Multiple Kernel Fusion Research Articles

HKFGCN: A novel multiple kernel fusion framework on graph convolutional network to predict microbe-drug associations

Accumulating clinical studies have consistently demonstrated that the microbes in the human body closely interact with the human host, actively participating in the regulation of drug effectiveness. Identifying the associations between microbes and drugs can facilitate the development of drug discovery, and microbes have become a new target in antimicrobial drug development. However, the discovery of microbe-drug associations relies on clinical or biological experiments, which are not only time-consuming but also financially burdensome. Thus, the utilization of computational methods to predict microbe-drug associations holds promise for reducing costs and enhancing the efficiency of biological experiments. Here, we introduce a new computational method, called HKFGCN (Heterogeneous information Kernel Fusion Graph Convolution Network), to predict the microbe-drug associations. Instead of extracting feature from a single network in previous studies, HKFGCN separately extracts topological information features from different networks, and further refines them by generating Gaussian kernel features. HKFGCN consists of three main steps. Firstly, we constructed two similarity networks and a microbe-drug association network based on numerous biological data. Second, we employed two types of encoders to extract features from these networks. Next, Gaussian kernel features were obtained from the drug and microbe features at each layer. Finally, we reconstructed the bipartite microbe-drug graph based on the learned representations. Experimental results demonstrate the excellent performance of the HKFGCN model across different datasets using the cross-validation scheme. Additionally, we conduced case studies on human immunodeficiency virus, and the results were corroborated by existing literatures. The prediction model’s code is available at https://github.com/roll-of-bubble/HKFGCN.

Lq-norm multiple kernel fusion regression for self-cleansing sediment transport

Experimental and modeling studies have been conducted to develop an approach for self-cleansing rigid boundary open channel design such as drainage and sewer systems. Self-cleansing experiments in the literature are mostly performed on circular channel cross-section, while a few studies considered self-cleansing sediment transport in small rectangular channels. Experiments in this study were carried out in a rectangular channel with a length of 12.5 m, a width of 0.6 m, a depth of 0.7 m and having an automatic control system for regulating channel slope, discharge and sediment rate. Behind utilizing collected experimental data in this study, existing data in the literature for rectangular channels are used to develop self-cleansing models applicable for channel design. Through the modeling procedure, this study recommends Lq-norm multiple kernel fusion regression (LMKFR) techniques for self-cleansing sediment transport. The LMKFR is a regression technique based on the regularized kernel regression method which benefits from the combination of multiple information sources to improve the performance using the Lq-norm multiple kernel learning framework. The results obtained by LMKFR are compared to support vector regression benchmark and existing conventional regression self-cleansing sediment transport models in the literature for rectangular channels. The superiority of LMKFR is illustrated in an accurate modeling as compared with its alternatives in terms of various statistical error measurement criteria. The encouraging results of LMKFR can be linked to utilization of several kernels which are fused effectively using an Lq-norm prior that captures the intrinsic sparsity of the problem at hand. Promising performance of LMKFR technique in this study suggests it as an effective technique to be examined in similar environmental, hydrological and hydraulic problems.

SMGCN: Multiple Similarity and Multiple Kernel Fusion Based Graph Convolutional Neural Network for Drug-Target Interactions Prediction.

Accurately identifying potential drug-target interactions (DTIs) is a critical step in accelerating drug discovery. Despite many studies that have been conducted over the past decades, detecting DTIs remains a highly challenging and complicated process. Therefore, we propose a novel method called SMGCN, which combines multiple similarity and multiple kernel fusion based on Graph Convolutional Network (GCN) to predict DTIs. In order to capture the features of the network structure and fully explore direct or indirect relationships between nodes, we propose the method of multiple similarity, which combines similarity fusion matrices with Random Walk with Restart (RWR) and cosine similarity. Then, we use GCN to extract multi-layer low-dimensional embedding features. Unlike traditional GCN methods, we incorporate Multiple Kernel Learning (MKL). Finally, we use the Dual Laplace Regularized Least Squares method to predict novel DTIs through combinatorial kernels in drug and target spaces. We conduct experiments on a golden standard dataset, and demonstrate the effectiveness of our proposed model in predicting DTIs through showing significant improvements in Area Under the Curve (AUC) and Area Under the Precision-Recall Curve (AUPR). In addition, our model can also discover some new DTIs, which can be verified by the KEGG BRITE Database and relevant literature.

