Self-tuning Spectral Clustering Research Articles

JSCSNCP-LMA: a method for predicting the association of lncRNA–miRNA

Non-coding RNAs (ncRNAs) have long been considered the "white elephant" on the genome because they lack the ability to encode proteins. However, in recent years, more and more biological experiments and clinical reports have proved that ncRNAs account for a large proportion in organisms. At the same time, they play a decisive role in the biological processes such as gene expression and cell growth and development. Recently, it has been found that short sequence non-coding RNA(miRNA) and long sequence non-coding RNA(lncRNA) can regulate each other, which plays an important role in various complex human diseases. In this paper, we used a new method (JSCSNCP-LMA) to predict lncRNA–miRNA with unknown associations. This method combined Jaccard similarity algorithm, self-tuning spectral clustering similarity algorithm, cosine similarity algorithm and known lncRNA–miRNA association networks, and used the consistency projection to complete the final prediction. The results showed that the AUC values of JSCSNCP-LMA in fivefold cross validation (fivefold CV) and leave-one-out cross validation (LOOCV) were 0.9145 and 0.9268, respectively. Compared with other models, we have successfully proved its superiority and good extensibility. Meanwhile, the model also used three different lncRNA–miRNA datasets in the fivefold CV experiment and obtained good results with AUC values of 0.9145, 0.9662 and 0.9505, respectively. Therefore, JSCSNCP-LMA will help to predict the associations between lncRNA and miRNA.

A Hybrid Method for Traffic State Classification Using K-Medoids Clustering and Self-Tuning Spectral Clustering

As an important part of intelligent transportation systems, traffic state classification plays a vital role for traffic managers when formulating measures to alleviate traffic congestion. The proliferation of traffic data brings new opportunities for traffic state classification. In this paper, we propose a hybrid new traffic state classification method based on unsupervised clustering. Firstly, the k-medoids clustering algorithm is used to cluster the daily traffic speed data from multiple detection points in the selected area, and then the cluster-center detection points of the cluster with congestion are selected for further analysis. Then, the self-tuning spectral clustering algorithm is used to cluster the speed, flow, and occupancy data of the target detection point to obtain the traffic state classification results. Finally, several state-of-the-art methods are introduced for comparison, and the results show that performance of the proposed method are superior to comparable methods.

QuasiSeq: profiling viral quasispecies via self-tuning spectral clustering with PacBio long sequencing reads.

The existence of quasispecies in the viral population causes difficulties for disease prevention and treatment. High-throughput sequencing provides opportunity to determine rare quasispecies and long sequencing reads covering full genomes reduce quasispecies determination to a clustering problem. The challenge is high similarity of quasispecies and high error rate of long sequencing reads. We developed QuasiSeq using a novel signature-based self-tuning clustering method, SigClust, to profile viral mixtures with high accuracy and sensitivity. QuasiSeq can correctly identify quasispecies even using low-quality sequencing reads (accuracy <80%) and produce quasispecies sequences with high accuracy (≥99.55%). Using high-quality circular consensus sequencing reads, QuasiSeq can produce quasispecies sequences with 100% accuracy. QuasiSeq has higher sensitivity and specificity than similar published software. Moreover, the requirement of the computational resource can be controlled by the size of the signature, which makes it possible to handle big sequencing data for rare quasispecies discovery. Furthermore, parallel computation is implemented to process the clusters and further reduce the runtime. Finally, we developed a web interface for the QuasiSeq workflow with simple parameter settings based on the quality of sequencing data, making it easy to use for users without advanced data science skills. QuasiSeq is open source and freely available at https://github.com/LHRI-Bioinformatics/QuasiSeq. The current release (v1.0.0) is archived and available at https://zenodo.org/badge/latestdoi/340494542. Supplementary data are available at Bioinformatics online.

