Spectral Dictionaries Research Articles

Total Utility Metric Based Dictionary Pruning for Sparse Hyperspectral Unmixing

Given a spectral library, sparse unmixing aims to estimate the fractional proportions in each pixel of a hyperspectral image scene. However, the ever-growing dimensionality of spectral dictionaries strongly limits the performance of sparse unmixing algorithms. In this study, we propose a novel dictionary pruning (DP) approach to improve the performance of sparse unmixing algorithms, making them more accurate and time-efficient. We quantify the relative importance of each spectral dictionary atom using the total utility metric at virtually no cost. In this way, we have quantitative insights into how well the elements in the dictionary represent the hyperspectral scene. We evaluate the performance of the proposed dictionary pruning approach on several simulated data sets and one real data. We also compare the experimental results with two well-known dictionary pruning methods both visually and quantitatively and demonstrate the superiority of our proposed method through extensive experimental analysis.

Learning of robust spectral graph dictionaries for distributed processing

We consider the problem of distributed representation of signals in sensor networks, where sensors exchange quantized information with their neighbors. The signals of interest are assumed to have a sparse representation with spectral graph dictionaries. We further model the spectral dictionaries as polynomials of the graph Laplacian operator. We first study the impact of the quantization noise in the distributed computation of matrix-vector multiplications, such as the forward and the adjoint operator, which are used in many classical signal processing tasks. It occurs that the performance is clearly penalized by the quantization noise, whose impact directly depends on the structure of the spectral graph dictionary. Next, we focus on the problem of sparse signal representation and propose an algorithm to learn polynomial graph dictionaries that are both adapted to the graph signals of interest and robust to quantization noise. Simulation results show that the learned dictionaries are efficient in processing graph signals in sensor networks where bandwidth constraints impose quantization of the messages exchanged in the network.

Binaural Localization of Multiple Sound Sources by Non-Negative Tensor Factorization

This paper presents non-negative factorization of audio signals for the binaural localization of multiple sound sources within realistic and unknown sound environments. Non-negative tensor factorization (NTF) provides a sparse representation of multichannel audio signals in time, frequency, and space that can be exploited in computational audio scene analysis and robot audition for the separation and localization of sound sources. In the proposed formulation, each sound source is represented by means of spectral dictionaries, temporal activation, and its distribution within each channel (here, left and right ears). This distribution, being dependent on the frequency, can be interpreted as an explicit estimation of the Head-Related Transfer Function (HRTF) of a binaural head which can then be converted into the estimated sound source position. Moreover, the semisupervised formulation of the non-negative factorization allows us to integrate prior knowledge about some sound sources of interest whose dictionaries can be learned in advance, whereas the remaining sources are considered as background sound, which remains unknown and is estimated on the fly. The proposed NTF-based sound source localization is applied here to binaural sound source localization of multiple speakers within realistic sound environments.

A Dynamic Unmixing Framework for Plant Production System Monitoring

Hyperspectral remote sensing or imaging spectroscopy is an emerging technology in plant production monitoring and management. The continuous reflectance spectra allow for the intensive monitoring of biophysical and biochemical tree characteristics during growth, through for instance the use of vegetation indices. Yet, since most of the pixels in hyperspectral images are mixed, the evaluation of the actual vegetation state on the ground directly from the measured spectra is degraded by the presence of other endmembers, such as soil. Spectral unmixing, then, becomes a necessary processing step to improve the interpretation of vegetation indices. In this sense, an active research direction is based on the use of large collections of pure spectra, called spectral libraries or dictionaries, which model a wide variety of possible states of the endmembers of interest on the ground, i.e., vegetation and soil. Under the linear mixing model (LMM), the observed spectra are assumed to be linear combinations of spectra from the available dictionary. Combinatorial techniques (e.g., MESMA) and sparse regression algorithms (e.g., SUnSAL) are widely used to tackle the unmixing problem in this case. However, both combinatorial and sparse techniques benefit from appropriate library reduction strategies. In this paper, we develop a new efficient method for library reduction (or dictionary pruning), which exploits the fact that hyperspectral data generally lives in a lower-dimensional subspace. Specifically, we present a slight modification of the MUSIC-CSR algorithm, a two-step method which aims first at pruning the dictionary and second at infering high-quality reconstruction of the vegetation spectra on the ground (this application being called signal unmixing in remote sensing), using the pruned dictionary as input to available unmixing methods. Our goal is two-fold: 1) to obtain high-accuracy unmixing output using sparse unmixing, with low-execution time; and 2) to improve MESMA performances in terms of accuracy. Our experiments, which have been conducted in a multi-temporal case study, show that the method achieves these two goals and proposes sparse unmixing as a reliable and robust alternative to the combinatorial methods in plant production monitoring applications. We further demonstrate that the proposed methodology of combining a library pruning approach with spectral unmixing provides a solid framework for the year-round monitoring of plant production systems.