Inferring circRNA-drug sensitivity associations via dual hierarchical attention networks and multiple kernel fusion

Increasing evidence has shown that the expression of circular RNAs (circRNAs) can affect the drug sensitivity of cells and significantly influence drug efficacy. Therefore, research into the relationships between circRNAs and drugs can be of great significance in increasing the comprehension of circRNAs function, as well as contributing to the discovery of new drugs and the repurposing of existing drugs. However, it is time-consuming and costly to validate the function of circRNA with traditional medical research methods. Therefore, the development of efficient and accurate computational models that can assist in discovering the potential interactions between circRNAs and drugs is urgently needed. In this study, a novel method is proposed, called DHANMKF , that aims to predict potential circRNA-drug sensitivity interactions for further biomedical screening and validation. Firstly, multimodal networks were constructed by DHANMKF using multiple sources of information on circRNAs and drugs. Secondly, comprehensive intra-type and inter-type node representations were learned using bi-typed multi-relational heterogeneous graphs, which are attention-based encoders utilizing a hierarchical process. Thirdly, the multi-kernel fusion method was used to fuse intra-type embedding and inter-type embedding. Finally, the Dual Laplacian Regularized Least Squares method (DLapRLS) was used to predict the potential circRNA-drug sensitivity associations using the combined kernel in circRNA and drug spaces. Compared with the other methods, DHANMKF obtained the highest AUC value on two datasets. Code is available at https://github.com/cuntjx/DHANMKF.

NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction.

Prediction of drug-target interactions (DTIs) plays a significant role in drug development and drug discovery. Although this task requires a large investment in terms of time and cost, especially when it is performed experimentally, the results are not necessarily significant. Computational DTI prediction is a shortcut to reduce the risks of experimental methods. In this study, we propose an effective approach of nonnegative matrix tri-factorization, referred to as NMTF-DTI, to predict the interaction scores between drugs and targets. NMTF-DTI utilizes multiple kernels (similarity measures) for drugs and targets and Laplacian regularization to boost the prediction performance. The performance of NMTF-DTI is evaluated via cross-validation and is compared with existing DTI prediction methods in terms of the area under the receiver operating characteristic (ROC) curve (AUC) and the area under the precision and recall curve (AUPR). We evaluate our method on four gold standard datasets, comparing to other state-of-the-art methods. Cross-validation and a separate, manually created dataset are used to set parameters. The results show that NMTF-DTI outperforms other competing methods. Moreover, the results of a case study also confirm the superiority of NMTF-DTI.

Multiple kernel fusion: A novel approach for lake water depth modeling

Multiple kernel fusion (MKF) refers to the task of combining multiple sources of information in the Hilbert space for improved performance. Very often the combined kernel is formed as a linear composition of multiple base kernels where the combination weights are learned from the data. As the first application of an MKF approach in hydrological modeling, lake water depth as one of the pivot factors in the reservoir analysis is simulated by considering different hydro-meteorological variables. The role of each individual input parameter is initially investigated by applying a kernel regression approach. We then illustrate the utility of an MKF formalism which learns kernel combination of weights to yield an optimal composition for kernel regression. A set of 40-year data collected from 27 groundwater and streamflow stations and 7 meteorological stations for precipitation and evaporation parameters in the vicinity of Lake Urmia are utilized for model development. Both visual and quantitative statistical performance criteria illustrate a superior performance for the MKF approach compared to kernel ridge regression (KRR), the support vector regression (SVR), back propagation neural network (BPNN) and auto regressive (AR) models. More specifically, while each individual input parameter fails to provide an accurate prediction for lake water depth modeling, an optimal combination of all input parameters incorporating the groundwater level, streamflow, precipitation and evaporation via a multiple kernel learning approach enhances the predictive performance of the model accuracy in the multiple scenarios. The promising results (RMSE = 0.098 m; R2 = 0.987; NSE = 0.986) may motivate the application of a MKF approach towards solving alternative and complex hydrological problems.

