A regularized nonnegative canonical polyadic decomposition algorithm with preprocessing for 3D fluorescence spectroscopy

International audienceWe consider blind source separation in chemical analysis focussing on the 3D fluorescence spectroscopy framework. We present an alternative method to process the Fluorescence Excitation-Emission Matrices (FEEM): first, a preprocessing is applied to eliminate the Raman and Rayleigh scattering peaks that clutter the FEEM. To improve its robustness versus possible improper settings, we suggest to associate the classical Zepp's method with a morphological image filtering technique. Then, in a second stage, the Canonical Polyadic (CP or Cande-comp/Parafac) decomposition of a nonnegative 3-way array has to be computed. In the fluorescence spectroscopy context, the constituent vectors of the loading matrices should be nonnegative (since standing for spectra and concentrations). Thus, we suggest a new NonNegative third order CP decomposition algorithm (NNCP) based on a non linear conjugate gradient optimisation algorithm with regularization terms and periodic restarts. Computer simulations performed on real experimental data are provided to enlighten the effectiveness and robustness of the whole processing chain and to validate the approach

Nonnegative matrix factorization: a blind spectra separation method for in vivo fluorescent optical imaging

International audienceFluorescence imaging in diffusive media is an emerging imaging modality for medical applications that uses injected fluorescent markers that bind to specific targets, e.g., carcinoma. The region of interest is illuminated with near-IR light and the emitted back fluorescence is analyzed to localize the fluorescence sources. To investigate a thick medium, as the fluorescence signal decreases with the light travel distance, any disturbing signal, such as biological tissues intrinsic fluorescence (called autofluorescence) is a limiting factor. Several specific markers may also be simultaneously injected to bind to different molecules, and one may want to isolate each specific fluorescent signal from the others. To remove the unwanted fluorescence contributions or separate different specific markers, a spectroscopic approach is explored. The nonnegative matrix factorization (NMF) is the blind positive source separation method we chose. We run an original regularized NMF algorithm we developed on experimental data, and successfully obtain separated in vivo fluorescence spectra

In vivo fluorescence spectra unmixing and autofluorescence removal by sparse Non-negative Matrix Factorization

International audienceFluorescence imaging locates fluorescent markers that specifically bind to targets, as tumors: markers are injected to a patient, optimally excited with near infrared light, and located thanks to emitted back fluorescence analysis. To investigate thick and diffusive media, as the fluorescence signal decreases with the light travel distance, the autofluorescence of biological tissues comes to be a limiting factor. To remove autofluorescence and isolate specific fluorescence, a spectroscopic approach, based on Non-negative Matrix Factorization (NMF), is explored. To improve results on spatially sparse markers detection, we suggest a new constrained NMF algorithm which takes sparsity constraints into account. A comparative study between both algorithms is proposed on simulated and in vivo data

Hyperspectral Unmixing Overview: Geometrical, Statistical, and Sparse Regression-Based Approaches

Imaging spectrometers measure electromagnetic energy scattered in their instantaneous field view in hundreds or thousands of spectral channels with higher spectral resolution than multispectral cameras. Imaging spectrometers are therefore often referred to as hyperspectral cameras (HSCs). Higher spectral resolution enables material identification via spectroscopic analysis, which facilitates countless applications that require identifying materials in scenarios unsuitable for classical spectroscopic analysis. Due to low spatial resolution of HSCs, microscopic material mixing, and multiple scattering, spectra measured by HSCs are mixtures of spectra of materials in a scene. Thus, accurate estimation requires unmixing. Pixels are assumed to be mixtures of a few materials, called endmembers. Unmixing involves estimating all or some of: the number of endmembers, their spectral signatures, and their abundances at each pixel. Unmixing is a challenging, ill-posed inverse problem because of model inaccuracies, observation noise, environmental conditions, endmember variability, and data set size. Researchers have devised and investigated many models searching for robust, stable, tractable, and accurate unmixing algorithms. This paper presents an overview of unmixing methods from the time of Keshava and Mustard's unmixing tutorial [1] to the present. Mixing models are first discussed. Signal-subspace, geometrical, statistical, sparsity-based, and spatial-contextual unmixing algorithms are described. Mathematical problems and potential solutions are described. Algorithm characteristics are illustrated experimentally.Comment: This work has been accepted for publication in IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensin

Active Wavelength Selection for Chemical Identification Using Tunable Spectroscopy

Spectrometers are the cornerstone of analytical chemistry. Recent advances in microoptics manufacturing provide lightweight and portable alternatives to traditional spectrometers. In this dissertation, we developed a spectrometer based on Fabry-Perot interferometers (FPIs). A FPI is a tunable (it can only scan one wavelength at a time) optical filter. However, compared to its traditional counterparts such as FTIR (Fourier transform infrared spectroscopy), FPIs provide lower resolution and lower signal-noiseratio (SNR). Wavelength selection can help alleviate these drawbacks. Eliminating uninformative wavelengths not only speeds up the sensing process but also helps improve accuracy by avoiding nonlinearity and noise. Traditional wavelength selection algorithms follow a training-validation process, and thus they are only optimal for the target analyte. However, for chemical identification, the identities are unknown. To address the above issue, this dissertation proposes active sensing algorithms that select wavelengths online while sensing. These algorithms are able to generate analytedependent wavelengths. We envision this algorithm deployed on a portable chemical gas platform that has low-cost sensors and limited computation resources. We develop three algorithms focusing on three different aspects of the chemical identification problems. First, we consider the problem of single chemical identification. We formulate the problem as a typical classification problem where each chemical is considered as a distinct class. We use Bayesian risk as the utility function for wavelength selection, which calculates the misclassification cost between classes (chemicals), and we select the wavelength with the maximum reduction in the risk. We evaluate this approach on both synthesized and experimental data. The results suggest that active sensing outperforms the passive method, especially in a noisy environment. Second, we consider the problem of chemical mixture identification. Since the number of potential chemical mixtures grows exponentially as the number of components increases, it is intractable to formulate all potential mixtures as classes. To circumvent combinatorial explosion, we developed a multi-modal non-negative least squares (MMNNLS) method that searches multiple near-optimal solutions as an approximation of all the solutions. We project the solutions onto spectral space, calculate the variance of the projected spectra at each wavelength, and select the next wavelength using the variance as the guidance. We validate this approach on synthesized and experimental data. The results suggest that active approaches are superior to their passive counterparts especially when the condition number of the mixture grows larger (the analytes consist of more components, or the constituent spectra are very similar to each other). Third, we consider improving the computational speed for chemical mixture identification. MM-NNLS scales poorly as the chemical mixture becomes more complex. Therefore, we develop a wavelength selection method based on Gaussian process regression (GPR). GPR aims to reconstruct the spectrum rather than solving the mixture problem, thus, its computational cost is a function of the number of wavelengths. We evaluate the approach on both synthesized and experimental data. The results again demonstrate more accurate and robust performance in contrast to passive algorithms

An investigation of the utility of monaural sound source separation via nonnegative matrix factorization applied to acoustic echo and reverberation mitigation for hands-free telephony