Peptide Identification by Database Search of Mixture Tandem Mass Spectra

In high-throughput proteomics the development of computational methods and novel experimental strategies often rely on each other. In certain areas, mass spectrometry methods for data acquisition are ahead of computational methods to interpret the resulting tandem mass spectra. Particularly, although there are numerous situations in which a mixture tandem mass spectrum can contain fragment ions from two or more peptides, nearly all database search tools still make the assumption that each tandem mass spectrum comes from one peptide. Common examples include mixture spectra from co-eluting peptides in complex samples, spectra generated from data-independent acquisition methods, and spectra from peptides with complex post-translational modifications. We propose a new database search tool (MixDB) that is able to identify mixture tandem mass spectra from more than one peptide. We show that peptides can be reliably identified with up to 95% accuracy from mixture spectra while considering only a 0.01% of all possible peptide pairs (four orders of magnitude speedup). Comparison with current database search methods indicates that our approach has better or comparable sensitivity and precision at identifying single-peptide spectra while simultaneously being able to identify 38% more peptides from mixture spectra at significantly higher precision.

Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra

Generating all plausible de novo interpretations of a peptide tandem mass (MS/MS) spectrum (Spectral Dictionary) and quickly matching them against the database represent a recently emerged alternative approach to peptide identification. However, the sizes of the Spectral Dictionaries quickly grow with the peptide length making their generation impractical for long peptides. We introduce Gapped Spectral Dictionaries (all plausible de novo interpretations with gaps) that can be easily generated for any peptide length thus addressing the limitation of the Spectral Dictionary approach. We show that Gapped Spectral Dictionaries are small thus opening a possibility of using them to speed-up MS/MS searches. Our MS-Gapped-Dictionary algorithm (based on Gapped Spectral Dictionaries) enables proteogenomics applications (such as searches in the six-frame translation of the human genome) that are prohibitively time consuming with existing approaches. MS-Gapped-Dictionary generates gapped peptides that occupy a niche between accurate but short peptide sequence tags and long but inaccurate full length peptide reconstructions. We show that, contrary to conventional wisdom, some high-quality spectra do not have good peptide sequence tags and introduce gapped tags that have advantages over the conventional peptide sequence tags in MS/MS database searches.

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search

Recent emergence of new mass spectrometry techniques (e.g. electron transfer dissociation, ETD) and improved availability of additional proteases (e.g. Lys-N) for protein digestion in high-throughput experiments raised the challenge of designing new algorithms for interpreting the resulting new types of tandem mass (MS/MS) spectra. Traditional MS/MS database search algorithms such as SEQUEST and Mascot were originally designed for collision induced dissociation (CID) of tryptic peptides and are largely based on expert knowledge about fragmentation of tryptic peptides (rather than machine learning techniques) to design CID-specific scoring functions. As a result, the performance of these algorithms is suboptimal for new mass spectrometry technologies or nontryptic peptides. We recently proposed the generating function approach (MS-GF) for CID spectra of tryptic peptides. In this study, we extend MS-GF to automatically derive scoring parameters from a set of annotated MS/MS spectra of any type (e.g. CID, ETD, etc.), and present a new database search tool MS-GFDB based on MS-GF. We show that MS-GFDB outperforms Mascot for ETD spectra or peptides digested with Lys-N. For example, in the case of ETD spectra, the number of tryptic and Lys-N peptides identified by MS-GFDB increased by a factor of 2.7 and 2.6 as compared with Mascot. Moreover, even following a decade of Mascot developments for analyzing CID spectra of tryptic peptides, MS-GFDB (that is not particularly tailored for CID spectra or tryptic peptides) resulted in 28% increase over Mascot in the number of peptide identifications. Finally, we propose a statistical framework for analyzing multiple spectra from the same precursor (e.g. CID/ETD spectral pairs) and assigning p values to peptide-spectrum-spectrum matches.

Spectral Dictionaries: Integrating de novo Peptide Sequencing with Database Search of Tandem Mass Spectra

Database search tools identify peptides by matching tandem mass spectra against a protein database. We study an alternative approach when all plausible de novo interpretations of a spectrum (spectral dictionary) are generated and then quickly matched against the database. We present a new MS-Dictionary algorithm for efficiently generating spectral dictionaries and demonstrate that MS-Dictionary can identify spectra that are missed in the database search. We argue that MS-Dictionary enables proteogenomics searches in six-frame translation of genomic sequences that may be prohibitively time-consuming for existing database search approaches. We show that such searches allow one to correct sequencing errors and find programmed frameshifts.