Iterative Conditional Modes Algorithm Research Articles

MC-SSM: Nonparametric Semantic Image Segmentation With the ICM Algorithm

In the last few years, there has been considerable interest in scene parsing. This task consists of assigning a predefined class label to each pixel (or pre-segmented region) in an image. To best address the complexity challenge of this task, first, we propose a new geometric retrieval strategy to select nearest neighbors from a database containing fully segmented and annotated images. Then, we introduce a novel and simple energy-minimization model. The proposed cost function of this model combines efficiently different global nonparametric semantic likelihood energy terms. These terms are computed from the (pre-)segmented regions of the (query) image and their structural properties (location, texture, color, context, and shape). Different from the traditional approaches, we use a simple and local optimization procedure derived from the iterative conditional modes algorithm to optimize our energy-based model. Experimental results on two challenging datasets: 1) microsoft research Cambridge dataset and 2) Stanford background dataset demonstrate the feasibility and the success of the proposed approach. Compared to existing annotation methods that require training classifiers for each object and learning many parameters, our method is easy to implement, has a few parameters, and combines different criteria.

Improving SAR-Based Urban Change Detection by Combining MAP-MRF Classifier and Nonlocal Means Similarity Weights

In remote sensing change detection, Markov random field (MRF) has been used successfully to model the prior probability using class-labels dependencies. MRF has played an important role in the detection of complex urban changes using optical images. However, the preservation of details in urban change analysis turns out to be a highly complex task if multitemporal SAR images with their speckle are to be used. Here, the ability of MRF to preserve geometric details and to combat speckle effect at the same time becomes questionable. Blob-region phenomenon and fine structures removal are common consequences of the application of traditional MRF-based change detection algorithm. To overcome these limitations, the iterated conditional modes (ICM) framework for the optimization of the maximum a posteriori (MAP-MRF) criterion function is extended to include a nonlocal probability maximization step. This probability model, which characterizes the relationship between pixels' class-labels in a nonlocal scale, has the potential to preserve spatial details and to reduce speckle effects. Two multitemporal SAR datasets were used to assess the proposed algorithm. Experimental results using three density functions [i.e., the log normal (LN), generalized Gaussian (GG), and normal distributions (ND)] have demonstrated the efficiency of the proposed approach in terms of detail preservation and noise suppression. Compared with the traditional MRF algorithm, the proposed approach proved to be less-sensitive to the value of the contextual parameter and the chosen density function. The proposed approach has also shown less sensitivity to the quality of the initial change map when compared with the ICM algorithm.

A Fast Iterated Conditional Modes Algorithm for Water–Fat Decomposition in MRI

Decomposition of water and fat in magnetic resonance imaging (MRI) is important for biomedical research and clinical applications. In this paper, we propose a two-phased approach for the three-point water-fat decomposition problem. Our contribution consists of two components: 1) a background-masked Markov random field (MRF) energy model to formulate the local smoothness of field inhomogeneity; 2) a new iterated conditional modes (ICM) algorithm accounting for high-performance optimization of the MRF energy model. The MRF energy model is integrated with background masking to prevent error propagation of background estimates as well as improve efficiency. The central component of our new ICM algorithm is the stability tracking (ST) mechanism intended to dynamically track iterative stability on pixels so that computation per iteration is performed only on instable pixels. The ST mechanism significantly improves the efficiency of ICM. We also develop a median-based initialization algorithm to provide good initial guesses for ICM iterations, and an adaptive gradient-based scheme for parametric configuration of the MRF model. We evaluate the robust of our approach with high-resolution mouse datasets acquired from 7T MRI.

Discriminação de fitofisionomias de floresta de várzea a partir do algoritmo Iterated Conditional Modes aplicado aos dados SAR/R99 (QUAD-POL/Banda L)

Utilizando-se dados do sensor aerotransportado SAR R99, adquiridos na banda L (1,28 GHz) em amplitude e com quatro polarizações (HH, VV, HV e VH), avaliou-se a distinção de fitofisionomias de floresta de várzea existentes nas Reservas de Desenvolvimento Sustentável Amanã e Mamirauá e áreas adjacentes, com a aplicação do algoritmo Iterated Conditional Modes (ICM) de classificação polarimétrica pontual/contextual. Os resultados mostraram que o uso das distribuições multivariadas em amplitude, conjuntamente com uma banda de textura, produziu classificações de qualidade superior àquelas obtidas com dados polarimétricos uni/bivariados. Esta abordagem permitiu a obtenção de um índice Kappa de 0,8963, discriminando as três classes vegetacionais de interesse, comprovando assim o potencial dos dados do SAR R99 e do algoritmo ICM no mapeamento de florestas de várzea da Amazônia.

