scholarly journals Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

2020 ◽  
Author(s):  
Andreas Tjärnberg ◽  
Omar Mahmood ◽  
Christopher A Jackson ◽  
Giuseppe-Antonio Saldi ◽  
Kyunghyun Cho ◽  
...  
Keyword(s):  
Objective Function ◽  
Single Cell ◽  
Missing Values ◽  
Nearest Neighbor ◽  
Projection Methods ◽  
Future Research ◽  
Specific Gene ◽  
K Nearest Neighbor ◽  
Single Cell Genomics ◽  
And Diffusion

AbstractThe analysis of single-cell genomics data presents several statistical challenges, and extensive efforts have been made to produce methods for the analysis of this data that impute missing values, address sampling issues and quantify and correct for noise. In spite of such efforts, no consensus on best practices has been established and all current approaches vary substantially based on the available data and empirical tests. The k-Nearest Neighbor Graph (kNN-G) is often used to infer the identities of, and relationships between, cells and is the basis of many widely used dimensionality-reduction and projection methods. The kNN-G has also been the basis for imputation methods using, e.g., neighbor averaging and graph diffusion. However, due to the lack of an agreed-upon optimal objective function for choosing hyperparameters, these methods tend to oversmooth data, thereby resulting in a loss of information with regard to cell identity and the specific gene-to-gene patterns underlying regulatory mechanisms. In this paper, we investigate the tuning of kNN- and diffusion-based denoising methods with a novel non-stochastic method for optimally preserving biologically relevant informative variance in single-cell data. The framework, Denoising Expression data with a Weighted Affinity Kernel and Self-Supervision (DEWÄKSS), uses a self-supervised technique to tune its parameters. We demonstrate that denoising with optimal parameters selected by our objective function (i) is robust to preprocessing methods using data from established benchmarks, (ii) disentangles cellular identity and maintains robust clusters over dimension-reduction methods, (iii) maintains variance along several expression dimensions, unlike previous heuristic-based methods that tend to oversmooth data variance, and (iv) rarely involves diffusion but rather uses a fixed weighted kNN graph for denoising. Together, these findings provide a new understanding of kNN- and diffusion-based denoising methods and serve as a foundation for future research. Code and example data for DEWÄKSS is available at https://gitlab.com/Xparx/dewakss/-/tree/Tjarnberg2020branch.

scholarly journals Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

2021 ◽  
Vol 17 (1) ◽  
pp. e1008569
Author(s):  
Andreas Tjärnberg ◽  
Omar Mahmood ◽  
Christopher A. Jackson ◽  
Giuseppe-Antonio Saldi ◽  
Kyunghyun Cho ◽  
...  
Keyword(s):  
Objective Function ◽  
Single Cell ◽  
Missing Values ◽  
Nearest Neighbor ◽  
Projection Methods ◽  
Specific Gene ◽  
K Nearest Neighbor ◽  
Single Cell Genomics ◽  
Nearest Neighbor Graph ◽  
And Diffusion

The analysis of single-cell genomics data presents several statistical challenges, and extensive efforts have been made to produce methods for the analysis of this data that impute missing values, address sampling issues and quantify and correct for noise. In spite of such efforts, no consensus on best practices has been established and all current approaches vary substantially based on the available data and empirical tests. The k-Nearest Neighbor Graph (kNN-G) is often used to infer the identities of, and relationships between, cells and is the basis of many widely used dimensionality-reduction and projection methods. The kNN-G has also been the basis for imputation methods using, e.g., neighbor averaging and graph diffusion. However, due to the lack of an agreed-upon optimal objective function for choosing hyperparameters, these methods tend to oversmooth data, thereby resulting in a loss of information with regard to cell identity and the specific gene-to-gene patterns underlying regulatory mechanisms. In this paper, we investigate the tuning of kNN- and diffusion-based denoising methods with a novel non-stochastic method for optimally preserving biologically relevant informative variance in single-cell data. The framework, Denoising Expression data with a Weighted Affinity Kernel and Self-Supervision (DEWÄKSS), uses a self-supervised technique to tune its parameters. We demonstrate that denoising with optimal parameters selected by our objective function (i) is robust to preprocessing methods using data from established benchmarks, (ii) disentangles cellular identity and maintains robust clusters over dimension-reduction methods, (iii) maintains variance along several expression dimensions, unlike previous heuristic-based methods that tend to oversmooth data variance, and (iv) rarely involves diffusion but rather uses a fixed weighted kNN graph for denoising. Together, these findings provide a new understanding of kNN- and diffusion-based denoising methods. Code and example data for DEWÄKSS is available at https://gitlab.com/Xparx/dewakss/-/tree/Tjarnberg2020branch.

scholarly journals A Survey On Missing Data in Machine Learning

2021 ◽  
Author(s):  
Tlamelo Emmanuel ◽  
Thabiso Maupong ◽  
Dimane Mpoeleng ◽  
Thabo Semong ◽  
Mphago Banyatsang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Missing Data ◽  
Human Error ◽  
Missing Values ◽  
Nearest Neighbor ◽  
Research Direction ◽  
Machine Learning Techniques ◽  
Future Research ◽  
Learning Approaches ◽  
K Nearest Neighbor

Abstract Machine learning has been the corner stone in analysing and extracting information from data and often a problem of missing values is encountered. Missing values occur as a result of various factors like missing completely at random, missing at random or missing not at random. All these may be as a result of system malfunction during data collection or human error during data pre-processing. Nevertheless, it is important to deal with missing values before analysing data since ignoring or omitting missing values may result in biased or misinformed analysis. In literature there have been several proposals for handling missing values. In this paper we aggregate some of the literature on missing data particularly focusing on machine learning techniques. We also give insight on how the machine learning approaches work by highlighting the key features of the proposed techniques, how they perform, their limitations and the kind of data they are most suitable for. Finally, we experiment on the K nearest neighbor and random forest imputation techniques on novel power plant induced fan data and offer some possible future research direction.

scholarly journals A survey on missing data in machine learning

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Tlamelo Emmanuel ◽  
Thabiso Maupong ◽  
Dimane Mpoeleng ◽  
Thabo Semong ◽  
Banyatsang Mphago ◽  
...  
Keyword(s):  
Machine Learning ◽  
Missing Data ◽  
Human Error ◽  
Missing Values ◽  
Nearest Neighbor ◽  
Research Direction ◽  
Machine Learning Techniques ◽  
Future Research ◽  
Learning Approaches ◽  
K Nearest Neighbor

AbstractMachine learning has been the corner stone in analysing and extracting information from data and often a problem of missing values is encountered. Missing values occur because of various factors like missing completely at random, missing at random or missing not at random. All these may result from system malfunction during data collection or human error during data pre-processing. Nevertheless, it is important to deal with missing values before analysing data since ignoring or omitting missing values may result in biased or misinformed analysis. In literature there have been several proposals for handling missing values. In this paper, we aggregate some of the literature on missing data particularly focusing on machine learning techniques. We also give insight on how the machine learning approaches work by highlighting the key features of missing values imputation techniques, how they perform, their limitations and the kind of data they are most suitable for. We propose and evaluate two methods, the k nearest neighbor and an iterative imputation method (missForest) based on the random forest algorithm. Evaluation is performed on the Iris and novel power plant fan data with induced missing values at missingness rate of 5% to 20%. We show that both missForest and the k nearest neighbor can successfully handle missing values and offer some possible future research direction.

Symmetry Breaking and Training from Incomplete Data with Radial Basis Boltzmann Machines

1997 ◽  
Vol 08 (03) ◽  
pp. 301-315 ◽  
Author(s):  
Marcel J. Nijman ◽  
Hilbert J. Kappen
Keyword(s):  
Symmetry Breaking ◽  
Incomplete Data ◽  
Missing Values ◽  
Nearest Neighbor ◽  
Boltzmann Machine ◽  
K Nearest Neighbor ◽  
Data Set ◽  
Input Space ◽  
Learning Rules ◽  
Radial Basis

A Radial Basis Boltzmann Machine (RBBM) is a specialized Boltzmann Machine architecture that combines feed-forward mapping with probability estimation in the input space, and for which very efficient learning rules exist. The hidden representation of the network displays symmetry breaking as a function of the noise in the dynamics. Thus, generalization can be studied as a function of the noise in the neuron dynamics instead of as a function of the number of hidden units. We show that the RBBM can be seen as an elegant alternative of k-nearest neighbor, leading to comparable performance without the need to store all data. We show that the RBBM has good classification performance compared to the MLP. The main advantage of the RBBM is that simultaneously with the input-output mapping, a model of the input space is obtained which can be used for learning with missing values. We derive learning rules for the case of incomplete data, and show that they perform better on incomplete data than the traditional learning rules on a 'repaired' data set.

