scholarly journals Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees

2019 ◽  
Author(s):  
Daniel Probst ◽  
Jean-Louis Reymond
Keyword(s):  
Particle Physics ◽  
Spanning Trees ◽  
High Dimensional Data ◽  
Large Data ◽  
High Dimensional ◽  
Data Sets ◽  
Chemical Structures ◽  
Data Points ◽  
Global And Local ◽  
Human Inspection

<p>The chemical sciences are producing an unprecedented amount of large, high-dimensional data sets containing chemical structures and associated properties. However, there are currently no algorithms to visualize such data while preserving both global and local features with a sufficient level of detail to allow for human inspection and interpretation. Here, we propose a solution to this problem with a new data visualization method, TMAP, capable of representing data sets of up to millions of data points and arbitrary high dimensionality as a two-dimensional tree (http://tmap.gdb.tools). Visualizations based on TMAP are better suited than t-SNE or UMAP for the exploration and interpretation of large data sets due to their tree-like nature, increased local and global neighborhood and structure preservation, and the transparency of the methods the algorithm is based on. We apply TMAP to the most used chemistry data sets including databases of molecules such as ChEMBL, FDB17, the Natural Products Atlas, DSSTox, DrugBank, as well as to the MoleculeNet benchmark collection of data sets. We also show its broad applicability with further examples from biology, particle physics, and literature.</p>

scholarly journals Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees

2019 ◽  
Author(s):  
Daniel Probst ◽  
Jean-Louis Reymond
Keyword(s):  
Particle Physics ◽  
Spanning Trees ◽  
High Dimensional Data ◽  
Large Data ◽  
High Dimensional ◽  
Data Sets ◽  
Chemical Structures ◽  
Data Points ◽  
Global And Local ◽  
Human Inspection

<p>The chemical sciences are producing an unprecedented amount of large, high-dimensional data sets containing chemical structures and associated properties. However, there are currently no algorithms to visualize such data while preserving both global and local features with a sufficient level of detail to allow for human inspection and interpretation. Here, we propose a solution to this problem with a new data visualization method, TMAP, capable of representing data sets of up to millions of data points and arbitrary high dimensionality as a two-dimensional tree (http://tmap.gdb.tools). Visualizations based on TMAP are better suited than t-SNE or UMAP for the exploration and interpretation of large data sets due to their tree-like nature, increased local and global neighborhood and structure preservation, and the transparency of the methods the algorithm is based on. We apply TMAP to the most used chemistry data sets including databases of molecules such as ChEMBL, FDB17, the Natural Products Atlas, DSSTox, DrugBank, as well as to the MoleculeNet benchmark collection of data sets. We also show its broad applicability with further examples from biology, particle physics, and literature.</p>

scholarly journals Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees

2019 ◽  
Author(s):  
Daniel Probst ◽  
Jean-Louis Reymond
Keyword(s):  
Data Visualization ◽  
Particle Physics ◽  
Cancer Biology ◽  
Spanning Trees ◽  
Minimum Spanning Tree ◽  
High Dimensional Data ◽  
Locality Sensitive Hashing ◽  
High Dimensional ◽  
Data Sets ◽  
Data Set

<div>Here, we introduce a new data visualization and exploration method, TMAP (tree-map), which exploits locality sensitive hashing, Kruskal’s minimum-spanning-tree algorithm, and a multilevel multipole-based graph layout algorithm to represent large and high dimensional data sets as a tree structure, which is readily understandable and explorable. Compared to other data visualization methods such as t-SNE or UMAP, TMAP increases the size of data sets that can be visualized due to its significantly lower memory requirements and running time and should find broad applicability in the age of big data. We exemplify TMAP in the area of cheminformatics with interactive maps for 1.16 million drug-like molecules from ChEMBL, 10.1 million small molecule fragments from FDB17, and 131 thousand 3D-structures of biomolecules from the PDB Databank, and to visualize data from literature (GUTENBERG data set), cancer biology (PANSCAN data set) and particle physics (MiniBooNE data set). TMAP is available as a Python package. Installation, usage instructions and application examples can be found at http://tmap.gdb.tools.</div>

Mahalanobis distance informed by clustering

2018 ◽  
Vol 8 (2) ◽  
pp. 377-406
Author(s):  
Almog Lahav ◽  
Ronen Talmon ◽  
Yuval Kluger
Keyword(s):  
Mahalanobis Distance ◽  
High Dimensional Data ◽  
Hidden Variables ◽  
Real Data ◽  
Risk Groups ◽  
High Dimensional ◽  
Data Sets ◽  
Kaplan Meier ◽  
Data Points ◽  
Survival Plot

Abstract A fundamental question in data analysis, machine learning and signal processing is how to compare between data points. The choice of the distance metric is specifically challenging for high-dimensional data sets, where the problem of meaningfulness is more prominent (e.g. the Euclidean distance between images). In this paper, we propose to exploit a property of high-dimensional data that is usually ignored, which is the structure stemming from the relationships between the coordinates. Specifically, we show that organizing similar coordinates in clusters can be exploited for the construction of the Mahalanobis distance between samples. When the observable samples are generated by a nonlinear transformation of hidden variables, the Mahalanobis distance allows the recovery of the Euclidean distances in the hidden space. We illustrate the advantage of our approach on a synthetic example where the discovery of clusters of correlated coordinates improves the estimation of the principal directions of the samples. Our method was applied to real data of gene expression for lung adenocarcinomas (lung cancer). By using the proposed metric we found a partition of subjects to risk groups with a good separation between their Kaplan–Meier survival plot.

