Protein Remote Homology Detection Based on an Ensemble Learning Approach.
Ontology highlight
ABSTRACT:
SUBMITTER: Chen J
PROVIDER: S-EPMC4875977 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BackgroundProtein remote homology detection plays a vital role in studies of protein structures and functions. Almost all of the traditional machine leaning methods require fixed length features to represent the protein sequences. However, it is never an easy task to extract the discriminative features with limited knowledge of proteins. On the other hand, deep learning technique has demonstrated its advantage in automatically learning representations. It is worthwhile to explore the applications of deep learning techniques to the protein remote homology detection.ResultsIn this study, we employ the Bidirectional Long Short-Term Memory (BLSTM) to learn effective features from pseudo proteins, also propose a predictor called ProDec-BLSTM: it includes input layer, bidirectional LSTM, time distributed dense layer and output layer. This neural network can automatically extract the discriminative features by using bidirectional LSTM and the time distributed dense layer.ConclusionExperimental results on a widely-used benchmark dataset show that ProDec-BLSTM outperforms other related methods in terms of both the mean ROC and mean ROC50 scores. This promising result shows that ProDec-BLSTM is a useful tool for protein remote homology detection. Furthermore, the hidden patterns learnt by ProDec-BLSTM can be interpreted and visualized, and therefore, additional useful information can be obtained.
| S-EPMC5634958 | biostudies-literature
Project description:In recent years, the increased population has led to an increase in the demand for various industrially processed edibles and other consumable products. These industries regularly alter the proteins found in raw materials to generate more commercially viable end-products in order to keep up with consumer demand. These modifications result in a substance that may cause allergic reactions in consumers, thereby creating a protein allergen. The detection of such proteins in various substances is essential for the prevention, diagnosis and treatment of allergic conditions. Bioinformatics and computational methods can be used to analyze the information contained in amino-acid sequences to detect possible allergens. The article presents a deep learning based ensemble approach to identify protein allergens using Extra Tree, Deep Belief Network (DBN), and CatBoost models. The proposed ensemble model achieves higher detection accuracy by combining the prediction results of the three models using majority voting. The evaluation of the proposed model was carried out on the benchmark protein allergen dataset, and the performance analysis revealed that the proposed model outperforms the other state-of-the-art literature techniques with a protein allergen detection accuracy of 89.16%.
| S-EPMC10588724 | biostudies-literature
Project description:With the exponential increase in malware, homology analysis has become a hot research topic in the malware detection field. This paper proposes MHAS, a malware homology analysis system based on ensemble learning and multifeatures. MHAS generates grayscale images from malware binary files and then uses the opcode tool IDA Pro to extract opcode sequences and system call graphs. Thus, RGB images and M-images are generated on the image matrix. Then, MHAS uses convolutional neural networks (CNNs) as base learners to perform bagging ensemble learning to learn features from the grayscale images, RGB images and M-images. Next, MHAS integrates the nine base learners using voting, learning and selective ensemble (in that order) and maps the integration results to the result matrix. Finally, the result matrix is again integrated using the learning method to obtain the final malware classification result. To verify the accuracy of MHAS, we performed a malware family classification experiment, that included samples of 10 malware families. The results showed that MHAS can reach an accuracy rate of 99.17%, meaning that it can effectively analyze and identify malware families.
| S-EPMC6709908 | biostudies-literature
Project description:Detecting chemical compounds using electronic noses is important in many gas sensing related applications. A gas detection system is supposed to indicate a significant event, such as the presence of new chemical compounds or a noteworthy change of concentration levels. Existing gas detection methods typically rely on prior knowledge of target analytes to prepare a dedicated, supervised learning model. However, in some scenarios, such as emergency response, not all the analytes of concern are a priori known and their presence are unlikely to be controlled. In this paper, we take a step towards addressing this issue by proposing an ensemble learning based approach (ELBA) that integrates several one-class classifiers and learns online. The proposed approach is initialized by training several one-class models using clean air only. During the sampling process, the initialized system detects the presence of chemicals, allowing to learn another one-class model and update existing models with self-labelled data. We validated the proposed approach with real-world experiments, in which a mobile robot equipped with an e-nose was remotely controlled to interact with different chemical analytes in an uncontrolled environment. We demonstrated that the ELBA algorithm not only can detect gas exposures but also recognize baseline responses under a suspect short-term sensor drift condition. Depending on the problem setups in practical applications, the present work can be easily hybridized to integrate other supervised learning models when the prior knowledge of target analytes is partially available.
