Bioinformatics in Toxicology: Statistical Methods for Supervised Learning in High-Dimensional Omics Data

2018 ◽  
pp. 447-472
Author(s):  
N. Sedaghat ◽  
I.B. Stanway ◽  
S.Z. Zangeneh ◽  
T. Bammler ◽  
A. Shojaie
Keyword(s):  
Supervised Learning ◽  
Statistical Methods ◽  
High Dimensional ◽  
Omics Data

scholarly journals Tropical Balls and Its Applications to K Nearest Neighbor over the Space of Phylogenetic Trees

Mathematics ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 779
Author(s):  
Ruriko Yoshida
Keyword(s):  
Supervised Learning ◽  
Phylogenetic Trees ◽  
Nearest Neighbor ◽  
Nearest Neighbors ◽  
High Dimensional ◽  
Learning Method ◽  
Dimensional Vector ◽  
K Nearest Neighbor ◽  
K Nearest Neighbors

A tropical ball is a ball defined by the tropical metric over the tropical projective torus. In this paper we show several properties of tropical balls over the tropical projective torus and also over the space of phylogenetic trees with a given set of leaf labels. Then we discuss its application to the K nearest neighbors (KNN) algorithm, a supervised learning method used to classify a high-dimensional vector into given categories by looking at a ball centered at the vector, which contains K vectors in the space.

scholarly journals A generalization of t-SNE and UMAP to single-cell multimodal omics

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Van Hoan Do ◽  
Stefan Canzar
Keyword(s):  
Dimensionality Reduction ◽  
Single Cell ◽  
Cell Types ◽  
High Dimensional ◽  
Omics Data ◽  
Relative Contribution ◽  
Reduction Techniques ◽  
Dimensionality Reduction Techniques ◽  
Concise Representation ◽  
Cellular Identity

AbstractEmerging single-cell technologies profile multiple types of molecules within individual cells. A fundamental step in the analysis of the produced high-dimensional data is their visualization using dimensionality reduction techniques such as t-SNE and UMAP. We introduce j-SNE and j-UMAP as their natural generalizations to the joint visualization of multimodal omics data. Our approach automatically learns the relative contribution of each modality to a concise representation of cellular identity that promotes discriminative features but suppresses noise. On eight datasets, j-SNE and j-UMAP produce unified embeddings that better agree with known cell types and that harmonize RNA and protein velocity landscapes.

scholarly journals Semi-Supervised Deep Learning for High-Dimensional Uncertainty Quantification

2020 ◽  
Author(s):  
Zequn Wang ◽  
Mingyang Li
Keyword(s):  
Uncertainty Quantification ◽  
Reliability Analysis ◽  
Supervised Learning ◽  
Dimensional Space ◽  
Limit State ◽  
Failure Surface ◽  
Simulation Method ◽  
High Dimensional ◽  
State Function ◽  
Latent Space

Abstract Conventional uncertainty quantification methods usually lacks the capability of dealing with high-dimensional problems due to the curse of dimensionality. This paper presents a semi-supervised learning framework for dimension reduction and reliability analysis. An autoencoder is first adopted for mapping the high-dimensional space into a low-dimensional latent space, which contains a distinguishable failure surface. Then a deep feedforward neural network (DFN) is utilized to learn the mapping relationship and reconstruct the latent space, while the Gaussian process (GP) modeling technique is used to build the surrogate model of the transformed limit state function. During the training process of the DFN, the discrepancy between the actual and reconstructed latent space is minimized through semi-supervised learning for ensuring the accuracy. Both labeled and unlabeled samples are utilized for defining the loss function of the DFN. Evolutionary algorithm is adopted to train the DFN, then the Monte Carlo simulation method is used for uncertainty quantification and reliability analysis based on the proposed framework. The effectiveness is demonstrated through a mathematical example.

scholarly journals An R Package for Divergence Analysis of Omics Data

2019 ◽  
Author(s):  
Wikum Dinalankara ◽  
Qian Ke ◽  
Donald Geman ◽  
Luigi Marchionni
Keyword(s):  
High Throughput Sequencing ◽  
R Package ◽  
The Cancer Genome Atlas ◽  
High Dimensional ◽  
Omics Data ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Ternary Code ◽  
Cancer Genome Atlas ◽  
Level Analysis

