Stochastic chemical reaction networks constitute a model class to quantitatively describe dynamics and cell-to-cell variability in biological systems. The topology of these networks typically is only partially characterized due to experimental limitations. Current approaches for refining network topology are based on the explicit enumeration of alternative topologies and are therefore restricte...

Kernelized LASSO (Least Absolute Selection and Shrinkage Operator) has been investigated in two separate recent papers [Gao, J., Antolovich, M., & Kwan, P. H. (2008). L1 LASSO and its Bayesian inference. In W. Wobcke, & M. Zhang (Eds.), Lecture notes in computer science: Vol. 5360 (pp. 318-324); Wang, G., Yeung, D. Y., & Lochovsky, F. (2007). The kernel path in kernelized LASSO. In Internationa...

Ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are attractive for genome-driven discovery and re-engineering, but limitations in bioinformatic methods and exponentially increasing genomic data make large-scale mining of RiPP data difficult. We report RODEO (Rapid ORF Description and Evaluation Online), which combines hidden-Markov-model-based analysis,...

We propose a new class of variable selection techniques for regression in high dimensional linear models based on a forward selection version of the LASSO, adaptive LASSO or elastic net, respectively to be called as forward iterative regression and shrinkage technique (FIRST), adaptive FIRST and elastic FIRST. These methods seem to work effectively for extremely sparse high dimensional linear m...

The lasso-based L1-graph is used in many applications since it can effectively model a set of data points as a graph. The lasso is a popular regression approach and the L1-graph represents data points as nodes by using the regression result. More specifically, by solving the L1-optimization problem of the lasso, the sparse regression coefficients are used to obtain the weights of the edges in t...

Professors McShane and Wyner have written a thought-provoking paper that intends to challenge some of the conventional wisdom in the paleoclimate literature. Rather than commenting on the merits of the entire methodology we focus on one topic. Namely, we discuss theoretical and practical aspects of the use of the least absolute shrinkage and selection operator [Tibshirani (1996)], more popularl...

We investigate the variable selection problem for Cox’s proportional hazards model, and propose a unified model selection and estimation procedure with desired theoretical properties and computational convenience. The new method is based on a penalized log partial likelihood with the adaptively-weighted L1 penalty on regression coefficients, and is named adaptive-LASSO (ALASSO) estimator. Inste...

Variable selection in genome-wide association studies can be a daunting task and statistically challenging because there are more variables than subjects. We propose an approach that uses principal-component analysis (PCA) and least absolute shrinkage and selection operator (LASSO) to identify gene-gene interaction in genome-wide association studies. A PCA was used to first reduce the dimension...

In this paper, we introduce Adaptive Cluster Lasso(ACL) method for variable selection in high dimensional sparse regression models with strongly correlated variables. To handle correlated variables, the concept of clustering or grouping variables and then pursuing model fitting is widely accepted. When the dimension is very high, finding an appropriate group structure is as difficult as the ori...

The Lasso is a popular and computationally efficient procedure for automatically performing both variable selection and coefficient shrinkage on linear regression models. One limitation of the Lasso is that the same tuning parameter is used for both variable selection and shrinkage. As a result, it typically ends up selecting a model with too many variables to prevent over shrinkage of the regr...