Inverse-Free Extreme Learning Machine With Optimal Information Updating

A Pseudoinversion-Free Method for Weight Updating in Broad Learning System

Neural networks have evolved into one of the most critical tools in the field of artificial intelligence. As a kind of shallow feedforward neural network, the broad learning system (BLS) uses a training process based on random and pseudoinverse methods, and it does not need to go through a complete training cycle to obtain new parameters when adding nodes. Instead, it performs rapid update iterations on the basis of existing parameters through a series of dynamic update algorithms, which enables BLS to combine high efficiency and accuracy flexibly. The training strategy of BLS is completely different from the existing mainstream neural network training strategy based on the gradient descent algorithm, and the superiority of the former has been proven in many experiments. This article applies an ingenious method of pseudoinversion to the weight updating process in BLS and employs it as an alternative strategy for the dynamic update algorithms in the original BLS. Theoretical analyses and numerical experiments demonstrate the efficiency and effectiveness of BLS aided with this method. The research presented in this article can be regarded as an extended study of the BLS theory, providing an innovative idea and direction for future research on BLS.

Functional extreme learning machine

Introduction

Extreme learning machine (ELM) is a training algorithm for single hidden layer feedforward neural network (SLFN), which converges much faster than traditional methods and yields promising performance. However, the ELM also has some shortcomings, such as structure selection, overfitting and low generalization performance.

Methods

This article a new functional neuron (FN) model is proposed, we takes functional neurons as the basic unit, and uses functional equation solving theory to guide the modeling process of FELM, a new functional extreme learning machine (FELM) model theory is proposed.

Results

The FELM implements learning by adjusting the coefficients of the basis function in neurons. At the same time, a simple, iterative-free and high-precision fast parameter learning algorithm is proposed.

Discussion

The standard data sets UCI and StatLib are selected for regression problems, and compared with the ELM, support vector machine (SVM) and other algorithms, the experimental results show that the FELM achieves better performance.

A Novel Convolutional Neural Network Model Based on Beetle Antennae Search Optimization Algorithm for Computerized Tomography Diagnosis

Convolutional neural networks (CNNs) are widely used in the field of medical imaging diagnosis but have the disadvantages of slow training speed and low diagnostic accuracy due to the initialization of parameters before training. In this article, a CNN optimization method based on the beetle antennae search (BAS) optimization algorithm is proposed. The method optimizes the initial parameters of the CNN through the BAS optimization algorithm. Based on this optimization approach, a novel CNN model with a pretrained BAS optimization algorithm was developed and applied to the analysis and diagnosis of medical imaging data for intracranial hemorrhage. Experimental results on 330 test images show that the proposed method has a better diagnostic performance than the traditional CNN. The proposed method achieves a diagnostic accuracy of 93.9394% and 100% recall, and the diagnosis of 66 human head computerized tomography image data only takes 0.1596 s. Moreover, the proposed method has more advantages than the three other optimization algorithms.

Growing Echo State Network With an Inverse-Free Weight Update Strategy

An echo state network (ESN) draws widespread attention and is applied in many scenarios. As the most typical approach for solving the ESN, the matrix inverse operation of high computational complexity is involved. However, in the modern big data era, addressing the heavy computational burden problem is necessary. In order to reduce the computational load, an inverse-free ESN (IFESN) is proposed for the first time in this article. Besides, an incremental IFESN is constructed to attain the network topology with theoretical proof on the training error's monotone decline property. Simulations and experiments are conducted on several numerical and real-world time-series benchmarks, and corresponding results indicate that the proposed model is superior to some existing models and possesses excellent practical application potential. The source code is publicly available at https://github.com/LongJin-lab/the-supplementary-file-for-CYB-E-2021-04-0944.

