Modified FDP cluster algorithm and its application in protein conformation clustering analysis

The density peaks clustering (DPC) algorithm can identify clusters with various shapes and densities in the underlying dataset. However, the DPC algorithm cannot exactly find the true quantity of clustering centers when computing the local density, and it is difficult to handle non-convex datasets. Moreover, the DPC algorithm is difficult to identify boundary points and outliers without a reasonable allocation strategy when dealing with low-density points. To solve these limitations, a novel deviation density peaks clustering (DeDPC) algorithm is proposed. First, the local deviation of the spatial distance of datasets with different structures is utilised to replace the local density to generate a more reasonable clustering center decision graph. Second, a threshold is defined to further divide and process low-density points. Finally, outliers in low-density points can be accurately found to accurately cluster the dataset. To evaluate the performance of the DeDPC algorithm, experiments are conducted on synthetic and real-world datasets and the DeDPC is compared with other clustering methods. The DeDPC is also applied to medical image segmentation to further demonstrate its capability for medical image processing. The simulation results show that the DeDPC method has good validity and utility for both non-convex datasets and medical image segmentation.

Water flooding flowing area identification for oil reservoirs based on the method of streamline clustering artificial intelligence

As a relatively novel density-based clustering algorithm, Density peak clustering (DPC) has been widely studied in recent years. DPC sorts all points in descending order of local density and finds neighbors for each point in turn to assign all points to the appropriate clusters. The algorithm is simple and effective but has some limitations in applicable scenarios. If the density difference between clusters is large or the data distribution is in a nested structure, the clustering effect of this algorithm is poor. This study incorporates the idea of connectivity into the original algorithm and proposes an improved density peak clustering algorithm ConDPC. ConDPC modifies the strategy of obtaining clustering center points and assigning neighbors and improves the clustering accuracy of the original density peak clustering algorithm. In this study, clustering comparison experiments were conducted on synthetic data sets and real-world data sets. The compared algorithms include original DPC, DBSCAN, K-means and two improved algorithms over DPC. The comparison results prove the effectiveness of ConDPC.

Density Peaks Clustering (DPC) algorithm identifies cluster centers based on local density and relative distance, disregarding the effect of the sample's environment on its density. This makes it challenging to identify cluster centers in low-density regions. Moreover, the single-step allocation strategy of DPC algorithm lacks fault tolerance. If a sample point is incorrectly allocated, it can trigger a cascade of subsequent allocation error. To solve the aforementioned issue, a density peak clustering algorithm based on natural neighbors and diffusion allocation (NNDA-DPC) is proposed. Firstly, the concept of natural neighbors is introduced, and the local density of sample points is redefined by considering the density of sample points and the environment in which the sample points are located. This is done to reduce the influence of the sparsity of class clusters on the selection of class cluster centers. The clustering centers are automatically determined by computing the decision value. Secondly, the natural neighbor points of the selected clustering centers are assigned to the corresponding clustering centers to form the initial microclusters. Finally, the initial microclusters are formed based on the remaining sample points and the initial clusters. The final clustering result is obtained by assigning the sample points based on the correlation between the remaining sample points and the initial clusters, which helps prevent the cascading effect of assignment errors. We compared the NNDA-DPC algorithm with DPC and its enhanced versions on artificial and UCI datasets. The experimental results demonstrate that the NNDA-DPC algorithm can efficiently cluster the datasets.

Density peaks clustering based on superior nodes and fuzzy correlation

Clustering is one of the most important topics in data mining and machine learning. The density peaks clustering (DPC) algorithm is a well-known density-based clustering method that can efficiently and effectively deal with non-spherical clusters. However, the computational methods of the local density and the distance measure are simple and easily ignore the correlation and the similarity between samples, and the manual setting of parameters has a great influence on the clustering results; therefore, the clustering performance of DPC is poor on the high-dimensional datasets. To address these issues, this paper presents an adaptive DPC algorithm with Fisher linear discriminant for the clustering of complex datasets, called ADPC-FLD. First, the kernel density estimation function is introduced to calculate the local density of the sample points. Pearson correlation coefficient between samples as weight is employed to construct a weighted Euclidean distance function to measure the distance between samples. This considers both the spatial structure and the correlation of the samples. Then, a novel density estimation entropy is proposed, and based on the minimization of density estimation entropy, the density estimation parameters are adaptively selected according to the distribution characteristics of the data, which can efficiently eliminate the influence of manual setting. Third, an adaptive strategy of cluster center selection is designed to avoid the error caused by the noise data as the cluster centers and the uncertainty of manually selecting the cluster centers. Finally, Fisher linear discriminant algorithm is used to eliminate the irrelevant information and reduce the dimensionality of high-dimensional data, following on which an adaptive DPC method is implemented on six synthetic datasets, thirteen UCI datasets and seven gene expression datasets for comparing with other related algorithms. The experimental results on 26 datasets show that the proposed algorithm significantly outperforms several outstanding clustering approaches in terms of clustering accuracy and efficiency.

