Factor-Adjusted Regularized Model Selection.
Ontology highlight
ABSTRACT:
SUBMITTER: Fan J
PROVIDER: S-EPMC7141573 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Regularized logistic regression is a standard classification method used in statistics and machine learning. Unlike regularized least squares problems such as ridge regression, the parameter estimates cannot be computed in closed-form and instead must be estimated using an iterative technique. This paper addresses the computational problem of regularized logistic regression that is commonly encountered in model selection and classifier statistical significance testing, in which a large number of related logistic regression problems must be solved for. Our proposed approach solves the problems simultaneously through an iterative technique, which also garners computational efficiencies by leveraging the redundancies across the related problems. We demonstrate analytically that our method provides a substantial complexity reduction, which is further validated by our results on real-world datasets.
| S-EPMC3875235 | biostudies-literature
Project description:We propose two model selection criteria relying on the bootstrap approach, denoted by QAICb1 and QAICb2, in the framework of linear mixed models. Similar to the justification of Akaike Information Criterion (AIC), the proposed QAICb1 and QAICb2 are proved as asymptotically unbiased estimators of the Kullback-Leibler discrepancy between a candidate model and the true model. However, they are defined on the quasi-likelihood function instead of the likelihood and are proven to be asymptotically equivalent. The proposed selection criteria are constructed by the quasi-likelihood of a candidate model and a bias estimation term in which the bootstrap method is adopted to improve the estimation for the bias caused by using the candidate model to estimate the true model. The simulations across a variety of mixed model settings are conducted to demonstrate that the proposed selection criteria outperform some other existing model selection criteria in selecting the true model. Generalized estimating equations (GEE) are utilized to calculate QAICb1 and QAICb2 in the simulations. The effectiveness of the proposed selection criteria is also demonstrated in an application of Parkinson's Progression Markers Initiative (PPMI) data.
| S-EPMC10896141 | biostudies-literature
Project description:Despite extensive research efforts, reconstruction of gene regulatory networks (GRNs) from transcriptomics data remains a pressing challenge in systems biology. While non-linear approaches for reconstruction of GRNs show improved performance over simpler alternatives, we do not yet have understanding if joint modelling of multiple target genes may improve performance, even under linearity assumptions. To address this problem, we propose two novel approaches that cast the GRN reconstruction problem as a blend between regularized multivariate regression and graphical models that combine the L2,1-norm with classical regularization techniques. We used data and networks from the DREAM5 challenge to show that the proposed models provide consistently good performance in comparison to contenders whose performance varies with data sets from simulation and experiments from model unicellular organisms Escherichia coli and Saccharomyces cerevisiae. Since the models' formulation facilitates the prediction of master regulators, we also used the resulting findings to identify master regulators over all data sets as well as their plasticity across different environments. Our results demonstrate that the identified master regulators are in line with experimental evidence from the model bacterium E. coli. Together, our study demonstrates that simultaneous modelling of several target genes results in improved inference of GRNs and can be used as an alternative in different applications.
| S-EPMC10414675 | biostudies-literature
Project description:Case-cohort designs are commonly used in large epidemiological studies to reduce the cost associated with covariate measurement. In many such studies the number of covariates is very large. An efficient variable selection method is needed for case-cohort studies where the covariates are only observed in a subset of the sample. Current literature on this topic has been focused on the proportional hazards model. However, in many studies the additive hazards model is preferred over the proportional hazards model either because the proportional hazards assumption is violated or the additive hazards model provides more relevent information to the research question. Motivated by one such study, the Atherosclerosis Risk in Communities (ARIC) study, we investigate the properties of a regularized variable selection procedure in stratified case-cohort design under an additive hazards model with a diverging number of parameters. We establish the consistency and asymptotic normality of the penalized estimator and prove its oracle property. Simulation studies are conducted to assess the finite sample performance of the proposed method with a modified cross-validation tuning parameter selection methods. We apply the variable selection procedure to the ARIC study to demonstrate its practical use.
| S-EPMC5787409 | biostudies-literature
Project description:In cancer studies, it is common that multiple microarray experiments are conducted to measure the same clinical outcome and expressions of the same set of genes. An important goal of such experiments is to identify a subset of genes that can potentially serve as predictive markers for cancer development and progression. Analyses of individual experiments may lead to unreliable gene selection results because of the small sample sizes. Meta analysis can be used to pool multiple experiments, increase statistical power, and achieve more reliable gene selection. The meta analysis of cancer microarray data is challenging because of the high dimensionality of gene expressions and the differences in experimental settings amongst different experiments.We propose a Meta Threshold Gradient Descent Regularization (MTGDR) approach for gene selection in the meta analysis of cancer microarray data. The MTGDR has many advantages over existing approaches. It allows different experiments to have different experimental settings. It can account for the joint effects of multiple genes on cancer, and it can select the same set of cancer-associated genes across multiple experiments. Simulation studies and analyses of multiple pancreatic and liver cancer experiments demonstrate the superior performance of the MTGDR.The MTGDR provides an effective way of analyzing multiple cancer microarray studies and selecting reliable cancer-associated genes.