A hidden Markov random field model for genome-wide association studies.

Genome-wide association studies (GWAS) are increasingly utilized for identifying novel susceptible genetic variants for complex traits, but there is little consensus on analysis methods for such data. Most commonly used methods include single single nucleotide polymorphism (SNP) analysis or haplotype analysis with Bonferroni correction for multiple comparisons. Since the SNPs in typical GWAS are often in linkage disequilibrium (LD), at least locally, Bonferroni correction of multiple comparisons often leads to conservative error control and therefore lower statistical power. In this paper, we propose a hidden Markov random field model (HMRF) for GWAS analysis based on a weighted LD graph built from the prior LD information among the SNPs and an efficient iterative conditional mode algorithm for estimating the model parameters. This model effectively utilizes the LD information in calculating the posterior probability that an SNP is associated with the disease. These posterior probabilities can then be used to define a false discovery controlling procedure in order to select the disease-associated SNPs. Simulation studies demonstrated the potential gain in power over single SNP analysis. The proposed method is especially effective in identifying SNPs with borderline significance at the single-marker level that nonetheless are in high LD with significant SNPs. In addition, by simultaneously considering the SNPs in LD, the proposed method can also help to reduce the number of false identifications of disease-associated SNPs. We demonstrate the application of the proposed HMRF model using data from a case-control GWAS of neuroblastoma and identify 1 new SNP that is potentially associated with neuroblastoma.

Estimating Kinetic Parameter Maps From Dynamic Contrast-Enhanced MRI Using Spatial Prior Knowledge

Dynamic contrast-enhanced magnetic resonance (DCE-MR) imaging can be used to study microvascular structure in vivo by monitoring the abundance of an injected diffusible contrast agent over time. The resulting spatially resolved intensity-time curves are usually interpreted in terms of kinetic parameters obtained by fitting a pharmacokinetic model to the observed data. Least squares estimates of the highly nonlinear model parameters, however, can exhibit high variance and can be severely biased. As a remedy, we bring to bear spatial prior knowledge by means of a generalized Gaussian Markov random field (GGMRF). By using information from neighboring voxels and computing the maximum a posteriori solution for entire parameter maps at once, both bias and variance of the parameter estimates can be reduced thus leading to smaller root mean square error (RMSE). Since the number of variables gets very big for common image resolutions, sparse solvers have to be employed. To this end, we propose a generalized iterated conditional modes (ICM) algorithm operating on blocks instead of sites which is shown to converge considerably faster than the conventional ICM algorithm. Results on simulated DCE-MR images show a clear reduction of RMSE and variance as well as, in some cases, reduced estimation bias. The mean residual bias (MRB) is reduced on the simulated data as well as for all 37 patients of a prostate DCE-MRI dataset. Using the proposed algorithm, average computation times only increase by a factor of 1.18 (871 ms per voxel) for a Gaussian prior and 1.51 (1.12 s per voxel) for an edge-preserving prior compared to the single voxel approach (740 ms per voxel).

Combining a deformable model and a probabilistic framework for an automatic 3D segmentation of prostate on MRI

Accurate localization and contouring of prostate are crucial issues in prostate cancer diagnosis and/or therapies. Although several semi-automatic and automatic segmentation methods have been proposed, manual expert correction remains necessary. We introduce a new method for automatic 3D segmentation of the prostate gland from magnetic resonance imaging (MRI) scans. A statistical shape model was used as an a priori knowledge, and gray levels distribution was modeled by fitting histogram modes with a Gaussian mixture. Markov fields were used to introduce contextual information regarding voxels' neighborhoods. Final labeling optimization is based on Bayesian a posteriori classification, estimated with the iterative conditional mode algorithm. We compared the accuracy of this method, free from any manual correction, with contours outlined by an expert radiologist. In 12 cases, including prostates with cancer and benign prostatic hypertrophy, the mean Hausdorff distance and overlap ratio were 9.94 mm and 0.83, respectively. This new automatic prostate MRI segmentation method produces satisfactory results, even at prostate's base and apex. The method is computationally feasible and efficient.