Semi-supervised classification of lower-ionospheric perturbations using GNSS radio occultation observations from Spire Global’s Cubesat Constellation

This study presents a new methodology to automatically classify perturbations in the lower ionosphere using GNSS radio occultation (RO) observations collected using Spire’s constellation of CubeSats. This methodology combines signal processing techniques with semi-supervised machine learning by applying spectral clustering in a metric space of wavelet spectra. A “bottom-up” algorithm was applied to extract E layer information directly from Spire’s high-rate (50 Hz) GNSS-RO profiles by subtracting the effect of the F layers. This processing algorithm has been implemented in our ground segment to operationally produce high rate sTEC profiles with a vertical resolution of better than 100 m. The key idea behind the semi-supervised classification is to produce a database of labeled clusters that can be used to classify new unlabeled data by determining which cluster it belongs to. A dataset of more than 12,000 GNSS-RO profiles collected in 2019 containing sTEC perturbations is used to find the initial clusters. This dataset is used to represent the climatology of ionospheric perturbations, such as MSTIDs and sporadic Es. The wavelet power spectrum (WPS) is computed for these profiles, and a metric space is defined using the Earth mover’s distance (EMD) between the WPS. A self-tuning spectral clustering algorithm is used to cluster the profiles in this metric space. These clusters are used as a reference database of perturbations to classify new sTEC profiles by finding the cluster of the closest profile of the clustered dataset in the EMD metric space. This new methodology is used to construct an automated system to monitor ionospheric perturbations on a global scale.

WITHDRAWN: An efficient self-tuning spectral clustering algorithm for chronic kidney disease prediction

Abstract Recently, Chronic Kidney Disease (CKD) is an increasingly severe problem which considered as a global health problem. To control CKD disease, early detection and characterization are considered to be important factors. In literature, many techniques were developed to identify CKD at an early stage but it fails to accurate identification because of redundancy and high dimension data. To solve the abovementioned problems, the efficient data mining technique must be utilized which increases accuracy for the identification of CKD. Hence, in this paper, self-tuning spectral clustering is introduced to reduce the high dimension and redundancy problem in data. The self-tuning spectral clustering is shown to extract and reveal required information from laboratory and clinical patient data which most helpful to assist physicians in increasing the accuracy of CKD identification before reach a severe stage. The clustering results are applying to machine learning techniques such as Deep Neural Network (DNN), Artificial Neural Network (ANN), Support Vector Machine (SVM), Random Forest (RF) and K-Nearest Neighbour (KNN). The proposed technique is implemented in the Phython and performance is evaluated. The performance of the proposed technique is analyzed with statistical measurements such as accuracy, specificity, precision, recall, sensitivity and F_score. In comparison analysis, our finding shows that SVM and KNN provide better identification of CKD with clustering technique and maximum 0.96% accuracy.

Robust self-tuning spectral clustering

Clustering, as an effective data analysis technique, is widely used in industrial application and science research. In this paper, we have proposed a novel spectral clustering method to solve three problems of spectral clustering, i.e., cluster-initialization, cluster-specification, and noise-robustness. To do this, we first learn a high-quality affinity matrix, and then capture an inherent clustering pattern in real feature space and projected subspace, and finally extract connected components to conduct clustering. By comparing to five comparison methods in six real data sets, our proposed method has achieved a competitive clustering performance in terms of four evaluation metrics.

Curvature Integration in a 5D Kernel for Extracting Vessel Connections in Retinal Images.

Tree-like structures, such as retinal images, are widely studied in computer-aided diagnosis systems for large-scale screening programs. Despite several segmentation and tracking methods proposed in the literature, there still exist several limitations specifically when two or more curvilinear structures cross or bifurcate, or in the presence of interrupted lines or highly curved blood vessels. In this paper, we propose a novel approach based on multi-orientation scores augmented with a contextual affinity matrix, which both are inspired by the geometry of the primary visual cortex (V1) and their contextual connections. The connectivity is described with a 5D kernel obtained as the fundamental solution of the Fokker-Planck equation modeling the cortical connectivity in the lifted space of positions, orientations, curvatures, and intensity. It is further used in a self-tuning spectral clustering step to identify the main perceptual units in the stimuli. The proposed method has been validated on several easy as well as challenging structures in a set of artificial images and actual retinal patches. Supported by quantitative and qualitative results, the method is capable of overcoming the limitations of current state-of-the-art techniques.

Abnormal Activity Detection Using Pyroelectric Infrared Sensors.

