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In order to solve the problem of low recognition accuracy of traditional pig sound recognition methods, deep neural network (DNN) and Hidden Markov Model (HMM) theory were used as the basis of pig sound signal recognition in this study. In this study, the sounds made by 10 landrace pigs during eating, estrus, howling, humming and panting were collected and preprocessed by Kalman filtering and an improved endpoint detection algorithm based on empirical mode decomposition-Teiger energy operator (EMD-TEO) cepstral distance. The extracted 39-dimensional mel-frequency cepstral coefficients (MFCCs) were then used as a dataset for network learning and recognition to build a DNN- and HMM-based sound recognition model for pig states. The results show that in the pig sound dataset, the recognition accuracy of DNN-HMM reaches 83%, which is 22% and 17% higher than that of the baseline models HMM and GMM-HMM, and possesses a better recognition effect. In a sub-dataset of the publicly available dataset AudioSet, DNN-HMM achieves a recognition accuracy of 79%, which is 8% and 4% higher than the classical models SVM and ResNet18, respectively, with better robustness.

Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.

Background HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins. Results We developed a single-instruction multiple-data (SIMD) vectorized implementation of the Viterbi algorithm for profile HMM alignment and introduced various other speed-ups. These accelerated the search methods HHsearch by a factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is ∼10× faster than PSI-BLAST and ∼20× faster than HMMER3. Jobs to perform HHsearch and HHblits searches with many query profile HMMs can be parallelized over cores and over cluster servers using OpenMP and message passing interface (MPI). The free, open-source, GPLv3-licensed software is available at https://github.com/soedinglab/hh-suite . Conclusion The added functionalities and increased speed of HHsearch and HHblits should facilitate their use in large-scale protein structure and function prediction, e.g. in metagenomics and genomics projects.

This manuscript introduces the end-to-end embedding of a CNN into a HMM, while interpreting the outputs of the CNN in a Bayesian framework. The hybrid CNN-HMM combines the strong discriminative abilities of CNNs with the sequence modelling capabilities of HMMs. Most current approaches in the field of gesture and sign language recognition disregard the necessity of dealing with sequence data both for training and evaluation. With our presented end-to-end embedding we are able to improve over the state-of-the-art on three challenging benchmark continuous sign language recognition tasks by between 15 and 38% relative reduction in word error rate and up to 20% absolute. We analyse the effect of the CNN structure, network pretraining and number of hidden states. We compare the hybrid modelling to a tandem approach and evaluate the gain of model combination.

Audio-visual speech recognition (AVSR) system is thought to be one of the most promising solutions for reliable speech recognition, particularly when the audio is corrupted by noise. However, cautious selection of sensory features is crucial for attaining high recognition performance. In the machine-learning community, deep learning approaches have recently attracted increasing attention because deep neural networks can effectively extract robust latent features that enable various recognition algorithms to demonstrate revolutionary generalization capabilities under diverse application conditions. This study introduces a connectionist-hidden Markov model (HMM) system for noise-robust AVSR. First, a deep denoising autoencoder is utilized for acquiring noise-robust audio features. By preparing the training data for the network with pairs of consecutive multiple steps of deteriorated audio features and the corresponding clean features, the network is trained to output denoised audio features from the corresponding features deteriorated by noise. Second, a convolutional neural network (CNN) is utilized to extract visual features from raw mouth area images. By preparing the training data for the CNN as pairs of raw images and the corresponding phoneme label outputs, the network is trained to predict phoneme labels from the corresponding mouth area input images. Finally, a multi-stream HMM (MSHMM) is applied for integrating the acquired audio and visual HMMs independently trained with the respective features. By comparing the cases when normal and denoised mel-frequency cepstral coefficients (MFCCs) are utilized as audio features to the HMM, our unimodal isolated word recognition results demonstrate that approximately 65 % word recognition rate gain is attained with denoised MFCCs under 10 dB signal-to-noise-ratio (SNR) for the audio signal input. Moreover, our multimodal isolated word recognition results utilizing MSHMM with denoised MFCCs and acquired visual features demonstrate that an additional word recognition rate gain is attained for the SNR conditions below 10 dB.

We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public repository, RVDB-prot aims to provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) protein profiles database for distant protein searching.