Region-Based Classification of Polarimetric SAR Images Using Wishart MRF

The scattering measurements of individual pixels in polarimetric SAR images are affected by speckle; hence, the performance of classification approaches, taking individual pixels as elements, would be damaged. By introducing the spatial relation between adjacent pixels, a novel classification method, taking regions as elements, is proposed using a Markov random field (MRF). In this method, an image is oversegmented into a large amount of rectangular regions first. Then, to use fully the statistical a priori knowledge of the data and the spatial relation of neighboring pixels, a Wishart MRF model, combining the Wishart distribution with the MRF, is proposed, and an iterative conditional mode algorithm is adopted to adjust oversegmentation results so that the shapes of all regions match the ground truth better. Finally, a Wishart-based maximum likelihood, based on regions, is used to obtain a classification map. Real polarimetric images are used in experiments. Compared with the other three frequently used methods, higher accuracy is observed, and classification maps are in better agreement with the initial ground maps, using the proposed method.

Estimating Local Ancestry in Admixed Populations

Large-scale genotyping of SNPs has shown a great promise in identifying markers that could be linked to diseases. One of the major obstacles involved in performing these studies is that the underlying population substructure could produce spurious associations. Population substructure can be caused by the presence of two distinct subpopulations or a single pool of admixed individuals. In this work, we focus on the latter, which is significantly harder to detect in practice. New advances in this research direction are expected to play a key role in identifying loci that are different among different populations and are still associated with a disease. We evaluated current methods for inference of population substructure in such cases and show that they might be quite inaccurate even in relatively simple scenarios. We therefore introduce a new method, LAMP (Local Ancestry in adMixed Populations), which infers the ancestry of each individual at every single-nucleotide polymorphism (SNP). LAMP computes the ancestry structure for overlapping windows of contiguous SNPs and combines the results with a majority vote. Our empirical results show that LAMP is significantly more accurate and more efficient than existing methods for inferring locus-specific ancestries, enabling it to handle large-scale datasets. We further show that LAMP can be used to estimate the individual admixture of each individual. Our experimental evaluation indicates that this extension yields a considerably more accurate estimate of individual admixture than state-of-the-art methods such as STRUCTURE or EIGENSTRAT, which are frequently used for the correction of population stratification in association studies.

Segmentation Framework Based on Label Field Fusion

In this paper, we put forward a novel fusion framework that mixes together label fields instead of observation data as is usually the case. Our framework takes as input two label fields: a quickly estimated and to-be-refined segmentation map and a spatial region map that exhibits the shape of the main objects of the scene. These two label fields are fused together with a global energy function that is minimized with a deterministic iterative conditional mode algorithm. As explained in the paper, the energy function may implement a pure fusion strategy or a fusion-reaction function. In the latter case, a data-related term is used to make the optimization problem well posed. We believe that the conceptual simplicity, the small number of parameters, the use of a simple and fast deterministic optimizer that admits a natural implementation on a parallel architecture are among the main advantages of our approach. Our fusion framework is adapted to various computer vision applications among which are motion segmentation, motion estimation and occlusion detection.

Bayesian Complex Amplitude Estimation and Adaptive Matched Filter Detection in Low-Rank Interference

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We propose a Bayesian method for complex amplitude estimation in low-rank interference. We assume that the received signal follows the generalized multivariate analysis of variance (GMANOVA) patterned-mean structure and is corrupted by low-rank spatially correlated interference and white noise. An iterated conditional modes (ICM) algorithm is developed for estimating the unknown complex signal amplitudes and interference and noise parameters. We also discuss initialization of the ICM algorithm and propose a (non-Bayesian) adaptive-matched-filter (AMF) signal detector that utilizes the ICM estimation results. Numerical simulations demonstrate the performance of the proposed methods. </para>

ALLEVIATION OF AN INDETERMINACY PROBLEM AFFECTING TWO CLASSICAL ITERATIVE IMAGE THRESHOLDING ALGORITHMS

Thresholding algorithms are being increasingly used in a wide variety of disciplines to objectively discern patterns and objects in micrographs, still pictures or remotely-sensed images. Our experience has shown that three common thresholding algorithms exhibit indeterminacy, in that different operator inputs may lead to very different pattern characterizations. A grayscale image of a soil profile is used to illustrate this phenomemon in the case of the intermeans (IM), minimum error (ME), and Besag's iterated conditional modes (ICM) algorithms. For the illustrative example, the IM algorithm depends only weakly on the starting point of the iterative process — it converges to only two adjacent threshold values. In contrast, the ME algorithm converges to 14 different threshold values plus a segmentation that identifies the entire image as dye, and one that identifies none of it as dye. The ICM algorithm converges to an even wider variety of final segmentations, depending on its starting point. A noniterative modification of the IM and ME algorithms is proposed, providing a consistent method for choosing from among a set of apparently equally-valid segmentations.

