AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal

Amplicon identification using SparsE representation of multiplex PYROsequencing signal (AdvISER-M-PYRO): application to bacterial resistance genotyping

MOTIVATION Pyrosequencing is a cost-effective DNA sequencing technology that has many applications, including rapid genotyping of a broad spectrum of bacteria. When molecular typing requires to genotype multiple DNA stretches, several pyrosequencing primers could be used simultaneously but this would create overlapping primer-specific signals, which are visually uninterpretable. Accordingly, th...

Sparse Signal Representation using Overlapping Frames

Signal expansions using frames may be considered as generalizations of signal representations based on transforms and filter banks. Frames for sparse signal representations may be designed using an iterative method with two main steps: (1) Frame vector selection and expansion coefficient determination for signals in a training set, – selected to be representative of the signals for which compac...

Sparse Signal Representation: Image Compression using Sparse Bayesian Learning

with Φ ∈ RN×M , M ≥ N , and some noise . The challenge is to determine the sparsest representation of reconstruction coefficients w = [w1, . . . , wM ] . Finding a sparse representation of a signal in an overcomplete dictionary is equivalent to solving a regularized linear inverse. For a given dictionary Φ, finding the maximally sparse w is an NP-hard problem [1]. A great deal of recent researc...

Modeling Category Identification Using Sparse Instance Representation

We study the problem of category identification, which involves making inferences about category membership (e.g., a ‘cat’) given a set of features (e.g., has a tail, has four legs). We note that this problem is closely related to classification problems in machine learning, for which standard methods exist, and new methods continue to be developed. Using a large database of associations of fea...

Analysis of Microbial Diversity by Amplicon Pyrosequencing