AbstractGiven the ever-increasing amount of high-dimensional and complex omics data becoming available, it is increasingly important to discover simple but effective methods of analysis. Divergence analysis transforms each entry of a high-dimensional omics profile into a digitized (binary or ternary) code based on the deviation of the entry from a given baseline population. This is a novel framework that is significantly different from existing omics data analysis methods: it allows digitization of continuous omics data at the univariate or multivariate level, facilitates sample level analysis, and is applicable on many different omics platforms. The divergence package, available on the R platform through the Bioconductor repository collection, provides easy-to-use functions for carrying out this transformation. Here we demonstrate how to use the package with sample high throughput sequencing data from the Cancer Genome Atlas.

scholarly journals An R package for divergence analysis of omics data

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249002
Author(s):  
Wikum Dinalankara ◽  
Qian Ke ◽  
Donald Geman ◽  
Luigi Marchionni
Keyword(s):  
R Package ◽  
The Cancer Genome Atlas ◽  
High Dimensional ◽  
Omics Data ◽  
Ternary Code ◽  
Cancer Genome Atlas ◽  
Level Analysis ◽  
Data Analysis Methods ◽  
Genome Atlas ◽  
Omics Data Analysis

Given the ever-increasing amount of high-dimensional and complex omics data becoming available, it is increasingly important to discover simple but effective methods of analysis. Divergence analysis transforms each entry of a high-dimensional omics profile into a digitized (binary or ternary) code based on the deviation of the entry from a given baseline population. This is a novel framework that is significantly different from existing omics data analysis methods: it allows digitization of continuous omics data at the univariate or multivariate level, facilitates sample level analysis, and is applicable on many different omics platforms. The divergence package, available on the R platform through the Bioconductor repository collection, provides easy-to-use functions for carrying out this transformation. Here we demonstrate how to use the package with data from the Cancer Genome Atlas.

scholarly journals Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data

2019 ◽  
Author(s):  
Robert Krueger ◽  
Johanna Beyer ◽  
Won-Dong Jang ◽  
Nam Wook Kim ◽  
Artem Sokolov ◽  
...  
Keyword(s):  
Supervised Learning ◽  
Visual Analytics ◽  
Cancer Biology ◽  
Large Scale ◽  
Hierarchical Structures ◽  
Image Data ◽  
Automated Analysis ◽  
Cell Types ◽  
High Dimensional ◽  
Exploration Process

AbstractFacetto is a scalable visual analytics application that is used to discover single-cell phenotypes in high-dimensional multi-channel microscopy images of human tumors and tissues. Such images represent the cutting edge of digital histology and promise to revolutionize how diseases such as cancer are studied, diagnosed, and treated. Highly multiplexed tissue images are complex, comprising 109or more pixels, 60-plus channels, and millions of individual cells. This makes manual analysis challenging and error-prone. Existing automated approaches are also inadequate, in large part, because they are unable to effectively exploit the deep knowledge of human tissue biology available to anatomic pathologists. To overcome these challenges, Facetto enables a semi-automated analysis of cell types and states. It integrates unsupervised and supervised learning into the image and feature exploration process and offers tools for analytical provenance. Experts can cluster the data to discover new types of cancer and immune cells and use clustering results to train a convolutional neural network that classifies new cells accordingly. Likewise, the output of classifiers can be clustered to discover aggregate patterns and phenotype subsets. We also introduce a new hierarchical approach to keep track of analysis steps and data subsets created by users; this assists in the identification of cell types. Users can build phenotype trees and interact with the resulting hierarchical structures of both high-dimensional feature and image spaces. We report on use-cases in which domain scientists explore various large-scale fluorescence imaging datasets. We demonstrate how Facetto assists users in steering the clustering and classification process, inspecting analysis results, and gaining new scientific insights into cancer biology.

Semi-supervised learning using multiple one-dimensional embedding based adaptive interpolation

2016 ◽  
Vol 14 (02) ◽  
pp. 1640002 ◽  
Author(s):  
Jianzhong Wang
Keyword(s):  
Supervised Learning ◽  
High Dimensional ◽  
One Dimensional ◽  
Large Size ◽  
Adaptive Interpolation

We propose a novel semi-supervised learning (SSL) scheme using adaptive interpolation on multiple one-dimensional (1D) embedded data. For a given high-dimensional dataset, we smoothly map it onto several different 1D sequences, so that the labeled subset is converted to a 1D subset for each of these sequences. Applying the cubic interpolation of the labeled subset, we obtain a subset of unlabeled points, which are assigned to the same label in all interpolations. Selecting a proportion of these points at random and adding them to the current labeled subset, we build a larger labeled subset for the next interpolation. Repeating the embedding and interpolation, we enlarge the labeled subset gradually, and finally reach a labeled set with a reasonable large size, based on which the final classifier is constructed. We explore the use of the proposed scheme in the classification of handwritten digits and show promising results.

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