MFIDMA: A Multiple Information Integration Model for the Prediction of Drug-miRNA Associations

Abnormal microRNA (miRNA) functions play significant roles in various pathological processes. Thus, predicting drug-miRNA associations (DMA) may hold great promise for identifying the potential targets of drugs. However, discovering the associations between drugs and miRNAs through wet experiments is time-consuming and laborious. Therefore, it is significant to develop computational prediction methods to improve the efficiency of identifying DMA on a large scale. In this paper, a multiple features integration model (MFIDMA) is proposed to predict drug-miRNA association. Specifically, we first formulated known DMA as a bipartite graph and utilized structural deep network embedding (SDNE) to learn the topological features from the graph. Second, the Word2vec algorithm was utilized to construct the attribute features of the miRNAs and drugs. Third, two kinds of features were entered into the convolution neural network (CNN) and deep neural network (DNN) to integrate features and predict potential target miRNAs for the drugs. To evaluate the MFIDMA model, it was implemented on three different datasets under a five-fold cross-validation and achieved average AUCs of 0.9407, 0.9444 and 0.8919. In addition, the MFIDMA model showed reliable results in the case studies of Verapamil and hsa-let-7c-5p, confirming that the proposed model can also predict DMA in real-world situations. The model was effective in analyzing the neighbors and topological features of the drug-miRNA network by SDNE. The experimental results indicated that the MFIDMA is an accurate and robust model for predicting potential DMA, which is significant for miRNA therapeutics research and drug discovery.

A State Space Modeling Method for Aero-Engine Based on AFOS-ELM

State space models (SSMs) are important for multi-variable performance analysis and controller design of aero-engines. In order to solve the problems of the traditional state space modeling methods that rely on component-level models (CLMs) and cannot be carried out in real time, an aero-engine state space modeling method based on adaptive forgetting factor online sequential extreme learning machine (AFOS-ELM) is proposed in this paper. The structure of the extreme learning machine (ELM) is determined according to the form of the state space model, and the inverse-free ELM algorithm is used to automatically select the appropriate number of hidden nodes to improve the efficiency of offline initialization. The focus of the ELM on current operation performance is enhanced by the adaptive renewed forgetting factor, which reduces the impact of aero-engine history and deviated data on the current output and improves the accuracy of the model. Then, according to the analytical equation of the ELM model, the state space model of an aero-engine at each sampling time is obtained by using the partial derivative method. The simulation results based on engine test data show that the real-time performance and accuracy of the state space model established online in this paper can meet the needs of aero-engine control system requirement.

Anti-cancer Peptide Recognition Based on Grouped Sequence and Spatial Dimension Integrated Networks

The diversification of the characteristic sequences of anti-cancer peptides has imposed difficulties on research. To effectively predict new anti-cancer peptides, this paper proposes a more suitable feature grouping sequence and spatial dimension-integrated network algorithm for anti-cancer peptide sequence prediction called GRCI-Net. The main process is as follows: First, we implemented the fusion reduction of binary structure features and K-mer sparse matrix features through principal component analysis and generated a set of new features; second, we constructed a new bidirectional long- and short-term memory network. We used traditional convolution and dilated convolution to acquire features in the spatial dimension using the memory network's grouping sequence model, which is designed to better handle the diversification of anti-cancer peptide feature sequences and to fully learn the contextual information between features. Finally, we achieved the fusion of grouping sequence features and spatial dimensional integration features through two sets of dense network layers, achieved the prediction of anti-cancer peptides through the sigmoid function, and verified the approach with two public datasets, ACP740 (accuracy reached 0.8230) and ACP240 (accuracy reached 0.8750). The following is a link to the model code and datasets mentioned in this article: https://github.com/ YouHongfeng101/ACP-DL.

New Super-Twisting Zeroing Neural-Dynamics Model for Tracking Control of Parallel Robots: A Finite-Time and Robust Solution

Parallel robots are usually required to perform real-time tracking control tasks in the presence of external disturbances in the complex environment. Conventional zeroing neural-dynamics (ZNDs) provide an alternative solution for the real-time tracking control of parallel robots due to its capacity of parallel processing and nonlinearity handling. However, it is still a challenge for the solution in a unified framework of the ZND to deal with the external disturbances, and simultaneously possess a finite-time convergence property. In this paper, a novel ZND model by exploring the super-twisting (ST) algorithm, named ST-ZND model, is proposed. The theoretical analyses on the global stability, finite-time convergence, as well as the robustness against the external disturbances are rigorously presented. Finally, the effectiveness and superiority of the ST-ZND model for the real-time tracking control of parallel robots are demonstrated by two illustrative examples, comparisons, and convergence tests.

