scholarly journals Relative Performance of Cluster Algorithms and Validation Indices in Maize Genome-wide Structure Patterns

2021 ◽  
Author(s):  
María Eugenia Videla ◽  
Juliana Iglesias ◽  
Cecilia Bruno
Keyword(s):  
Clustering Algorithms ◽  
Misclassification Rate ◽  
Clustering Methods ◽  
Cluster Assignment ◽  
Crop Species ◽  
Internal Validation ◽  
Cluster Membership ◽  
Cluster Algorithms ◽  
Genome Wide ◽  
Degree Of Confidence

Abstract A number of clustering algorithms are available to depict population genetic structure (PGS) with genomic data; however, there is no consensus on which methods are the best performing ones. We conducted a simulation study of three PGS scenarios with subpopulations k=2, 5 and 10, recreating several maize genomes as a model to: (i) compare three well-known clustering methods: UPGMA, k-means and, Bayesian method (BM), (ii) asses four internal validation indices: CH, Connectivity, Dunn and Silhouette, to determine the reliable number of groups defining a PGS, and (iii) estimate the misclassification rate for each validation index. Moreover, a publicly available maize dataset was used to illustrate the outcomes of our simulation. BM was the best method to classify individuals in all tested scenarios, without assignment errors. Conversely, UPGMA was the method with the highest misclassification rate. In scenarios with 5 and 10 subpopulations, CH and Connectivity indices had the maximum underestimation of group number for all cluster algorithms. Dunn and Silhouette indices showed the best performance with BM. Nevertheless, since Silhouette measures the degree of confidence in cluster assignment, and BM measures the probability of cluster membership, these results should be considered with caution. In this study we found that BM showed to be efficient to depict the PGS in both simulated and real maize datasets. This study offers a robust alternative to unveil the existing PGS, thereby facilitating population studies and breeding strategies in maize programs. Moreover, the present findings may have implications for other crop species.

scholarly journals mbkmeans: Fast clustering for single cell data using mini-batch k-means

2021 ◽  
Vol 17 (1) ◽  
pp. e1008625
Author(s):  
Stephanie C. Hicks ◽  
Ruoxi Liu ◽  
Yuwei Ni ◽  
Elizabeth Purdom ◽  
Davide Risso
Keyword(s):  
Single Cell ◽  
Clustering Algorithms ◽  
Large Datasets ◽  
Clustering Methods ◽  
Cell Clustering ◽  
Genome Wide ◽  
Data Representations ◽  
Computing Performance ◽  
Cell Data ◽  
Genome Wide Gene Expression

Single-cell RNA-Sequencing (scRNA-seq) is the most widely used high-throughput technology to measure genome-wide gene expression at the single-cell level. One of the most common analyses of scRNA-seq data detects distinct subpopulations of cells through the use of unsupervised clustering algorithms. However, recent advances in scRNA-seq technologies result in current datasets ranging from thousands to millions of cells. Popular clustering algorithms, such as k-means, typically require the data to be loaded entirely into memory and therefore can be slow or impossible to run with large datasets. To address this problem, we developed the mbkmeans R/Bioconductor package, an open-source implementation of the mini-batch k-means algorithm. Our package allows for on-disk data representations, such as the common HDF5 file format widely used for single-cell data, that do not require all the data to be loaded into memory at one time. We demonstrate the performance of the mbkmeans package using large datasets, including one with 1.3 million cells. We also highlight and compare the computing performance of mbkmeans against the standard implementation of k-means and other popular single-cell clustering methods. Our software package is available in Bioconductor at https://bioconductor.org/packages/mbkmeans.

scholarly journals MONET: Multi-omic patient module detection by omic selection

2020 ◽  
Author(s):  
Nimrod Rappoport ◽  
Roy Safra ◽  
Ron Shamir
Keyword(s):  
Clustering Algorithms ◽  
Simulated Data ◽  
Cell Types ◽  
Clustering Methods ◽  
Data Types ◽  
Common Structure ◽  
Genome Wide ◽  
Distinct Cluster ◽  
Genome Wide Data ◽  
Unique Approach

