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Full-Text Articles in Physical Sciences and Mathematics
Supervised Detection Of Regulatory Motifs In Dna Sequences, Sunduz Keles, Mark J. Van Der Laan, Sandrine Dudoit, Biao Xing, Michael B. Eisen
Supervised Detection Of Regulatory Motifs In Dna Sequences, Sunduz Keles, Mark J. Van Der Laan, Sandrine Dudoit, Biao Xing, Michael B. Eisen
U.C. Berkeley Division of Biostatistics Working Paper Series
Identification of transcription factor binding sites (regulatory motifs) is a major interest in contemporary biology. We propose a new likelihood based method, COMODE, for identifying structural motifs in DNA sequences. Commonly used methods (e.g. MEME, Gibbs sampler) model binding sites as families of sequences described by a position weight matrix (PWM) and identify PWMs that maximize the likelihood of observed sequence data under a simple multinomial mixture model. This model assumes that the positions of the PWM correspond to independent multinomial distributions with four cell probabilities. We address supervising the search for DNA binding sites using the information derived from …
A New Class Of Entropy Estimators For Multi-Dimensional Densities, Erik G. Learned-Miller
A New Class Of Entropy Estimators For Multi-Dimensional Densities, Erik G. Learned-Miller
Erik G Learned-Miller
We present a new class of estimators for approximating the entropy of multi-dimensional probability densities based on a sample of the density. These estimators extend the classic "m-spacing" estimators of Vasicek (1976) and others for estimating entropies of one-dimensional probability densities. Unlike plug-in estimators of entropy, which first estimate a probability density and then compute its entropy. our estimators avoid the difficult intermediate step of density estimation. For fixed dimension. the estimators an polynomial in the sample size. Similarities to consistent and asymptotically efficient one-dimensional estimators of entropy suggest that our estimators may sham these properties.
Entropy And Generalized Least Square Methods In Assessment Of The Regional Value Of Streamgages, Momcilo Markus, H. Vernon Knapp, Gary D. Tasker
Entropy And Generalized Least Square Methods In Assessment Of The Regional Value Of Streamgages, Momcilo Markus, H. Vernon Knapp, Gary D. Tasker
United States Geological Survey: Staff Publications
The Illinois State Water Survey performed a study to assess the streamgaging network in the State of Illinois. One of the important aspects of the study was to assess the regional value of each station through an assessment of the information transfer among gaging records for low, average, and high flow conditions. This analysis was performed for the main hydrologic regions in the State, and the stations were initially evaluated using a new approach based on entropy analysis. To determine the regional value of each station within a region, several information parameters, including total net information, were defined based on …