scholarly journals Efficient High-Dimensional Kernel k-Means with Random Projection++

2021 ◽  
Vol 11 (15) ◽  
pp. 6963
Author(s):  
Jan Y. K. Chan ◽  
Alex Po Leung ◽  
Yunbo Xie
Keyword(s):  
Kernel Methods ◽  
Dimensional Space ◽  
Random Projection ◽  
High Dimensional ◽  
Random Projections ◽  
Input Feature ◽  
Data Points ◽  
Speed Up ◽  
Lower Dimensional Space ◽  
Lower Dimensional

Using random projection, a method to speed up both kernel k-means and centroid initialization with k-means++ is proposed. We approximate the kernel matrix and distances in a lower-dimensional space Rd before the kernel k-means clustering motivated by upper error bounds. With random projections, previous work on bounds for dot products and an improved bound for kernel methods are considered for kernel k-means. The complexities for both kernel k-means with Lloyd’s algorithm and centroid initialization with k-means++ are known to be O(nkD) and Θ(nkD), respectively, with n being the number of data points, the dimensionality of input feature vectors D and the number of clusters k. The proposed method reduces the computational complexity for the kernel computation of kernel k-means from O(n2D) to O(n2d) and the subsequent computation for k-means with Lloyd’s algorithm and centroid initialization from O(nkD) to O(nkd). Our experiments demonstrate that the speed-up of the clustering method with reduced dimensionality d=200 is 2 to 26 times with very little performance degradation (less than one percent) in general.

scholarly journals Deep Clustering with Self-supervision using Pairwise Data Similarities

2021 ◽  
Author(s):  
Mohammadreza Sadeghi ◽  
Narges Armanfard
Keyword(s):  
Dimensional Space ◽  
Second Phase ◽  
Similar Data ◽  
Number Of Clusters ◽  
Latent Space ◽  
Benchmark Datasets ◽  
Data Points ◽  
Complex Cluster ◽  
Lower Dimensional Space ◽  
Lower Dimensional

<div>Deep clustering incorporates embedding into clustering to find a lower-dimensional space appropriate for clustering. In this paper we propose a novel deep clustering framework with self-supervision using pairwise data similarities (DCSS). The proposed method consists of two successive phases. In the first phase we propose to form hypersphere-like groups of similar data points, i.e. one hypersphere per cluster, employing an autoencoder which is trained using cluster-specific losses. The hyper-spheres are formed in the autoencoder’s latent space. In the second phase, we propose to employ pairwise data similarities to create a K-dimensional space that is capable of accommodating more complex cluster distributions; hence, providing more accurate clustering performance. K is the number of clusters. The autoencoder’s latent space obtained in the first phase is used as the input of the second phase. Effectiveness of both phases are demonstrated on seven benchmark datasets through conducting a rigorous set of experiments.</div>

Methods for Binary Multidimensional Scaling

2002 ◽  
Vol 14 (5) ◽  
pp. 1195-1232 ◽  
Author(s):  
Douglas L. T. Rohde
Keyword(s):  
Neural Networks ◽  
Multidimensional Scaling ◽  
Dimensional Space ◽  
Discrete Space ◽  
High Dimensional ◽  
Continuous Space ◽  
Low Dimensional ◽  
Set Of Points ◽  
Lower Dimensional Space ◽  
Lower Dimensional

Multidimensional scaling (MDS) is the process of transforming a set of points in a high-dimensional space to a lower-dimensional one while preserving the relative distances between pairs of points. Although effective methods have been developed for solving a variety of MDS problems, they mainly depend on the vectors in the lower-dimensional space having real-valued components. For some applications, the training of neural networks in particular, it is preferable or necessary to obtain vectors in a discrete, binary space. Unfortunately, MDS into a low-dimensional discrete space appears to be a significantly harder problem than MDS into a continuous space. This article introduces and analyzes several methods for performing approximately optimized binary MDS.

scholarly journals Optimization of the multidimensional signal interpolator in a lower dimensional space

2019 ◽  
Vol 43 (4) ◽  
pp. 653-660 ◽  
Author(s):  
M.V. Gashnikov
Keyword(s):  
Experimental Study ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Multidimensional Signals ◽  
Multidimensional Signal ◽  
Signal Sample ◽  
Lower Dimensional Space ◽  
Lower Dimensional ◽  
Selection Of

Adaptive multidimensional signal interpolators are developed. These interpolators take into account the presence and direction of boundaries of flat signal regions in each local neighborhood based on the automatic selection of the interpolating function for each signal sample. The selection of the interpolating function is performed by a parameterized rule, which is optimized in a parametric lower dimensional space. The dimension reduction is performed using rank filtering of local differences in the neighborhood of each signal sample. The interpolating functions of adaptive interpolators are written for the multidimensional, three-dimensional and two-dimensional cases. The use of adaptive interpolators in the problem of compression of multidimensional signals is also considered. Results of an experimental study of adaptive interpolators for real multidimensional signals of various types are presented.

