arXiv subjects

Thomas Oberlin

Publications and source records attributed to Thomas Oberlin.

32 records · Page 2Linked to original sources

arXiv2020

Compartment model-based nonlinear unmixing for kinetic analysis of dynamic PET images

When no arterial input function is available, quantification of dynamic PET images requires a previous step devoted to the extraction of a reference time-activity curve (TAC). Factor analysis is often applied for this purpose. This paper introduces a novel approach that conducts a new kind of nonlinear factor analysis relying on a compartment model, and computes the kinetic parameters of specific binding tissues jointly. To this end, it capitalizes on data-driven parametric imaging methods to provide a physical description of the underlying PET data, directly relating the specific binding with the kinetics of the non-specific binding in the corresponding tissues. This characterization is introduced into the factor analysis formulation to yield a novel nonlinear unmixing model designed for PET image analysis. This model also explicitly introduces global kinetic parameters that allow for a direct estimation of the binding potential with respect to the free fractions in each non-specific binding tissue. The performance of the method is evaluated on synthetic and real data to demonstrate its potential interest.

eess.IV↗

arXiv2020

Ordinal Non-negative Matrix Factorization for Recommendation

We introduce a new non-negative matrix factorization (NMF) method for ordinal data, called OrdNMF. Ordinal data are categorical data which exhibit a natural ordering between the categories. In particular, they can be found in recommender systems, either with explicit data (such as ratings) or implicit data (such as quantized play counts). OrdNMF is a probabilistic latent factor model that generalizes Bernoulli-Poisson factorization (BePoF) and Poisson factorization (PF) applied to binarized data. Contrary to these methods, OrdNMF circumvents binarization and can exploit a more informative representation of the data. We design an efficient variational algorithm based on a suitable model augmentation and related to variational PF. In particular, our algorithm preserves the scalability of PF and can be applied to huge sparse datasets. We report recommendation experiments on explicit and implicit datasets, and show that OrdNMF outperforms BePoF and PF applied to binarized data.

cs.LG↗

arXiv2020

Fast reconstruction of atomic-scale STEM-EELS images from sparse sampling

This paper discusses the reconstruction of partially sampled spectrum-images to accelerate the acquisition in scanning transmission electron microscopy (STEM). The problem of image reconstruction has been widely considered in the literature for many imaging modalities, but only a few attempts handled 3D data such as spectral images acquired by STEM electron energy loss spectroscopy (EELS). Besides, among the methods proposed in the microscopy literature, some are fast but inaccurate while others provide accurate reconstruction but at the price of a high computation burden. Thus none of the proposed reconstruction methods fulfills our expectations in terms of accuracy and computation complexity. In this paper, we propose a fast and accurate reconstruction method suited for atomic-scale EELS. This method is compared to popular solutions such as beta process factor analysis (BPFA) which is used for the first time on STEM-EELS images. Experiments based on real as synthetic data will be conducted.

eess.IV↗

arXiv2020

Simulated JWST datasets for multispectral and hyperspectral image fusion

This paper aims at providing a comprehensive framework to generate an astrophysical scene and to simulate realistic hyperspectral and multispectral data acquired by two JWST instruments, namely NIRCam Imager and NIRSpec IFU. We want to show that this simulation framework can be resorted to assess the benefits of fusing these images to recover an image of high spatial and spectral resolutions. To do so, we create a synthetic scene associated with a canonical infrared source, the Orion Bar. This scene combines pre-existing modelled spectra provided by the JWST Early Release Science Program 1288 and real high resolution spatial maps from the Hubble space and ALMA telescopes. We develop forward models including corresponding noises for the two JWST instruments based on their technical designs and physical features. JWST observations are then simulated by applying the forward models to the aforementioned synthetic scene. We test a dedicated fusion algorithm we developed on these simulated observations. We show the fusion process reconstructs the high spatio-spectral resolution scene with a good accuracy on most areas, and we identify some limitations of the method to be tackled in future works. The synthetic scene and observations presented in the paper are made publicly available and can be used for instance to evaluate instrument models (aboard the JWST or on the ground), pipelines, or more sophisticated algorithms dedicated to JWST data analysis. Besides, fusion methods such as the one presented in this paper are shown to be promising tools to fully exploit the unprecedented capabilities of the JWST.

astro-ph.IM↗

arXiv2019

Hyperspectral and multispectral image fusion under spectrally varying spatial blurs -- Application to high dimensional infrared astronomical imaging

