Change Point Detection in Correlation Networks.
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ABSTRACT:
SUBMITTER: Barnett I
PROVIDER: S-EPMC4703970 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundTo detect changes in biological processes, samples are often studied at several time points. We examined expression data measured at different developmental stages, or more broadly, historical data. Hence, the main assumption of our proposed methodology was the independence between the examined samples over time. In addition, however, the examinations were clustered at each time point by measuring littermates from relatively few mother mice at each developmental stage. As each examination was lethal, we had an independent data structure over the entire history, but a dependent data structure at a particular time point. Over the course of these historical data, we wanted to identify abrupt changes in the parameter of interest - change points.ResultsIn this study, we demonstrated the application of generalized hypothesis testing using a linear mixed effects model as a possible method to detect change points. The coefficients from the linear mixed model were used in multiple contrast tests and the effect estimates were visualized with their respective simultaneous confidence intervals. The latter were used to determine the change point(s). In small simulation studies, we modelled different courses with abrupt changes and compared the influence of different contrast matrices. We found two contrasts, both capable of answering different research questions in change point detection: The Sequen contrast to detect individual change points and the McDermott contrast to find change points due to overall progression. We provide the R code for direct use with provided examples. The applicability of those tests for real experimental data was shown with in-vivo data from a preclinical study.ConclusionSimultaneous confidence intervals estimated by multiple contrast tests using the model fit from a linear mixed model were capable to determine change points in clustered expression data. The confidence intervals directly delivered interpretable effect estimates representing the strength of the potential change point. Hence, scientists can define biologically relevant threshold of effect strength depending on their research question. We found two rarely used contrasts best fitted for detection of a possible change point: the Sequen and McDermott contrasts.
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Project description:Conventional computers based on the von Neumann architecture perform computation by repeatedly transferring data between their physically separated processing and memory units. As computation becomes increasingly data centric and the scalability limits in terms of performance and power are being reached, alternative computing paradigms with collocated computation and storage are actively being sought. A fascinating such approach is that of computational memory where the physics of nanoscale memory devices are used to perform certain computational tasks within the memory unit in a non-von Neumann manner. We present an experimental demonstration using one million phase change memory devices organized to perform a high-level computational primitive by exploiting the crystallization dynamics. Its result is imprinted in the conductance states of the memory devices. The results of using such a computational memory for processing real-world data sets show that this co-existence of computation and storage at the nanometer scale could enable ultra-dense, low-power, and massively-parallel computing systems.
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Project description:Phylogenetic recombination detection is a fundamental task in bioinformatics and evolutionary biology. Most of the computational tools developed to attack this important problem are not integrated into the growing suite of R packages for statistical analysis of molecular sequences. Here, we present an R package, rbrothers, that makes a Bayesian multiple change-point model, one of the most sophisticated model-based phylogenetic recombination tools, available to R users. Moreover, we equip the Bayesian change-point model with a set of pre- and post- processing routines that will broaden the application domain of this recombination detection framework. Specifically, we implement an algorithm that forms the set of input trees required by multiple change-point models. We also provide functionality for checking Markov chain Monte Carlo convergence and creating estimation result summaries and graphics. Using rbrothers, we perform a comparative analysis of two Salmonella enterica genes, fimA and fimH, that encode major and adhesive subunits of the type 1 fimbriae, respectively. We believe that rbrothers, available at R-Forge: http://evolmod.r-forge.r-project.org/, will allow researchers to incorporate recombination detection into phylogenetic workflows already implemented in R.
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Project description:A clinical decision support system (CDSS) and its components can malfunction due to various reasons. Monitoring the system and detecting its malfunctions can help one to avoid any potential mistakes and associated costs. In this paper, we investigate the problem of detecting changes in the CDSS operation, in particular its monitoring and alerting subsystem, by monitoring its rule firing counts. The detection should be performed online, that is whenever a new datum arrives, we want to have a score indicating how likely there is a change in the system. We develop a new method based on Seasonal-Trend decomposition and likelihood ratio statistics to detect the changes. Experiments on real and simulated data show that our method has a lower delay in detection compared with existing change-point detection methods.
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Project description:A method is presented for detecting changes in the axial peak tibial acceleration while adapting to self-discovered lower-impact running. Ten runners with high peak tibial acceleration were equipped with a wearable auditory biofeedback system. They ran on an athletic track without and with real-time auditory biofeedback at the instructed speed of 3.2 m·s-1. Because inter-subject variation may underline the importance of individualized retraining, a change-point analysis was used for each subject. The tuned change-point application detected major and subtle changes in the time series. No changes were found in the no-biofeedback condition. In the biofeedback condition, a first change in the axial peak tibial acceleration occurred on average after 309 running gait cycles (3'40"). The major change was a mean reduction of 2.45 g which occurred after 699 running gait cycles (8'04") in this group. The time needed to achieve the major reduction varied considerably between subjects. Because of the individualized approach to gait retraining and its relatively quick response due to a strong sensorimotor coupling, we want to highlight the potential of a stand-alone biofeedback system that provides real-time, continuous, and auditory feedback in response to the axial peak tibial acceleration for lower-impact running.