scholarly journals GENETIC ALGORITHMS FOR MULTIDIMENSIONAL SCALING / GENETINIŲ ALGORITMŲ TAIKYMAS DAUGIAMATĖMS SKALĖMS

2015 ◽  
Vol 7 (3) ◽  
pp. 275-279 ◽  
Author(s):  
Agnė Dzidolikaitė
Keyword(s):  
Genetic Algorithm ◽  
Genetic Algorithms ◽  
Multidimensional Scaling ◽  
Optimization Problem ◽  
Dimensional Space ◽  
Local Solution ◽  
Multidimensional Data ◽  
Global Optimization Problem ◽  
Lower Dimensional Space ◽  
Lower Dimensional

The paper analyzes global optimization problem. In order to solve this problem multidimensional scaling algorithm is combined with genetic algorithm. Using multidimensional scaling we search for multidimensional data projections in a lower-dimensional space and try to keep dissimilarities of the set that we analyze. Using genetic algorithms we can get more than one local solution, but the whole population of optimal points. Different optimal points give different images. Looking at several multidimensional data images an expert can notice some qualities of given multidimensional data. In the paper genetic algorithm is applied for multidimensional scaling and glass data is visualized, and certain qualities are noticed. Analizuojamas globaliojo optimizavimo uždavinys. Jis apibrėžiamas kaip netiesinės tolydžiųjų kintamųjų tikslo funkcijos optimizavimas leistinojoje srityje. Optimizuojant taikomi įvairūs algoritmai. Paprastai taikant tikslius algoritmus randamas tikslus sprendinys, tačiau tai gali trukti labai ilgai. Dažnai norima gauti gerą sprendinį per priimtiną laiko tarpą. Tokiu atveju galimi kiti – euristiniai, algoritmai, kitaip dar vadinami euristikomis. Viena iš euristikų yra genetiniai algoritmai, kopijuojantys gyvojoje gamtoje vykstančią evoliuciją. Sudarant algoritmus naudojami evoliuciniai operatoriai: paveldimumas, mutacija, selekcija ir rekombinacija. Taikant genetinius algoritmus galima rasti pakankamai gerus sprendinius tų uždavinių, kuriems nėra tikslių algoritmų. Genetiniai algoritmai taip pat taikytini vizualizuojant duomenis daugiamačių skalių metodu. Taikant daugiamates skales ieškoma daugiamačių duomenų projekcijų mažesnio skaičiaus matmenų erdvėje siekiant išsaugoti analizuojamos aibės panašumus arba skirtingumus. Taikant genetinius algoritmus gaunamas ne vienas lokalusis sprendinys, o visa optimumų populiacija. Skirtingi optimumai atitinka skirtingus vaizdus. Matydamas kelis daugiamačių duomenų variantus, ekspertas gali įžvelgti daugiau daugiamačių duomenų savybių. Straipsnyje genetinis algoritmas pritaikytas daugiamatėms skalėms. Parodoma, kad daugiamačių skalių algoritmą galima kombinuoti su genetiniu algoritmu ir panaudoti daugiamačiams duomenims vizualizuoti.

Projected Clustering for Biological Data Analysis

2011 ◽  
pp. 1617-1622
Author(s):  
Ping Deng ◽  
Qingkai Ma ◽  
Weili Wu
Keyword(s):  
Nearest Neighbor ◽  
Dimensional Space ◽  
Clustering Algorithms ◽  
Biological Data ◽  
High Dimensional ◽  
Projected Clustering ◽  
Cluster Data ◽  
Biological Data Analysis ◽  
Data Points ◽  
Entire Dataset

Clustering can be considered as the most important unsupervised learning problem. It has been discussed thoroughly by both statistics and database communities due to its numerous applications in problems such as classification, machine learning, and data mining. A summary of clustering techniques can be found in (Berkhin, 2002). Most known clustering algorithms such as DBSCAN (Easter, Kriegel, Sander, & Xu, 1996) and CURE (Guha, Rastogi, & Shim, 1998) cluster data points based on full dimensions. When the dimensional space grows higher, the above algorithms lose their efficiency and accuracy because of the so-called “curse of dimensionality”. It is shown in (Beyer, Goldstein, Ramakrishnan, & Shaft, 1999) that computing the distance based on full dimensions is not meaningful in high dimensional space since the distance of a point to its nearest neighbor approaches the distance to its farthest neighbor as dimensionality increases. Actually, natural clusters might exist in subspaces. Data points in different clusters may be correlated with respect to different subsets of dimensions. In order to solve this problem, feature selection (Kohavi & Sommerfield, 1995) and dimension reduction (Raymer, Punch, Goodman, Kuhn, & Jain, 2000) have been proposed to find the closely correlated dimensions for all the data and the clusters in such dimensions. Although both methods reduce the dimensionality of the space before clustering, the case where clusters may exist in different subspaces of full dimensions is not handled well. Projected clustering has been proposed recently to effectively deal with high dimensionalities. Finding clusters and their relevant dimensions are the objectives of projected clustering algorithms. Instead of projecting the entire dataset on the same subspace, projected clustering focuses on finding specific projection for each cluster such that the similarity is reserved as much as possible.

