Ten quick tips for effective dimensionality reduction

Decoding movement direction from cortical microelectrode recordings using an LSTM-based neural network

Brain-machine interfaces (BMIs) allow individuals to communicate with computers using neural signals, and Kalman Filter (KF) are prevailingly used to decode movement directions from these neural signals. In this paper, we implemented a multi-layer long short-term memory (LSTM)based artificial neural network (ANN) for decoding BMI neural signals. We collected motor cortical neural signals from a nonhuman primate (NHP), implanted with microelectrode array (MEA) while performing a directional joystick task. Next, we compared the LSTM model in decoding the joystick trajectories from the neural signals against the prevailing KF model. The results showed that the LSTM model yielded significantly improved decoding accuracy measured by mean correlation coefficient (0.84, p < 10^-7) than the KF model (0.72). In addition, using a principal component analysis (PCA)-based dimensionality reduction technique yielded slightly deteriorated accuracies for both the LSTM (0.80) and KF (0.70) models, but greatly reduced the computational complexity. The results showed that the LSTM decoding model holds promise to improve decoding in BMIs for paralyzed humans.

Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data

Integrative, single-cell analyses may provide unprecedented insights into cellular and spatial diversity of the tumor microenvironment. The sparsity, noise, and high dimensionality of these data present unique challenges. Whilst approaches for integrating single-cell data are emerging and are far from being standardized, most data integration, cell clustering, cell trajectory, and analysis pipelines employ a dimension reduction step, frequently principal component analysis (PCA), a matrix factorization method that is relatively fast, and can easily scale to large datasets when used with sparse-matrix representations. In this review, we provide a guide to PCA and related methods. We describe the relationship between PCA and singular value decomposition, the difference between PCA of a correlation and covariance matrix, the impact of scaling, log-transforming, and standardization, and how to recognize a horseshoe or arch effect in a PCA. We describe canonical correlation analysis (CCA), a popular matrix factorization approach for the integration of single-cell data from different platforms or studies. We discuss alternatives to CCA and why additional preprocessing or weighting datasets within the joint decomposition should be considered.

Unsupervised dimensionality reduction for exposome research

Understanding the effect of the environment on human health has benefited from progress made in measuring the exposome. High resolution mass spectrometry (HRMS) has made it possible to measure small molecules across a large dynamic range, allowing researchers to study the role of low abundance environmental toxicants in causing human disease. HRMS data have a high dimensional structure (number of predictors >> number of observations), generating information on the abundance of many chemical features (predictors) which may be highly correlated. Unsupervised dimension reduction techniques can allow dimensionality reduction of the various features into components that capture the essence of the variability in the exposome dataset. We illustrate and discuss the relevance of three different unsupervised dimension reduction techniques: principal component analysis, factor analysis, and non-negative matrix factorization. We focus on the utility of each method in understanding the relationship between the exposome and a disease outcome and describe their strengths and limitations. While the utility of these methods is context specific, it remains important to focus on the interpretability of results from each method.

Exploring dimension-reduced embeddings with Sleepwalk

Dimension-reduction methods, such as t-SNE or UMAP, are widely used when exploring high-dimensional data describing many entities, for example, RNA-seq data for many single cells. However, dimension reduction is commonly prone to introducing artifacts, and we hence need means to see where a dimension-reduced embedding is a faithful representation of the local neighborhood and where it is not. We present Sleepwalk, a simple but powerful tool that allows the user to interactively explore an embedding, using color to depict original or any other distances from all points to the cell under the mouse cursor. We show how this approach not only highlights distortions but also reveals otherwise hidden characteristics of the data, and how Sleepwalk's comparative modes help integrate multisample data and understand differences between embedding and preprocessing methods. Sleepwalk is a versatile and intuitive tool that unlocks the full power of dimension reduction and will be of value not only in single-cell RNA-seq but also in any other area with matrix-shaped big data.

Interpretation of omics data analyses

Omics studies attempt to extract meaningful messages from large-scale and high-dimensional data sets by treating the data sets as a whole. The concept of treating data sets as a whole is important in every step of the data-handling procedures: the pre-processing step of data records, the step of statistical analyses and machine learning, translation of the outputs into human natural perceptions, and acceptance of the messages with uncertainty. In the pre-processing, the method by which to control the data quality and batch effects are discussed. For the main analyses, the approaches are divided into two types and their basic concepts are discussed. The first type is the evaluation of many items individually, followed by interpretation of individual items in the context of multiple testing and combination. The second type is the extraction of fewer important aspects from the whole data records. The outputs of the main analyses are translated into natural languages with techniques, such as annotation and ontology. The other technique for making the outputs perceptible is visualization. At the end of this review, one of the most important issues in the interpretation of omics data analyses is discussed. Omics studies have a large amount of information in their data sets, and every approach reveals only a very restricted aspect of the whole data sets. The understandable messages from these studies have unavoidable uncertainty.