Towards deeper match for multi-view oriented multiple kernel learning

Multi-view representation learning aims to exploit the complementary information underlying multiple view data to enhance the expressive power of data representation. Given that kernels in multiple kernel learning naturally correspond to different views, previous shallow similarity learning models cannot fully capture the complex hierarchical information. This work presents an effective deeper match model for multi-view oriented kernel (DMMV) learning which brings a deeper insight into the kernel match for similarity based multi-view representation fusion. Specifically, we propose local deep view-specific self-kernel (LDSvK) by mimicking the deep neural networks to faithfully characterize the local similarity between view-specific samples. Thus, the representation capacity of each view can be saliently analyzed. We build the global deep multi-view fusion kernel (GDMvK) by learning deep fusion of LDSvKs to learn a comprehensive measurement of the cross-view similarity. Notably, the proposed learning framework of the deeper local information extraction and global deep multiple kernel fusion provides a robust way in fitting multi-view data, and yields better learning performance. Experimental results on several multi-view benchmark datasets well demonstrate the effectiveness of our DMMV over other state-of-the-art methods.

Inferring human miRNA-disease associations via multiple kernel fusion on GCNII.

Increasing evidence shows that the occurrence of human complex diseases is closely related to the mutation and abnormal expression of microRNAs(miRNAs). MiRNAs have complex and fine regulatory mechanisms, which makes it a promising target for drug discovery and disease diagnosis. Therefore, predicting the potential miRNA-disease associations has practical significance. In this paper, we proposed an miRNA–disease association predicting method based on multiple kernel fusion on Graph Convolutional Network via Initial residual and Identity mapping (GCNII), called MKFGCNII. Firstly, we built a heterogeneous network of miRNAs and diseases to extract multi-layer features via GCNII. Secondly, multiple kernel fusion method was applied to weight fusion of embeddings at each layer. Finally, Dual Laplacian Regularized Least Squares was used to predict new miRNA–disease associations by the combined kernel in miRNA and disease spaces. Compared with the other methods, MKFGCNII obtained the highest AUC value of 0.9631. Code is available at https://github.com/cuntjx/bioInfo.

Monogenic features based single sample face recognition by kernel sparse representation on multiple Riemannian manifolds

This paper presents a novel method for single sample face recognition, characterized by the use of grayscale monogenic features of the face images, and the kernel sparse representation on multiple Riemannian manifolds. To indicate regional face discriminability, the multi-scale extended monogenic features are firstly locally extracted from different regions of an image, according to a specific face partition scheme, and then the intrinsic subspace of the feature vector set corresponding to each region is further extracted and modeled as a point of a Grassmann manifold. The congeneric local feature scheme is also exploited to entire image for the extraction of co-occurrence distributions of the grouped feature images of intersectional dimensions, based on a special binarization scheme applied to the resultant feature images. This derives the auxiliary marginal distribution-based descriptors residing on the closures of multiple multinomial manifolds. To train the kernel sparse representation classifier using the combined descriptors for a recognition task, the strategy of kernel alignment combining column L2-norm-based kernel matrix normalization are adopted for multiple kernel fusion, where the used kernels are all derived from Riemannian geometries of two types of manifolds. The superiority of our method is demonstrated through extensive experiments.

Predicting the function of rice proteins through Multi-instance Multi-label Learning based on multiple features fusion.

There are a large number of unannotated proteins with unknown functions in rice, which are difficult to be verified by biological experiments. Therefore, computational method is one of the mainstream methods for rice proteins function prediction. Two representative rice proteins, indica protein and japonica protein, are selected as the experimental dataset. In this paper, two feature extraction methods (the residue couple model method and the pseudo amino acid composition method) and the Principal Component Analysis method are combined to design protein descriptive features. Moreover, based on the state-of-the-art MIML algorithm EnMIMLNN, a novel MIML learning framework MK-EnMIMLNN is proposed. And the MK-EnMIMLNN algorithm is designed by learning multiple kernel fusion function neural network. The experimental results show that the hybrid feature extraction method is better than the single feature extraction method. More importantly, the MK-EnMIMLNN algorithm is superior to most classic MIML learning algorithms, which proves the effectiveness of the MK-EnMIMLNN algorithm in rice proteins function prediction.