Hyperspectral imaging has become a significant source of valuable data for astronomers over the past decades. Current instrumental and observing time constraints allow direct acquisition of multispectral images, with high spatial but low spectral resolution, and hyperspectral images, with low spatial but high spectral resolution. To enhance scientific interpretation of the data, we propose a data fusion method which combines the benefits of each image to recover a high spatio-spectral resolution datacube. The proposed inverse problem accounts for the specificities of astronomical instruments, such as spectrally variant blurs. We provide a fast implementation by solving the problem in the frequency domain and in a low-dimensional subspace to efficiently handle the convolution operators as well as the high dimensionality of the data. We conduct experiments on a realistic synthetic dataset of simulated observation of the upcoming James Webb Space Telescope, and we show that our fusion algorithm outperforms state-of-the-art methods commonly used in remote sensing for Earth observation.

cs.CV↗

arXiv2019

Coupled dictionary learning for unsupervised change detection between multi-sensor remote sensing images

Archetypal scenarios for change detection generally consider two images acquired through sensors of the same modality. However, in some specific cases such as emergency situations, the only images available may be those acquired through sensors of different modalities. This paper addresses the problem of unsupervisedly detecting changes between two observed images acquired by sensors of different modalities with possibly different resolutions. These sensor dissimilarities introduce additional issues in the context of operational change detection that are not addressed by most of the classical methods. This paper introduces a novel framework to effectively exploit the available information by modelling the two observed images as a sparse linear combination of atoms belonging to a pair of coupled overcomplete dictionaries learnt from each observed image. As they cover the same geographical location, codes are expected to be globally similar, except for possible changes in sparse spatial locations. Thus, the change detection task is envisioned through a dual code estimation which enforces spatial sparsity in the difference between the estimated codes associated with each image. This problem is formulated as an inverse problem which is iteratively solved using an efficient proximal alternating minimization algorithm accounting for nonsmooth and nonconvex functions. The proposed method is applied to real images with simulated yet realistic and real changes. A comparison with state-of-the-art change detection methods evidences the accuracy of the proposed strategy.

eess.IV↗

arXiv2019

Recommendation from Raw Data with Adaptive Compound Poisson Factorization

Count data are often used in recommender systems: they are widespread (song play counts, product purchases, clicks on web pages) and can reveal user preference without any explicit rating from the user. Such data are known to be sparse, over-dispersed and bursty, which makes their direct use in recommender systems challenging, often leading to pre-processing steps such as binarization. The aim of this paper is to build recommender systems from these raw data, by means of the recently proposed compound Poisson Factorization (cPF). The paper contributions are three-fold: we present a unified framework for discrete data (dcPF), leading to an adaptive and scalable algorithm; we show that our framework achieves a trade-off between Poisson Factorization (PF) applied to raw and binarized data; we study four specific instances that are relevant to recommendation and exhibit new links with combinatorics. Experiments with three different datasets show that dcPF is able to effectively adjust to over-dispersion, leading to better recommendation scores when compared with PF on either raw or binarized data.

cs.IR↗

arXiv2019

Factor analysis of dynamic PET images: beyond Gaussian noise

Factor analysis has proven to be a relevant tool for extracting tissue time-activity curves (TACs) in dynamic PET images, since it allows for an unsupervised analysis of the data. Reliable and interpretable results are possible only if considered with respect to suitable noise statistics. However, the noise in reconstructed dynamic PET images is very difficult to characterize, despite the Poissonian nature of the count-rates. Rather than explicitly modeling the noise distribution, this work proposes to study the relevance of several divergence measures to be used within a factor analysis framework. To this end, the $β$-divergence, widely used in other applicative domains, is considered to design the data-fitting term involved in three different factor models. The performances of the resulting algorithms are evaluated for different values of $β$, in a range covering Gaussian, Poissonian and Gamma-distributed noises. The results obtained on two different types of synthetic images and one real image show the interest of applying non-standard values of $β$ to improve factor analysis.

eess.IV↗

arXiv2018

Reconstruction of partially sampled multi-band images - Application to STEM-EELS imaging

Electron microscopy has shown to be a very powerful tool to map the chemical nature of samples at various scales down to atomic resolution. However, many samples can not be analyzed with an acceptable signal-to-noise ratio because of the radiation damage induced by the electron beam. This is particularly crucial for electron energy loss spectroscopy (EELS) which acquires spectral-spatial data and requires high beam intensity. Since scanning transmission electron microscopes (STEM) are able to acquire data cubes by scanning the electron probe over the sample and recording a spectrum for each spatial position, it is possible to design the scan pattern and to sample only specific pixels. As a consequence, partial acquisition schemes are now conceivable, provided a reconstruction of the full data cube is conducted as a post-processing step. This paper proposes two reconstruction algorithms for multi-band images acquired by STEM-EELS which exploits the spectral structure and the spatial smoothness of the image. The performance of the proposed schemes is illustrated thanks to experiments conducted on a realistic phantom dataset as well as real EELS spectrum-images.

