This letter reports an experimental study aimed at establishing the questionable usefulness of scattering attributes for ship classification from moderate-resolution SAR images. About 2700 example images representing four ship types have been extracted from the OpenSARShip annotated data set and used to form the training and test sets for random forest models. After importance ranking and cross-validation, different subsets of both geometric and scattering attributes were selected from a fixed training set and used to train the classifier. The results from the validation using the test sets show that the scattering attributes give a significant contribution in terms of overall classification accuracy.

A method and a stand-alone Python code to estimate the 3D chromatin structure from chromosome conformation capture data are presented. The method is based on a multiresolution, modified-bead-chain chromatin model, evolved through quaternion operators in a Monte Carlo sampling. The solution space to be sampled is generated by a score function with a data-fit part and a constraint part where the available prior knowledge is implicitly coded. The final solution is a set of 3D configurations that are compatible with both the data and the prior knowledge. The iterative code, provided here as additional material, is equipped with a graphical user interface and stores its results in standard-format files for 3D visualization. We describe the mathematical-computational aspects of the method and explain the details of the code. Some experimental results are reported, with a demonstration of their fit to the data.

We present a method to infer 3D chromatin configurations from Chromosome Conformation Capture data. Quite a few methods have been proposed to estimate the structure of the nuclear dna in homogeneous populations of cells from this kind of data. Many of them transform contact frequencies into euclidean distances between pairs of chromatin fragments, and then reconstruct the structure by solving a distance-to-geometry problem. To avoid inconsistencies, our method is based on a score function that does not require any frequency-to-distance translation. We propose a multiscale chromatin model where the chromatin fiber is suitably partitioned at each scale. The partial structures are estimated independently, and connected to rebuild the whole fiber. Our score function consists of a data-fit part and a penalty part, balanced automatically at each scale and each subchain. The penalty part enforces soft geometric constraints. As many different structures can fit the data, our sampling strategy produces a set of solutions with similar scores. The procedure contains a few parameters, independent of both the scale and the genomic segment treated. The partition of the fiber, along with intrinsically parallel parts, make this method computationally efficient. Results from human genome data support the biological plausibility of our solutions.

Bleed-through is a pervasive degradation in ancient documents, caused by the ink of the opposite side of the sheet that has seeped through the paper fiber, and appears as an extra, interfering text. Bleed-through severely impairs document readability and makes it difficult to decipher the contents. Digital image restoration techniques have been successfully employed to remove or significantly reduce this distortion. The main theme is to identify the bleedthrough pixels and estimate an appropriate replacement for them, in accordance to their surrounding. This paper proposes a two-step image restoration method, exploiting information from the recto and verso images. First, based on a non-stationary linear model of the two texts overlapped in the recto-verso pair, the bleed through pixels are identified. In the second step, a sparse representation based image inpainting technique, with a non-negative sparsity constraint, is used to find an appropriate replacement for the bleedthough pixels. Thanks to the power of dictionary learning and sparse image reconstruction methods, the natural texture of the background is well reproduced in the bleed-through areas, and even a their possible overestimation is effectively corrected, so that the original appearance of the document is preserved. The experiments are conducted on the images of a popular database of ancient documents, and the results validate the performance of the proposed method compared to the state of the art.

We present a parallelizzable, multilevel algorithm for the study of three-dimensional structure of biological macromolecules, applied to two fundamental topics: the 3D reconstruction of Chromatin and the elaboration of motion of proteins. For Chromatin, starting from contact data obtained through Chromosome Conformation Capture techniques, our method first subdivides the data matrix in biologically relevant blocks, and then treats them separately, at several levels, depending on the initial data resolution. The result is a family of configurations for the entire fiber, each one compatible with both experimental data and prior knowledge about specific genomes. For Proteins, the method is conceived as a solution for the problem of identifying motion and alternative conformations to the deposited structures. The algorithm, using quaternions, processes the main chain and the aminoacid side chian independently; it then exploits a Monte Carlo method for selection of biologically acceptable conformations, based on energy evaluation, and finally returns a family of conformations and of trajectories at single atom resolution.

BACKGROUND: The knowledge of the spatial organisation of the chromatin fibre in cell nuclei helps researchers to understand the nuclear machinery that regulates DNA activity. Recent experimental techniques of the type Chromosome Conformation Capture (3C, or similar) provide high-resolution, high-throughput data consisting in the number of times any possible pair of DNA fragments is found to be in contact, in a certain population of cells. As these data carry information on the structure of the chromatin fibre, several attempts have been made to use them to obtain high-resolution 3D reconstructions of entire chromosomes, or even an entire genome. The techniques proposed treat the data in different ways, possibly exploiting physical-geometric chromatin models. One popular strategy is to transform contact data into Euclidean distances between pairs of fragments, and then solve a classical distance-to-geometry problem. RESULTS: We developed and tested a reconstruction technique that does not require translating contacts into distances, thus avoiding a number of related drawbacks. Also, we introduce a geometrical chromatin chain model that allows us to include sound biochemical and biological constraints in the problem. This model can be scaled at different genomic resolutions, where the structures of the coarser models are influenced by the reconstructions at finer resolutions. The search in the solution space is then performed by a classical simulated annealing, where the model is evolved efficiently through quaternion operators. The presence of appropriate constraints permits the less reliable data to be overlooked, so the result is a set of plausible chromatin configurations compatible with both the data and the prior knowledge. CONCLUSIONS: To test our method, we obtained a number of 3D chromatin configurations from Hi-C data available in the literature for the long arm of human chromosome 1, and validated their features against known properties of gene density and transcriptional activity. Our results are compatible with biological features not introduced a priori in the problem: structurally different regions in our reconstructions highly correlate with functionally different regions as known from literature and genomic repositories.

