Factor analysis of dynamic PET images

Thanks to its ability to evaluate metabolic functions in tissues from the temporal evolution of a previously injected radiotracer, dynamic positron emission tomography (PET) has become an ubiquitous analysis tool to quantify biological processes. Several quantification techniques from the PET imaging literature require a previous estimation of global time-activity curves (TACs) (herein called \textit{factors}) representing the concentration of tracer in a reference tissue or blood over time. To this end, factor analysis has often appeared as an unsupervised learning solution for the extraction of factors and their respective fractions in each voxel. Inspired by the hyperspectral unmixing literature, this manuscript addresses two main drawbacks of general factor analysis techniques applied to dynamic PET. The first one is the assumption that the elementary response of each tissue to tracer distribution is spatially homogeneous. Even though this homogeneity assumption has proven its effectiveness in several factor analysis studies, it may not always provide a sufficient description of the underlying data, in particular when abnormalities are present. To tackle this limitation, the models herein proposed introduce an additional degree of freedom to the factors related to specific binding. To this end, a spatially-variant perturbation affects a nominal and common TAC representative of the high-uptake tissue. This variation is spatially indexed and constrained with a dictionary that is either previously learned or explicitly modelled with convolutional nonlinearities affecting non-specific binding tissues. The second drawback is related to the noise distribution in PET images. Even though the positron decay process can be described by a Poisson distribution, the actual noise in reconstructed PET images is not expected to be simply described by Poisson or Gaussian distributions. Therefore, we propose to consider a popular and quite general loss function, called the $\beta$-divergence, that is able to generalize conventional loss functions such as the least-square distance, Kullback-Leibler and Itakura-Saito divergences, respectively corresponding to Gaussian, Poisson and Gamma distributions. This loss function is applied to three factor analysis models in order to evaluate its impact on dynamic PET images with different reconstruction characteristics

A Method for Unsupervised Semi-Quantification of Inmunohistochemical Staining with Beta Divergences

In many research laboratories, it is essential to determine the relative expression levels of some proteins of interest in tissue samples. The semi-quantitative scoring of a set of images consists of establishing a scale of scores ranging from zero or one to a maximum number set by the researcher and assigning a score to each image that should represent some predefined characteristic of the IHC staining, such as its intensity. However, manual scoring depends on the judgment of an observer and therefore exposes the assessment to a certain level of bias. In this work, we present a fully automatic and unsupervised method for comparative biomarker quantification in histopathological brightfield images. The method relies on a color separation method that discriminates between two chromogens expressed as brown and blue colors robustly, independent of color variation or biomarker expression level. For this purpose, we have adopted a two-stage stain separation approach in the optical density space. First, a preliminary separation is performed using a deconvolution method in which the color vectors of the stains are determined after an eigendecomposition of the data. Then, we adjust the separation using the non-negative matrix factorization method with beta divergences, initializing the algorithm with the matrices resulting from the previous step. After that, a feature vector of each image based on the intensity of the two chromogens is determined. Finally, the images are annotated using a systematically initialized k-means clustering algorithm with beta divergences. The method clearly defines the initial boundaries of the categories, although some flexibility is added. Experiments for the semi-quantitative scoring of images in five categories have been carried out by comparing the results with the scores of four expert researchers yielding accuracies that range between 76.60% and 94.58%. These results show that the proposed automatic scoring system, which is definable and reproducible, produces consistent results.FEDER / Junta de Andalucía-Consejería de Economía y Conocimiento US-1264994Fondo de Desarrollo (FEDER). Unión Europea PGC2018-096244-B-I00, SAF2016-75442-RMinisterio de Economía, Industria y Competitividad (MINECO). España TEC2017- 82807-

