Plug-in Algorithm Research Articles

Forecasting economic growth by combining local linear and standard approaches

Today, developing economies are of major importance for global macroeconomic development. However, the empirical analysis and especially the forecasting of macroeconomic time series remain difficult due to a lack of sufficient data, data frequency, high volatility, and non-linear developments. These difficulties require more sophisticated approaches to obtain reliable forecasts. Therefore, we propose an improved forecasting method especially for growth data based on a data-driven local linear trend estimation with an extended iterative plug-in algorithm for determining the bandwidth endogenously. This approach allows a smooth trend estimation that takes care of temporary changes in trend processes. Further, the naïve random walk model is extended for forecasting by including a local linear, time-varying drift. We apply this method to GDP development for six developing and two advanced economies and compare different forecast combinations. The combinations that include the local linear approach and the random walk with a local linear trend improve forecasting accuracy and reduce variance.

Th17 Cell-Related Gene Biomarkers in Osteoporosis: Comprehensive Bioinformatics Analysis and In Vivo Validation.

The interaction between the bone and immune systems has a major role in osteoporosis regulation. However, the infiltration of T helper 17 (Th17) cells and their associated genes in osteoporosis remains unclear. The GSE35959 dataset was obtained from the Gene Expression Omnibus (GEO) database, and the Immune Cell Abundance Identifier (ImmuCellAI) program was used to evaluate the abundance of 24 immune cell types, including Th17 cells. Differential analysis and relevance analysis were performed to identify differentially expressed Th17 cell-related genes (DETh17RGs) in osteoporosis. The potential functions of DETh17RGs were analyzed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment. Hub DETh17RGs were obtained through comprehensive analysis using Weighted Gene Co-Expression Network Analysis (WGCNA) and the CytoHubba plug-in algorithm. The expression levels of hub genes were validated using additional osteoporosis datasets. Additionally, the transcript levels of Hub genes in a mice model of osteoporosis were examined using quantitative PCR (qPCR). 464 DETh17RGs were identified in this study, with 421 genes showing positive associations and 43 genes showing negative associations. Among these, seven genes (CD44, TGFB1, ACTN4, ARHGDIA, ESR1, TLN1, FLNA) were considered as Hub DETh17RGs. The qPCR transcript levels of hub DETh17RGs in a mice model of osteoporosis exhibited consistent expression trends with the bioinformatics analysis. This research enhances our understanding of the molecular mechanisms involving Th17 cells in the development of osteoporosis and contributes to the discovery of potential biomarkers.

An extended exponential SEMIFAR model with application in R

The article at hand provides a detailed description of the esemifar R-package, which is an extension of the already published smoots R-package, enabling the data-driven local-polynomial smoothing of trend-stationary time series with long memory. In this regard, a simple data-driven algorithm is proposed based on the well-known iterative plug-in algorithm for SEMIFAR (semiparametric fractional autoregressive) models. Two new functions for data-driven estimation of the trend and its derivatives in the presence of long memory are introduced. esemifar is applied to various environmental and financial time series with long memory, for example, mean monthly Northern Hemisphere temperature changes, daily observations of the air quality index of London (Britain), quarterly G7-GDP and daily trading volume of the S & P500. It is worth mentioning that this package can be applied to any suitable time series.

Identification of hub genes associated with osteoporosis development by comprehensive bioinformatics analysis.

Osteoporosis (OP) is a systemic bone disease caused by various factors, including, the decrease of bone density and quality, the destruction of bone microstructure, and the increase of bone fragility. It is a disease with a high incidence in a large proportion of the world's elderly population. However, osteoporosis lacks obvious symptoms and sensitive biomarkers. Therefore, it is extremely urgent to discover and identify disease-related biomarkers for early clinical diagnosis and effective intervention for osteoporosis. In our study, the Linear Models for Microarray Data (LIMMA) tool was used to screen differential expressed genes from transcriptome sequencing data of OP blood samples downloaded from the GEO database, and cluster Profiler was used for enriching analysis of differently expressed genes. In order to analyzed the relevance of gene modules, clinical symptoms, and the most related module setting genes associated with disease progression, we adapted Weighted Gene Co-expression Network Analysis (WGCNA) to screen and analyze the related pathways and relevant molecules. We used the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database to construct protein interaction network of key modules, and Cytoscape software was used to complete network visualization and screen of core genes in the network. Various plug-in algorithms of cytoHubba were used to identify key genes of OP. Finally, correlation analysis and single-gene gene probe concentration analysis (GSEA) analysis were performed for each core gene. Results of a total of 8 key genes that were closely related to the occurrence and development of OP were screened out, which provided a brand-new idea for the clinical diagnosis and early prevention of OP. Quantitative real-time PCR (qRT-PCR) was performed for validation, the expression levels of CUL1, PTEN and STAT1 genes in the OS group were significantly higher than in the non-OS groups. Receiver operating characteristic analysis demonstrated that CUL1, PTEN and STAT1 displayed considerable diagnostic accuracy for OS.