Two New Discrete-Time Neurodynamic Algorithms Applied to Online Future Matrix Inversion With Nonsingular or Sometimes-Singular Coefficient

In this paper, a high-precision general discretization formula using six time instants is first proposed to approximate the first-order derivative. Then, such a formula is studied to discretize two continuous-time neurodynamic models, both of which are derived by applying the neurodynamic approaches based on neural networks (i.e., zeroing neurodynamics and gradient neurodynamics). Originating from the general six-instant discretization (6ID) formula, a specific 6ID formula is further presented. Subsequently, two new discrete-time neurodynamic algorithms, i.e., 6ID-type discrete-time zeroing neurodynamic (DTZN) algorithm and 6ID-type discrete-time gradient neurodynamic (DTGN) algorithm, are proposed and investigated for online future matrix inversion (OFMI). In addition to analyzing the usual nonsingular situation of the coefficient, this paper investigates the sometimes-singular situation of the coefficient for OFMI. Finally, two illustrative numerical examples, including an application to the inverse-kinematic control of a PUMA560 robot manipulator, are provided to show respective characteristics and advantages of the proposed 6ID-type DTZN and DTGN algorithms for OFMI in different situations, where the coefficient matrix to be inverted is always-nonsingular or sometimes-singular during time evolution.

ACP-DL: A Deep Learning Long Short-Term Memory Model to Predict Anticancer Peptides Using High-Efficiency Feature Representation

Cancer is a well-known killer of human beings, which has led to countless deaths and misery. Anticancer peptides open a promising perspective for cancer treatment, and they have various attractive advantages. Conventional wet experiments are expensive and inefficient for finding and identifying novel anticancer peptides. There is an urgent need to develop a novel computational method to predict novel anticancer peptides. In this study, we propose a deep learning long short-term memory (LSTM) neural network model, ACP-DL, to effectively predict novel anticancer peptides. More specifically, to fully exploit peptide sequence information, we developed an efficient feature representation approach by integrating binary profile feature and k-mer sparse matrix of the reduced amino acid alphabet. Then we implemented a deep LSTM model to automatically learn how to identify anticancer peptides and non-anticancer peptides. To our knowledge, this is the first time that the deep LSTM model has been applied to predict anticancer peptides. It was demonstrated by cross-validation experiments that the proposed ACP-DL remarkably outperformed other comparison methods with high accuracy and satisfied specificity on benchmark datasets. In addition, we also contributed two new anticancer peptides benchmark datasets, ACP740 and ACP240, in this work. The source code and datasets are available at https://github.com/haichengyi/ACP-DL.

A New Varying-Parameter Recurrent Neural-Network for Online Solution of Time-Varying Sylvester Equation

Solving Sylvester equation is a common algebraic problem in mathematics and control theory. Different from the traditional fixed-parameter recurrent neural networks, such as gradient-based recurrent neural networks or Zhang neural networks, a novel varying-parameter recurrent neural network, [called varying-parameter convergent-differential neural network (VP-CDNN)] is proposed in this paper for obtaining the online solution to the time-varying Sylvester equation. With time passing by, this kind of new varying-parameter neural network can achieve super-exponential performance. Computer simulation comparisons between the fixed-parameter neural networks and the proposed VP-CDNN via using different kinds of activation functions demonstrate that the proposed VP-CDNN has better convergence and robustness properties.