Adaptive multiple kernel fusion model using spatial-statistical information for high resolution SAR image classification

The current high-resolution (HR) synthetic aperture radar (SAR) image classification is confronted with the challenges of the complex spatial patterns and highly variable backscattering of objects. Data-based methods, such as convolutional neural networks (CNNs), can well extract spatial features but ignore valuable statistical knowledge of SAR data. Model-based methods can utilize the non-stationary and non-Gaussian statistical properties of SAR images, while they fail to encode the local spatial patterns. In this paper, an adaptive multiple kernel fusion model with superpixel regularization (AMKFM-SPR) is proposed for HR SAR image classification, which combines the advantages of both deep spatial features and multiscale statistical properties to improve classification accuracy. For the deep spatial features, multilayer features are extracted by using the pre-trained CNN model. Then, a hybrid pooling strategy is designed to encode the feature maps into more distinguishable features from the perspective of spatial structure and local statistics. For the scattering statistical features, the Gabor magnitudes of HR SAR data are modeled by the log-normal distribution and projected into the cumulative distribution function space. Further, the covariance matrix is calculated for mapped multivariate data to build global statistical features. For the feature fusion, multiple kernels are constructed to describe the spatial and statistical information. An improved centered kernel alignment (ICKA) scheme is utilized to adaptively determine the kernel weights and effectively exploit the complementarity among different features. Next, the fusion kernel is fed into a support vector machine to produce the initial classification map. Finally, to compensate for the limitations of the patch-based classification way, superpixel regularization (SPR) is performed on the class probability map to enhance label consistency and refine the spatial detail. Experiments on three real HR SAR images show the superiority of the proposed method over other related algorithms.

Inferring human microbe–drug associations via multiple kernel fusion on graph neural network

Complex and diverse microbial communities have certain impacts on human health, and specific drugs are needed to treat diseases caused by microbes. However, most of the discovery of associations between microbes and drugs is through biological experiments, which are time-consuming and expensive. Therefore, it is crucial to develop an effective and computational model to detect novel microbe–drug associations. In this study, we propose a model based on Multiple Kernel fusion on Graph Convolutional Network, called MKGCN, for inferring novel microbe–drug associations. Our model is built on the heterogeneous network of microbes and drugs to extract multi-layer features, through Graph Convolutional Network (GCN). Then, we respectively calculate the kernel matrix by embedding features on each layer, and fuse multiple kernel matrices based on the average weighting method. Finally, Dual Laplacian Regularized Least Squares is used to infer new microbe–drug associations by the combined kernel in microbe and drug spaces. Compared with the existing tools for detecting biological bipartite networks, our model has excellent prediction effect on three datasets via three types of cross-validation. Furthermore, we also conduct a case study of the SARS-Cov-2 virus and make a deduction about drugs that may be able to associate with COVID-19. We have proved the accuracy of the prediction results through the existing literature.

MvKFN-MDA: Multi-view Kernel Fusion Network for miRNA-disease association prediction

Predicting the associations between microRNAs (miRNAs) and diseases is of great significance for identifying miRNAs related to human diseases. Since it is time-consuming and costly to identify the association between miRNA and disease through biological experiments, computational methods are currently used as an effective supplement to identify the potential association between disease and miRNA. This paper presents a Multi-view Kernel Fusion Network (MvKFN) based prediction method (MvKFN-MDA) to address the problem of miRNA-disease associations prediction. A novel multiple kernel fusion framework Multi-view Kernel Fusion Network (MvKFN) is first proposed to effectively fuse different views similarity kernels constructed from different data sources in a highly nonlinear way. Using MvKFNs, both different base similarity kernels for miRNA, such as sequence, functional, semantic, Gaussian profile kernels and different base similarity kernels for diseases, such as semantic, Gaussian profile kernel are nonlinearly fused into two integrated similarity kernels, one for miRNA, another for disease. Then, miRNA and disease feature representations are extracted from the miRNA and disease integrated similarity kernels respectively. These features are then fed into a neural matrix completion framework which finally outputs the association prediction scores. The parameters of MvKFN-MDA are learned based on the known miRNA-disease association matrix in a supervised end-to-end way. We compare the proposed method with other state-of-the-art methods. The AUCs of our proposed method were superior to the existing methods in both 5-FCV and LOOCV on two open experimental datasets. Furthermore, 49, 48, and 47 of the top 50 predicted miRNAs for three high-risk human diseases, namely, colon cancer, lymphoma, and kidney cancer, are verified respectively using experimental literature. Finally, 100% accuracy from the top 50 predicted miRNAs is achieved when breast cancer is used as a case study to evaluate the ability of MvKFN-MDA for predicting a new disease without any known related miRNAs.