AbstractRecent advances in experimental biology allow creation of datasets where several genome-wide data types (called omics) are measured per sample. Integrative analysis of multi-omic datasets in general, and clustering of samples in such datasets specifically, can improve our understanding of biological processes and discover different disease subtypes. In this work we present Monet (Multi Omic clustering by Non-Exhaustive Types), which presents a unique approach to multi-omic clustering. Monet discovers modules of similar samples, such that each module is allowed to have a clustering structure for only a subset of the omics. This approach differs from most extant multi-omic clustering algorithms, which assume a common structure across all omics, and from several recent algorithms that model distinct cluster structures using Bayesian statistics. We tested Monet extensively on simulated data, on an image dataset, and on ten multi-omic cancer datasets from TCGA. Our analysis shows that Monet compares favorably with other multi-omic clustering methods. We demonstrate Monet’s biological and clinical relevance by analyzing its results for Ovarian Serous Cystadenocarcinoma. We also show that Monet is robust to missing data, can cluster genes in multi-omic dataset, and reveal modules of cell types in single-cell multi-omic data. Our work shows that Monet is a valuable tool that can provide complementary results to those provided by extant algorithms for multi-omic analysis.

scholarly journals A Deep Learning Approach to Population Structure Inference in Inbred Lines of Maize

2020 ◽  
Vol 11 ◽  
Author(s):  
Xaviera Alejandra López-Cortés ◽  
Felipe Matamala ◽  
Carlos Maldonado ◽  
Freddy Mora-Poblete ◽  
Carlos Alberto Scapim
Keyword(s):  
Population Structure ◽  
Deep Learning ◽  
Principal Component ◽  
Inbred Lines ◽  
Clustering Methods ◽  
Crop Species ◽  
Reduction Techniques ◽  
Field Corn ◽  
Genome Wide ◽  
Linear Dimensionality Reduction

Analysis of population genetic variation and structure is a common practice for genome-wide studies, including association mapping, ecology, and evolution studies in several crop species. In this study, machine learning (ML) clustering methods, K-means (KM), and hierarchical clustering (HC), in combination with non-linear and linear dimensionality reduction techniques, deep autoencoder (DeepAE) and principal component analysis (PCA), were used to infer population structure and individual assignment of maize inbred lines, i.e., dent field corn (n = 97) and popcorn (n = 86). The results revealed that the HC method in combination with DeepAE-based data preprocessing (DeepAE-HC) was the most effective method to assign individuals to clusters (with 96% of correct individual assignments), whereas DeepAE-KM, PCA-HC, and PCA-KM were assigned correctly 92, 89, and 81% of the lines, respectively. These findings were consistent with both Silhouette Coefficient (SC) and Davies–Bouldin validation indexes. Notably, DeepAE-HC also had better accuracy than the Bayesian clustering method implemented in InStruct. The results of this study showed that deep learning (DL)-based dimensional reduction combined with ML clustering methods is a useful tool to determine genetically differentiated groups and to assign individuals into subpopulations in genome-wide studies without having to consider previous genetic assumptions.

A New semi-supervised clustering for incomplete data

2021 ◽  
pp. 1-13
Author(s):  
Sonia Goel ◽  
Meena Tushir
Keyword(s):  
Incomplete Data ◽  
Missing Values ◽  
Clustering Algorithms ◽  
Complete Data ◽  
Unlabeled Data ◽  
Misclassification Rate ◽  
Data Sets ◽  
Clustering Methods ◽  
Data Set ◽  
Supervised Clustering

Semi-supervised clustering technique partitions the unlabeled data based on prior knowledge of labeled data. Most of the semi-supervised clustering algorithms exist only for the clustering of complete data, i.e., the data sets with no missing features. In this paper, an effort has been made to check the effectiveness of semi-supervised clustering when applied to incomplete data sets. The novelty of this approach is that it considers the missing features along with available knowledge (labels) of the data set. The linear interpolation imputation technique initially imputes the missing features of the data set, thus completing the data set. A semi-supervised clustering is now employed on this complete data set, and missing features are regularly updated within the clustering process. In the proposed work, the labeled percentage range used is 30, 40, 50, and 60% of the total data. Data is further altered by arbitrarily eliminating certain features of its components, which makes the data incomplete with partial labeling. The proposed algorithm utilizes both labeled and unlabeled data, along with certain missing values in the data. The proposed algorithm is evaluated using three performance indices, namely the misclassification rate, random index metric, and error rate. Despite the additional missing features, the proposed algorithm has been successfully implemented on real data sets and showed better/competing results than well-known standard semi-supervised clustering methods.

scholarly journals Identifying and characterizing high-risk clusters in a heterogeneous ICU population with deep embedded clustering

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
José Castela Forte ◽  
Galiya Yeshmagambetova ◽  
Maureen L. van der Grinten ◽  
Bart Hiemstra ◽  
Thomas Kaufmann ◽  
...  
Keyword(s):  
Machine Learning ◽  
High Risk ◽  
Mortality Risk ◽  
Clustering Algorithms ◽  
Kidney Injury ◽  
Risk Groups ◽  
Admission Diagnosis ◽  
Dutch Hospital ◽  
Cluster Membership