Automated high-content image-based characterization of microorganism behavioral diversity and distribution

Microorganisms have evolved complex systems to respond to environmental signals. Gradients of particular molecules and elemental ions alter the behavior of microbes and their distribution within their environment. Microdevices coupled with automated image-based methods are now employed to analyze the instantaneous distribution and motion behaviors of microbial species in controlled environments at small temporal scales, mimicking, to some extent, macro conditions. Such technologies have so far been adopted for investigations mainly on individual species. Similar versatile approaches must now be developed for the characterization of multiple and complex interactions between a microbial community and its environment. Here, we provide a comprehensive step-by-step method for the characterization of species-specific behavior in a synthetic mixed microbial suspension in response to an environmental driver. By coupling accessible microfluidic devices with automated image analysis approaches, we evaluated the behavioral response of three morphologically different telluric species (Phytophthora parasitica, Vorticella microstoma, Enterobacter aerogenes) to a potassium gradient driver. Using the TrackMate plug-in algorithm, we performed morphometric and then motion analyses to characterize the response of each microbial species to the driver. Such an approach enabled to confirm the different morphological features of the three species and simultaneously characterize their specific motion in reaction to the driver and their co-interaction dynamics. By increasing the complexity of suspensions, this approach could be integrated in a framework for phenotypic analysis in microbial ecology research, helping to characterize how key drivers influence microbiota assembly at microbiota host-environment interfaces.

Targeted Search for Individualized Clinical Decision Rules to Optimize Clinical Outcomes.

Novel biomarkers, in combination with currently available clinical information, have been sought to enhance clinical decision making in many branches of medicine, including screening, surveillance and prognosis. An individualized clinical decision rule (ICDR) is a decision rule that matches subgroups of patients with tailored medical regimen based on patient characteristics. We proposed new approaches to identify ICDRs by directly optimizing a risk-adjusted clinical benefit function that acknowledges the tradeoff between detecting disease and over-treating patients with benign conditions. In particular, we developed a novel plug-in algorithm to optimize the risk-adjusted clinical benefit function, which leads to the construction of both nonparametric and linear parametric ICDRs. In addition, we proposed a novel approach based on the direct optimization of a smoothed ramp loss function to further enhance the robustness of a linear ICDR. We studied the asymptotic theories of the proposed estimators. Simulation results demonstrated good finite sample performance for the proposed estimators and improved clinical utilities when compared to standard approaches. The methods were applied to a prostate cancer biomarker study.

Gene Biomarkers Related to Th17 Cells in Macular Edema of Diabetic Retinopathy: Cutting-Edge Comprehensive Bioinformatics Analysis and In Vivo Validation.