Mineral identification using data-mining in hyperspectral infrared imagery

Les applications de l’imagerie infrarouge dans le domaine de la géologie sont principalement des applications hyperspectrales. Elles permettent entre autre l’identification minérale, la cartographie, ainsi que l’estimation de la portée. Le plus souvent, ces acquisitions sont réalisées in-situ soit à l’aide de capteurs aéroportés, soit à l’aide de dispositifs portatifs. La découverte de minéraux indicateurs a permis d’améliorer grandement l’exploration minérale. Ceci est en partie dû à l’utilisation d’instruments portatifs. Dans ce contexte le développement de systèmes automatisés permettrait d’augmenter à la fois la qualité de l’exploration et la précision de la détection des indicateurs. C’est dans ce cadre que s’inscrit le travail mené dans ce doctorat. Le sujet consistait en l’utilisation de méthodes d’apprentissage automatique appliquées à l’analyse (au traitement) d’images hyperspectrales prises dans les longueurs d’onde infrarouge. L’objectif recherché étant l’identification de grains minéraux de petites tailles utilisés comme indicateurs minéral -ogiques. Une application potentielle de cette recherche serait le développement d’un outil logiciel d’assistance pour l’analyse des échantillons lors de l’exploration minérale. Les expériences ont été menées en laboratoire dans la gamme relative à l’infrarouge thermique (Long Wave InfraRed, LWIR) de 7.7m à 11.8 m. Ces essais ont permis de proposer une méthode pour calculer l’annulation du continuum. La méthode utilisée lors de ces essais utilise la factorisation matricielle non négative (NMF). En utlisant une factorisation du premier ordre on peut déduire le rayonnement de pénétration, lequel peut ensuite être comparé et analysé par rapport à d’autres méthodes plus communes. L’analyse des résultats spectraux en comparaison avec plusieurs bibliothèques existantes de données a permis de mettre en évidence la suppression du continuum. Les expérience ayant menés à ce résultat ont été conduites en utilisant une plaque Infragold ainsi qu’un objectif macro LWIR. L’identification automatique de grains de différents matériaux tels que la pyrope, l’olivine et le quartz a commencé. Lors d’une phase de comparaison entre des approches supervisées et non supervisées, cette dernière s’est montrée plus approprié en raison du comportement indépendant par rapport à l’étape d’entraînement. Afin de confirmer la qualité de ces résultats quatre expériences ont été menées. Lors d’une première expérience deux algorithmes ont été évalués pour application de regroupements en utilisant l’approche FCC (False Colour Composite). Cet essai a permis d’observer une vitesse de convergence, jusqu’a vingt fois plus rapide, ainsi qu’une efficacité significativement accrue concernant l’identification en comparaison des résultats de la littérature. Cependant des essais effectués sur des données LWIR ont montré un manque de prédiction de la surface du grain lorsque les grains étaient irréguliers avec présence d’agrégats minéraux. La seconde expérience a consisté, en une analyse quantitaive comparative entre deux bases de données de Ground Truth (GT), nommée rigid-GT et observed-GT (rigide-GT: étiquet manuel de la région, observée-GT:étiquetage manuel les pixels). La précision des résultats était 1.5 fois meilleur lorsque l’on a utlisé la base de données observed-GT que rigid-GT. Pour les deux dernières epxérience, des données venant d’un MEB (Microscope Électronique à Balayage) ainsi que d’un microscopie à fluorescence (XRF) ont été ajoutées. Ces données ont permis d’introduire des informations relatives tant aux agrégats minéraux qu’à la surface des grains. Les résultats ont été comparés par des techniques d’identification automatique des minéraux, utilisant ArcGIS. Cette dernière a montré une performance prometteuse quand à l’identification automatique et à aussi été utilisée pour la GT de validation. Dans l’ensemble, les quatre méthodes de cette thèse représentent des méthodologies bénéfiques pour l’identification des minéraux. Ces méthodes présentent l’avantage d’être non-destructives, relativement précises et d’avoir un faible coût en temps calcul ce qui pourrait les qualifier pour être utilisée dans des conditions de laboratoire ou sur le terrain.The geological applications of hyperspectral infrared imagery mainly consist in mineral identification, mapping, airborne or portable instruments, and core logging. Finding the mineral indicators offer considerable benefits in terms of mineralogy and mineral exploration which usually involves application of portable instrument and core logging. Moreover, faster and more mechanized systems development increases the precision of identifying mineral indicators and avoid any possible mis-classification. Therefore, the objective of this thesis was to create a tool to using hyperspectral infrared imagery and process the data through image analysis and machine learning methods to identify small size mineral grains used as mineral indicators. This system would be applied for different circumstances to provide an assistant for geological analysis and mineralogy exploration. The experiments were conducted in laboratory conditions in the long-wave infrared (7.7μm to 11.8μm - LWIR), with a LWIR-macro lens (to improve spatial resolution), an Infragold plate, and a heating source. The process began with a method to calculate the continuum removal. The approach is the application of Non-negative Matrix Factorization (NMF) to extract Rank-1 NMF and estimate the down-welling radiance and then compare it with other conventional methods. The results indicate successful suppression of the continuum from the spectra and enable the spectra to be compared with spectral libraries. Afterwards, to have an automated system, supervised and unsupervised approaches have been tested for identification of pyrope, olivine and quartz grains. The results indicated that the unsupervised approach was more suitable due to independent behavior against training stage. Once these results obtained, two algorithms were tested to create False Color Composites (FCC) applying a clustering approach. The results of this comparison indicate significant computational efficiency (more than 20 times faster) and promising performance for mineral identification. Finally, the reliability of the automated LWIR hyperspectral infrared mineral identification has been tested and the difficulty for identification of the irregular grain’s surface along with the mineral aggregates has been verified. The results were compared to two different Ground Truth(GT) (i.e. rigid-GT and observed-GT) for quantitative calculation. Observed-GT increased the accuracy up to 1.5 times than rigid-GT. The samples were also examined by Micro X-ray Fluorescence (XRF) and Scanning Electron Microscope (SEM) in order to retrieve information for the mineral aggregates and the grain’s surface (biotite, epidote, goethite, diopside, smithsonite, tourmaline, kyanite, scheelite, pyrope, olivine, and quartz). The results of XRF imagery compared with automatic mineral identification techniques, using ArcGIS, and represented a promising performance for automatic identification and have been used for GT validation. In overall, the four methods (i.e. 1.Continuum removal methods; 2. Classification or clustering methods for mineral identification; 3. Two algorithms for clustering of mineral spectra; 4. Reliability verification) in this thesis represent beneficial methodologies to identify minerals. These methods have the advantages to be a non-destructive, relatively accurate and have low computational complexity that might be used to identify and assess mineral grains in the laboratory conditions or in the field