We adopt clustering algorithm to improve segmentation accuracy. In this paper, 3D laser scanning platform was built to obtain the spatial 3D point cloud data. And then we extracted the point cloud data for two planar features. K-means algorithm, density-based clustering algorithm and density peak clustering algorithm were employed to split the 3D point cloud of the two planes. After clustering, we compared and analyzed the clustering results of the three clustering algorithms. More importantly, we also found that for peak density clustering, the threshold value is related to its sensitivity to noise points. After fitting the two planes, the verticality of two planes was also calculated. We analyzed the results and summarized the criterion for selecting thresholds.

In software‐defined wide area networks (SD‐WANs), finding an optimal number of controllers and their placement is termed as the controller placement problem. The existing solutions based on multi‐objective optimisation techniques incur high computation time. Heuristic algorithms based methods quickly converge to local optimum solutions and clustering‐based approaches demand that the number of controllers required to be predefined. In SD‐WANs, computationally simple solutions for controller placement can be developed using non‐parametric clustering algorithms. The proposed modified density peak (modified‐DP) clustering algorithm decides the multi‐controller placement for the selected networks from the Internet Topology Zoo. The computed performance metrics are compared with hierarchical k‐means, modified affinity propagation (modified‐AP), and basic DP (basic‐DP) clustering algorithms. The criteria importance through inter‐criteria correlation method calculates weights of each performance metric, and a normalised weighted additive utility function computes the utility value for the controller placement using each algorithm. The modified‐DP computes the minimum utility value and optimal placement of SDN controllers compared to hierarchical k‐means, modified‐AP, and basic‐DP. The Cbench tool calculates the maximum throughput for the controller placement in each network topology. The calculated fairness in the utilisation of the controllers justifies the optimal controller placement using modified‐DP.

Density Peak Clustering (DPC) is a widely used clustering method that automatically identifies cluster centers based on local density and distance metrics. However, DPC tends to converge to local optimal solutions when processing datasets with uneven density distributions. This paper proposes DPC-DIST, an improved algorithm that addresses this limitation through a geometric distribution coefficient δ . By incorporating spatial distribution characteristics into density calculations, DPC-DIST effectively prevents convergence to suboptimal solutions. Comprehensive experiments on six benchmark datasets (Wine, Iris, Seeds, Blobs, R15, R3) demonstrate that DPC-DIST consistently outperforms the original DPC, K-means++, and spectral clustering algorithms. Significant improvements were observed in high-dimensional data processing, with 9.3 % increase in Silhouette Coefficient and 47.7 % improvement in Calinski-Harabasz Score on the Wine dataset. The algorithm shows particular advantages in facility location optimization and logistics planning applications, demonstrating its practical value for real-world scenarios.

Outlier detection is an important field in data mining, which can be used in fraud detection, fault detection, and other fields. This article focuses on the problem where the density peak clustering algorithm needs a manual parameter setting and time complexity is high; the first is to use the k nearest neighbors clustering algorithm to replace the density peak of the density estimate, which adopts the KD-Tree index data structure calculation of data objects k close neighbors. Then it adopts the method of the product of density and distance automatic selection of clustering centers. In addition, the central relative distance and fast density peak clustering outliers were defined to characterize the degree of outliers of data objects. Then, based on fast density peak clustering outliers, an outlier detection algorithm was devised. Experiments on artificial and real data sets are performed to validate the algorithm, and the validity and time efficiency of the proposed algorithm are validated when compared to several conventional and innovative algorithms.

