scholarly journals Dropout-based feature selection for scRNASeq

2016 ◽  
Author(s):  
Tallulah S. Andrews ◽  
Martin Hemberg
Keyword(s):  
Feature Selection ◽  
Dimensionality Reduction ◽  
Single Cell ◽  
Relevant Information ◽  
Features Selection ◽  
Technical Noise ◽  
Biologically Relevant ◽  
Selection For ◽  
Cell Expression ◽  
Variable Genes

AbstractFeatures selection is a key step in many single-cell RNASeq (scRNASeq) analyses. Feature selection is intended to preserve biologically relevant information while removing genes only subject to technical noise. As it is frequently performed prior to dimensionality reduction, clustering and pseudotime analyses, feature selection can have a major impact on the results. Several different approaches have been proposed for unsupervised feature selection from unprocessed single-cell expression matrices, most based upon identifying highly variable genes in the dataset. We present two methods which take advantage of the prevalence of zeros (dropouts) in scRNASeq data to identify features. We show that dropout-based feature selection outperforms variance-based feature selection for multiple applications of single-cell RNASeq.

scholarly journals M3Drop: dropout-based feature selection for scRNASeq

2018 ◽  
Vol 35 (16) ◽  
pp. 2865-2867 ◽  
Author(s):  
Tallulah S Andrews ◽  
Martin Hemberg
Keyword(s):  
Feature Selection ◽  
Single Cell ◽  
R Package ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Selection Methods ◽  
Functional Responses ◽  
Technical Noise ◽  
New Methods ◽  
Selection For

Abstract Motivation Most genomes contain thousands of genes, but for most functional responses, only a subset of those genes are relevant. To facilitate many single-cell RNASeq (scRNASeq) analyses the set of genes is often reduced through feature selection, i.e. by removing genes only subject to technical noise. Results We present M3Drop, an R package that implements popular existing feature selection methods and two novel methods which take advantage of the prevalence of zeros (dropouts) in scRNASeq data to identify features. We show these new methods outperform existing methods on simulated and real datasets. Availability and implementation M3Drop is freely available on github as an R package and is compatible with other popular scRNASeq tools: https://github.com/tallulandrews/M3Drop. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Michael F. Z. Wang ◽  
Madhav Mantri ◽  
Shao-Pei Chou ◽  
Gaetano J. Scuderi ◽  
David W. McKellar ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Annotation ◽  
Gene Annotation ◽  
Active Regions ◽  
Sequencing Analysis ◽  
Biologically Relevant ◽  
Mole Rat ◽  
Genome Annotations ◽  
Cell Expression ◽  
High Quality Genome

AbstractConventional scRNA-seq expression analyses rely on the availability of a high quality genome annotation. Yet, as we show here with scRNA-seq experiments and analyses spanning human, mouse, chicken, mole rat, lemur and sea urchin, genome annotations are often incomplete, in particular for organisms that are not routinely studied. To overcome this hurdle, we created a scRNA-seq analysis routine that recovers biologically relevant transcriptional activity beyond the scope of the best available genome annotation by performing scRNA-seq analysis on any region in the genome for which transcriptional products are detected. Our tool generates a single-cell expression matrix for all transcriptionally active regions (TARs), performs single-cell TAR expression analysis to identify biologically significant TARs, and then annotates TARs using gene homology analysis. This procedure uses single-cell expression analyses as a filter to direct annotation efforts to biologically significant transcripts and thereby uncovers biology to which scRNA-seq would otherwise be in the dark.

scholarly journals Effective Feature Selection for 5G IM Applications Traffic Classification

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Muhammad Shafiq ◽  
Xiangzhan Yu ◽  
Asif Ali Laghari ◽  
Dawei Wang
Keyword(s):  
Feature Selection ◽  
Classification Accuracy ◽  
Statistical Test ◽  
Traffic Classification ◽  
Features Selection ◽  
Traffic Flows ◽  
Selection Algorithm ◽  
Feature Selection Algorithm ◽  
Wrapper Method ◽  
Selection For

Recently, machine learning (ML) algorithms have widely been applied in Internet traffic classification. However, due to the inappropriate features selection, ML-based classifiers are prone to misclassify Internet flows as that traffic occupies majority of traffic flows. To address this problem, a novel feature selection metric named weighted mutual information (WMI) is proposed. We develop a hybrid feature selection algorithm named WMI_ACC, which filters most of the features with WMI metric. It further uses a wrapper method to select features for ML classifiers with accuracy (ACC) metric. We evaluate our approach using five ML classifiers on the two different network environment traces captured. Furthermore, we also apply Wilcoxon pairwise statistical test on the results of our proposed algorithm to find out the robust features from the selected set of features. Experimental results show that our algorithm gives promising results in terms of classification accuracy, recall, and precision. Our proposed algorithm can achieve 99% flow accuracy results, which is very promising.