eess.IV↗

arXiv2018

Negative Binomial Matrix Factorization for Recommender Systems

We introduce negative binomial matrix factorization (NBMF), a matrix factorization technique specially designed for analyzing over-dispersed count data. It can be viewed as an extension of Poisson matrix factorization (PF) perturbed by a multiplicative term which models exposure. This term brings a degree of freedom for controlling the dispersion, making NBMF more robust to outliers. We show that NBMF allows to skip traditional pre-processing stages, such as binarization, which lead to loss of information. Two estimation approaches are presented: maximum likelihood and variational Bayes inference. We test our model with a recommendation task and show its ability to predict user tastes with better precision than PF.

cs.LG↗

arXiv2017

Unmixing dynamic PET images with variable specific binding kinetics

To analyze dynamic positron emission tomography (PET) images, various generic multivariate data analysis techniques have been considered in the literature, such as principal component analysis (PCA), independent component analysis (ICA), factor analysis and nonnegative matrix factorization (NMF). Nevertheless, these conventional approaches neglect any possible nonlinear variations in the time activity curves describing the kinetic behavior of tissues with specific binding, which limits their ability to recover a reliable, understandable and interpretable description of the data. This paper proposes an alternative analysis paradigm that accounts for spatial fluctuations in the exchange rate of the tracer between a free compartment and a specifically bound ligand compartment. The method relies on the concept of linear unmixing, usually applied on the hyperspectral domain, which combines NMF with a sum-to-one constraint that ensures an exhaustive description of the mixtures. The spatial variability of the signature corresponding to the specific binding tissue is explicitly modeled through a perturbed component. The performance of the method is assessed on both synthetic and real data and is shown to compete favorably when compared to other conventional analysis methods. The proposed method improved both factor estimation and proportions extraction for specific binding. Modeling the variability of the specific binding factor has a strong potential impact for dynamic PET image analysis.

cs.CV↗

arXiv2017

EEG reconstruction and skull conductivity estimation using a Bayesian model promoting structured sparsity

M/EEG source localization is an open research issue. To solve it, it is important to have good knowledge of several physical parameters to build a reliable head operator. Amongst them, the value of the conductivity of the human skull has remained controversial. This report introduces a novel hierarchical Bayesian framework to estimate the skull conductivity jointly with the brain activity from the M/EEG measurements to improve the reconstruction quality. A partially collapsed Gibbs sampler is used to draw samples asymptotically distributed according to the associated posterior. The generated samples are then used to estimate the brain activity and the model hyperparameters jointly in a completely unsupervised framework. We use synthetic and real data to illustrate the improvement of the reconstruction. The performance of our method is also compared with two optimization algorithms introduced by Vallaghé \textit{et al.} and Gutierrez \textit{et al.} respectively, showing that our method is able to provide results of similar or better quality while remaining applicable in a wider array of situations.

stat.ME↗

arXiv2015

Bayesian Structured Sparsity Priors for EEG Source Localization Technical Report

This report introduces a new hierarchical Bayesian model for the EEG source localization problem. This model promotes structured sparsity to search for focal brain activity. This sparsity is obtained via a multivariate Bernoulli Laplacian prior assigned to the brain activity approximating an $\ell_{20}$ pseudo norm regularization in a Bayesian framework. A partially collapsed Gibbs sampler is used to draw samples asymptotically distributed according to the posterior associated with the proposed Bayesian model. The generated samples are used to estimate the brain activity and the model hyperparameters jointly in an unsupervised framework. Two different kinds of Metropolis-Hastings moves are introduced to accelerate the convergence of the Gibbs sampler. The first move is based on multiple dipole shifts within each MCMC chain whereas the second one exploits proposals associated with different MCMC chains. We use both synthetic and real data to compare the performance of the proposed method with the weighted $\ell_{21}$ mixed norm regularization and a method based on a multiple sparse prior, showing that our algorithm presents advantages in several scenarios.

stat.ME↗

arXiv2012

The Monogenic Synchrosqueezed Wavelet Transform: A tool for the Decomposition/Demodulation of AM-FM images

The synchrosqueezing method aims at decomposing 1D functions as superpositions of a small number of "Intrinsic Modes", supposed to be well separated both in time and frequency. Based on the unidimensional wavelet transform and its reconstruction properties, the synchrosqueezing transform provides a powerful representation of multicomponent signals in the time-frequency plane, together with a reconstruction of each mode. In this paper, a bidimensional version of the synchrosqueezing transform is defined, by considering a well-adapted extension of the concept of analytic signal to images: the monogenic signal. The natural bidimensional counterpart of the notion of Intrinsic Mode is then the concept of "Intrinsic Monogenic Mode" that we define. Thereafter, we investigate the properties of its associated Monogenic Wavelet Decomposition. This leads to a natural bivariate extension of the Synchrosqueezed Wavelet Transform, for decomposing and processing multicomponent images. Numerical tests validate the effectiveness of the method for different examples.

math.NA↗