A peak preserving algorithm for the removal of colored noise from signals

We employ the simulated annealing method in order to restore signals that may contain peaks we wish to preserve but, otherwise, are smooth and buried in colored noise. The problem is formulated as a global optimization one. We propose a piecewise linear model for the noise-free signal that is appropriate for preserving peaks that are often encountered in biomedical or industrial signals. An iterative algorithm is proposed. The restored signal is used to estimate the model parameters that are subsequently used to improve the signal estimation. The algorithm stops when self-consistency has been achieved, i.e., the estimated values of the noise model parameters agree to within the accuracy of their estimation with the parameters used to restore the signal. Application of the method to simulated data with various levels of noise showed that the underlying signal can be restored sufficiently well. The algorithm is also applied to some evoked-response magneto-encephalographic data, as well as to some signals from an automatic industrial inspection problem. Our results are compared with those obtained by using the iterative conditional modes algorithm and shown to be better in terms of preserving the peaks in the signals.

Contextual clustering for analysis of functional MRI data.

We present a contextual clustering procedure for statistical parametric maps (SPM) calculated from time varying three-dimensional images. The algorithm can be used for the detection of neural activations from functional magnetic resonance images (fMRI). An important characteristic of SPM is that the intensity distribution of background (nonactive area) is known whereas the distributions of activation areas are not. The developed contextual clustering algorithm divides an SPM into background and activation areas so that the probability of detecting false activations by chance is controlled, i.e., hypothesis testing is performed. Unlike the much used voxel-by-voxel testing, neighborhood information is utilized, an important difference. This is achieved by using a Markov random field prior and iterated conditional modes (ICM) algorithm. However, unlike in the conventional use of ICM algorithm, the classification is based only on the distribution of background. The results from our simulations and human fMRI experiments using visual stimulation demonstrate that a better sensitivity is achieved with a given specificity in comparison to the voxel-by-voxel thresholding technique. The algorithm is computationally efficient and can be used to detect and delineate objects from a noisy background in other applications.

NOTE: Blind Restoration of Degraded Binary Markov Random Field Images

The problem of restoring binary images degraded by region-dependent flip-flap noises is considered. The real image is described by a Markov random field (MRF). The iterative conditional modes (ICM) algorithm is adopted. It is shown that under certain conditions the ICM algorithm is insensitive to either the MRF model or the noise parameters. Using this property, we propose a blind restoration algorithm that has the following two basic properties: (a) it does not require full knowledge about the model and noise parameters; (b) it can be fully implemented in parallel. To show the effectiveness of the algorithm, simulation results are presented on the applications of the algorithm to degraded hand-drawn and synthetic images.

A Bayesian approach to subvoxel tissue classification in NMR microscopic images of trabecular bone.

NMR microscopy is currently being used as an investigational tool for the evaluation of micromorphometric parameters of trabecular bone as a possible means to assess its strength. Since, typically, the image voxel size is not significantly smaller than individual trabecular elements, partial volume blurring can be a major complication for accurate tissue classification. In this paper, a Bayesian segmentation technique is reported that achieves improved subvoxel tissue classification. Each voxel is subdivided either into eight subvoxels twice the original resolution, or up to four subvoxels along the transaxial direction and the subvoxels optimally classified as volume blurring, the likelihood for the number of marrow subvoxels in each voxel can be computed on the basis of its measured signal. To resolve the ambiguity of the location of the marrow subvoxels, a Gibbs distribution is introduced to model the interaction between the subvoxels. Neighboring subvoxel pairs with the same tissue label are encouraged, and pairs with distinct labels are penalized. The segmentation is achieved by maximizing the a posteriori probability of the label image using the block ICM (iterative conditional mode) algorithm. The potential of the proposed technique is demonstrated in real and synthetic NMR microscopic images.