In this thesis we investigate the applicability and utility of Monaural Sound Source Separation (MSSS) via Nonnegative Matrix Factorization (NMF) for various problems related to audio for hands-free telephony. We first investigate MSSS via NMF as an alternative acoustic echo reduction approach to existing approaches such as Acoustic Echo Cancellation (AEC). To this end, we present the single-channel acoustic echo problem as an MSSS problem, in which the objective is to extract the users signal from a mixture also containing acoustic echo and noise. To perform separation, NMF is used to decompose the near-end microphone signal onto the union of two nonnegative bases in the magnitude Short Time Fourier Transform domain. One of these bases is for the spectral energy of the acoustic echo signal, and is formed from the in- coming far-end user’s speech, while the other basis is for the spectral energy of the near-end speaker, and is trained with speech data a priori. In comparison to AEC, the speaker extraction approach obviates Double-Talk Detection (DTD), and is demonstrated to attain its maximal echo mitigation performance immediately upon initiation and to maintain that performance during and after room changes for similar computational requirements. Speaker extraction is also shown to introduce distortion of the near-end speech signal during double-talk, which is quantified by means of a speech distortion measure and compared to that of AEC. Subsequently, we address Double-Talk Detection (DTD) for block-based AEC algorithms. We propose a novel block-based DTD algorithm that uses the available signals and the estimate of the echo signal that is produced by NMF-based speaker extraction to compute a suitably normalized correlation-based decision variable, which is compared to a fixed threshold to decide on doubletalk. Using a standard evaluation technique, the proposed algorithm is shown to have comparable detection performance to an existing conventional block-based DTD algorithm. It is also demonstrated to inherit the room change insensitivity of speaker extraction, with the proposed DTD algorithm generating minimal false doubletalk indications upon initiation and in response to room changes in comparison to the existing conventional DTD. We also show that this property allows its paired AEC to converge at a rate close to the optimum. Another focus of this thesis is the problem of inverting a single measurement of a non- minimum phase Room Impulse Response (RIR). We describe the process by which percep- tually detrimental all-pass phase distortion arises in reverberant speech filtered by the inverse of the minimum phase component of the RIR; in short, such distortion arises from inverting the magnitude response of the high-Q maximum phase zeros of the RIR. We then propose two novel partial inversion schemes that precisely mitigate this distortion. One of these schemes employs NMF-based MSSS to separate the all-pass phase distortion from the target speech in the magnitude STFT domain, while the other approach modifies the inverse minimum phase filter such that the magnitude response of the maximum phase zeros of the RIR is not fully compensated. Subjective listening tests reveal that the proposed schemes generally produce better quality output speech than a comparable inversion technique

An investigation of the utility of monaural sound source separation via nonnegative matrix factorization applied to acoustic echo and reverberation mitigation for hands-free telephony

In this thesis we investigate the applicability and utility of Monaural Sound Source Separation (MSSS) via Nonnegative Matrix Factorization (NMF) for various problems related to audio for hands-free telephony. We first investigate MSSS via NMF as an alternative acoustic echo reduction approach to existing approaches such as Acoustic Echo Cancellation (AEC). To this end, we present the single-channel acoustic echo problem as an MSSS problem, in which the objective is to extract the users signal from a mixture also containing acoustic echo and noise. To perform separation, NMF is used to decompose the near-end microphone signal onto the union of two nonnegative bases in the magnitude Short Time Fourier Transform domain. One of these bases is for the spectral energy of the acoustic echo signal, and is formed from the in- coming far-end user’s speech, while the other basis is for the spectral energy of the near-end speaker, and is trained with speech data a priori. In comparison to AEC, the speaker extraction approach obviates Double-Talk Detection (DTD), and is demonstrated to attain its maximal echo mitigation performance immediately upon initiation and to maintain that performance during and after room changes for similar computational requirements. Speaker extraction is also shown to introduce distortion of the near-end speech signal during double-talk, which is quantified by means of a speech distortion measure and compared to that of AEC. Subsequently, we address Double-Talk Detection (DTD) for block-based AEC algorithms. We propose a novel block-based DTD algorithm that uses the available signals and the estimate of the echo signal that is produced by NMF-based speaker extraction to compute a suitably normalized correlation-based decision variable, which is compared to a fixed threshold to decide on doubletalk. Using a standard evaluation technique, the proposed algorithm is shown to have comparable detection performance to an existing conventional block-based DTD algorithm. It is also demonstrated to inherit the room change insensitivity of speaker extraction, with the proposed DTD algorithm generating minimal false doubletalk indications upon initiation and in response to room changes in comparison to the existing conventional DTD. We also show that this property allows its paired AEC to converge at a rate close to the optimum. Another focus of this thesis is the problem of inverting a single measurement of a non- minimum phase Room Impulse Response (RIR). We describe the process by which percep- tually detrimental all-pass phase distortion arises in reverberant speech filtered by the inverse of the minimum phase component of the RIR; in short, such distortion arises from inverting the magnitude response of the high-Q maximum phase zeros of the RIR. We then propose two novel partial inversion schemes that precisely mitigate this distortion. One of these schemes employs NMF-based MSSS to separate the all-pass phase distortion from the target speech in the magnitude STFT domain, while the other approach modifies the inverse minimum phase filter such that the magnitude response of the maximum phase zeros of the RIR is not fully compensated. Subjective listening tests reveal that the proposed schemes generally produce better quality output speech than a comparable inversion technique