AbstractCritically ill patients constitute a highly heterogeneous population, with seemingly distinct patients having similar outcomes, and patients with the same admission diagnosis having opposite clinical trajectories. We aimed to develop a machine learning methodology that identifies and provides better characterization of patient clusters at high risk of mortality and kidney injury. We analysed prospectively collected data including co-morbidities, clinical examination, and laboratory parameters from a minimally-selected population of 743 patients admitted to the ICU of a Dutch hospital between 2015 and 2017. We compared four clustering methodologies and trained a classifier to predict and validate cluster membership. The contribution of different variables to the predicted cluster membership was assessed using SHapley Additive exPlanations values. We found that deep embedded clustering yielded better results compared to the traditional clustering algorithms. The best cluster configuration was achieved for 6 clusters. All clusters were clinically recognizable, and differed in in-ICU, 30-day, and 90-day mortality, as well as incidence of acute kidney injury. We identified two high mortality risk clusters with at least 60%, 40%, and 30% increased. ICU, 30-day and 90-day mortality, and a low risk cluster with 25–56% lower mortality risk. This machine learning methodology combining deep embedded clustering and variable importance analysis, which we made publicly available, is a possible solution to challenges previously encountered by clustering analyses in heterogeneous patient populations and may help improve the characterization of risk groups in critical care.

A Hard C-Means Clustering Algorithm Incorporating Membership KL Divergence and Local Data Information for Noisy Image Segmentation

2017 ◽  
Vol 32 (04) ◽  
pp. 1850012 ◽  
Author(s):  
R. R. Gharieb ◽  
G. Gendy ◽  
H. Selim
Keyword(s):  
Image Segmentation ◽  
Membership Function ◽  
Clustering Algorithm ◽  
Clustering Algorithms ◽  
Cluster Center ◽  
Local Data ◽  
Cluster Membership ◽  
Kl Divergence ◽  
Clustering Approach ◽  
Center Distance

In this paper, the standard hard C-means (HCM) clustering approach to image segmentation is modified by incorporating weighted membership Kullback–Leibler (KL) divergence and local data information into the HCM objective function. The membership KL divergence, used for fuzzification, measures the proximity between each cluster membership function of a pixel and the locally-smoothed value of the membership in the pixel vicinity. The fuzzification weight is a function of the pixel to cluster-centers distances. The used pixel to a cluster-center distance is composed of the original pixel data distance plus a fraction of the distance generated from the locally-smoothed pixel data. It is shown that the obtained membership function of a pixel is proportional to the locally-smoothed membership function of this pixel multiplied by an exponentially distributed function of the minus pixel distance relative to the minimum distance provided by the nearest cluster-center to the pixel. Therefore, since incorporating the locally-smoothed membership and data information in addition to the relative distance, which is more tolerant to additive noise than the absolute distance, the proposed algorithm has a threefold noise-handling process. The presented algorithm, named local data and membership KL divergence based fuzzy C-means (LDMKLFCM), is tested by synthetic and real-world noisy images and its results are compared with those of several FCM-based clustering algorithms.

scholarly journals Genome-wide association studies: assessing trait characteristics in model and crop plants

2021 ◽  
Author(s):  
Saleh Alseekh ◽  
Dimitrina Kostova ◽  
Mustafa Bulut ◽  
Alisdair R. Fernie
Keyword(s):  
Biotic Resistance ◽  
Association Studies ◽  
Critical Evaluation ◽  
Genome Wide Association ◽  
Functional Study ◽  
Genome Wide Association Studies ◽  
Future Perspectives ◽  
Crop Species ◽  
Genome Wide ◽  
Single Feature

AbstractGWAS involves testing genetic variants across the genomes of many individuals of a population to identify genotype–phenotype association. It was initially developed and has proven highly successful in human disease genetics. In plants genome-wide association studies (GWAS) initially focused on single feature polymorphism and recombination and linkage disequilibrium but has now been embraced by a plethora of different disciplines with several thousand studies being published in model and crop species within the last decade or so. Here we will provide a comprehensive review of these studies providing cases studies on biotic resistance, abiotic tolerance, yield associated traits, and metabolic composition. We also detail current strategies of candidate gene validation as well as the functional study of haplotypes. Furthermore, we provide a critical evaluation of the GWAS strategy and its alternatives as well as future perspectives that are emerging with the emergence of pan-genomic datasets.

scholarly journals RFCell: A Gene Selection Approach for scRNA-seq Clustering Based on Permutation and Random Forest