Healthy aging is one of the most important social issues. In this paper, we propose a method for abnormal activity detection without any manual labeling of the training samples. By leveraging the Field of View (FOV) modulation, the spatio-temporal characteristic of human activity is encoded into low-dimension data stream generated by the ceiling-mounted Pyroelectric Infrared (PIR) sensors. The similarity between normal training samples are measured based on Kullback-Leibler (KL) divergence of each pair of them. The natural clustering of normal activities is discovered through a self-tuning spectral clustering algorithm with unsupervised model selection on the eigenvectors of a modified similarity matrix. Hidden Markov Models (HMMs) are employed to model each cluster of normal activities and form feature vectors. One-Class Support Vector Machines (OSVMs) are used to profile the normal activities and detect abnormal activities. To validate the efficacy of our method, we conducted experiments in real indoor environments. The encouraging results show that our method is able to detect abnormal activities given only the normal training samples, which aims to avoid the laborious and inconsistent data labeling process.

Dynamic aurora sequence recognition using Volume Local Directional Pattern with local and global features

Aurora event consists of the spatial structure and temporal evolution of aurora luminosity, which attributes to the effects of the solar wind-magnetosphere interaction and the physics of the magnetosphere-ionosphere interaction. Dynamic aurora event provides a meaningful projection of effects from plasma processes of outer space and also reveals some certain physical phenomenon and principle. Aurora sequence recognition is one of the key procedure in the analysis of dynamic aurora event. Lots of effective features for static aurora image classification are proposed. If these features for static image classification are utilized to recognize the dynamic aurora sequence, it will result in higher computational complexity. The dynamic features of aurora sequence are seldom proposed due to its complexity. To this end, this paper proposes an efficient aurora sequence descriptor which combines local and global spatial information with temporal location information, which is called as Volume Local Directional Patterns. The ring-section spatial pyramid partition structure is used in the VLDP code image which is coded by Volume Local Directional Patterns to obtain the local spatial feature. After combining the global feature of VLDP code image, the final RSPLDP feature is obtained. Finally, the STSC (self-tuning spectral clustering) method is used to classify the aurora sequence. The experimental results on the dataset which is captured from All-sky Imager (ASI) at the Chinese Yellow River Station demonstrate the effectiveness of the proposed classification scheme.

Texture Image Segmentation Using Affinity Propagation and Spectral Clustering

Clustering is a popular and effective method for image segmentation. However, existing cluster methods often suffer the following problems: (1) Need a huge space and a lot of computation when the input data are large. (2) Need to assign some parameters (e.g. number of clusters) in advance which will affect the clustering results greatly. To save the space and computation, reduce the sensitivity of the parameters, and improve the effectiveness and efficiency of the clustering algorithms, we construct a new clustering algorithm for image segmentation. The new algorithm consists of two phases: coarsening clustering and exact clustering. First, we use Affinity Propagation (AP) algorithm for coarsening. Specifically, in order to save the space and computational cost, we only compute the similarity between each point and its t nearest neighbors, and get a condensed similarity matrix (with only t columns, where t &lt;&lt; N and N is the number of data points). Second, to further improve the efficiency and effectiveness of the proposed algorithm, the Self-tuning Spectral Clustering (SSC) is used to the resulted points (the representative points gotten in the first phase) to do the exact clustering. As a result, the proposed algorithm can quickly and precisely realize the clustering for texture image segmentation. The experimental results show that the proposed algorithm is more efficient than the compared algorithms FCM, K-means and SOM.

Statistical background model-based target detection

This paper proposes a statistical background modeling framework to deal with the issue of target detection, where the global and local information is utilized to achieve more accurate detection of moving objects. Specifically, for the target detection problem under illumination change conditions, a novel self-adaptive Gaussian mixture model mixed with the global information is utilized to construct a statistical background model to detect moving objects; for the target detection problem under dynamic background conditions, the self-tuning spectral clustering method is first utilized to cluster background images, and then the kernel density estimation method mixed with the local information is utilized to construct a statistical background model to detect moving objects. Experimental results demonstrate that the proposed framework can improve the detection performance under illumination change conditions or dynamic background conditions.

An Adaptive Spectral Clustering Algorithm Based on the Importance of Shared Nearest Neighbors

The construction of a similarity matrix is one significant step for the spectral clustering algorithm; while the Gaussian kernel function is one of the most common measures for constructing the similarity matrix. However, with a fixed scaling parameter, the similarity between two data points is not adaptive and appropriate for multi-scale datasets. In this paper, through quantitating the value of the importance for each vertex of the similarity graph, the Gaussian kernel function is scaled, and an adaptive Gaussian kernel similarity measure is proposed. Then, an adaptive spectral clustering algorithm is gotten based on the importance of shared nearest neighbors. The idea is that the greater the importance of the shared neighbors between two vertexes, the more possible it is that these two vertexes belong to the same cluster; and the importance value of the shared neighbors is obtained with an iterative method, which considers both the local structural information and the distance similarity information, so as to improve the algorithm’s performance. Experimental results on different datasets show that our spectral clustering algorithm outperforms the other spectral clustering algorithms, such as the self-tuning spectral clustering and the adaptive spectral clustering based on shared nearest neighbors in clustering accuracy on most datasets.

