Γ -convergence of Onsager–Machlup functionals: I. With applications to maximum a posteriori estimation in Bayesian inverse problems

The Bayesian solution to a statistical inverse problem can be summarised by a mode of the posterior distribution, i.e. a maximum a posteriori (MAP) estimator. The MAP estimator essentially coincides with the (regularised) variational solution to the inverse problem, seen as minimisation of the Onsager–Machlup (OM) functional of the posterior measure. An open problem in the stability analysis of inverse problems is to establish a relationship between the convergence properties of solutions obtained by the variational approach and by the Bayesian approach. To address this problem, we propose a general convergence theory for modes that is based on the Γ-convergence of OM functionals, and apply this theory to Bayesian inverse problems with Gaussian and edge-preserving Besov priors. Part II of this paper considers more general prior distributions.

Graph of graphs analysis for multiplexed data with application to imaging mass cytometry

Imaging Mass Cytometry (IMC) combines laser ablation and mass spectrometry to quantitate metal-conjugated primary antibodies incubated in intact tumor tissue slides. This strategy allows spatially-resolved multiplexing of dozens of simultaneous protein targets with 1μm resolution. Each slide is a spatial assay consisting of high-dimensional multivariate observations (m-dimensional feature space) collected at different spatial positions and capturing data from a single biological sample or even representative spots from multiple samples when using tissue microarrays. Often, each of these spatial assays could be characterized by several regions of interest (ROIs). To extract meaningful information from the multi-dimensional observations recorded at different ROIs across different assays, we propose to analyze such datasets using a two-step graph-based approach. We first construct for each ROI a graph representing the interactions between the m covariates and compute an m dimensional vector characterizing the steady state distribution among features. We then use all these m-dimensional vectors to construct a graph between the ROIs from all assays. This second graph is subjected to a nonlinear dimension reduction analysis, retrieving the intrinsic geometric representation of the ROIs. Such a representation provides the foundation for efficient and accurate organization of the different ROIs that correlates with their phenotypes. Theoretically, we show that when the ROIs have a particular bi-modal distribution, the new representation gives rise to a better distinction between the two modalities compared to the maximum a posteriori (MAP) estimator. We applied our method to predict the sensitivity to PD-1 axis blockers treatment of lung cancer subjects based on IMC data, achieving 97.3% average accuracy on two IMC datasets. This serves as empirical evidence that the graph of graphs approach enables us to integrate multiple ROIs and the intra-relationships between the features at each ROI, giving rise to an informative representation that is strongly associated with the phenotypic state of the entire image.

Graph of graphs analysis for multiplexed data with application to imaging mass cytometry

Hyper spectral imaging, sensor networks, spatial multiplexed proteomics, and spatial transcriptomics assays is a representative subset of distinct technologies from diverse domains of science and engineering that share common data structures. The data in all these modalities consist of high-dimensional multivariate observations (m-dimensional feature space) collected at different spatial positions and therefore can be analyzed using similar computational methodologies. Furthermore, in many studies practitioners collect datasets consisting of multiple spatial assays of this type, each capturing such data from a single biological sample, patient, or hyper spectral image, etc. Each of these spatial assays could be characterized by several regions of interest (ROIs). The focus of this paper is on a particular application, imaging mass cytometry (IMC), which falls into this problem setup. To extract meaningful information from the multi-dimensional observations recorded at different ROIs across different assays, we propose to analyze such datasets using a two-step graph-based approach. We first construct for each ROI a graph representing the interactions between the m covariates and compute an m dimensional vector characterizing the steady state distribution among features. We then use all these m-dimensional vectors to construct a graph between the ROIs from all assays. This second graph is subjected to a nonlinear dimension reduction analysis, retrieving the intrinsic geometric representation of the ROIs. Such a representation provides the foundation for efficient and accurate organization of the different ROIs that correlates with their phenotypes. Theoretically, we show that when the ROIs have a particular bi-modal distribution, the new representation gives rise to a better distinction between the two modalities compared to the maximum a posteriori (MAP) estimator. We applied our method to predict the sensitivity to PD-1 axis blockers treatment of lung cancer subjects based on IMC data, achieving 92% accuracy. This serves as empirical evidence that the graph of graphs approach enables us to integrate multiple ROIs and the intra-relationships between the features at each ROI, giving rise to an informative representation that is strongly associated with the phenotypic state of the entire image. Importantly, this approach is applicable to other modalities such as spatial transcriptomics.Author summaryWe propose a two-step graph-based analyses for high-dimensional multiplexed datasets characterizing ROIs and their inter-relationships. The first step consists of extracting the steady state distribution of the random walk on the graph, which captures the mutual relations between the covariates of each ROI. The second step employs a nonlinear dimensionality reduction on the steady state distributions to construct a map that unravels the intrinsic geometric structure of the ROIs. We show theoretically that when the ROIs have a two-class structure, our method accentuates the distinction between the classes. Particularly, in a setting with Gaussian distribution it outperforms the MAP estimator, implying that the mutual relations between the covariates and spatial coordinates are well captured by the steady state distributions. We apply our method to imaging mass cytometry (IMC). Our analysis provides a representation that facilitates prediction of the sensitivity to PD-1 axis blockers treatment of lung cancer subjects. Particularly, our approach achieves state of the art results with accuracy of 92%.