Differential abundance testing on single-cell data using k-nearest neighbor graphs

2021 ◽  
Author(s):  
Emma Dann ◽  
Neil C. Henderson ◽  
Sarah A. Teichmann ◽  
Michael D. Morgan ◽  
John C. Marioni
Keyword(s):  
Single Cell ◽  
Nearest Neighbor ◽  
K Nearest Neighbor ◽  
Differential Abundance ◽  
Cell Data

scholarly journals The K Nearest Neighbor Algorithm for Imputation of Missing Longitudinal Prenatal Alcohol Data

2021 ◽  
Author(s):  
Ayesha Sania ◽  
Nicolo Pini ◽  
Morgan Nelson ◽  
Michael Myers ◽  
Lauren Shuffrey ◽  
...  
Keyword(s):  
Missing Data ◽  
Missing Values ◽  
Nearest Neighbor ◽  
Learning Algorithm ◽  
Drinking Behavior ◽  
Nearest Neighbors ◽  
First Trimester ◽  
Epidemiologic Studies ◽  
K Nearest Neighbor ◽  
Timeline Followback

Abstract Background — Missing data are a source of bias in epidemiologic studies. This is problematic in alcohol research where data missingness is linked to drinking behavior. Methods — The Safe Passage study was a prospective investigation of prenatal drinking and fetal/infant outcomes (n=11,083). Daily alcohol consumption for last reported drinking day and 30 days prior was recorded using Timeline Followback method. Of 3.2 million person-days, data were missing for 0.36 million. We imputed missing data using a machine learning algorithm; “K Nearest Neighbor” (K-NN). K-NN imputes missing values for a participant using data of participants closest to it. Imputed values were weighted for the distances from nearest neighbors and matched for day of week. Validation was done on randomly deleted data for 5-15 consecutive days. Results — Data from 5 nearest neighbors and segments of 55 days provided imputed values with least imputation error. After deleting data segments from with no missing days first trimester, there was no difference between actual and predicted values for 64% of deleted segments. For 31% of the segments, imputed data were within +/-1 drink/day of the actual. Conclusions — K-NN can be used to impute missing data in longitudinal studies of alcohol use during pregnancy with high accuracy.

scholarly journals PERBANDINGAN METODE HOT-DECK IMPUTATION DAN METODE KNNI DALAM MENGATASI MISSING VALUES

2020 ◽  
Vol 2019 (1) ◽  
pp. 275-285
Author(s):  
Iman Jihad Fadillah ◽  
Siti Muchlisoh
Keyword(s):  
Missing Values ◽  
Nearest Neighbor ◽  
K Nearest Neighbor ◽  
Running Time ◽  
Hot Deck Imputation ◽  
Nearest Neighbor Imputation