Audio source separation for music in low-latency and high-latency scenarios

Aquesta tesi proposa mètodes per tractar les limitacions de les tècniques existents de separació de fonts musicals en condicions de baixa i alta latència. En primer lloc, ens centrem en els mètodes amb un baix cost computacional i baixa latència. Proposem l'ús de la regularització de Tikhonov com a mètode de descomposició de l'espectre en el context de baixa latència. El comparem amb les tècniques existents en tasques d'estimació i seguiment dels tons, que són passos crucials en molts mètodes de separació. A continuació utilitzem i avaluem el mètode de descomposició de l'espectre en tasques de separació de veu cantada, baix i percussió. En segon lloc, proposem diversos mètodes d'alta latència que milloren la separació de la veu cantada, gràcies al modelatge de components específics, com la respiració i les consonants. Finalment, explorem l'ús de correlacions temporals i anotacions manuals per millorar la separació dels instruments de percussió i dels senyals musicals polifònics complexes.Esta tesis propone métodos para tratar las limitaciones de las técnicas existentes de separación de fuentes musicales en condiciones de baja y alta latencia. En primer lugar, nos centramos en los métodos con un bajo coste computacional y baja latencia. Proponemos el uso de la regularización de Tikhonov como método de descomposición del espectro en el contexto de baja latencia. Lo comparamos con las técnicas existentes en tareas de estimación y seguimiento de los tonos, que son pasos cruciales en muchos métodos de separación. A continuación utilizamos y evaluamos el método de descomposición del espectro en tareas de separación de voz cantada, bajo y percusión. En segundo lugar, proponemos varios métodos de alta latencia que mejoran la separación de la voz cantada, gracias al modelado de componentes que a menudo no se toman en cuenta, como la respiración y las consonantes. Finalmente, exploramos el uso de correlaciones temporales y anotaciones manuales para mejorar la separación de los instrumentos de percusión y señales musicales polifónicas complejas.This thesis proposes specific methods to address the limitations of current music source separation methods in low-latency and high-latency scenarios. First, we focus on methods with low computational cost and low latency. We propose the use of Tikhonov regularization as a method for spectrum decomposition in the low-latency context. We compare it to existing techniques in pitch estimation and tracking tasks, crucial steps in many separation methods. We then use the proposed spectrum decomposition method in low-latency separation tasks targeting singing voice, bass and drums. Second, we propose several high-latency methods that improve the separation of singing voice by modeling components that are often not accounted for, such as breathiness and consonants. Finally, we explore using temporal correlations and human annotations to enhance the separation of drums and complex polyphonic music signals

Contributions au traitement des images multivariées

Ce mémoire résume mon activité pédagogique et scientifique en vue de l’obtention de l’habilitation à diriger des recherches

Blind source separation using statistical nonnegative matrix factorization

PhD ThesisBlind Source Separation (BSS) attempts to automatically extract and track a signal of interest in real world scenarios with other signals present. BSS addresses the problem of recovering the original signals from an observed mixture without relying on training knowledge. This research studied three novel approaches for solving the BSS problem based on the extensions of non-negative matrix factorization model and the sparsity regularization methods. 1) A framework of amalgamating pruning and Bayesian regularized cluster nonnegative tensor factorization with Itakura-Saito divergence for separating sources mixed in a stereo channel format: The sparse regularization term was adaptively tuned using a hierarchical Bayesian approach to yield the desired sparse decomposition. The modified Gaussian prior was formulated to express the correlation between different basis vectors. This algorithm automatically detected the optimal number of latent components of the individual source. 2) Factorization for single-channel BSS which decomposes an information-bearing matrix into complex of factor matrices that represent the spectral dictionary and temporal codes: A variational Bayesian approach was developed for computing the sparsity parameters for optimizing the matrix factorization. This approach combined the advantages of both complex matrix factorization (CMF) and variational -sparse analysis. BLIND SOURCE SEPARATION USING STATISTICAL NONNEGATIVE MATRIX FACTORIZATION ii 3) An imitated-stereo mixture model developed by weighting and time-shifting the original single-channel mixture where source signals can be modelled by the AR processes. The proposed mixing mixture is analogous to a stereo signal created by two microphones with one being real and another virtual. The imitated-stereo mixture employed the nonnegative tensor factorization for separating the observed mixture. The separability analysis of the imitated-stereo mixture was derived using Wiener masking. All algorithms were tested with real audio signals. Performance of source separation was assessed by measuring the distortion between original source and the estimated one according to the signal-to-distortion (SDR) ratio. The experimental results demonstrate that the proposed uninformed audio separation algorithms have surpassed among the conventional BSS methods; i.e. IS-cNTF, SNMF and CMF methods, with average SDR improvement in the ranges from 2.6dB to 6.4dB per source.Payap Universit