| S-EPMC9096169 | biostudies-literature
Project description:BackgroundClassification of protein sequences is a central problem in computational biology. Currently, among computational methods discriminative kernel-based approaches provide the most accurate results. However, kernel-based methods often lack an interpretable model for analysis of discriminative sequence features, and predictions on new sequences usually are computationally expensive.ResultsIn this work we present a novel kernel for protein sequences based on average word similarity between two sequences. We show that this kernel gives rise to a feature space that allows analysis of discriminative features and fast classification of new sequences. We demonstrate the performance of our approach on a widely-used benchmark setup for protein remote homology detection.ConclusionOur word correlation approach provides highly competitive performance as compared with state-of-the-art methods for protein remote homology detection. The learned model is interpretable in terms of biologically meaningful features. In particular, analysis of discriminative words allows the identification of characteristic regions in biological sequences. Because of its high computational efficiency, our method can be applied to ranking of potential homologs in large databases.
| S-EPMC2438326 | biostudies-literature
Project description:MotivationOwing to its importance in both basic research (such as molecular evolution and protein attribute prediction) and practical application (such as timely modeling the 3D structures of proteins targeted for drug development), protein remote homology detection has attracted a great deal of interest. It is intriguing to note that the profile-based approach is promising and holds high potential in this regard. To further improve protein remote homology detection, a key step is how to find an optimal means to extract the evolutionary information into the profiles.ResultsHere, we propose a novel approach, the so-called profile-based protein representation, to extract the evolutionary information via the frequency profiles. The latter can be calculated from the multiple sequence alignments generated by PSI-BLAST. Three top performing sequence-based kernels (SVM-Ngram, SVM-pairwise and SVM-LA) were combined with the profile-based protein representation. Various tests were conducted on a SCOP benchmark dataset that contains 54 families and 23 superfamilies. The results showed that the new approach is promising, and can obviously improve the performance of the three kernels. Furthermore, our approach can also provide useful insights for studying the features of proteins in various families. It has not escaped our notice that the current approach can be easily combined with the existing sequence-based methods so as to improve their performance as well.Availability and implementationFor users' convenience, the source code of generating the profile-based proteins and the multiple kernel learning was also provided at http://bioinformatics.hitsz.edu.cn/main/~binliu/remote/
| S-EPMC7537947 | biostudies-literature
Project description:Protein remote homology detection is one of the most important problems in bioinformatics. Discriminative methods such as support vector machines (SVM) have shown superior performance. However, the performance of SVM-based methods depends on the vector representations of the protein sequences. Prior works have demonstrated that sequence-order effects are relevant for discrimination, but little work has explored how to incorporate the sequence-order information along with the amino acid physicochemical properties into the prediction. In order to incorporate the sequence-order effects into the protein remote homology detection, the physicochemical distance transformation (PDT) method is proposed. Each protein sequence is converted into a series of numbers by using the physicochemical property scores in the amino acid index (AAIndex), and then the sequence is converted into a fixed length vector by PDT. The sequence-order information can be efficiently included into the feature vector with little computational cost by this approach. Finally, the feature vectors are input into a support vector machine classifier to detect the protein remote homologies. Our experiments on a well-known benchmark show the proposed method SVM-PDT achieves superior or comparable performance with current state-of-the-art methods and its computational cost is considerably superior to those of other methods. When the evolutionary information extracted from the frequency profiles is combined with the PDT method, the profile-based PDT approach can improve the performance by 3.4% and 11.4% in terms of ROC score and ROC50 score respectively. The local sequence-order information of the protein can be efficiently captured by the proposed PDT and the physicochemical properties extracted from the amino acid index are incorporated into the prediction. The physicochemical distance transformation provides a general framework, which would be a valuable tool for protein-level study.