Design, Analysis, and Representation of Novel Five-Step DTZD Algorithm for Time-Varying Nonlinear Optimization

Continuous-time and discrete-time forms of Zhang dynamics (ZD) for time-varying nonlinear optimization have been developed recently. In this paper, a novel discrete-time ZD (DTZD) algorithm is proposed and investigated based on the previous research. Specifically, the DTZD algorithm for time-varying nonlinear optimization is developed by adopting a new Taylor-type difference rule. This algorithm is a five-step iteration process, and thus, is referred to as the five-step DTZD algorithm in this paper. Theoretical analysis and results of the proposed five-step DTZD algorithm are presented to highlight its excellent computational performance. The geometric representation of the proposed algorithm for time-varying nonlinear optimization is also provided. Comparative numerical results are illustrated with four examples to substantiate the efficacy and superiority of the proposed five-step DTZD algorithm for time-varying nonlinear optimization compared with the previous DTZD algorithms.

ADMM-Based Algorithm for Training Fault Tolerant RBF Networks and Selecting Centers

In the training stage of radial basis function (RBF) networks, we need to select some suitable RBF centers first. However, many existing center selection algorithms were designed for the fault-free situation. This brief develops a fault tolerant algorithm that trains an RBF network and selects the RBF centers simultaneously. We first select all the input vectors from the training set as the RBF centers. Afterward, we define the corresponding fault tolerant objective function. We then add an -norm term into the objective function. As the -norm term is able to force some unimportant weights to zero, center selection can be achieved at the training stage. Since the -norm term is nondifferentiable, we formulate the original problem as a constrained optimization problem. Based on the alternating direction method of multipliers framework, we then develop an algorithm to solve the constrained optimization problem. The convergence proof of the proposed algorithm is provided. Simulation results show that the proposed algorithm is superior to many existing center selection algorithms.

Robust Fuzzy Adaptive Tracking Control for Nonaffine Stochastic Nonlinear Switching Systems

This paper is concerned with the trajectory tracking control problem of a class of nonaffine stochastic nonlinear switched systems with the nonlower triangular form under arbitrary switching. Fuzzy systems are employed to tackle the problem from packaged unknown nonlinearities, and the backstepping and robust adaptive control techniques are applied to design the controller by adopting the structural characteristics of fuzzy systems and the common Lyapunov function approach. By using Lyapunov stability theory, the semiglobally uniformly ultimate boundness in the fourth-moment of all closed-loop signals is guaranteed, and the system output is ensured to converge to a small neighborhood of the given trajectory. The main advantages of this paper lie in the fact that both the completely nonaffine form and nonlower triangular structure are taken into account for the controlled systems, and the increasing property of whole state functions is removed by using the structural characteristics of fuzzy systems. The developed control method is verified through a numerical example.

ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes

MOTIVATION

Protein-protein interactions (PPIs) play a key role in many cellular processes. Most annotations of PPIs mix experimental and computational data. The mix optimizes coverage, but obfuscates the annotation origin. Some resources excel at focusing on reliable experimental data. Here, we focused on new pairs of interacting proteins for several model organisms based solely on sequence-based prediction methods.

RESULTS

We extracted reliable experimental data about which proteins interact (binary) for eight diverse model organisms from public databases, namely from Escherichia coli, Schizosaccharomyces pombe, Plasmodium falciparum, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, and for the previously used Homo sapiens and Saccharomyces cerevisiae. Those data were the base to develop a PPI prediction method for each model organism. The method used evolutionary information through a profile-kernel Support Vector Machine (SVM). With the resulting eight models, we predicted all possible protein pairs in each organism and made the top predictions available through a web application. Almost all of the PPIs made available were predicted between proteins that have not been observed in any interaction, in particular for less well-studied organisms. Thus, our work complements existing resources and is particularly helpful for designing experiments because of its uniqueness. Experimental annotations and computational predictions are strongly influenced by the fact that some proteins have many partners and others few. To optimize machine learning, recent methods explicitly ignored such a network-structure and rely either on domain knowledge or sequence-only methods. Our approach is independent of domain-knowledge and leverages evolutionary information. The database interface representing our results is accessible from https://rostlab.org/services/ppipair/. The data can also be downloaded from https://figshare.com/collections/ProfPPI-DB/4141784.