| S-EPMC7147709 | biostudies-literature
Project description:MotivationThis work is motivated by the problem of identifying homozygosity islands on the genome of individuals in a population. Our method directly tackles the issue of identification of the homozygosity islands at the population level, without the need of analysing single individuals and then combine the results, as is made nowadays in state-of-the-art approaches.ResultsWe propose regularized offline change-point methods to detect changes in the parameters of a multidimensional distribution when we have several aligned, independent samples of fixed resolution. We present a penalized maximum likelihood approach that can be efficiently computed by a dynamic programming algorithm or approximated by a fast binary segmentation algorithm. Both estimators are shown to converge almost surely to the set of change-points without the need of specifying a priori the number of change-points. In simulation, we observed similar performances from the exact and greedy estimators. Moreover, we provide a new methodology for the selection of the regularization constant which has the advantage of being automatic, consistent, and less prone to subjective analysis.Availability and implementationThe data used in the application are from the Human Genome Diversity Project (HGDP) and is publicly available. Algorithms were implemented using the R software R Core Team (R: A Language and Environment for Statistical Computing. Vienna (Austria): R Foundation for Statistical Computing, 2020.) in the R package blockcpd, found at https://github.com/Lucas-Prates/blockcpd.
| S-EPMC10112956 | biostudies-literature
Project description:Research on change-point detection, the classical problem of detecting abrupt changes in sequential data, has focused predominantly on datasets with a single observable. A growing number of time series datasets, however, involve many observables, often with the property that a given change typically affects only a few of the observables. We introduce a general statistical method that, given many noisy observables, detects points in time at which various subsets of the observables exhibit simultaneous changes in data distribution and explicitly identifies those subsets. Our work is motivated by the problem of identifying the nature and timing of biologically interesting conformational changes that occur during atomic-level simulations of biomolecules such as proteins. This problem has proved challenging both because each such conformational change might involve only a small region of the molecule and because these changes are often subtle relative to the ever-present background of faster structural fluctuations. We show that our method is effective in detecting biologically interesting conformational changes in molecular dynamics simulations of both folded and unfolded proteins, even in cases where these changes are difficult to detect using alternative techniques. This method may also facilitate the detection of change points in other types of sequential data involving large numbers of observables--a problem likely to become increasingly important as such data continue to proliferate in a variety of application domains.
| S-EPMC4475967 | biostudies-literature
Project description:BackgroundTranscriptional regulation is primarily mediated by the binding of factors to non-coding regions in DNA. Identification of these binding regions enhances understanding of tissue formation and potentially facilitates the development of gene therapies. However, successful identification of binding regions is made difficult by the lack of a universal biological code for their characterisation.ResultsWe extend an alignment-based method, changept, and identify clusters of biological significance, through ontology and de novo motif analysis. Further, we apply a Bayesian method to estimate and combine binary classifiers on the clusters we identify to produce a better performing composite.ConclusionsThe analysis we describe provides a computational method for identification of conserved binding sites in the human genome and facilitates an alternative interrogation of combinations of existing data sets with alignment data.
| S-EPMC8790847 | biostudies-literature
Project description:Identifying macroeconomic events that are responsible for dramatic changes of economy is of particular relevance to understanding the overall economic dynamics. We introduce an open-source available efficient Python implementation of a Bayesian multi-trend change point analysis, which solves significant memory and computing time limitations to extract crisis information from a correlation metric. Therefore, we focus on the recently investigated S&P500 mean market correlation in a period of roughly 20 years that includes the dot-com bubble, the global financial crisis, and the Euro crisis. The analysis is performed two-fold: first, in retrospect on the whole dataset and second, in an online adaptive manner in pre-crisis segments. The online sensitivity horizon is roughly determined to be 80 up to 100 trading days after a crisis onset. A detailed comparison to global economic events supports the interpretation of the mean market correlation as an informative macroeconomic measure by a rather good agreement of change point distributions and major crisis events. Furthermore, the results hint at the importance of the U.S. housing bubble as a trigger of the global financial crisis, provide new evidence for the general reasoning of locally (meta)stable economic states, and could work as a comparative impact rating of specific economic events.
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Project description:In a natural environment, sensory systems are faced with ever-changing stimuli that can occur, disappear or change their properties at any time. For the animal to react adequately the sensory systems must be able to detect changes in external stimuli based on its neuronal responses. Since the nervous system has no prior knowledge of the stimulus timing, changes in stimulus need to be inferred from the changes in neuronal activity, in particular increase or decrease of the spike rate, its variability, and shifted response latencies. From a mathematical point of view, this problem can be rephrased as detecting changes of statistical properties in a time series. In neuroscience, the CUSUM (cumulative sum) method has been applied to recorded neuronal responses for detecting a single stimulus change. Here, we investigate the applicability of the CUSUM approach for detecting single as well as multiple stimulus changes that induce increases or decreases in neuronal activity. Like the nervous system, our algorithm relies exclusively on previous neuronal population activities, without using knowledge about the timing or number of external stimulus changes. We apply our change point detection methods to experimental data obtained by multi-electrode recordings from turtle retinal ganglion cells, which react to changes in light stimulation with a range of typical neuronal activity patterns. We systematically examine how variations of mathematical assumptions (Poisson, Gaussian, and Gamma distributions) used for the algorithms may affect the detection of an unknown number of stimulus changes in our data and compare these CUSUM methods with the standard Rate Change method. Our results suggest which versions of the CUSUM algorithm could be useful for different types of specific data sets.
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