Automatic speech recognition, especially large vocabulary continuous speech recognition, is an important issue in the field of machine learning. For a long time, the hidden Markov model (HMM)-Gaussian mixed model (GMM) has been the mainstream speech recognition framework. But recently, HMM-deep neural network (DNN) model and the end-to-end model using deep learning has achieved performance beyond HMM-GMM. Both using deep learning techniques, these two models have comparable performances. However, the HMM-DNN model itself is limited by various unfavorable factors such as data forced segmentation alignment, independent hypothesis, and multi-module individual training inherited from HMM, while the end-to-end model has a simplified model, joint training, direct output, no need to force data alignment and other advantages. Therefore, the end-to-end model is an important research direction of speech recognition. In this paper we review the development of end-to-end model. This paper first introduces the basic ideas, advantages and disadvantages of HMM-based model and end-to-end models, and points out that end-to-end model is the development direction of speech recognition. Then the article focuses on the principles, progress and research hotspots of three different end-to-end models, which are connectionist temporal classification (CTC)-based, recurrent neural network (RNN)-transducer and attention-based, and makes theoretically and experimentally detailed comparisons. Their respective advantages and disadvantages and the possible future development of the end-to-end model are finally pointed out. Automatic speech recognition is a pattern recognition task in the field of computer science, which is a subject area of Symmetry.

Based on the combination of improved Local Mean Decomposition (LMD), Multi-scale Permutation Entropy (MPE) and Hidden Markov Model (HMM), the fault types of bearings are diagnosed. Improved LMD is proposed based on the self-similarity of roller bearing vibration signal by extending the right and left side of the original signal to suppress its edge effect. First, the vibration signals of the rolling bearing are decomposed into several product function (PF) components by improved LMD respectively. Then, the phase space reconstruction of the PF1 is carried out by using the mutual information (MI) method and the false nearest neighbor (FNN) method to calculate the delay time and the embedding dimension, and then the scale is set to obtain the MPE of PF1. After that, the MPE features of rolling bearings are extracted. Finally, the features of MPE are used as HMM training and diagnosis. The experimental results show that the proposed method can effectively identify the different faults of the rolling bearing.

Following an avalanche, one of the factors that affect victims’ chance of survival is the speed with which they are located and dug out. Rescue teams use techniques like trained rescue dogs and electronic transceivers to locate victims. However, the resources and time required to deploy rescue teams are major bottlenecks that decrease a victim’s chance of survival. Advances in the field of Unmanned Aerial Vehicles (UAVs) have enabled the use of flying robots equipped with sensors like optical cameras to assess the damage caused by natural or manmade disasters and locate victims in the debris. In this paper, we propose assisting avalanche search and rescue (SAR) operations with UAVs fitted with vision cameras. The sequence of images of the avalanche debris captured by the UAV is processed with a pre-trained Convolutional Neural Network (CNN) to extract discriminative features. A trained linear Support Vector Machine (SVM) is integrated at the top of the CNN to detect objects of interest. Moreover, we introduce a pre-processing method to increase the detection rate and a post-processing method based on a Hidden Markov Model to improve the prediction performance of the classifier. Experimental results conducted on two different datasets at different levels of resolution show that the detection performance increases with an increase in resolution, while the computation time increases. Additionally, they also suggest that a significant decrease in processing time can be achieved thanks to the pre-processing step.

CLV3/ESR (CLE) proteins are important signaling peptides in plants. The short CLE peptide (12–13 amino acids) is cleaved from a larger pre-propeptide and functions as an extracellular ligand. The CLE family is large and has resisted attempts at classification because the CLE domain is too short for reliable phylogenetic analysis and the pre-propeptide is too variable. We used a model-based search for CLE domains from 57 plant genomes and used the entire pre-propeptide for comprehensive clustering analysis. In total, 1628 CLE genes were identified in land plants, with none recognizable from green algae. These CLEs form 12 groups within which CLE domains are largely conserved and pre-propeptides can be aligned. Most clusters contain sequences from monocots, eudicots and Amborella trichopoda, with sequences from Picea abies, Selaginella moellendorffii and Physcomitrella patens scattered in some clusters. We easily identified previously known clusters involved in vascular differentiation and nodulation. In addition, we found a number of discrete groups whose function remains poorly characterized. Available data indicate that CLE proteins within a cluster are likely to share function, whereas those from different clusters play at least partially different roles. Our analysis provides a foundation for future evolutionary and functional studies.