Locally adaptive multiple kernel clustering

Conventional multiple kernel learning aims to construct a global combination of multiple kernels in input space. For a data set which has varying local distributions in input space, using a uniform combination of multiple kernels may not always work well. In this paper, we proposed a localized multiple kernel learning method for clustering. Instead of using a uniform combinational kernel over the whole input space, our method associates to each cluster a localized kernel. We assign to each cluster a weight vector for feature selection and combine each weight vector with a Gaussian kernel to form a unique kernel for the corresponding cluster. By optimizing the weight vector and the width parameter of Gaussian kernel jointly for each cluster, each kernel can be localized to match the data distribution of its corresponding cluster. A locally adaptive strategy based on the kernel k-means clustering is used to optimize the kernel for each cluster. We experimentally compared our methods to the kernel k-means clustering, averaged multiple kernel clustering, self-tuning spectral clustering and Variable Bandwidth Mean Shift algorithm. Experimental results demonstrate the effectiveness of our method.

Automatic image segmentation using constraint learning and propagation

In this paper, we propose automatic image segmentation using constraint learning and propagation. Recently, kernel learning is receiving much attention because a learned kernel can fit the given data better than a predefined kernel. To effectively learn the constraints generated by initial seeds for image segmentation, we employ kernel propagation (KP) based on kernel learning. The key idea of KP is first to learn a small-sized seed-kernel matrix and then propagate it into a large-sized full-kernel matrix. By applying KP to automatic image segmentation, we design a novel segmentation method to achieve high performance. First, we generate pairwise constraints, i.e., must-link and cannot-link, from initially selected seeds to make the seed-kernel matrix. To select the optimal initial seeds, we utilize global k-means clustering (GKM) and self-tuning spectral clustering (SSC). Next, we propagate the seed-kernel matrix into the full-kernel matrix of the entire image, and thus image segmentation results are obtained. We test our method on the Berkeley segmentation database, and the experimental results demonstrate that the proposed method is very effective in automatic image segmentation.

Spectral clustering with fuzzy similarity measure

Spectral clustering algorithms have been successfully used in the field of pattern recognition and computer vision. The widely used similarity measure for spectral clustering is Gaussian kernel function which measures the similarity between data points. However, it is difficult for spectral clustering to choose the suitable scaling parameter in Gaussian kernel similarity measure. In this paper, utilizing the prototypes and partition matrix obtained by fuzzy c-means clustering algorithm, we develop a fuzzy similarity measure for spectral clustering (FSSC). Furthermore, we introduce the K-nearest neighbor sparse strategy into FSSC and apply the sparse FSSC to texture image segmentation. In our experiments, we firstly perform some experiments on artificial data to verify the efficiency of the proposed fuzzy similarity measure. Then we analyze the parameters sensitivity of our method. Finally, we take self-tuning spectral clustering and Nystrom methods for baseline comparisons, and apply these three methods to the synthetic texture and remote sensing image segmentation. The experimental results show that the proposed method is significantly effective and stable.

Local density adaptive similarity measurement for spectral clustering

Similarity measurement is crucial to the performance of spectral clustering. The Gaussian kernel function is usually adopted as the similarity measure. However, with a fixed kernel parameter, the similarity between two data points is only determined by their Euclidean distance, and is not adaptive to their surroundings. In this paper, a local density adaptive similarity measure is proposed, which uses the local density between two data points to scale the Gaussian kernel function. The proposed similarity measure satisfies the clustering assumption and has an effect of amplifying intra-cluster similarity, thus making the affinity matrix clearly block diagonal. Experimental results on both synthetic and real world data sets show that the spectral clustering algorithm with our local density adaptive similarity measure outperforms the traditional spectral clustering algorithm, the path-based spectral clustering algorithm and the self-tuning spectral clustering algorithm.