In this paper we review a maximum a posteriori (MAP) approach detection method in a Bayesian scheme which incorporates prior information about the source flux distribution, the locations and the number of sources of extragalactic point sources in images of the Cosmic Microwave Background. This new technique allows us to obtain fast solutions and to fix the number of detected sources in a non-arbitrary way. The performance of the method is superior to that of the standard frequentist approach based on the matched filter.

We propose to model the image differentials of astrophysical source maps by Student's t-distribution and to use them in the Bayesian source separation method as priors. We introduce an efficient Markov Chain Monte Carlo (MCMC) sampling scheme to unmix the astrophysical sources and describe the derivation details. In this scheme, we use the Langevin stochastic equation for transitions, which enables parallel drawing of random samples from the posterior, and reduces the computation time significantly (by two orders of magnitude). In addition, Student's t-distribution parameters are updated throughout the iterations. The results on astrophysical source separation are assessed with two performance criteria defined in the pixel and the frequency domains.

We propose a system to process multispectral scans of double-sided documents. It can co-register any number of recto and verso channel maps, and reduce the bleed-through/show-through distortions by exploiting blind source separation. From RGB scans, it is also able to recover the original colors, thus improving the readability of a document while maintaining its original appearance. The recto and verso patterns obtained can then be further analyzed. Many approaches to this problem are based on single-channel or multichannel recto-verso scans. In any case, getting rid of the unwanted interferences is a challenging problem. All the methods relying on pixel intensities, such as the one presented here, need a very accurate co-registration, and this is difficult for recto-verso pairs since the relevant information is often very sparse.

We propose an adaptive Monte Carlo Markov Chain (MCMC) simulation for the Bayesian source separation problem and apply it to the unmixing of astrophysical components. In this method, we use the Langevin stochastic equation for transitions, which enables parallel drawing of random samples from the posterior, and which reduces the computation time significantly (by two orders of magnitude). In addition to this, the parameters of the Markov Random Field (MRF) model are updated via Maximum Likelihood (ML) throughout the iterations.

This paper deals with blind separation of images from noisy linear mixtures with unknown coefficients, formulated as a Bayesian estimation problem. This is a flexible framework, where any kind of prior knowledge about the source images and the mixing matrix can be accounted for. In particular, we describe local correlation within the individual images through the use of Markov random field (MRF) image models. These are naturally suited to express the joint pdf of the sources in a factorized form, so that the statistical independence requirements of most independent component analysis approaches to blind source separation are retained. Our model also includes edge variables to preserve intensity discontinuities. MRF models have been proved to be very efficient in many visual reconstruction problems, such as blind image restoration, and allow separation and edge detection to be performed simultaneously. We propose an expectation-maximization algorithm with the mean field approximation to derive a procedure for estimating the mixing matrix, the sources, and their edge maps. We tested this procedure on both synthetic and real images, in the fully blind case (i.e., no prior information on mixing is exploited) and found that a source model accounting for local autocorrelation is able to increase robustness against noise, even space variant. Furthermore, when the model closely fits the source characteristics, independence is no longer a strict requirement, and cross-correlated sources can be separated, as well.

A microwave sky map results from a combination of signals from various astrophysical sources, such as cosmic microwave background radiation, synchrotron radiation and galactic dust radiation. To derive information about these sources, one needs to separate them from the measured maps on different frequency channels. Our insufficient knowledge of the weights to be given to the individual signals at different frequencies makes this a difficult task. Recent work on the problem led to only limited success due to ignoring the noise and to the lack of a suitable statistical model for the sources. In this paper, we derive the statistical distribution of some source realizations, and check the appropriateness of a Gaussian mixture model for them. A source separation technique, namely, independent factor analysis, has been suggested recently in the literature for Gaussian mixture sources in the presence of noise. This technique employs a three layered neural network architecture which allows a simple, hierarchical treatment of the problem. We modify the algorithm proposed in the literature to accommodate for space-varying noise and test its performance on simulated astrophysical maps. We also compare the performances of an expectation-maximization and a simulated annealing learning algorithm in estimating the mixture matrix and the source model parameters. The problem with expectation-maximization is that it does not ensure global optimization, and thus the choice of the starting point is a critical task. Indeed, we did not succeed to reach good solutions for random initializations of the algorithm. Conversely, our experiments with simulated annealing yielded initialization-independent results. The mixing matrix and the means and coefficients in the source model were estimated with a good accuracy while some of the variances of the components in the mixture model were not estimated satisfactorily.

This paper deals with motion segmentation. We use an active contour method to segment the apparent motion computed from two successive frames of an image sequence. In order to obtain accurate segmentation, we combine both intensity and motion information. We examine two different ways for combination and we show results obtained on a real sequence.