| S-EPMC3460876 | biostudies-literature
Project description:BACKGROUND: Remote homology detection is a hard computational problem. Most approaches have trained computational models by using either full protein sequences or multiple sequence alignments (MSA), including all positions. However, when we deal with proteins in the "twilight zone" we can observe that only some segments of sequences (motifs) are conserved. We introduce a novel logical representation that allows us to represent physico-chemical properties of sequences, conserved amino acid positions and conserved physico-chemical positions in the MSA. From this, Inductive Logic Programming (ILP) finds the most frequent patterns (motifs) and uses them to train propositional models, such as decision trees and support vector machines (SVM). RESULTS: We use the SCOP database to perform our experiments by evaluating protein recognition within the same superfamily. Our results show that our methodology when using SVM performs significantly better than some of the state of the art methods, and comparable to other. However, our method provides a comprehensible set of logical rules that can help to understand what determines a protein function. CONCLUSIONS: The strategy of selecting only the most frequent patterns is effective for the remote homology detection. This is possible through a suitable first-order logical representation of homologous properties, and through a set of frequent patterns, found by an ILP system, that summarizes essential features of protein functions.
| S-EPMC3078102 | biostudies-literature
Project description:Termite mushrooms are edible fungi that provide significant economic, nutritional, and medicinal value. However, identifying these mushroom species based on morphology and traditional knowledge is ineffective due to their short development time and seasonal nature. This study proposes a novel method for classifying termite mushroom species. The method utilizes Gradient Boosting machine learning techniques and sequence encoding on the Internal Transcribed Spacer (ITS) gene dataset to construct a machine learning model for identifying termite mushroom species. The model is trained using ITS sequences obtained from the National Center for Biotechnology Information (NCBI) and the Barcode of Life Data Systems (BOLD). Ensemble learning techniques are applied to classify termite mushroom species. The proposed model achieves good results on the test dataset, with an accuracy of 0.91 and an average AUCROC value of 0.99. To validate the model, eight ITS sequences collected from termite mushroom samples in An Linh commune, Phu Giao district, Binh Duong province, Vietnam were used as the test data. The results show consistent species identification with predictions from the NCBI BLAST software. The results of species identification were consistent with the NCBI BLAST prediction software. This machine-learning model shows promise as an automatic solution for classifying termite mushroom species. It can help researchers better understand the local growth of these termite mushrooms and develop conservation plans for this rare and valuable plant resource.
| S-EPMC10598762 | biostudies-literature
Project description:Recently, object detection methods have developed rapidly and have been widely used in many areas. In many scenarios, helmet wearing detection is very useful, because people are required to wear helmets to protect their safety when they work in construction sites or cycle in the streets. However, for the problem of helmet wearing detection in complex scenes such as construction sites and workshops, the detection accuracy of current approaches still needs to be improved. In this work, we analyze the mechanism and performance of several detection algorithms and identify two feasible base algorithms that have complementary advantages. We use one base algorithm to detect relatively large heads and helmets. Also, we use the other base algorithm to detect relatively small heads, and we add another convolutional neural network to detect whether there is a helmet above each head. Then, we integrate these two base algorithms with an ensemble method. In this method, we first propose an approach to merge information of heads and helmets from the base algorithms, and then propose a linear function to estimate the confidence score of the identified heads and helmets. Experiments on a benchmark data set show that, our approach increases the precision and recall for base algorithms, and the mean Average Precision of our approach is 0.93, which is better than many other approaches. With GPU acceleration, our approach can achieve real-time processing on contemporary computers, which is useful in practice.
| S-EPMC7924479 | biostudies-literature