An Introduction to Machine Learning

In the last few years, machine learning (ML) and artificial intelligence have seen a new wave of publicity fueled by the huge and ever-increasing amount of data and computational power as well as the discovery of improved learning algorithms. However, the idea of a computer learning some abstract concept from data and applying them to yet unseen situations is not new and has been around at least since the 1950s. Many of these basic principles are very familiar to the pharmacometrics and clinical pharmacology community. In this paper, we want to introduce the foundational ideas of ML to this community such that readers obtain the essential tools they need to understand publications on the topic. Although we will not go into the very details and theoretical background, we aim to point readers to relevant literature and put applications of ML in molecular biology as well as the fields of pharmacometrics and clinical pharmacology into perspective.

Improved cell composition deconvolution method of bulk gene expression profiles to quantify subsets of immune cells

Background

To facilitate the investigation of the pathogenic roles played by various immune cells in complex tissues such as tumors, a few computational methods for deconvoluting bulk gene expression profiles to predict cell composition have been created. However, available methods were usually developed along with a set of reference gene expression profiles consisting of imbalanced replicates across different cell types. Therefore, the objective of this study was to create a new deconvolution method equipped with a new set of reference gene expression profiles that incorporate more microarray replicates of the immune cells that have been frequently implicated in the poor prognosis of cancers, such as T helper cells, regulatory T cells and macrophage M1/M2 cells.

Methods

Our deconvolution method was developed by choosing ε-support vector regression (ε-SVR) as the core algorithm assigned with a loss function subject to the L1-norm penalty. To construct the reference gene expression signature matrix for regression, a subset of differentially expressed genes were chosen from 148 microarray-based gene expression profiles for 9 types of immune cells by using ANOVA and minimizing condition number. Agreement analyses including mean absolute percentage errors and Bland-Altman plots were carried out to compare the performances of our method and CIBERSORT.

Results

In silico cell mixtures, simulated bulk tissues, and real human samples with known immune-cell fractions were used as the test datasets for benchmarking. Our method outperformed CIBERSORT in the benchmarks using in silico breast tissue-immune cell mixtures in the proportions of 30:70 and 50:50, and in the benchmark using 164 human PBMC samples. Our results suggest that the performance of our method was at least comparable to that of a state-of-the-art tool, CIBERSORT.

Conclusions

We developed a new cell composition deconvolution method and the implementation was entirely based on the publicly available R and Python packages. In addition, we compiled a new set of reference gene expression profiles, which might allow for a more robust prediction of the immune cell fractions from the expression profiles of cell mixtures. The source code of our method could be downloaded from https://github.com/holiday01/deconvolution-to-estimate-immune-cell-subsets.

BOLD and EEG signal variability at rest differently relate to aging in the human brain

Variability of neural activity is regarded as a crucial feature of healthy brain function, and several neuroimaging approaches have been employed to assess it noninvasively. Studies on the variability of both evoked brain response and spontaneous brain signals have shown remarkable changes with aging but it is unclear if the different measures of brain signal variability - identified with either hemodynamic or electrophysiological methods - reflect the same underlying physiology. In this study, we aimed to explore age differences of spontaneous brain signal variability with two different imaging modalities (EEG, fMRI) in healthy younger (25 ​± ​3 years, N ​= ​135) and older (67 ​± ​4 years, N ​= ​54) adults. Consistent with the previous studies, we found lower blood oxygenation level dependent (BOLD) variability in the older subjects as well as less signal variability in the amplitude of low-frequency oscillations (1-12 ​Hz), measured in source space. These age-related reductions were mostly observed in the areas that overlap with the default mode network. Moreover, age-related increases of variability in the amplitude of beta-band frequency EEG oscillations (15-25 ​Hz) were seen predominantly in temporal brain regions. There were significant sex differences in EEG signal variability in various brain regions while no significant sex differences were observed in BOLD signal variability. Bivariate and multivariate correlation analyses revealed no significant associations between EEG- and fMRI-based variability measures. In summary, we show that both BOLD and EEG signal variability reflect aging-related processes but are likely to be dominated by different physiological origins, which relate differentially to age and sex.

A Guide to Representational Similarity Analysis for Social Neuroscience

Representational similarity analysis (RSA) is a computational technique that uses pairwise comparisons of stimuli to reveal their representation in higher-order space. In the context of neuroimaging, mass-univariate analyses and other multivariate analyses can provide information on what and where information is represented but have limitations in their ability to address how information is represented. Social neuroscience is a field that can particularly benefit from incorporating RSA techniques to explore hypotheses regarding the representation of multidimensional data, how representations can predict behavior, how representations differ between groups and how multimodal data can be compared to inform theories. The goal of this paper is to provide a practical as well as theoretical guide to implementing RSA in social neuroscience studies.