35 research outputs found
Templates for Convex Cone Problems with Applications to Sparse Signal Recovery
This paper develops a general framework for solving a variety of convex cone
problems that frequently arise in signal processing, machine learning,
statistics, and other fields. The approach works as follows: first, determine a
conic formulation of the problem; second, determine its dual; third, apply
smoothing; and fourth, solve using an optimal first-order method. A merit of
this approach is its flexibility: for example, all compressed sensing problems
can be solved via this approach. These include models with objective
functionals such as the total-variation norm, ||Wx||_1 where W is arbitrary, or
a combination thereof. In addition, the paper also introduces a number of
technical contributions such as a novel continuation scheme, a novel approach
for controlling the step size, and some new results showing that the smooth and
unsmoothed problems are sometimes formally equivalent. Combined with our
framework, these lead to novel, stable and computationally efficient
algorithms. For instance, our general implementation is competitive with
state-of-the-art methods for solving intensively studied problems such as the
LASSO. Further, numerical experiments show that one can solve the Dantzig
selector problem, for which no efficient large-scale solvers exist, in a few
hundred iterations. Finally, the paper is accompanied with a software release.
This software is not a single, monolithic solver; rather, it is a suite of
programs and routines designed to serve as building blocks for constructing
complete algorithms.Comment: The TFOCS software is available at http://tfocs.stanford.edu This
version has updated reference
Constraining the electric charges of some astronomical bodies in Reissner-Nordstrom spacetimes and generic r^-2-type power-law potentials from orbital motions
We put model-independent, dynamical constraints on the net electric charge Q
of some astronomical and astrophysical objects by assuming that their exterior
spacetimes are described by the Reissner-Nordstroem metric, which induces an
additional potential U_RN \propto Q^2 r^-2. Our results extend to other
hypothetical power-law interactions inducing extra-potentials U_pert = r^-2 as
well (abridged).Comment: LaTex2e, 16 pages, 3 figures, no tables, 128 references. Version
matching the one at press in General Relativity and Gravitation (GRG). arXiv
admin note: substantial text overlap with arXiv:1112.351
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism