Hydrophobicity Analysis of Protein Primary Structures to Identify Helical Regions

2004 ◽  
Vol 43 (01) ◽  
pp. 102-105 ◽  
Author(s):  
S. Cerutti ◽  
L. Pattini
Keyword(s):  
Neural Networks ◽  
Amino Acid ◽  
Secondary Structure ◽  
Markov Models ◽  
Hidden Markov ◽  
Single Amino Acid ◽  
Helical Structures ◽  
Alpha Helices ◽  
Primary Structures ◽  
Hydrophobicity Analysis

Summary Objectives: A wavelet based approach for the hydrophobicity analysis of protein primary structures is proposed to predict the presence of alpha helices in the secondary structure. Methods: The information about hydropathy profile periodicity content together with a score of probability of occurrence of a single amino acid allows the localization of alpha helices. Results: The accuracy is comparable to other consolidated predictors based on different techniques (i.e.: neural networks, hidden markov models). Conclusion: This method is particularly suitable to capture the amphiphilic character of the helical structures.

scholarly journals FIND: Identifying Functionally and Structurally Important Features in Protein Sequences with Deep Neural Networks

2019 ◽  
Author(s):  
Ranjani Murali ◽  
James Hemp ◽  
Victoria Orphan ◽  
Yonatan Bisk
Keyword(s):  
Neural Networks ◽  
Amino Acid ◽  
Hidden Markov Models ◽  
Markov Models ◽  
Genomic Sequence ◽  
Hidden Markov ◽  
Amino Acid Sequences ◽  
Homologous Proteins ◽  
Biological Studies ◽  
Insight Into

AbstractThe ability to correctly predict the functional role of proteins from their amino acid sequences would significantly advance biological studies at the molecular level by improving our ability to understand the biochemical capability of biological organisms from their genomic sequence. Existing methods that are geared towards protein function prediction or annotation mostly use alignment-based approaches and probabilistic models such as Hidden-Markov Models. In this work we introduce a deep learning architecture (FunctionIdentification withNeuralDescriptions orFIND) which performs protein annotation from primary sequence. The accuracy of our methods matches state of the art techniques, such as protein classifiers based on Hidden Markov Models. Further, our approach allows for model introspection via a neural attention mechanism, which weights parts of the amino acid sequence proportionally to their relevance for functional assignment. In this way, the attention weights automatically uncover structurally and functionally relevant features of the classified protein and find novel functional motifs in previously uncharacterized proteins. While this model is applicable to any database of proteins, we chose to apply this model to superfamilies of homologous proteins, with the aim of extracting features inherent to divergent protein families within a larger superfamily. This provided insight into the functional diversification of an enzyme superfamily and its adaptation to different physiological contexts. We tested our approach on three families (nitrogenases, cytochromebd-type oxygen reductases and heme-copper oxygen reductases) and present a detailed analysis of the sequence characteristics identified in previously characterized proteins in the heme-copper oxygen reductase (HCO) superfamily. These are correlated with their catalytic relevance and evolutionary history. FIND was then applied to discover features in previously uncharacterized members of the HCO superfamily, providing insight into their unique sequence features. This modeling approach demonstrates the power of neural networks to recognize patterns in large datasets and can be utilized to discover biochemically and structurally important features in proteins from their amino acid sequences.Author summary

scholarly journals Conserved Peptides Recognition by Ensemble of Neural Networks for Mining Protein Data – LPMO Case Study

2020 ◽  
Vol 15 (2) ◽  
pp. 429-440
Author(s):  
G.S. Dotsenko ◽  
A.S. Dotsenko
Keyword(s):  
Neural Networks ◽  
Amino Acid ◽  
Markov Models ◽  
Amino Acid Sequences ◽  
Peptide Pattern ◽  
Novel Approach ◽  
Polysaccharide Monooxygenases ◽  
Promising Area ◽  
Peptide Pattern Recognition ◽  
Bacterial Proteomes

Mining protein data is a recent promising area of modern bioinformatics. In this work, we suggested a novel approach for mining protein data – conserved peptides recognition by ensemble of neural networks (CPRENN). This approach was applied for mining lytic polysaccharide monooxygenases (LPMOs) in 19 ascomycete, 18 basidiomycete, and 18 bacterial proteomes. LPMOs are recently discovered enzymes and their mining is of high relevance for biotechnology of lignocellulosic materials. CPRENN was compared with two conventional bioinformatic methods for mining protein data – profile hidden Markov models (HMMs) search (HMMER program) and peptide pattern recognition (PPR program combined with Hotpep application). The maximum number of hypothetical LPMO amino acid sequences was discovered by HMMER. Profile HMMs search proved to be more sensitive method for mining LPMOs than conserved peptides recognition. Totally, CPRENN found 76 %, 67 %, and 65 % of hypothetical ascomycete, basidiomycete, and bacterial LPMOs discovered by HMMER, respectively. For AA9, AA10, and AA11 families which contain the major part of all LPMOs in the carbohydrate-active enzymes database (CAZy), CPRENN and PPR + Hotpep found 69–98 % and 62–95 % of amino acid sequences discovered by HMMER, respectively. In contrast with PPR + Hotpep, CPRENN possessed perfect precision and provided more complete mining of basidiomycete and bacterial LPMOs.