scholarly journals Discovering a sparse set of pairwise discriminating features in high-dimensional data

2020 ◽  
Author(s):  
Samuel Melton ◽  
Sharad Ramanathan
Keyword(s):  
Single Cell ◽  
Dimensional Space ◽  
Cell Types ◽  
Dimensional Subspace ◽  
Supplementary Information ◽  
High Dimensional ◽  
Technological Advances ◽  
Data Points ◽  
Low Dimensional ◽  
Sparse Set

Abstract Motivation Recent technological advances produce a wealth of high-dimensional descriptions of biological processes, yet extracting meaningful insight and mechanistic understanding from these data remains challenging. For example, in developmental biology, the dynamics of differentiation can now be mapped quantitatively using single-cell RNA sequencing, yet it is difficult to infer molecular regulators of developmental transitions. Here, we show that discovering informative features in the data is crucial for statistical analysis as well as making experimental predictions. Results We identify features based on their ability to discriminate between clusters of the data points. We define a class of problems in which linear separability of clusters is hidden in a low-dimensional space. We propose an unsupervised method to identify the subset of features that define a low-dimensional subspace in which clustering can be conducted. This is achieved by averaging over discriminators trained on an ensemble of proposed cluster configurations. We then apply our method to single-cell RNA-seq data from mouse gastrulation, and identify 27 key transcription factors (out of 409 total), 18 of which are known to define cell states through their expression levels. In this inferred subspace, we find clear signatures of known cell types that eluded classification prior to discovery of the correct low-dimensional subspace. Availability and implementation https://github.com/smelton/SMD. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Interface-targeted seismic velocity estimation using machine learning

2019 ◽  
Vol 218 (1) ◽  
pp. 45-56 ◽  
Author(s):  
C Nur Schuba ◽  
Jonathan P Schuba ◽  
Gary G Gray ◽  
Richard G Davy
Keyword(s):  
Neural Network ◽  
Regression Model ◽  
Dimensional Space ◽  
Seismic Profile ◽  
Velocity Estimation ◽  
Seismic Survey ◽  
Wide Angle ◽  
Seismic Velocities ◽  
Lower Dimensional Space ◽  
Lower Dimensional

SUMMARY We present a new approach to estimate 3-D seismic velocities along a target interface. This approach uses an artificial neural network trained with user-supplied geological and geophysical input features derived from both a 3-D seismic reflection volume and a 2-D wide-angle seismic profile that were acquired from the Galicia margin, offshore Spain. The S-reflector detachment fault was selected as the interface of interest. The neural network in the form of a multilayer perceptron was employed with an autoencoder and a regression layer. The autoencoder was trained using a set of input features from the 3-D reflection volume. This set of features included the reflection amplitude and instantaneous frequency at the interface of interest, time-thicknesses of overlying major layers and ratios of major layer time-thicknesses to the total time-depth of the interface. The regression model was trained to estimate the seismic velocities of the crystalline basement and mantle from these features. The ‘true’ velocities were obtained from an independent full-waveform inversion along a 2-D wide-angle seismic profile, contained within the 3-D data set. The autoencoder compressed the vector of inputs into a lower dimensional space, then the regression layer was trained in the lower dimensional space to estimate velocities above and below the targeted interface. This model was trained on 50 networks with different initializations. A total of 37 networks reached minimum achievable error of 2 per cent. The low standard deviation (&lt;300  m s−1) between different networks and low errors on velocity estimations demonstrate that the input features were sufficient to capture variations in the velocity above and below the targeted S-reflector. This regression model was then applied to the 3-D reflection volume where velocities were predicted over an area of ∼400 km2. This approach provides an alternative way to obtain velocities across a 3-D seismic survey from a deep non-reflective lithology (e.g. upper mantle) , where conventional reflection velocity estimations can be unreliable.

scholarly journals Random projections and Hotelling’s T2 statistics for change detection in high-dimensional data streams

2013 ◽  
Vol 23 (2) ◽  
pp. 447-461 ◽  
Author(s):  
Ewa Skubalska-Rafajłowicz
Keyword(s):  
Discrete Time ◽  
Data Streams ◽  
Random Projection ◽  
Image Sequences ◽  
High Dimensional ◽  
Random Projections ◽  
Random Subspace ◽  
Noisy Image ◽  
Method Of Dimensionality Reduction ◽  
Diagnostic Properties

The method of change (or anomaly) detection in high-dimensional discrete-time processes using a multivariate Hotelling chart is presented. We use normal random projections as a method of dimensionality reduction. We indicate diagnostic properties of the Hotelling control chart applied to data projected onto a random subspace of Rn. We examine the random projection method using artificial noisy image sequences as examples.

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