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuan Zhao ◽  
Zhao-Yu Fang ◽  
Cui-Xiang Lin ◽  
Chao Deng ◽  
Yun-Pei Xu ◽  
...  
Keyword(s):  
Random Forest ◽  
Single Cell ◽  
Gene Selection ◽  
Clustering Algorithms ◽  
Selection Methods ◽  
Clustering Methods ◽  
Cell Type ◽  
Cell Type Specificity ◽  
Random Forest Classification ◽  
Forest Classification

In recent years, the application of single cell RNA-seq (scRNA-seq) has become more and more popular in fields such as biology and medical research. Analyzing scRNA-seq data can discover complex cell populations and infer single-cell trajectories in cell development. Clustering is one of the most important methods to analyze scRNA-seq data. In this paper, we focus on improving scRNA-seq clustering through gene selection, which also reduces the dimensionality of scRNA-seq data. Studies have shown that gene selection for scRNA-seq data can improve clustering accuracy. Therefore, it is important to select genes with cell type specificity. Gene selection not only helps to reduce the dimensionality of scRNA-seq data, but also can improve cell type identification in combination with clustering methods. Here, we proposed RFCell, a supervised gene selection method, which is based on permutation and random forest classification. We first use RFCell and three existing gene selection methods to select gene sets on 10 scRNA-seq data sets. Then, three classical clustering algorithms are used to cluster the cells obtained by these gene selection methods. We found that the gene selection performance of RFCell was better than other gene selection methods.

scholarly journals Comparison of dimensionality reduction and clustering methods for SARS-CoV-2 genome

2021 ◽  
Vol 10 (4) ◽  
pp. 2170-2180
Author(s):  
Untari N. Wisesty ◽  
Tati Rajab Mengko
Keyword(s):  
Dimensionality Reduction ◽  
Dimensional Reduction ◽  
Clustering Algorithm ◽  
Sequence Data ◽  
Clustering Algorithms ◽  
Gaussian Mixture Models ◽  
Reduction Process ◽  
Principal Component ◽  
Gaussian Mixture ◽  
Clustering Methods

This paper aims to conduct an analysis of the SARS-CoV-2 genome variation was carried out by comparing the results of genome clustering using several clustering algorithms and distribution of sequence in each cluster. The clustering algorithms used are K-means, Gaussian mixture models, agglomerative hierarchical clustering, mean-shift clustering, and DBSCAN. However, the clustering algorithm has a weakness in grouping data that has very high dimensions such as genome data, so that a dimensional reduction process is needed. In this research, dimensionality reduction was carried out using principal component analysis (PCA) and autoencoder method with three models that produce 2, 10, and 50 features. The main contributions achieved were the dimensional reduction and clustering scheme of SARS-CoV-2 sequence data and the performance analysis of each experiment on each scheme and hyper parameters for each method. Based on the results of experiments conducted, PCA and DBSCAN algorithm achieve the highest silhouette score of 0.8770 with three clusters when using two features. However, dimensionality reduction using autoencoder need more iterations to converge. On the testing process with Indonesian sequence data, more than half of them enter one cluster and the rest are distributed in the other two clusters.

scholarly journals PRIVACY PRESERVING CLUSTERING BASED ON LINEAR APPROXIMATION OF FUNCTION

2013 ◽  
Vol 12 (5) ◽  
pp. 3443-3451
Author(s):  
Rajesh Pasupuleti ◽  
Narsimha Gugulothu
Keyword(s):  
Linear Approximation ◽  
Clustering Algorithms ◽  
Similarity Measures ◽  
Privacy Preserving ◽  
Distance Measures ◽  
Clustering Methods ◽  
Sensitive Data ◽  
Processing Information ◽  
Data Objects ◽  
Approximation Of Function

Clustering analysis initiatives  a new direction in data mining that has major impact in various domains including machine learning, pattern recognition, image processing, information retrieval and bioinformatics. Current clustering techniques address some of the  requirements not adequately and failed in standardizing clustering algorithms to support for all real applications. Many clustering methods mostly depend on user specified parametric methods and initial seeds of clusters are randomly selected by  user.  In this paper, we proposed new clustering method based on linear approximation of function by getting over all idea of behavior knowledge of clustering function, then pick the initial seeds of clusters as the points on linear approximation line and perform clustering operations, unlike grouping data objects into clusters by using distance measures, similarity measures and statistical distributions in traditional clustering methods. We have shown experimental results as clusters based on linear approximation yields good  results in practice with an example of  business data are provided.  It also  explains privacy preserving clusters of sensitive data objects.

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