Seven clusters in genomic triplet distributions

Motivation: In several recent papers new algorithms were proposed for detecting coding regions without requiring learning dataset of already known genes. In this paper we studied cluster structure of several genomes in the space of codon usage. This allowed to interpret some of the results obtained in other studies and propose a simpler method, which is, nevertheless, fully functional. Results: Several complete genomic sequences were analyzed, using visualization of tables of triplet counts in a sliding window. The distribution of 64-dimensional vectors of triplet frequencies displays a well-detectable cluster structure. The structure was found to consist of seven clusters, corresponding to protein-coding information in three possible phases in one of the two complementary strands and in the non-coding regions. Awareness of the existence of this structure allows development of methods for the segmentation of sequences into regions with the same coding phase and non-coding regions. This method may be completely unsupervised or use some external information. Since the method does not need extraction of ORFs, it can be applied even for unassembled genomes. Accuracy calculated on the base-pair level (both sensitivity and specificity) exceeds 90%. This is not worse as compared to such methods as HMM, however, has the advantage to be much simpler and clear

Estimation of Viterbi path in Bayesian hidden Markov models

The article studies different methods for estimating the Viterbi path in the Bayesian framework. The Viterbi path is an estimate of the underlying state path in hidden Markov models (HMMs), which has a maximum joint posterior probability. Hence it is also called the maximum a posteriori (MAP) path. For an HMM with given parameters, the Viterbi path can be easily found with the Viterbi algorithm. In the Bayesian framework the Viterbi algorithm is not applicable and several iterative methods can be used instead. We introduce a new EM-type algorithm for finding the MAP path and compare it with various other methods for finding the MAP path, including the variational Bayes approach and MCMC methods. Examples with simulated data are used to compare the performance of the methods. The main focus is on non-stochastic iterative methods and our results show that the best of those methods work as well or better than the best MCMC methods. Our results demonstrate that when the primary goal is segmentation, then it is more reasonable to perform segmentation directly by considering the transition and emission parameters as nuisance parameters.Peer reviewe

Lower limb locomotion activity recognition of healthy individuals using semi-Markov model and single wearable inertial sensor

International audienceLower limb locomotion activity is of great interest in the field of human activity recognition. In this work, a triplet semi-Markov model-based method is proposed to recognize the locomotion activities of healthy individuals when lower limbs move periodically. In the proposed algorithm, the gait phases (or leg phases) are introduced into the hidden states, and Gaussian mixture density is introduced to represent the complex conditioned observation density. The introduced sojourn state forms the semi-Markov structure, which naturally replicates the real transition of activity and gait during motion. Then, batch mode and on-line Expectation-Maximization (EM) algorithms are proposed, respectively, for model training and adaptive on-line recognition. The algorithm is tested on two datasets collected from wearable inertial sensors. The batch mode recognition accuracy reaches up to 95.16%, whereas the adaptive on-line recognition gradually obtains high accuracy after the time required for model updating. Experimental results show an improvement in performance compared to the other competitive algorithm

Two-Step Active Learning for Instance Segmentation with Uncertainty and Diversity Sampling

Training high-quality instance segmentation models requires an abundance of labeled images with instance masks and classifications, which is often expensive to procure. Active learning addresses this challenge by striving for optimum performance with minimal labeling cost by selecting the most informative and representative images for labeling. Despite its potential, active learning has been less explored in instance segmentation compared to other tasks like image classification, which require less labeling. In this study, we propose a post-hoc active learning algorithm that integrates uncertainty-based sampling with diversity-based sampling. Our proposed algorithm is not only simple and easy to implement, but it also delivers superior performance on various datasets. Its practical application is demonstrated on a real-world overhead imagery dataset, where it increases the labeling efficiency fivefold.Comment: UNCV ICCV 202