Literacy by Way of Automatic Speech Recognition

2011 ◽  
pp. 2074-2118
Author(s):  
Russell Gluck ◽  
John Fulcher
Keyword(s):  
Neural Networks ◽  
Speech Recognition ◽  
Automatic Speech Recognition ◽  
Markov Models ◽  
Hidden Markov ◽  
Time Warping ◽  
Oral Storytelling ◽  
Pattern Recognition Techniques ◽  
Dynamic Time ◽  
Over Time

The chapter commences with an overview of automatic speech recognition (ASR), which covers not only the de facto standard approach of hidden Markov models (HMMs), but also the tried-and-proven techniques of dynamic time warping and artificial neural networks (ANNs). The coverage then switches to Gluck’s (2004) draw-talk-write (DTW) process, developed over the past two decades to assist non-text literate people become gradually literate over time through telling and/or drawing their own stories. DTW has proved especially effective with “illiterate” people from strong oral, storytelling traditions. The chapter concludes by relating attempts to date in automating the DTW process using ANN-based pattern recognition techniques on an Apple Macintosh G4™ platform.

A New Modular Strategy For Action Sequence Automation Using Neural Networks And Hidden Markov Models

2013 ◽  
Vol 2 (3) ◽  
pp. 18-35 ◽  
Author(s):  
Mohamed Adel Taher ◽  
Mostapha Abdeljawad
Keyword(s):  
Neural Networks ◽  
Hidden Markov Models ◽  
Fuzzy Systems ◽  
Markov Models ◽  
Hidden Markov ◽  
Current System ◽  
Action Sequence ◽  
Hybrid Strategy ◽  
Automatic Control Theory ◽  
Welding Automation

In this paper, the authors propose a new hybrid strategy (using artificial neural networks and hidden Markov models) for skill automation. The strategy is based on the concept of using an “adaptive desired” that is introduced in the paper. The authors explain how using an adaptive desired can help a system for which an explicit model is not available or is difficult to obtain to smartly cope with environmental disturbances without requiring explicit rules specification (as with fuzzy systems). At the same time, unlike the currently available hidden Markov-based systems, the system does not merely replay a memorized skill. Instead, it takes into account the current system state as reported by sensors. The authors approach can be considered a bridge between the spirit of conventional automatic control theory and fuzzy/hidden Markov-based thinking. To demonstrate the different aspects of the proposed strategy, the authors discuss its application to underwater welding automation.

Hidden Markov model interpretations of neural networks

2000 ◽  
Vol 23 (4) ◽  
pp. 494-495
Author(s):  
Ingmar Visser
Keyword(s):  
Neural Networks ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Hidden Markov Models ◽  
Markov Models ◽  
Hidden Markov ◽  
Distributed Representations ◽  
Hidden Layer

Page's manifesto makes a case for localist representations in neural networks, one of the advantages being ease of interpretation. However, even localist networks can be hard to interpret, especially when at some hidden layer of the network distributed representations are employed, as is often the case. Hidden Markov models can be used to provide useful interpretable representations.

Infant Cry Recognition System

2019 ◽  
Vol 11 (1) ◽  
pp. 15-32
Author(s):  
Yosra Abdulaziz Mohammed
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Markov Models ◽  
Hidden Markov ◽  
Recognition System ◽  
Acoustic Features ◽  
Infant Cry ◽  
Identification Rate ◽  
The One ◽  
Better Than

Cries of infants can be seen as an indicator of pain. It has been proven that crying caused by pain, hunger, fear, stress, etc., show different cry patterns. The work presented here introduces a comparative study between the performance of two different classification techniques implemented in an automatic classification system for identifying two types of infants' cries, pain, and non-pain. The techniques are namely, Continuous Hidden Markov Models (CHMM) and Artificial Neural Networks (ANN). Two different sets of acoustic features were extracted from the cry samples, those are MFCC and LPCC, the feature vectors generated by each were eventually fed into the classification module for the purpose of training and testing. The results of this work showed that the system based on CDHMM have better performance than that based on ANN. CDHMM gives the best identification rate at 96.1%, which is much higher than 79% of ANN whereby in general the system based on MFCC features performed better than the one that utilizes LPCC features.

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