The effect of missing data on robust Bayesian spectral analysis

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.Published in: Machine Learning for Signal Processing (MLSP), 2013 IEEE International Workshop on Date of Conference: 22-25 Sept. 2013We investigate the effects of missing observations on the robust Bayesian model for spectral analysis introduced by Christmas [2013]. The model assumes Student-t distributed noise and uses an automatic relevance determination prior on the precisions of the amplitudes of the component sinusoids and it is not obvious what their effect will be when some of the otherwise temporally uniformly sampled data is missing

Noise and nonlinearities in high-throughput data

High-throughput data analyses are becoming common in biology, communications, economics and sociology. The vast amounts of data are usually represented in the form of matrices and can be considered as knowledge networks. Spectra-based approaches have proved useful in extracting hidden information within such networks and for estimating missing data, but these methods are based essentially on linear assumptions. The physical models of matching, when applicable, often suggest non-linear mechanisms, that may sometimes be identified as noise. The use of non-linear models in data analysis, however, may require the introduction of many parameters, which lowers the statistical weight of the model. According to the quality of data, a simpler linear analysis may be more convenient than more complex approaches. In this paper, we show how a simple non-parametric Bayesian model may be used to explore the role of non-linearities and noise in synthetic and experimental data sets.Comment: 12 pages, 3 figure

Accounting for Calibration Uncertainties in X-ray Analysis: Effective Areas in Spectral Fitting

While considerable advance has been made to account for statistical uncertainties in astronomical analyses, systematic instrumental uncertainties have been generally ignored. This can be crucial to a proper interpretation of analysis results because instrumental calibration uncertainty is a form of systematic uncertainty. Ignoring it can underestimate error bars and introduce bias into the fitted values of model parameters. Accounting for such uncertainties currently requires extensive case-specific simulations if using existing analysis packages. Here we present general statistical methods that incorporate calibration uncertainties into spectral analysis of high-energy data. We first present a method based on multiple imputation that can be applied with any fitting method, but is necessarily approximate. We then describe a more exact Bayesian approach that works in conjunction with a Markov chain Monte Carlo based fitting. We explore methods for improving computational efficiency, and in particular detail a method of summarizing calibration uncertainties with a principal component analysis of samples of plausible calibration files. This method is implemented using recently codified Chandra effective area uncertainties for low-resolution spectral analysis and is verified using both simulated and actual Chandra data. Our procedure for incorporating effective area uncertainty is easily generalized to other types of calibration uncertainties.Comment: 61 pages double spaced, 8 figures, accepted for publication in Ap

DART-ID increases single-cell proteome coverage.

Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce the number of confidently sequenced peptides. To alleviate this reduction, we developed Data-driven Alignment of Retention Times for IDentification (DART-ID). DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches. When applied to bulk or to single-cell samples, DART-ID increased the number of data points by 30-50% at 1% FDR, and thus decreased missing data. Benchmarks indicate excellent quantification of peptides upgraded by DART-ID and support their utility for quantitative analysis, such as identifying cell types and cell-type specific proteins. The additional datapoints provided by DART-ID boost the statistical power and double the number of proteins identified as differentially abundant in monocytes and T-cells. DART-ID can be applied to diverse experimental designs and is freely available at http://dart-id.slavovlab.net

Recognition of Harmonic Sounds in Polyphonic Audio using a Missing Feature Approach: Extended Report

A method based on local spectral features and missing feature techniques is proposed for the recognition of harmonic sounds in mixture signals. A mask estimation algorithm is proposed for identifying spectral regions that contain reliable information for each sound source and then bounded marginalization is employed to treat the feature vector elements that are determined as unreliable. The proposed method is tested on musical instrument sounds due to the extensive availability of data but it can be applied on other sounds (i.e. animal sounds, environmental sounds), whenever these are harmonic. In simulations the proposed method clearly outperformed a baseline method for mixture signals

SZ contribution to characterize the shape of galaxy cluster haloes

We present the on-going activity to characterize the geometrical properties of the gas and dark matter haloes using multi-wavelength observations of galaxy clusters. The role of the SZ signal in describing the gas distribution is discussed for the pilot case of the CLASH object MACS J1206.2-0847