Unseen Face Presentation Attack Detection Using Sparse Multiple Kernel Fisher Null-Space

We address the face presentation attack detection problem in the challenging conditions of an unseen attack scenario where the system is exposed to novel presentation attacks that were not available in the training stage. To this aim, we pose the unseen face presentation attack detection (PAD) problem as the one-class kernel Fisher null-space regression and present a new face PAD approach that only uses bona fide (genuine) samples for training. Drawing on the proposed kernel Fisher null-space face PAD method and motivated by the availability of multiple information sources, next, we propose a multiple kernel fusion anomaly detection approach to combine the complementary information provided by different views of the problem for improved detection performance. And the last but not the least, we introduce a sparse variant of our multiple kernel Fisher null-space face PAD approach to improve inference speed at the operational phase without compromising much on the detection performance. The results of an experimental evaluation on the OULU-NPU, Replay-Mobile, Replay-Attack and MSU-MFSD datasets illustrate that the proposed method outperforms other methods operating in an unseen attack detection scenario while achieving very competitive performance to multi-class methods (that benefit from presentation attack data for training) despite using only bona fide samples in the training stage.

Identification of Drug–Target Interactions via Dual Laplacian Regularized Least Squares with Multiple Kernel Fusion

Detection of Drug–Target Interactions (DTIs) is the time-consuming and laborious experiment via biochemical approaches. Machine learning based methods have been widely used to mine meaningful information of drug research. In this study, we establish a novel computational method to predict DTIs via Dual Laplacian Regularized Least Squares model (DLapRLS) with Hilbert–Schmidt Independence Criterion-based Multiple Kernel Learning (HSIC-MKL). Multiple kernels are built from different information sources (drug and target spaces). Then, above corresponding kernels are integrated by HSIC-MKL. At last, DLapRLS model is trained by Alternating Least Squares Algorithm (ALSA) and employed to predict new DTIs. On four benchmark datasets, the results of our method are comparable and even better than existing models.

Discovering Cancer Subtypes via an Accurate Fusion Strategy on Multiple Profile Data.

Discovering cancer subtypes is useful for guiding clinical treatment of multiple cancers. Progressive profile technologies for tissue have accumulated diverse types of data. Based on these types of expression data, various computational methods have been proposed to predict cancer subtypes. It is crucial to study how to better integrate these multiple profiles of data. In this paper, we collect multiple profiles of data for five cancers on The Cancer Genome Atlas (TCGA). Then, we construct three similarity kernels for all patients of the same cancer by gene expression, miRNA expression and isoform expression data. We also propose a novel unsupervised multiple kernel fusion method, Similarity Kernel Fusion (SKF), in order to integrate three similarity kernels into one combined kernel. Finally, we make use of spectral clustering on the integrated kernel to predict cancer subtypes. In the experimental results, the P-values from the Cox regression model and survival curve analysis can be used to evaluate the performance of predicted subtypes on three datasets. Our kernel fusion method, SKF, has outstanding performance compared with single kernel and other multiple kernel fusion strategies. It demonstrates that our method can accurately identify more accurate subtypes on various kinds of cancers. Our cancer subtype prediction method can identify essential genes and biomarkers for disease diagnosis and prognosis, and we also discuss the possible side effects of therapies and treatment.

