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Sparse and Compositionally Robust Inference of Microbial Ecological Networks
tl;dr
We present SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference), a statistical method for the inference of microbial ecological networks from amplicon sequencing datasets that addresses both of these issues. Expand
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  • Open Access
Global Characterization of the CEC 2005 Fitness Landscapes Using Fitness-Distance Analysis
tl;dr
We interpret real-valued black-box optimization problems over continuous domains as high-dimensional, complex landscapes. Expand
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Particle Swarm CMA Evolution Strategy for the optimization of multi-funnel landscapes
tl;dr
We extend the Evolution Strategy with Covariance Matrix Adaptation (CMA-ES) by collaborative concepts from Particle Swarm Optimization (PSO). Expand
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  • Open Access
Optimization of Convex Functions with Random Pursuit
We consider unconstrained randomized optimization of convex objective functions. We analyze the Random Pursuit algorithm, which iteratively computes an approximate solution to the optimizationExpand
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  • Open Access
Don't Fall for Tuning Parameters: Tuning-Free Variable Selection in High Dimensions With the TREX
tl;dr
We introduce TREX, an alternative to Lasso with an inherent calibration to all aspects of the model that can outperform cross-validated Lasso in terms of variable selection and computational efficiency. Expand
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  • Open Access
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
tl;dr
We describe 4C-ker, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus that can be important for gene regulation. Expand
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  • Open Access
A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity
Broad-spectrum antibiotics are frequently prescribed to children. Early childhood represents a dynamic period for the intestinal microbial ecosystem, which is readily shaped by environmental cues;Expand
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Gaussian Adaptation Revisited - An Entropic View on Covariance Matrix Adaptation
tl;dr
We revisit Gaussian Adaptation (GaA), a black-box optimizer for discrete and continuous problems that has been developed in the late 1960’s. Expand
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  • Open Access
Variable metric random pursuit
tl;dr
We analyze Random Pursuit algorithms with fixed (F-RP) and variable metric (V-RP). Expand
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  • Open Access
Microbial Networks in SPRING - Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data
High-throughput microbial sequencing techniques, such as targeted amplicon-based and metagenomic profiling, provide low-cost genomic survey data of microbial communities in their natural environment,Expand
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  • Open Access