Based on the traditional grid density clustering algorithm, proposing A Data Stream Clustering Algorithm Based on Density and Extended Grid(DEGDS). The algorithm combines the advantages of grid clustering algorithm and density clustering algorithm, by improving the defects of clustering parameters by artificially set, get any shape of the cluster. The algorithm uses the local density of each sample point and the distance from the other sample points, determining the number of clustering centers in the grid, and realizing the automatic determination of the clustering center, which avoids the influence of improper selection of initial centroid on clustering results. And in the process of combining the Spark parallel framework for partitioning the data to achieve its parallelization. For data points clustered outside the grid, the clustering within the grid has been effectively expanded by extending the grid, to ensure the accuracy of clustering. Introduced density estimation is connected and grid boundaries to merging grid, saving memory consumption. Using the attenuation factor to incremental update grid density, reflect the evolution of spatial data stream. The experimental results show that compared with the traditional clustering algorithm, the DEGDS algorithm has a large performance improvement in accuracy and efficiency, and can be effectively for large data clustering.

Density peak clustering based on relative density relationship

Aiming at the problem of video key frame extraction, a density peak clustering algorithm is proposed, which uses the HSV histogram to transform high-dimensional abstract video image data into quantifiable low-dimensional data, and reduces the computational complexity while capturing image features. On this basis, the density peak clustering algorithm is used to cluster these low-dimensional data and find the cluster centers. Combining the clustering results, the final key frames are obtained. A large number of key frame extraction experiments for different types of videos show that the algorithm can extract different number of key frames by combining video content, overcome the shortcoming of traditional key frame extraction algorithm which can only extract a fixed number of key frames, and the extracted key frames can represent the main content of video accurately.

The first synchronization clustering (SynC) algorithm based on an extensive Kuromato model was presented in 2010. In 2017, an effective synchronization clustering (ESynC) algorithm, inspired by SynC algorithm and a linear version of Vicsek model, was proposed. When facing complex data distributions, ESynC algorithm may regard an irregular and whole cluster as some micro-clusters. To conquer this shortcoming, a combined clustering algorithm based on ESynC algorithm and a merging judgement process of micro-clusters (CESynC) is presented. CESynC algorithm first uses ESynC algorithm to detect clusters or micro-clusters, then merges those conjoint micro-clusters by using a merging judgement process. For some datasets that ESynC and SynC cannot detect correct clusters, CESynC can capture natural clusters. From the simulation experiments, we observe that CESynC can get better (or the same) clustering results than (or as) that of ESynC in many cases. We also observe that the clustering results of CESynC and ESynC are often better than that of SynC. Therefore, we can say CESynC can often obtain better clustering quality than ESynC and SynC in some kinds of datasets. Further comparison experiments with some classical clustering algorithms demonstrate the clustering effect of CESynC.

Density peaks clustering (DPC) is a well-known density-based clustering algorithm that can deal with nonspherical clusters well. However, DPC has high computational complexity and space complexity in calculating local density ρ and distance δ , which makes it suitable only for small-scale data sets. In addition, for clustering high-dimensional data, the performance of DPC still needs to be improved. High-dimensional data not only make the data distribution more complex but also lead to more computational overheads. To address the above issues, we propose an improved density peaks clustering algorithm, which combines feature reduction and data sampling strategy. Specifically, features of the high-dimensional data are automatically extracted by principal component analysis (PCA), auto-encoder (AE), and t-distributed stochastic neighbor embedding (t-SNE). Next, in order to reduce the computational overhead, we propose a novel data sampling method for the low-dimensional feature data. Firstly, the data distribution in the low-dimensional feature space is estimated by the Quasi-Monte Carlo (QMC) sequence with low-discrepancy characteristics. Then, the representative QMC points are selected according to their cell densities. Next, the selected QMC points are used to calculate ρ and δ instead of the original data points. In general, the number of the selected QMC points is much smaller than that of the initial data set. Finally, a two-stage classification strategy based on the QMC points clustering results is proposed to classify the original data set. Compared with current works, our proposed algorithm can reduce the computational complexity from O n 2 to O N n , where N denotes the number of selected QMC points and n is the size of original data set, typically N ≪ n . Experimental results demonstrate that the proposed algorithm can effectively reduce the computational overhead and improve the model performance.