BackgroundPrevious studies have shown that T-helper 17 (Th17) cell-related cytokines are significantly increased in the vitreous of proliferative diabetic retinopathy (PDR), suggesting that Th17 cells play an important role in the inflammatory response of diabetic retinopathy (DR), but its cell infiltration and gene correlation in the retina of DR, especially in diabetic macular edema (DME), have not been studied.MethodsThe dataset GSE160306 was downloaded from the Gene Expression Omnibus (GEO) database, which contains 9 NPDR samples and 10 DME samples. ImmuCellAI algorithm was used to estimate the abundance of Th17 cells in 24 kinds of infiltrating immune cells. The differentially expressed Th17 related genes (DETh17RGs) between NPDR and DME were documented by difference analysis and correlation analysis. Through aggregate analyses such as gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analysis, a protein-protein interaction (PPI) network was constructed to analyze the potential function of DETh17RGs. CytoHubba plug-in algorithm, Lasso regression analysis and support vector machine recursive feature elimination (SVM-RFE) were implemented to comprehensively identify Hub DETh17RGs. The expression archetypes of Hub DETh17RGs were further verified in several other independent datasets related to DR. The Th17RG score was defined as the genetic characterization of six Hub DETh17RGs using the GSVA sample score method, which was used to distinguish early and advanced diabetic nephropathy (DN) as well as normal and diabetic nephropathy. Finally, real-time quantitative PCR (qPCR) was implemented to verify the transcription levels of Hub DETh17RGs in the STZ-induced DR model mice (C57BL/6J).Results238 DETh17RGs were identified, of which 212 genes were positively correlated while only 26 genes were negatively correlated. Six genes (CD44, CDC42, TIMP1, BMP7, RHOC, FLT1) were identified as Hub DETh17RGs. Because DR and DN have a strong correlation in clinical practice, the verification of multiple independent datasets related to DR and DN proved that Hub DETh17RGs can not only distinguish PDR patients from normal people, but also distinguish DN patients from normal people. It can also identify the initial and advanced stages of the two diseases (NPDR vs DME, Early DN vs Advanced DN). Except for CDC42 and TIMP1, the qPCR transcription levels and trends of other Hub DETh17RGs in STZ-induced DR model mice were consistent with the human transcriptome level in this study.ConclusionThis study will improve our understanding of Th17 cell-related molecular mechanisms in the progression of DME. At the same time, it also provides an updated basis for the molecular mechanism of Th17 cell crosstalk in the eye and kidney in diabetes.

The Use of the Modified Semi-bounded Plug-in Algorithm to Compare Neural and Bayesian Classifiers Stability

Despite of the widespread use of the neural networks in the industrial applications, their mathematical formulation remains difficult to analyze. This explains a limited amount of work that formally models their classification volatility. Referring to the statistical point of view, we attempt in this work to evaluate the classical and Bayesian neural networks stability degree compared to the statistical methods stressing their error rate probability densities. The comparison based on this new criterion is performed using the modified semi-bounded Plug-in algorithm.

The Generalised Plug-in Algorithm for the Diffeomorphism Kernel Estimate

The optimal value of the smoothing parameter of the Kernel estimator can be obtained by the well known Plug-in algorithm. The optimality is realised in the sense of Mean Integrated Square Error (MISE). In this paper, we propose to generalise this algorithm to the case of the difficult problem of the estimation of a distribution which has a bounded support. The proposed algorithm consists in searching the optimal smoothing parameter by iterations from the expression of MISE of the kernel-diffeomorphism estimator. By some simulations applied to some distribution having a support bounded and semi bounded, we show that the support of the pdf estimator respects the one of the theoretical distribution. We also prove that the proposed method minimizes the Gibbs phenomenon.

Chemputation and the Standardization of Chemical Informatics.

The explosion in the use of machine learning for automated chemical reaction optimization is gathering pace. However, the lack of a standard architecture that connects the concept of chemical transformations universally to software and hardware provides a barrier to using the results of these optimizations and could cause the loss of relevant data and prevent reactions from being reproducible or unexpected findings verifiable or explainable. In this Perspective, we describe how the development of the field of digital chemistry or chemputation, that is the universal code-enabled control of chemical reactions using a standard language and ontology, will remove these barriers allowing users to focus on the chemistry and plug in algorithms according to the problem space to be explored or unit function to be optimized. We describe a standard hardware (the chemical processing programming architecture—the ChemPU) to encompass all chemical synthesis, an approach which unifies all chemistry automation strategies, from solid-phase peptide synthesis, to HTE flow chemistry platforms, while at the same time establishing a publication standard so that researchers can exchange chemical code (χDL) to ensure reproducibility and interoperability. Not only can a vast range of different chemistries be plugged into the hardware, but the ever-expanding developments in software and algorithms can also be accommodated. These technologies, when combined will allow chemistry, or chemputation, to follow computation—that is the running of code across many different types of capable hardware to get the same result every time with a low error rate.

An annotated association mining approach for extracting and visualizing interesting clinical events