scholarly journals Data segmentation based on the local intrinsic dimension

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Michele Allegra ◽  
Elena Facco ◽  
Francesco Denti ◽  
Alessandro Laio ◽  
Antonietta Mira
Keyword(s):  
High Dimensional Data ◽  
Large Data ◽  
Large Data Sets ◽  
High Dimensional ◽  
Data Sets ◽  
Imaging Data ◽  
Unsupervised Segmentation ◽  
Real World Data ◽  
Data Set ◽  
Intrinsic Dimension

Abstract One of the founding paradigms of machine learning is that a small number of variables is often sufficient to describe high-dimensional data. The minimum number of variables required is called the intrinsic dimension (ID) of the data. Contrary to common intuition, there are cases where the ID varies within the same data set. This fact has been highlighted in technical discussions, but seldom exploited to analyze large data sets and obtain insight into their structure. Here we develop a robust approach to discriminate regions with different local IDs and segment the points accordingly. Our approach is computationally efficient and can be proficiently used even on large data sets. We find that many real-world data sets contain regions with widely heterogeneous dimensions. These regions host points differing in core properties: folded versus unfolded configurations in a protein molecular dynamics trajectory, active versus non-active regions in brain imaging data, and firms with different financial risk in company balance sheets. A simple topological feature, the local ID, is thus sufficient to achieve an unsupervised segmentation of high-dimensional data, complementary to the one given by clustering algorithms.

Visualization of High-Dimensional Data with Polar Coordinates

2011 ◽  
pp. 2062-2067
Author(s):  
Frank Rehm ◽  
Frank Klawonn ◽  
Rudolf Kruse
Keyword(s):  
High Dimensional Data ◽  
Computation Time ◽  
Large Data ◽  
Feature Space ◽  
Three Dimensions ◽  
Polar Coordinates ◽  
High Dimensional ◽  
Data Sets ◽  
Memory Space ◽  
Resource Requirements

Many applications in science and business such as signal analysis or costumer segmentation deal with large amounts of data which are usually high dimensional in the feature space. As a part of preprocessing and exploratory data analysis, visualization of the data helps to decide which kind of data mining method probably leads to good results or whether outliers or noisy data need to be treated before (Barnett & Lewis, 1994; Hawkins, 1980). Since the visual assessment of a feature space that has more than three dimensions is not possible, it becomes necessary to find an appropriate visualization scheme for such data sets. Multidimensional scaling (MDS) is a family of methods that seek to present the important structure of the data in a reduced number of dimensions. Due to the approach of distance preservation that is followed by conventional MDS techniques, resource requirements regarding memory space and computation time are fairly high and prevent their application to large data sets. In this work we will present two methods that visualize high-dimensional data on the plane using a new approach. An algorithm will be presented that allows applying our method on larger data sets. We will also present some results on a benchmark data set.

scholarly journals A Study On High Dimensional Clustering By Using Clique

2011 ◽  
pp. 101-104
Author(s):  
Raghunath Kar ◽  
Susanta Kumar Das
Keyword(s):  
Input Parameter ◽  
High Dimensional Data ◽  
Real Life ◽  
Multidimensional Data ◽  
High Dimensional ◽  
Data Sets ◽  
Data Points ◽  
A Cell ◽  
Low Dimensional ◽  
Partition Method

In real life clustering of high dimensional data is a big problem. To find out the dense regions from increasing dimensions is one of them. We have already studied the clustering techniques of low dimensional data sets like k-means, k-mediod, BIRCH, CLARANS, CURE, DBScan, PAM etc. If a region is dense then it consists with number of data points with a minimum support of input parameter ø other wise it cannot take into clustering. So in this approach we have implemented CLIQUE to find out the clusters from multidimensional data sets. In dimension growth subspace clustering the clustering process start at single dimensional subspaces and grows upward to higher dimensional ones. It is a partition method where each dimension divided like a grid structure. The grid is a cell where the data points are present. We check the dense units from the structure by applying different algorithms. Finally the clusters are formed from the high dimensional data sets.

scholarly journals Subspace Clustering of High-Dimensional Data: An Evolutionary Approach

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Singh Vijendra ◽  
Sahoo Laxman
Keyword(s):  
Clustering Algorithm ◽  
Dimensional Space ◽  
Clustering Algorithms ◽  
High Dimensional Data ◽  
Subspace Clustering ◽  
High Dimensional ◽  
Data Sets ◽  
Real World Data ◽  
Data Set ◽  
Data Points

Clustering high-dimensional data has been a major challenge due to the inherent sparsity of the points. Most existing clustering algorithms become substantially inefficient if the required similarity measure is computed between data points in the full-dimensional space. In this paper, we have presented a robust multi objective subspace clustering (MOSCL) algorithm for the challenging problem of high-dimensional clustering. The first phase of MOSCL performs subspace relevance analysis by detecting dense and sparse regions with their locations in data set. After detection of dense regions it eliminates outliers. MOSCL discovers subspaces in dense regions of data set and produces subspace clusters. In thorough experiments on synthetic and real-world data sets, we demonstrate that MOSCL for subspace clustering is superior to PROCLUS clustering algorithm. Additionally we investigate the effects of first phase for detecting dense regions on the results of subspace clustering. Our results indicate that removing outliers improves the accuracy of subspace clustering. The clustering results are validated by clustering error (CE) distance on various data sets. MOSCL can discover the clusters in all subspaces with high quality, and the efficiency of MOSCL outperforms PROCLUS.

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