Despeckling method of ultrasound images using closed-form shrinkage function based on cauchy distribution in wavelet domain

Speckle suppression and elimination are very important to improve the visual quality of ultrasound image and the diagnostic ability of the diseases. An effective technique of image denoising based on discrete wavelet transform is to employ a Bayesian maximum a posteriori (MAP) estimator. To suppress and remove the speckle noise using MAP estimator effectively, it must assign correctly the shrinkage function based on appropriate probability density functions (PDFs) for the wavelet coefficients of logarithmically transformed noise-free ultrasound image and speckle noise. In this paper, we introduce a new closed-form shrinkage function that is an analytical solution of a Bayesian MAP estimator for despeckling of the ultrasound images effectively in wavelet domain. We employ a Cauchy prior and Gaussian PDF to model the wavelet coefficients of logarithmically transformed noise-free ultrasound image and speckle noise, respectively. Firstly, we derive the CauchyShrinkGMAP that is a closed-form shrinkage function. In addition, we estimate the noise variance and parameter of MAP estimator. Next, we evaluate the despeckling performance of wavelet image denoising method using the CauchyShrinkGMAP compared to various despeckling method using median and Wiener filters, hard and soft thresholding and GaussShrinkGMAP and MCMAP3N shrinkage function. The experiment results show that PSNR of new closed-form shrinkage function is highest, MSE is smallest, and the correlation coefficient ([Formula: see text]) and SSIM are closer to one than the other existing image denoising methods for noisy synthetic ultrasound images at different speckle noise levels. Also, experiment results show that ENL of new closed-form shrinkage function is highest and that of EN and SD is smallest than the other existing image denoising methods for noisy real ultrasound image.

An Efficient Algorithm for Reconstruction Images Corrupted by Some Multiplicative Noises

In this paper, we propose a novel hybrid model for restoration of images corrupted by multiplicative noise. Using a MAP estimator, we can derive a functional whose minimizer corresponds to the denoised image we want to recover. The energies studied here are inspired by image restoration with non linear variable exponent [1, 2], and it is a combination of fast growth with respect to low gradient and slow growth when the gradient is large. We study a mathematical framework to prove the well posedness of the minimizer problem and we introduce the associated evolution problem, for which we derive numerical approaches. At last, compared experimental results distinctly demonstrate the superiority of the proposed model, in term of removing some muliplicative noise while preserving the edges and reducing the staircase effect.

SPECKLE REDUCTION IN SAR IMAGES USING A BAYESIAN MULTISCALE APPROACH

Synthetic aperture radar (SAR) images are corrupted by speckles, which influence the interpretation of the images. Therefore, to reduce speckles and obtain reliable information from images, researchers studied different methods. This study proposes a Bayesian multiscale method, to reduce speckles in SAR images. First, it was shown that Laplacian probability density function can capture the characteristics of noise-free curvelet coefficients, and then, a maximum a posteriori (MAP) estimator was designed for estimating them. Comparison of the results obtained with those obtained from conventional speckle filters, such as Lee, Kuan, Frost, and Gamma filters, and also curvelet non-Bayesian despeckling, shows better achievement of the proposed algorithm. For instance, the improvement in different parameters is as follows: ‘noise mean value’ (NMV) 0.24 times, ‘noise standard deviation’ (NSD) 0.34 times, ‘mean square difference’ (MSD) 2.6 times and ‘equivalent number of looks’ (ENL) 0.61 times.