Improving Prediction of Self-interacting Proteins Using Stacked Sparse Auto-Encoder with PSSM profiles

Self-interacting proteins (SIPs) play a significant role in the execution of most important molecular processes in cells, such as signal transduction, gene expression regulation, immune response and enzyme activation. Although the traditional experimental methods can be used to generate SIPs data, it is very expensive and time-consuming based only on biological technique. Therefore, it is important and urgent to develop an efficient computational method for SIPs detection. In this study, we present a novel SIPs identification method based on machine learning technology by combing the Zernike Moments (ZMs) descriptor on Position Specific Scoring Matrix (PSSM) with Probabilistic Classification Vector Machines (PCVM) and Stacked Sparse Auto-Encoder (SSAE). More specifically, an efficient feature extraction technique called ZMs is firstly utilized to generate feature vectors on Position Specific Scoring Matrix (PSSM); Then, Deep neural network is employed for reducing the feature dimensions and noise; Finally, the Probabilistic Classification Vector Machine is used to execute the classification. The prediction performance of the proposed method is evaluated on S.erevisiae and Human SIPs datasets via cross-validation. The experimental results indicate that the proposed method can achieve good accuracies of 92.55% and 97.47%, respectively. To further evaluate the advantage of our scheme for SIPs prediction, we also compared the PCVM classifier with the Support Vector Machine (SVM) and other existing techniques on the same data sets. Comparison results reveal that the proposed strategy is outperforms other methods and could be a used tool for identifying SIPs.

A Novel Recurrent Neural Network for Manipulator Control With Improved Noise Tolerance

In this paper, we propose a novel recurrent neural network to resolve the redundancy of manipulators for efficient kinematic control in the presence of noises in a polynomial type. Leveraging the high-order derivative properties of polynomial noises, a deliberately devised neural network is proposed to eliminate the impact of noises and recover the accurate tracking of desired trajectories in workspace. Rigorous analysis shows that the proposed neural law stabilizes the system dynamics and the position tracking error converges to zero in the presence of noises. Extensive simulations verify the theoretical results. Numerical comparisons show that existing dual neural solutions lose stability when exposed to large constant noises or time-varying noises. In contrast, the proposed approach works well and has a low tracking error comparable to noise-free situations.

Excavation Equipment Recognition Based on Novel Acoustic Statistical Features

Excavation equipment recognition attracts increasing attentions in recent years due to its significance in underground pipeline network protection and civil construction management. In this paper, a novel classification algorithm based on acoustics processing is proposed for four representative excavation equipments. New acoustic statistical features, namely, the short frame energy ratio, concentration of spectrum amplitude ratio, truncated energy range, and interval of pulse are first developed to characterize acoustic signals. Then, probability density distributions of these acoustic features are analyzed and a novel classifier is presented. Experiments on real recorded acoustics of the four excavation devices are conducted to demonstrate the effectiveness of the proposed algorithm. Comparisons with two popular machine learning methods, support vector machine and extreme learning machine, combined with the popular linear prediction cepstral coefficients are provided to show the generalization capability of our method. A real surveillance system using our algorithm is developed and installed in a metro construction site for real-time recognition performance validation.

Backstepping-Based Lyapunov Function Construction Using Approximate Dynamic Programming and Sum of Square Techniques

In this paper, backstepping for a class of block strict-feedback nonlinear systems is considered. Since the input function could be zero for each backstepping step, the backstepping technique cannot be applied directly. Based on the assumption that nonlinear systems are polynomials, for each backstepping step, Lypunov function can be constructed in a polynomial form by sum of square (SOS) technique. The virtual control can be obtained by the Sontag feedback formula, which is equivalent to an optimal control-the solution of a Hamilton-Jacobi-Bellman equation. Thus, approximate dynamic programming (ADP) could be used to estimate value functions (Lyapunov functions) instead of SOS. Through backstepping technique, the control Lyapunov function (CLF) of the full system is constructed finally making use of the strict-feedback structure and a stabilizable controller can be obtained through the constructed CLF. The contributions of the proposed method are twofold. On one hand, introducing ADP into backstepping can broaden the application of the backstepping technique. A class of block strict-feedback systems can be dealt by the proposed method and the requirement of nonzero input function for each backstepping step can be relaxed. On the other hand, backstepping with surface dynamic control actually reduces the computation complexity of ADP through constructing one part of the CLF by solving semidefinite programming using SOS. Simulation results verify contributions of the proposed method.

