We present single-cell interpretation via multikernel learning (SIMLR), an analytic framework and software which learns a similarity measure from single-cell RNA-seq data in order to perform dimension reduction, clustering and visualization. On seven published data sets, we benchmark SIMLR against state-of-the-art methods. We show that SIMLR is scalable and greatly enhances clustering performance while improving the visualization and interpretability of single-cell sequencing data.

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Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning.

Single-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical to identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. Here, we propose a novel similarity-learning framework, SIMLR (single-cell interpretation via multi-kernel learning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization. We show that SIMLR separates subpopulations more accurately in single-cell data sets than do existing dimension reduction methods. Additionally, SIMLR demonstrates high sensitivity and accuracy on high-throughput peripheral blood mononuclear cells (PBMC) data sets generated by the GemCode single-cell technology from 10x Genomics.

/pdf/visualization-and-analysis-of-single-cell-rna-seq-data-by-111algazw3.pdf

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

Although both online learning and kernel learning have been studied extensively in machine learning, there is limited effort in addressing the intersecting research problems of these two important topics. As an attempt to fill the gap, we address a new research problem, termed Online Multiple Kernel Classification (OMKC), which learns a kernel-based prediction function by selecting a subset of predefined kernel functions in an online learning fashion. OMKC is in general more challenging than typical online learning because both the kernel classifiers and the subset of selected kernels are unknown, and more importantly the solutions to the kernel classifiers and their combination weights are correlated. The proposed algorithms are based on the fusion of two online learning algorithms, i.e., the Perceptron algorithm that learns a classifier for a given kernel, and the Hedge algorithm that combines classifiers by linear weights. We develop stochastic selection strategies that randomly select a subset of kernels for combination and model updating, thus improving the learning efficiency. Our empirical study with 15 data sets shows promising performance of the proposed algorithms for OMKC in both learning efficiency and prediction accuracy.

/pdf/online-multiple-kernel-classification-3seefec54x.pdf

Online Multiple Kernel Classification

Multiple kernel learning (MKL) is a promising family of machine learning algorithms using multiple kernel functions for various challenging data mining tasks. Conventional MKL methods often formulate the problem as an optimization task of learning the optimal combinations of both kernels and classifiers, which usually results in some forms of challenging optimization tasks that are often difficult to be solved. Different from the existing MKL methods, in this paper, we investigate a boosting framework of MKL for classification tasks, i.e., we adopt boosting to solve a variant of MKL problem, which avoids solving the complicated optimization tasks. Specifically, we present a novel framework of Multiple kernel boosting (MKBoost), which applies the idea of boosting techniques to learn kernel-based classifiers with multiple kernels for classification problems. Based on the proposed framework, we propose several variants of MKBoost algorithms and extensively examine their empirical performance on a number of benchmark data sets in comparisons to various state-of-the-art MKL algorithms on classification tasks. Experimental results show that the proposed method is more effective and efficient than the existing MKL techniques.

https://ink.library.smu.edu.sg/cgi/viewcontent.cgi?article=3280&context=sis_research

MKBoost: A Framework of Multiple Kernel Boosting

Multiple Kernel Learning を用いた食べ物画像の分類

Traditional multiple kernel learning (MKL) algorithms are essentially supervised learning in the sense that the kernel learning task requires the class labels of training data. However, class labels may not always be available prior to the kernel learning task in some real world scenarios, e.g., an early preprocessing step of a classification task or an unsupervised learning task such as dimension reduction. In this paper, we investigate a problem of Unsupervised Multiple Kernel Learning (UMKL), which does not require class labels of training data as needed in a conventional multiple kernel learning task. Since a kernel essentially defines pairwise similarity between any two examples, our unsupervised kernel learning method mainly follows two intuitive principles: (1) a good kernel should allow every example to be well reconstructed from its localized bases weighted by the kernel values; (2) a good kernel should induce kernel values that are coincided with the local geometry of the data. We formulate the unsupervised multiple kernel learning problem as an optimization task and propose an efficient alternating optimization algorithm to solve it. Empirical results on both classification and dimension reductions tasks validate the efficacy of the proposed UMKL algorithm.

/pdf/unsupervised-multiple-kernel-learning-1sc79aojui.pdf

Xiangyang Lan

Papers

Unsupervised Multiple Kernel Learning