scholarly journals Research of Clustering Algorithms using Enhanced Feature Selection

2019 ◽  
Vol 9 (2) ◽  
pp. 4612-4615
Keyword(s):  
Feature Selection ◽  
Text Mining ◽  
Clustering Algorithms ◽  
Present Situation ◽  
Features Selection ◽  
Entity Extraction ◽  
Text Documents ◽  
Clustering Techniques ◽  
Selection For ◽  
Video And Audio

In Present situation, a huge quantity of data is recorded in variety of forms like text, image, video, and audio and is estimated to enhance in future. The major tasks related to text are entity extraction, information extraction, entity relation modeling, document summarization are performed by using text mining. This paper main focus is on document clustering, a sub task of text mining and to measure the performance of different clustering techniques. In this paper we are using an enhanced features selection for clustering of text documents to prove that it produces better results compared to traditional feature selection.

scholarly journals Feature Selection for Topological Proximity Prediction of Single-Cell Transcriptomic Profiles in Drosophila Embryo Using Genetic Algorithm

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 28
Author(s):  
Shruti Gupta ◽  
Ajay Kumar Verma ◽  
Shandar Ahmad
Keyword(s):  
Genetic Algorithm ◽  
Feature Selection ◽  
Single Cell ◽  
Gene Selection ◽  
Spatial Information ◽  
Single Cells ◽  
Drosophila Embryo ◽  
Main Challenge ◽  
Selection For

Single-cell transcriptomics data, when combined with in situ hybridization patterns of specific genes, can help in recovering the spatial information lost during cell isolation. Dialogue for Reverse Engineering Assessments and Methods (DREAM) consortium conducted a crowd-sourced competition known as DREAM Single Cell Transcriptomics Challenge (SCTC) to predict the masked locations of single cells from a set of 60, 40 and 20 genes out of 84 in situ gene patterns known in Drosophila embryo. We applied a genetic algorithm (GA) to predict the most important genes that carry positional and proximity information of the single-cell origins, in combination with the base distance mapping algorithm DistMap. Resulting gene selection was found to perform well and was ranked among top 10 in two of the three sub-challenges. However, the details of the method did not make it to the main challenge publication, due to an intricate aggregation ranking. In this work, we discuss the detailed implementation of GA and its post-challenge parameterization, with a view to identify potential areas where GA-based approaches of gene-set selection for topological association prediction may be improved, to be more effective. We believe this work provides additional insights into the feature-selection strategies and their relevance to single-cell similarity prediction and will form a strong addendum to the recently published work from the consortium.

Ensemble Feature Selection for Single Cell Chromatin Conformation Analysis

2021 ◽  
Author(s):  
Amirreza Rouhi ◽  
Luca Nanni ◽  
Arif Canakoglu ◽  
Pietro Pinoli ◽  
Stefano Ceri
Keyword(s):  
Feature Selection ◽  
Single Cell ◽  
Chromatin Conformation ◽  
Conformation Analysis ◽  
Selection For

scholarly journals Publisher Correction: Single-cell manifold-preserving feature selection for detecting rare cell populations

2021 ◽  
Author(s):  
Shaoheng Liang ◽  
Vakul Mohanty ◽  
Jinzhuang Dou ◽  
Qi Miao ◽  
Yuefan Huang ◽  
...  
Keyword(s):  
Feature Selection ◽  
Single Cell ◽  
Cell Populations ◽  
Selection For

Best Features Selection for Biomedical Data Classification Using Seven Spot Ladybird Optimization Algorithm

2018 ◽  
Vol 9 (3) ◽  
pp. 75-87 ◽  
Author(s):  
Noria Bidi ◽  
Zakaria Elberrichi
Keyword(s):  
Feature Selection ◽  
Optimization Algorithm ◽  
Feature Selection Method ◽  
Nearest Neighbors ◽  
Selection Method ◽  
Support Vector ◽  
Biomedical Data ◽  
Features Selection ◽  
Benchmark Datasets ◽  
Selection For

This article presents a new adaptive algorithm called FS-SLOA (Feature Selection-Seven Spot Ladybird Optimization Algorithm) which is a meta-heuristic feature selection method based on the foraging behavior of a seven spot ladybird. The new efficient technique has been applied to find the best subset features, which achieves the highest accuracy in classification using three classifiers: the Naive Bayes (NB), the Nearest Neighbors (KNN) and the Support Vector Machine (SVM). The authors' proposed approach has been experimented on four well-known benchmark datasets (Wisconsin Breast cancer, Pima Diabetes, Mammographic Mass, and Dermatology datasets) taken from the UCI machine learning repository. Experimental results prove that the classification accuracy of FS-SLOA is the best performing for different datasets.

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