Accurate prediction of protein-protein interactions by integrating potential evolutionary information embedded in PSSM profile and discriminative vector machine classifier

Identification of protein-protein interactions (PPIs) is of critical importance for deciphering the underlying mechanisms of almost all biological processes of cell and providing great insight into the study of human disease. Although much effort has been devoted to identifying PPIs from various organisms, existing high-throughput biological techniques are time-consuming, expensive, and have high false positive and negative results. Thus it is highly urgent to develop in silico methods to predict PPIs efficiently and accurately in this post genomic era. In this article, we report a novel computational model combining our newly developed discriminative vector machine classifier (DVM) and an improved Weber local descriptor (IWLD) for the prediction of PPIs. Two components, differential excitation and orientation, are exploited to build evolutionary features for each protein sequence. The main characteristics of the proposed method lies in introducing an effective feature descriptor IWLD which can capture highly discriminative evolutionary information from position-specific scoring matrixes (PSSM) of protein data, and employing the powerful and robust DVM classifier. When applying the proposed method to Yeast and H. pylori data sets, we obtained excellent prediction accuracies as high as 96.52% and 91.80%, respectively, which are significantly better than the previous methods. Extensive experiments were then performed for predicting cross-species PPIs and the predictive results were also pretty promising. To further validate the performance of the proposed method, we compared it with the state-of-the-art support vector machine (SVM) classifier on Human data set. The experimental results obtained indicate that our method is highly effective for PPIs prediction and can be taken as a supplementary tool for future proteomics research.

Robust and accurate prediction of protein self-interactions from amino acids sequence using evolutionary information

Self-interacting proteins (SIPs) play an essential role in cellular functions and the evolution of protein interaction networks (PINs). Due to the limitations of experimental self-interaction proteins detection technology, it is a very important task to develop a robust and accurate computational approach for SIPs prediction. In this study, we propose a novel computational method for predicting SIPs from protein amino acids sequence. Firstly, a novel feature representation scheme based on Local Binary Pattern (LBP) is developed, in which the evolutionary information, in the form of multiple sequence alignments, is taken into account. Then, by employing the Relevance Vector Machine (RVM) classifier, the performance of our proposed method is evaluated on yeast and human datasets using a five-fold cross-validation test. The experimental results show that the proposed method can achieve high accuracies of 94.82% and 97.28% on yeast and human datasets, respectively. For further assessing the performance of our method, we compared it with the state-of-the-art Support Vector Machine (SVM) classifier, and other existing methods, on the same datasets. Comparison results demonstrate that the proposed method is very promising and could provide a cost-effective alternative for predicting SIPs. In addition, to facilitate extensive studies for future proteomics research, a web server is freely available for academic use at .

Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix

Self-interacting Proteins (SIPs) play an essential role in a wide range of biological processes, such as gene expression regulation, signal transduction, enzyme activation and immune response. Because of the limitations for experimental self-interaction proteins identification, developing an effective computational method based on protein sequence to detect SIPs is much important. In the study, we proposed a novel computational approach called RVMBIGP that combines the Relevance Vector Machine (RVM) model and Bi-gram probability (BIGP) to predict SIPs based on protein sequence. The proposed prediction model includes as following steps: (1) an effective feature extraction method named BIGP is used to represent protein sequences on Position Specific Scoring Matrix (PSSM); (2) Principal Component Analysis (PCA) method is employed for integrating the useful information and reducing the influence of noise; (3) the robust classifier Relevance Vector Machine (RVM) is used to carry out classification. When performed on yeast and human datasets, the proposed RVMBIGP model can achieve very high accuracies of 95.48% and 98.80%, respectively. The experimental results show that our proposed method is very promising and may provide a cost-effective alternative for SIPs identification. In addition, to facilitate extensive studies for future proteomics research, the RVMBIGP server is freely available for academic use at http://219.219.62.123:8888/RVMBIGP.