Multispectral image change detection with kernel cross-modal factor analysis-based fusion of kernels

The utilization of the complementary information, the color feature, and the intensity-texture feature, in hue, saturation, and intensity space is limited in the change detection of multispectral images. A kernel fusing the complementary information of the color feature and the intensity-texture features is proposed. To construct the fusion kernel, color kernel and intensity-texture kernel are constructed based on Gaussian radial basis function kernel. Then, the kernel cross-modal factor analysis method is used to provide transformations of the kernels and the fusion kernel is obtained by multiple kernel fusion, thus achieving the capture of the complementary information. In this way, the obtained fusion kernel highlights the changed areas and its boundary using the color features, and meanwhile provides texture-intensity change information. Experiments on real multispectral images demonstrate the effectiveness of the fusion kernel, and illustrate that it can get smoother homogeneous areas, obtain more accurate edge locations, and provide strong noise immunity for multispectral image change detection.

EEG feature descriptors and discriminant analysis under Riemannian Manifold perspective

Abstract This paper presents a framework to classify motor imagery in the context of multi-class Brain Computer Interface based on electroencephalography (EEG). Covariance matrices are extracted as the EEG signal descriptors, and different dissimilarity metrics on the manifold of Symmetric Positive Definite (SPD) matrices are investigated to classify these covariance descriptors. Specifically, we compare the performance of the Log Euclidean distance, Stein divergence, Kullback–Leibler divergence and Von Neumann divergence. Furthermore, inspired from the conventional Common Spatial Pattern, discriminant analysis performed directly on the SPD manifold using different mentioned metrics are proposed to improve the classification accuracy. We also propose a new feature, namely Heterogeneous Orders Relevance Composition (HORC), by combining different relevance matrices, such as Covariance, Mutual Information or Kernel Matrix under the Tensor Framework and Multiple Kernel fusion. Multi-Class Multi-Kernel Relevance Vector Machine is adopted to provide a sparse classifier and Bayesian confidence prediction. Finally, we compare the performance of total 16 methods on the dataset IIa of the BCI Competition IV. The results shows that the mentioned dissimilarity metrics perform quite equally on the original manifold, whereas the proposed discrimination methods can improve the accuracy by 3–5% on the reduced dimension manifold.

A multiple kernel learning based fusion for earthquake detection from multimedia twitter data

An efficient way of extracting useful information from multiple sources of data is to use data fusion technology. This paper introduces a data fusion approach in multimedia data for earthquake detection in twitter by using kernel fusion. The fusion method applies to fuse two types of data. The first type is features extracted from text by using bag-of-words method which is based on the calculation of the term frequency-inverse document frequency. The second type is the visual features extracted from images by applying scale-invariant feature transform. A multiple kernel fusion is applied in order to fuse the information from these two sources. Our experiments have indicated that comparing to the approaches using single data source, the proposed approach of using multiple kernel learning algorithm as early fusion increased the accuracy for earthquake detection. Experimental results for the proposed method achieved a high accuracy of 0.94, comparing to accuracy of 0.89 with texts only, and accuracy of 0.83 with images only.

A new framework with multiple tasks for detecting and locating pain events in video

Automatically detecting and locating pain events in video is an important task in medical assessment. It is a challenging problem in facial expression analysis due to spontaneous faces, head movements and pose variations. In this paper, we explore the role of facial information at various time scales (frame, segment and sequence) and propose a new framework for pain event detection and locating in video. We introduce a feature-level fusion method for pain event detection and a multiple-task fusion method for locating pain events, respectively. Both spatial and spatial–temporal features are utilized in our study. At first, we employ the histogram of oriented gradients (HOG) of fiducial points (P-HOG) to extract spatial features from each video frame and train an SVM as a frame-based pain event detector. Secondly, HOG from Three Orthogonal Planes (named as HOG-TOP) is used to characterize the dynamic textures of a video segment, a segment-based classifier (SVM) is then trained for segment-level detection. We further apply a max pooling strategy to obtain the global P-HOG and HOG-TOP to represent the whole video sequence and a multiple kernel fusion is employed to find an optimal feature-level fusion. An SVM with multiple kernels is trained to perform sequence-level (pain event) detection. Finally, an effective probabilistic fusion method is proposed to integrate the detection results of the three different tasks (frame-level, segment-level and sequence-level detection) to locate pain events in video. Extensive experiments conducted on the UNBC-McMaster Shoulder Pain database show that our proposed method outperforms other state-of-the-art methods both in pain event detection and locating in video. Our sequence-level event detection method has also been applied to facial expression recognition in video with good results.