Protein Remote Homology Detection Based on an Ensemble Learning Approach.
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ABSTRACT:
SUBMITTER: Chen J
PROVIDER: S-EPMC4875977 | biostudies-literature |
REPOSITORIES: biostudies-literature
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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: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: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: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
Project description:Anomaly detection is a highly important task in the field of data analysis. Traditional anomaly detection approaches often strongly depend on data size, structure and features, while introducing the idea of ensemble into anomaly detection can greatly improve the generalization ability. Ensemble-based anomaly detection methods still face some challenges, however, such as data imbalance, time and space demand and the selection of base detectors. To this end, we propose a selective ensemble method for anomaly detection based on parallel learning (SEAD-PL). First, a differentiated stratified sampling method is designed to alleviate the problem of data imbalance. Then, a distributed parallel training frame is built to address the problem of excessive time and space consumption for base detector training. Finally, a clustering-based ensemble selection strategy is introduced to balance the accuracy and diversity of base detectors. Experiments are performed on six datasets, which demonstrate that the proposed method has obvious advantages over four selected methods.
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Project description:IoT devices have grown in popularity in recent years. Statistics show that the number of online IoT devices exceeded 35 billion in 2022. This rapid growth in adoption made these devices an obvious target for malicious actors. Attacks such as botnets and malware injection usually start with a phase of reconnaissance to gather information about the target IoT device before exploitation. In this paper, we introduce a machine-learning-based detection system for reconnaissance attacks based on an explainable ensemble model. Our proposed system aims to detect scanning and reconnaissance activity of IoT devices and counter these attacks at an early stage of the attack campaign. The proposed system is designed to be efficient and lightweight to operate in severely resource-constrained environments. When tested, the implementation of the proposed system delivered an accuracy of 99%. Furthermore, the proposed system showed low false positive and false negative rates at 0.6% and 0.05%, respectively, while maintaining high efficiency and low resource consumption.
| S-EPMC10256059 | biostudies-literature
Project description:The accuracy and interpretability of artificial intelligence (AI) are crucial for the advancement of optical coherence tomography (OCT) image detection, as it can greatly reduce the manual labor required by clinicians. By prioritizing these aspects during development and application, we can make significant progress towards streamlining the clinical workflow. In this paper, we propose an explainable ensemble approach that utilizes transfer learning to detect fundus lesion diseases through OCT imaging. Our study utilized a publicly available OCT dataset consisting of normal subjects, patients with dry age-related macular degeneration (AMD), and patients with diabetic macular edema (DME), each with 15 samples. The impact of pre-trained weights on the performance of individual networks was first compared, and then these networks were ensemble using majority soft polling. Finally, the features learned by the networks were visualized using Grad-CAM and CAM. The use of pre-trained ImageNet weights improved the performance from 68.17% to 92.89%. The ensemble model consisting of the three CNN models with pre-trained parameters loaded performed best, correctly distinguishing between AMD patients, DME patients and normal subjects 100% of the time. Visualization results showed that Grad-CAM could display the lesion area more accurately. It is demonstrated that the proposed approach could have good performance of both accuracy and interpretability in retinal OCT image detection.
| S-EPMC10959366 | biostudies-literature