Detecting Abrupt Changes in the Presence of Local Fluctuations and Autocorrelated Noise

DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection

To fully understand gene regulation, it is necessary to have a thorough understanding of both the transcriptome and the enzymatic and RNA-binding activities that shape it. While many RNA-Seq-based tools have been developed to analyze the transcriptome, most only consider the abundance of sequencing reads along annotated patterns (such as genes). These annotations are typically incomplete, leading to errors in the differential expression analysis. To address this issue, we present DiffSegR - an R package that enables the discovery of transcriptome-wide expression differences between two biological conditions using RNA-Seq data. DiffSegR does not require prior annotation and uses a multiple changepoints detection algorithm to identify the boundaries of differentially expressed regions in the per-base log2 fold change. In a few minutes of computation, DiffSegR could rightfully predict the role of chloroplast ribonuclease Mini-III in rRNA maturation and chloroplast ribonuclease PNPase in (3'/5')-degradation of rRNA, mRNA and tRNA precursors as well as intron accumulation. We believe DiffSegR will benefit biologists working on transcriptomics as it allows access to information from a layer of the transcriptome overlooked by the classical differential expression analysis pipelines widely used today. DiffSegR is available at https://aliehrmann.github.io/DiffSegR/index.html.

Causal Responsibility Division of Chronological Continuous Treatment Based on Change-Point Detection

This paper introduces a novel approach, called causal relation quantification, based on change-point detection to address the issue of harmonic responsibility division in power systems. The proposed method focuses on determining the causal effect of chronological continuous treatment, enabling the identification of crucial treatment intervals. Within each interval, three propensity-score-based algorithms are executed to assess their respective causal effects. By integrating the results from each interval, the overall causal effect of a chronological continuous treatment variable can be calculated. This calculated overall causal effect represents the causal responsibility of each harmonic customer. The effectiveness of the proposed method is evaluated through a simulation study and demonstrated in an empirical harmonic application. The results of the simulation study indicate that our method provides accurate and robust estimates, while the calculated results in the harmonic application align closely with the real-world scenario as verified by on-site investigations.

Automated selection of changepoints using empirical P-values and trimming

OBJECTIVES

One challenge that arises when analyzing mobile health (mHealth) data is that updates to the proprietary algorithms that process these data can change apparent patterns. Since the timings of these updates are not publicized, an analytic approach is necessary to determine whether changes in mHealth data are due to lifestyle behaviors or algorithmic updates. Existing methods for identifying changepoints do not consider multiple types of changepoints, may require prespecifying the number of changepoints, and often involve nonintuitive parameters. We propose a novel approach, Automated Selection of Changepoints using Empirical P-values and Trimming (ASCEPT), to select an optimal set of changepoints in mHealth data.

MATERIALS AND METHODS

ASCEPT involves 2 stages: (1) identification of a statistically significant set of changepoints from sequential iterations of a changepoint detection algorithm; and (2) trimming changepoints within linear and seasonal trends. ASCEPT is available at https://github.com/matthewquinn1/changepointSelect.

RESULTS

We demonstrate ASCEPT's utility using real-world mHealth data collected through the Precision VISSTA study. We also demonstrate that ASCEPT outperforms a comparable method, circular binary segmentation, and illustrate the impact when adjusting for changepoints in downstream analysis.

DISCUSSION

ASCEPT offers a practical approach for identifying changepoints in mHealth data that result from algorithmic updates. ASCEPT's only required parameters are a significance level and goodness-of-fit threshold, offering a more intuitive option compared to other approaches.

CONCLUSION

ASCEPT provides an intuitive and useful way to identify which changepoints in mHealth data are likely the result of updates to the underlying algorithms that process the data.

Investigation of Regression-Based Effect Size Methods Developed in Single-Subject Studies

The purpose of this study is to provide a brief introduction to effect size calculation in single-subject design studies, including a description of nonparametric and regression-based effect sizes. We then focus the rest of the tutorial on common regression-based methods used to calculate effect size in single-subject experimental studies. We start by first describing the difference between five regression-based methods (Gorsuch, White et al., Center et al., Allison and Gorman, Huitema and McKean). This is followed by an example using the five regression-based effect size methods and a demonstration how these methods can be applied using a sample data set. In this way, the question of how the values obtained from different effect size methods differ was answered. The specific regression models used in these five regression-based methods and how these models can be obtained from the SPSS program were shown. R² values obtained from these five methods were converted to Cohen's d value and compared in this study. The d values obtained from the same data set were estimated as 0.003, 0.357, 2.180, 3.470, and 2.108 for the Allison and Gorman, Gorsuch, White et al., Center et al., as well as for Huitema and McKean methods, respectively. A brief description of selected statistical programs available to conduct regression-based methods was given.

Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models

BACKGROUND

Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq). This technique provides a direct survey of the DNA regions associated to these modifications. In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed or adapted to analyze the massive amount of data it generates. Many of these algorithms were built around natural assumptions such as the Poisson distribution to model the noise in the count data. In this work we start from these natural assumptions and show that it is possible to improve upon them.

RESULTS

Our comparisons on seven reference datasets of histone modifications (H3K36me3 & H3K4me3) suggest that natural assumptions are not always realistic under application conditions. We show that the unconstrained multiple changepoint detection model with alternative noise assumptions and supervised learning of the penalty parameter reduces the over-dispersion exhibited by count data. These models, implemented in the R package CROCS ( https://github.com/aLiehrmann/CROCS ), detect the peaks more accurately than algorithms which rely on natural assumptions.

CONCLUSION

The segmentation models we propose can benefit researchers in the field of epigenetics by providing new high-quality peak prediction tracks for H3K36me3 and H3K4me3 histone modifications.