arXiv subjects

Jonathan G. Ligo

Publications and source records attributed to Jonathan G. Ligo.

3 recordsLinked to original sources

arXiv2016

Detecting Sparse Mixtures: Rate of Decay of Error Probability

We study the rate of decay of the probability of error for distinguishing between a sparse signal with noise, modeled as a sparse mixture, from pure noise. This problem has many applications in signal processing, evolutionary biology, bioinformatics, astrophysics and feature selection for machine learning. We let the mixture probability tend to zero as the number of observations tends to infinity and derive oracle rates at which the error probability can be driven to zero for a general class of signal and noise distributions via the likelihood ratio test. In contrast to the problem of detection of non-sparse signals, we see the log-probability of error decays sublinearly rather than linearly and is characterized through the $χ^2$-divergence rather than the Kullback-Leibler divergence for "weak" signals and can be independent of divergence for "strong" signals. Our contribution is the first characterization of the rate of decay of the error probability for this problem for both the false alarm and miss probabilities.

cs.IT↗

arXiv2013

MCUIUC -- A New Framework for Metagenomic Read Compression

Metagenomics is an emerging field of molecular biology concerned with analyzing the genomes of environmental samples comprising many different diverse organisms. Given the nature of metagenomic data, one usually has to sequence the genomic material of all organisms in a batch, leading to a mix of reads coming from different DNA sequences. In deep high-throughput sequencing experiments, the volume of the raw reads is extremely high, frequently exceeding 600 Gb. With an ever increasing demand for storing such reads for future studies, the issue of efficient metagenomic compression becomes of paramount importance. We present the first known approach to metagenome read compression, termed MCUIUC (Metagenomic Compression at UIUC). The gist of the proposed algorithm is to perform classification of reads based on unique organism identifiers, followed by reference-based alignment of reads for individually identified organisms, and metagenomic assembly of unclassified reads. Once assembly and classification are completed, lossless reference based compression is performed via positional encoding. We evaluate the performance of the algorithm on moderate sized synthetic metagenomic samples involving 15 randomly selected organisms and describe future directions for improving the proposed compression method.

q-bio.GN↗

arXiv2013

MetaPar: Metagenomic Sequence Assembly via Iterative Reclassification

We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with low memory usage. The gist of the approach is to iteratively perform read (re)classification based on phylogenetic marker genes and assembler outputs generated from random subsets of metagenomic reads. Once a sufficiently accurate classification within genera is performed, de novo metagenomic assemblers (such as Velvet or IDBA-UD) or reference based assemblers may be used for contig construction. We analyze the performance of MetaPar on synthetic data consisting of 15 randomly chosen species from the NCBI database through the effective gap and effective coverage metrics.

q-bio.QM↗