Highly Accurate Prediction of Protein-Protein Interactions via Incorporating Evolutionary Information and Physicochemical Characteristics

Protein-protein interactions (PPIs) occur at almost all levels of cell functions and play crucial roles in various cellular processes. Thus, identification of PPIs is critical for deciphering the molecular mechanisms and further providing insight into biological processes. Although a variety of high-throughput experimental techniques have been developed to identify PPIs, existing PPI pairs by experimental approaches only cover a small fraction of the whole PPI networks, and further, those approaches hold inherent disadvantages, such as being time-consuming, expensive, and having high false positive rate. Therefore, it is urgent and imperative to develop automatic in silico approaches to predict PPIs efficiently and accurately. In this article, we propose a novel mixture of physicochemical and evolutionary-based feature extraction method for predicting PPIs using our newly developed discriminative vector machine (DVM) classifier. The improvements of the proposed method mainly consist in introducing an effective feature extraction method that can capture discriminative features from the evolutionary-based information and physicochemical characteristics, and then a powerful and robust DVM classifier is employed. To the best of our knowledge, it is the first time that DVM model is applied to the field of bioinformatics. When applying the proposed method to the Yeast and Helicobacter pylori (H. pylori) datasets, we obtain excellent prediction accuracies of 94.35% and 90.61%, respectively. The computational results indicate that our method is effective and robust for predicting PPIs, and can be taken as a useful supplementary tool to the traditional experimental methods for future proteomics research.

An Efficient Leave-One-Out Cross-Validation-Based Extreme Learning Machine (ELOO-ELM) With Minimal User Intervention

It is well known that the architecture of the extreme learning machine (ELM) significantly affects its performance and how to determine a suitable set of hidden neurons is recognized as a key issue to some extent. The leave-one-out cross-validation (LOO-CV) is usually used to select a model with good generalization performance among potential candidates. The primary reason for using the LOO-CV is that it is unbiased and reliable as long as similar distribution exists in the training and testing data. However, the LOO-CV has rarely been implemented in practice because of its notorious slow execution speed. In this paper, an efficient LOO-CV formula and an efficient LOO-CV-based ELM (ELOO-ELM) algorithm are proposed. The proposed ELOO-ELM algorithm can achieve fast learning speed similar to the original ELM without compromising the reliability feature of the LOO-CV. Furthermore, minimal user intervention is required for the ELOO-ELM, thus it can be easily adopted by nonexperts and implemented in automation processes. Experimentation studies on benchmark datasets demonstrate that the proposed ELOO-ELM algorithm can achieve good generalization with limited user intervention while retaining the efficiency feature.

Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences

We propose a novel computational method known as RVM-LPQ that combines the Relevance Vector Machine (RVM) model and Local Phase Quantization (LPQ) to predict PPIs from protein sequences. The main improvements are the results of representing protein sequences using the LPQ feature representation on a Position Specific Scoring Matrix (PSSM), reducing the influence of noise using a Principal Component Analysis (PCA), and using a Relevance Vector Machine (RVM) based classifier. We perform 5-fold cross-validation experiments on Yeast and Human datasets, and we achieve very high accuracies of 92.65% and 97.62%, respectively, which is significantly better than previous works. To further evaluate the proposed method, we compare it with the state-of-the-art support vector machine (SVM) classifier on the Yeast dataset. The experimental results demonstrate that our RVM-LPQ method is obviously better than the SVM-based method. The promising experimental results show the efficiency and simplicity of the proposed method, which can be an automatic decision support tool for future proteomics research.