximization (EM)
algorithm for learning a sequence model to capture the temporal structure of
the data and automatically decompose nonlinear dynamics into stochastic
switching linear dynamical systems. Moreover, we show how this framework of
switching models enables extracting hierarchies of Markovian and
auto-regressive locally linear controllers from nonlinear experts in an
imitation learning scenario.Comment: 2nd Annual Conference on Learning for Dynamics and Contro
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis
Profile hidden Markov models (pHMMs) are widely employed in various
bioinformatics applications to identify similarities between biological
sequences, such as DNA or protein sequences. In pHMMs, sequences are
represented as graph structures. These probabilities are subsequently used to
compute the similarity score between a sequence and a pHMM graph. The
Baum-Welch algorithm, a prevalent and highly accurate method, utilizes these
probabilities to optimize and compute similarity scores. However, the
Baum-Welch algorithm is computationally intensive, and existing solutions offer
either software-only or hardware-only approaches with fixed pHMM designs. We
identify an urgent need for a flexible, high-performance, and energy-efficient
HW/SW co-design to address the major inefficiencies in the Baum-Welch algorithm
for pHMMs.
We introduce ApHMM, the first flexible acceleration framework designed to
significantly reduce both computational and energy overheads associated with
the Baum-Welch algorithm for pHMMs. ApHMM tackles the major inefficiencies in
the Baum-Welch algorithm by 1) designing flexible hardware to accommodate
various pHMM designs, 2) exploiting predictable data dependency patterns
through on-chip memory with memoization techniques, 3) rapidly filtering out
negligible computations using a hardware-based filter, and 4) minimizing
redundant computations.
ApHMM achieves substantial speedups of 15.55x - 260.03x, 1.83x - 5.34x, and
27.97x when compared to CPU, GPU, and FPGA implementations of the Baum-Welch
algorithm, respectively. ApHMM outperforms state-of-the-art CPU implementations
in three key bioinformatics applications: 1) error correction, 2) protein
family search, and 3) multiple sequence alignment, by 1.29x - 59.94x, 1.03x -
1.75x, and 1.03x - 1.95x, respectively, while improving their energy efficiency
by 64.24x - 115.46x, 1.75x, 1.96x.Comment: Accepted to ACM TAC
Learning a Hybrid Architecture for Sequence Regression and Annotation
When learning a hidden Markov model (HMM), sequen- tial observations can
often be complemented by real-valued summary response variables generated from
the path of hid- den states. Such settings arise in numerous domains, includ-
ing many applications in biology, like motif discovery and genome annotation.
In this paper, we present a flexible frame- work for jointly modeling both
latent sequence features and the functional mapping that relates the summary
response variables to the hidden state sequence. The algorithm is com- patible
with a rich set of mapping functions. Results show that the availability of
additional continuous response vari- ables can simultaneously improve the
annotation of the se- quential observations and yield good prediction
performance in both synthetic data and real-world datasets.Comment: AAAI 201
Diffusion of Context and Credit Information in Markovian Models
This paper studies the problem of ergodicity of transition probability
matrices in Markovian models, such as hidden Markov models (HMMs), and how it
makes very difficult the task of learning to represent long-term context for
sequential data. This phenomenon hurts the forward propagation of long-term
context information, as well as learning a hidden state representation to
represent long-term context, which depends on propagating credit information
backwards in time. Using results from Markov chain theory, we show that this
problem of diffusion of context and credit is reduced when the transition
probabilities approach 0 or 1, i.e., the transition probability matrices are
sparse and the model essentially deterministic. The results found in this paper
apply to learning approaches based on continuous optimization, such as gradient
descent and the Baum-Welch algorithm.Comment: See http://www.jair.org/ for any accompanying file
HMMConverter 1.0: a toolbox for hidden Markov models
Hidden Markov models (HMMs) and their variants are widely used in Bioinformatics applications that analyze and compare biological sequences. Designing a novel application requires the insight of a human expert to define the model's architecture. The implementation of prediction algorithms and algorithms to train the model's parameters, however, can be a time-consuming and error-prone task. We here present HMMConverter, a software package for setting up probabilistic HMMs, pair-HMMs as well as generalized HMMs and pair-HMMs. The user defines the model itself and the algorithms to be used via an XML file which is then directly translated into efficient C++ code. The software package provides linear-memory prediction algorithms, such as the Hirschberg algorithm, banding and the integration of prior probabilities and is the first to present computationally efficient linear-memory algorithms for automatic parameter training. Users of HMMConverter can thus set up complex applications with a minimum of effort and also perform parameter training and data analyses for large data sets
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