| S-EPMC2631520 | biostudies-literature
Project description:Clear cell renal cell carcinoma (ccRCC) is the most common subtype of RCC showing a significant percentage of mortality. One of the priorities of kidney cancer research is to identify RCC-specific biomarkers for early detection and screening of the disease. With the development of high-throughput technology, it is now possible to measure the expression levels of thousands of genes in parallel and assess the molecular profile of individual tumors. Studying the relationship between gene expression and survival outcome has been widely used to find genes associated with cancer survival, providing new information for clinical decision-making. One of the challenges of using transcriptomics data is their high dimensionality which can lead to instability in the selection of gene signatures. Here we identify potential prognostic biomarkers correlated to the survival outcome of ccRCC patients using two network-based regularizers (EN and TCox) applied to Cox models. Some genes always selected by each method were found (COPS7B, DONSON, GTF2E2, HAUS8, PRH2, and ZNF18) with known roles in cancer formation and progression. Afterward, different lists of genes ranked based on distinct metrics (logFC of DEGs or β coefficients of regression) were analyzed using GSEA to try to find over- or under-represented mechanisms and pathways. Some ontologies were found in common between the gene sets tested, such as nuclear division, microtubule and tubulin binding, and plasma membrane and chromosome regions. Additionally, genes that were more involved in these ontologies and genes selected by the regularizers were used to create a new gene set where we applied the Cox regression model. With this smaller gene set, we were able to significantly split patients into high/low risk groups showing the importance of studying these genes as potential prognostic factors to help clinicians better identify and monitor patients with ccRCC.
| S-EPMC9367278 | biostudies-literature
Project description:Speech emotion classification (SEC) has gained the utmost height and occupied a conspicuous position within the research community in recent times. Its vital role in Human-Computer Interaction (HCI) and affective computing cannot be overemphasized. Many primitive algorithmic solutions and deep neural network (DNN) models have been proposed for efficient recognition of emotion from speech however, the suitability of these methods to accurately classify emotion from speech with multi-lingual background and other factors that impede efficient classification of emotion is still demanding critical consideration. This study proposed an attention-based network with a pre-trained convolutional neural network and regularized neighbourhood component analysis (RNCA) feature selection techniques for improved classification of speech emotion. The attention model has proven to be successful in many sequence-based and time-series tasks. An extensive experiment was carried out using three major classifiers (SVM, MLP and Random Forest) on a publicly available TESS (Toronto English Speech Sentence) dataset. The result of our proposed model (Attention-based DCNN+RNCA+RF) achieved 97.8% classification accuracy and yielded a 3.27% improved performance, which outperforms state-of-the-art SEC approaches. Our model evaluation revealed the consistency of attention mechanism and feature selection with human behavioural patterns in classifying emotion from auditory speech.
| S-EPMC10368662 | biostudies-literature
Project description:In the presence of high-dimensional predictors, it is challenging to develop reliable regression models that can be used to accurately predict future outcomes. Further complications arise when the outcome of interest is an event time, which is often not fully observed due to censoring. In this article, we develop robust prediction models for event time outcomes by regularizing the Gehan's estimator for the accelerated failure time (AFT) model (Tsiatis, 1996, Annals of Statistics 18, 305-328) with least absolute shrinkage and selection operator (LASSO) penalty. Unlike existing methods based on the inverse probability weighting and the Buckley and James estimator (Buckley and James, 1979, Biometrika 66, 429-436), the proposed approach does not require additional assumptions about the censoring and always yields a solution that is convergent. Furthermore, the proposed estimator leads to a stable regression model for prediction even if the AFT model fails to hold. To facilitate the adaptive selection of the tuning parameter, we detail an efficient numerical algorithm for obtaining the entire regularization path. The proposed procedures are applied to a breast cancer dataset to derive a reliable regression model for predicting patient survival based on a set of clinical prognostic factors and gene signatures. Finite sample performances of the procedures are evaluated through a simulation study.
| S-EPMC3073158 | biostudies-literature
Project description:Variable selections for regression with high-dimensional big data have found many applications in bioinformatics and computational biology. One appealing approach is the L0 regularized regression which penalizes the number of nonzero features in the model directly. However, it is well known that L0 optimization is NP-hard and computationally challenging. In this paper, we propose efficient EM (L0EM) and dual L0EM (DL0EM) algorithms that directly approximate the L0 optimization problem. While L0EM is efficient with large sample size, DL0EM is efficient with high-dimensional (n ? m) data. They also provide a natural solution to all Lp ??p ? [0,2] problems, including lasso with p = 1 and elastic net with p ? [1,2]. The regularized parameter ? can be determined through cross validation or AIC and BIC. We demonstrate our methods through simulation and high-dimensional genomic data. The results indicate that L0 has better performance than lasso, SCAD, and MC+, and L0 with AIC or BIC has similar performance as computationally intensive cross validation. The proposed algorithms are efficient in identifying the nonzero variables with less bias and constructing biologically important networks with high-dimensional big data.
| S-EPMC5098106 | biostudies-literature
Project description:High-throughput phenotyping (HTP) technologies can produce data on thousands of phenotypes per unit being monitored. These data can be used to breed for economically and environmentally relevant traits (e.g., drought tolerance); however, incorporating high-dimensional phenotypes in genetic analyses and in breeding schemes poses important statistical and computational challenges. To address this problem, we developed regularized selection indices; the methodology integrates techniques commonly used in high-dimensional phenotypic regressions (including penalization and rank-reduction approaches) into the selection index (SI) framework. Using extensive data from CIMMYT's (International Maize and Wheat Improvement Center) wheat breeding program we show that regularized SIs derived from hyper-spectral data offer consistently higher accuracy for grain yield than those achieved by standard SIs, and by vegetation indices commonly used to predict agronomic traits. Regularized SIs offer an effective approach to leverage HTP data that is routinely generated in agriculture; the methodology can also be used to conduct genetic studies using high-dimensional phenotypes that are often collected in humans and model organisms including body images and whole-genome gene expression profiles.
| S-EPMC7235263 | biostudies-literature