Salah satu ciri data statistik yang berkualitas adalah completeness. Namun, pada penyelenggaraan sensus atau survei, sering kali ditemukan masalah data hilang atau tidak lengkap (missing values), tidak terkecuali pada data Survei Sosial Ekonomi Indonesia (Susenas). Berbagai masalah dapat ditimbulkan oleh missing values. Oleh karena itu, masalah missing values harus ditangani. Imputasi adalah cara yang sering digunakan untuk menangani masalah ini. Terdapat beberapa metode imputasi yang telah dikembangkan untuk menangani missing values. Hot-deck Imputation dan K-Nearest Neighbor Imputation (KNNI) merupakan metode yang dapat digunakan untuk menangani masalah missing values. Metode Hot-deck Imputation dan KNNI memanfaatkan variabel prediktor untuk melakukan proses imputasi dan tidak memerlukan asumsi yang rumit dalam penggunaannya. Algoritma dan cara penanganan missing values yang berbeda pada kedua metode tentunya dapat menghasilkan hasil estimasi yang berbeda pula. Penelitian ini membandingkan metode Hot-deck Imputation dan KNNI dalam mengatasi missing values. Analisis perbandingan dilakukan dengan melihat ketepatan estimator melalui nilai RMSE dan MAPE. Selain itu, diukur juga performa komputasi melalui penghitungan running time pada proses imputasi. Implementasi kedua metode pada data Susenas Maret Tahun 2017 menunjukkan bahwa, metode KNNI menghasilkan ketepatan estimator yang lebih baik dibandingkan Hot-deck Imputation. Namun, performa komputasi yang dihasilkan pada Hot-deck Imputation lebih baik dibandingkan KNNI.

scholarly journals Continuous visualization of differences between biological conditions in single-cell data

2018 ◽  
Author(s):  
Tyler J. Burns ◽  
Garry P. Nolan ◽  
Nikolay Samusik
Keyword(s):  
Single Cell ◽  
Nearest Neighbor ◽  
Developmental Trajectory ◽  
Functional Markers ◽  
Mass Cytometry ◽  
K Nearest Neighbor ◽  
Cell Frequency ◽  
Low Dimensional ◽  
Marker Shift ◽  
Cell Data

In high-dimensional single cell data, comparing changes in functional markers between conditions is typically done across manual or algorithm-derived partitions based on population-defining markers. Visualizations of these partitions is commonly done on low-dimensional embeddings (eg. t-SNE), colored by per-partition changes. Here, we provide an analysis and visualization tool that performs these comparisons across overlapping k-nearest neighbor (KNN) groupings. This allows one to color low-dimensional embeddings by marker changes without hard boundaries imposed by partitioning. We devised an objective optimization of k based on minimizing functional marker KNN imputation error. Proof-of-concept work visualized the exact location of an IL-7 responsive subset in a B cell developmental trajectory on a t-SNE map independent of clustering. Per-condition cell frequency analysis revealed that KNN is sensitive to detecting artifacts due to marker shift, and therefore can also be valuable in a quality control pipeline. Overall, we found that KNN groupings lead to useful multiple condition visualizations and efficiently extract a large amount of information from mass cytometry data. Our software is publicly available through the Bioconductor package Sconify.

scholarly journals Application of imputation methods for missing values of PM10 and O3 data: Interpolation, moving average and K-nearest neighbor methods

2021 ◽  
Vol 8 (3) ◽  
pp. 215-226
Author(s):  
Parisa Saeipourdizaj ◽  
Parvin Sarbakhsh ◽  
Akbar Gholampour
Keyword(s):  
Missing Data ◽  
Human Error ◽  
Missing Values ◽  
Nearest Neighbor ◽  
Moving Average ◽  
Classification And Regression Tree ◽  
Coefficient Of Determination ◽  
K Nearest Neighbor ◽  
Imputation Methods ◽  
Machine Failure

Background: PIn air quality studies, it is very often to have missing data due to reasons such as machine failure or human error. The approach used in dealing with such missing data can affect the results of the analysis. The main aim of this study was to review the types of missing mechanism, imputation methods, application of some of them in imputation of missing of PM10 and O3 in Tabriz, and compare their efficiency. Methods: Methods of mean, EM algorithm, regression, classification and regression tree, predictive mean matching (PMM), interpolation, moving average, and K-nearest neighbor (KNN) were used. PMM was investigated by considering the spatial and temporal dependencies in the model. Missing data were randomly simulated with 10, 20, and 30% missing values. The efficiency of methods was compared using coefficient of determination (R2 ), mean absolute error (MAE) and root mean square error (RMSE). Results: Based on the results for all indicators, interpolation, moving average, and KNN had the best performance, respectively. PMM did not perform well with and without spatio-temporal information. Conclusion: Given that the nature of pollution data always depends on next and previous information, methods that their computational nature is based on before and after information indicated better performance than others, so in the case of pollutant data, it is recommended to use these methods.

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