ObjectiveThis work aims at deriving interesting clinical events using association rule mining based on a user-annotated order of clinical features. Materials and methodsA user specifies a partial temporal order of features by indexing features of interest, with repeated and bundled indexes allowed as needed. An association mining algorithm plugin was designed to generate rules that adhere to the user-specified temporal order. The plugin uses temporal and sequence constraints to reduce rule permutations early in the rule generation process. The method was evaluated with a large medical claims dataset to generate clinical events. ResultsUsing the plug-in algorithm, the database is scanned to calculate the support of item sequences whose sequential order conforms with the user annotated feature order. In our experiments with 20,000 medical claim data records, our method generated rules in a significantly less time than the standalone Apriori algorithm. Our approach generates dendrograms to organize the rules into meaningful hierarchies and provides a graphical interface to navigate the rules and unfold interesting clinical events. DiscussionSince many associations in healthcare are of sequential nature, some of the derived rules may describe interesting clinical flows or events, while others may be contextually irrelevant. Our method exploits user-specified sequence constraints to eliminate irrelevant rules and reduce rule permutations, speeding up rule mining. ConclusionThis work can be the foundation for future association rule mining studies to extract sequential events based on interestingness. The work can support clinical education where the instructor defines feature sequence constraints, and students unfold and examine extracted sequential rules.

Cost effective stream workflow scheduling to handle application structural changes

Stream workflow is a network of big data streaming applications that acts as key enabler for real-time analysis from Internet of Things data. Smart traffic management and smart grid are examples of stream workflow. The focus of existing work is on streaming operator graphs which differs from stream workflow and handling data fluctuations without significant consideration of different dynamic forms that could happen in the structure of data pipelines. This paper investigates the scheduling problem of stream workflow to support runtime alterations of stream workflow deployment, so that scheduling plans will be revised to handle stream workflow applications with continuously changing characteristics. It proposes a pluggable dynamic scheduling technique that accepts user-defined algorithms to handle stream workflow runtime changes. It also presents three different plug-in algorithms and methods to enable auto-scaling of this workflow in a Multicloud environment. The experimental results of the quality of the solution showed that the proposed plug-in optimisation technique is more efficient than baseline and dynamic fair-share techniques to handle runtime changes.

Data-driven local polynomial for the trend and its derivatives in economic time series

ABSTRACTThe main purpose of this paper is the development of data-driven iterative plug-in algorithms for local polynomial estimation of the trend and its derivatives under dependent errors. Furthermore, a data-driven lag-window estimator for the variance factor in the bandwidth is proposed so that the nonparametric stage is carried out without any parametric assumption on the stationary errors. Analysis of the residuals using an ARMA model is further discussed. Moreover, some computational features of the data-driven algorithms are discussed in detail. Practical performance of the proposals is confirmed by a simulation study and a comparative study, and illustrated by quarterly US GDP and labour force data. An R package called ‘smoots’ (smoothing time series) for smoothing the trend and its derivatives in short-memory time series is developed based on the proposals of this paper.

Steady state adjusting trends using a data-driven local polynomial regression

Economic variables usually follow a dynamic trend pattern. However, it is difficult to estimate this trend precisely as numerous economically- and statistically-based estimation methods exist. This contribution proposes a data-driven nonparametric trend that is local polynomial, to improve arbitrary trend estimations of commonly used methods concerning the selection of the smoothing parameter and the dependence structure. An iterative plug-in (IPI) algorithm determines the bandwidth endogenously and allows a theory-based interpretation of the length of growth processes. This length of the bandwidth reflects the lengths of the steady state periods. Consequently, the bandwidth identifies the time period of stable economic conditions and can detect economic changes. To demonstrate the power of this estimation approach, an extensive simulation study is performed. Furthermore, examples using US and UK GDP data along with a guide for the optimal choice of algorithms for empirical applications are provided. This proposed method yields new insights for growth dynamics, cyclical movements and their dependence.

Secular stagnation? Is there statistical evidence of an unprecedented, systematic decline in growth?

So far it is difficult to establish firm evidence that the recent decline in growth is indeed systematic, unprecedented, and significant. In order to provide more statistical evidence of a decline in economic growth, we use a data-driven nonparametric estimation approach which improves boundary estimators, using an extended iterative plug-in (IPI) algorithm to determine the bandwidth endogenously. We identify continuously Moving Trends (MT) with a length of 18 years for US GDP. Two introduced tests demonstrate a persistent decline in US trends and growth rates since the dot.com bubble. Hence, the 2008 financial crisis merely revealed that GDP, labor, and multi-factor productivity trends were already stagnating.

Heterogeneous slot scheduling for real-time industrial wireless sensor networks

Real-time performance and reliability are two critical indicators in an industrial wireless sensor network (IWSN). Several time-division multiple-address (TDMA)-based industrial standards such as WirelessHART and ISA100 are widely used in IWSNs. However, to simplify the analysis, standard TDMA supports only one or two slot types in each frame, and each slot is usually 10 ms, which severely limits transmissibility and real-time responses in TDMA-based IWSNs where the number of transmissions is large but the length of most packets is small. In this paper, we propose a TDMA frame containing slots of different lengths to address this issue. The key ideas are to waste fewer slot resources and achieve on-demand slot allocation. First, we study the matching problem in a TDMA frame; then, we propose two scheduling methods, the split scheduling algorithm (SSA) and the double plug-in algorithm (DPA), under our TDMA frame. Extensive simulations and real testbed results show that the proposed solution DPA can significantly improve network performance and reliability. Real-time comparisons with other existing scheduling schemes show that the proposed solution improves the acceptance ratio by 48.8% compared to the rate-monotonic scheme.

Postnatal Developmental Changes in Fractal Complexity of Giemsa-Stained Chromatin in Mice Spleen Follicular Cells.

Although there are numerous recent works focusing on fractal properties of DNA and chromatin, many issues regarding changes in chromatin fractality during physiological aging remain unclear. In this study, we present results indicating that in mice, there is an age-related reduction of chromatin fractal complexity in a population of spleen follicular cells (SFCs). Spleen tissue was obtained from 16 mice and fixated in Carnoy solution. The youngest animal was newborn, and each animal was exactly 1 month older than the previous. We performed fractal analysis of SFC chromatin structure, stained using Giemsa technique. Fractal analysis was done in a plugin algorithm of ImageJ software. We also performed gray-level co-occurrence matrix (GLCM) analysis of all chromatin structures with the calculation of parameters such as angular second moment and inverse difference moment. Giemsa-stained SFC chromatin exhibited an age-dependent reduction of fractal dimension with statistically significant (p<0.01) linear trend. Moreover, there was a statistically significant increase of SFC chromatin lacunarity. The chromatin GLCM parameters did not significantly change. To our knowledge, this is the first study to perform fractal and GLCM analyses of SFC chromatin and to investigate potential changes of fractal parameters during postnatal development.

Slow Booms and Deep Busts: 160 Years of Business Cycles in Spain

Abstract This paper introduces an economically important new idea for detrending macroeconomic time series and examines the Spanish business cycle pattern with respect to potential asymmetries. To address difficulties in the trend and cycle decomposition, a nonparametric trend estimation approach is introduced and exemplary applied to the Spanish GDP data for the period 1850 to 2015. The application of an iterative plug-in (IPI) algorithm for endogenous bandwidth selection solves the problem of choosing an adequate smoothing parameter for nonparametric regression. The algorithm identifies continuously Moving Trends (MT) with a time length of 34 years. After we estimate the trend nonparametrically, we fit several time series models to the residuals for further analysis. Although asymmetry during expansion and recession phases is indicated, it is not unambiguous.

On the iterative plug-in algorithm for estimating diurnal patterns of financial trade durations

ABSTRACTThis paper discusses the detailed performance of an iterative plug-in (IPI) bandwidth selector for estimating the diurnal duration pattern in a Semi-ACD (semiparametric autoregressive conditional duration) model. For this purpose a large simulation study was carried out. The effects of different factors, which affect the selected bandwidth are discussed in detail. The simulated results and data examples show that the proposed IPI algorithm works very well in practice and that the Semi-ACD model in general is clearly superior to the parametric ACD model, if there is a deterministic trend in the duration data. It is also shown that the bandwidth selection, and the estimation of the diurnal pattern and the model parameters will all be clearly improved, if the sample size is enlarged. According to the goodness-of-fit of the estimated diurnal pattern, a best combination of the above-mentioned factors is found. Moreover, a comparative study shows that our proposal usually outperforms the commonly used cubic spline.

On trend estimation under monotone Gaussian subordination with long-memory: application to fossil pollen series

Fossil pollen data from stratigraphic cores are irregularly spaced in time due to non-linear age–depth relations. Moreover, their marginal distributions may vary over time. We address these features in a nonparametric regression model with errors that are monotone transformations of a latent continuous-time Gaussian process Z(T). Although Z(T) is unobserved, due to monotonicity, under suitable regularity conditions, it can be recovered facilitating further computations such as estimation of the long-memory parameter and the Hermite coefficients. The estimation of Z(T) itself involves estimation of the marginal distribution function of the regression errors. These issues are considered in proposing a plug-in algorithm for optimal bandwidth selection and construction of confidence bands for the trend function. Some high-resolution time series of pollen records from Lago di Origlio in Switzerland, which go back ca. 20,000 years are used to illustrate the methods.