Mutual Information Metric Research Articles

Implementation and evaluation of a new workflow for registration and segmentation of pulmonary MRI data for regional lung perfusion assessment

Recently it has been shown that regional lung perfusion can be assessed using time-resolved contrast-enhanced magnetic resonance (MR) imaging. Quantification of the perfusion images has been attempted, based on definition of small regions of interest (ROIs). Use of complete lung segmentations instead of ROIs could possibly increase quantification accuracy. Due to the low signal-to-noise ratio, automatic segmentation algorithms cannot be applied. On the other hand, manual segmentation of the lung tissue is very time consuming and can become inaccurate, as the borders of the lung to adjacent tissues are not always clearly visible. We propose a new workflow for semi-automatic segmentation of the lung from additionally acquired morphological HASTE MR images. First the lung is delineated semi-automatically in the HASTE image. Next the HASTE image is automatically registered with the perfusion images. Finally, the transformation resulting from the registration is used to align the lung segmentation from the morphological dataset with the perfusion images. We evaluated rigid, affine and locally elastic transformations, suitable optimizers and different implementations of mutual information (MI) metrics to determine the best possible registration algorithm. We located the shortcomings of the registration procedure and under which conditions automatic registration will succeed or fail. Segmentation results were evaluated using overlap and distance measures. Integration of the new workflow reduces the time needed for post-processing of the data, simplifies the perfusion quantification and reduces interobserver variability in the segmentation process. In addition, the matched morphological data set can be used to identify morphologic changes as the source for the perfusion abnormalities.

Incorporating Metric Flows and Sparse Jacobian Transformations in ITK

Various metrics have been proposed in the literature for performing intrinsic automatic image to image registration. Among these measures, mutual information is a very popular one because of its robustness and accuracy for a wide variety of applications. In this paper, we propose a filter for performing non-rigid registration by estimating a dense deformation field derived from the mutual information metric. This filter takes place in the ITK PDE deformable registration design like the Demons algorithm of Thirion. We also show how the concept of metric flow is conceptually linked to the concept of metric derivative for a prior transformation model by the transformation jacobian. We also suggest a sparse implementation of the GetJacobian() method for reducing the computation time of a metric derivative for local transformations models.

Intelligent unmanned ground vehicle navigation via information evaluation

Sensor-centric navigation of unmanned ground vehicles (UGVs) operating in rugged and expansive terrains requires the competency to evaluate the utility of sensor information such that it results in intelligent behavior of the vehicles. Highly imperfect, inconsistent information and incomplete a priori knowledge introduce uncertainty in such unmanned navigation systems. Understanding and quantifying uncertainty yields a measure of useful information that plays a critical role in several robotic navigation tasks such as sensor fusion, mapping, localization, path planning and control. In this article, within a probabilistic framework, the utility of estimation and information-theoretic concepts towards quantifying uncertainty using entropy and mutual information metrics in various contexts of UGV navigation via experimental results is demonstrated.

Entropy‐based motion extraction for motion capture animation

AbstractIn this paper, we present a new segmentation solution for extracting motion patterns from motion capture data by searching for critical keyposes in the motion sequence. A rank is established for critical keyposes that identifies the significance of the directional change in motion data. The method is based on entropy metrics, specifically the mutual information measure. Displacement histograms between frames are evaluated and the mutual information metric is employed in order to calculate the inter‐frame dependency. The most significant keypose identifies the largest directional change in the motion data. This will have the lowest mutual information level from all the candidate keyposes. Less significant keyposes are then listed with higher mutual information levels. The results show that the method has higher sensitivity in the directional change than methods based on the magnitude of the velocity alone. This method is intended to provide a summary of a motion clip by ranked keyposes, which is highly useful in motion browsing and motion retrieve database system. Copyright © 2005 John Wiley & Sons, Ltd.

SU‐FF‐J‐100: Mutual Information as a Metric of Multimodality Contrast Agent Efficacy

Purpose: Mutual information (MI) has been previously employed for image registration. Assuming a priori registration, MI becomes an estimator of image similarity. We apply the concept of MI to the analysis of a feature space formed from multimodality signal intensity distributions. We demonstrate the utility of this concept through the development of a reproducible inter‐image metric to evaluate the efficacy of a multimodal contrast agent for x‐ray computed tomography (CT) and magnetic resonance (MR) imaging. Method and Materials: MR and CT scans were acquired of an anesthetized rabbit in the presence of a multimodal contrast agent. MR and CT scans were acquired pre‐ and post‐injection at fixed time intervals. For each time interval, the MR and CT images were registered, the multimodality feature space was formed and the mutual information between MR and CT was computed using in‐house software. The resulting MI metric was compared with measurements of signal intensity enhancement in user‐defined regions‐of‐interest within the liver, kidneys and aorta. Results: The MI metric correlates with measurements of signal enhancement in MR and CT due to the presence of contrast agent as seen in the liver, kidneys and aorta. Voxels identified as contributing to the increase in MI correspond to areas of visual contrast enhancement observed on MR and CT. Conclusion: We have developed an inter‐image metric for the characterization and optimization of a multimodal contrast agent. The computation of the MI metric is automated and can be extended to 3D for the assessment of image volumes and allows for the inclusion of other modalities such as positron emission tomography. Future investigations will further the development of MI and multimodality feature space analysis as a tool in radiation therapy applications including image registration, target definition and treatment response monitoring.

Deciphering protein network organization using phylogenetic profile groups.

Phylogenetic profiling is now an effective computational method to detect functional associations between proteins. The method links two proteins in accordance with the similarity of their phyletic distributions across a set of genomes. While pair-wise linkage is useful, it misses correlations in higher order groups: triplets, quadruplets, and so on. Here we assess the probability of observing co-occurrence patterns of 3 binary profiles by chance and show that this probability is asymptotically the same as the mutual information in three profiles. We demonstrate the utility of the probability and the mutual information metrics in detecting overly represented triplets of orthologous proteins which could not be detected using pairwise profiles. These triplets serve as small building blocks, i.e. motifs in protein networks; they allow us to infer the function of uncharacterized members, and facilitate analysis of the local structure and global organization of the protein network. Our method is extendable to N-component clusters, and therefore serves as a general tool for high order protein function annotation.

Gene clustering based on clusterwide mutual information.

Cluster analysis of gene-wide expression data from DNA microarray hybridization studies has proved to be a useful tool for identifying biologically relevant groupings of genes and constructing gene regulatory networks. The motivation for considering mutual information is its capacity to measure a general dependence among gene random variables. We propose a novel clustering strategy based on minimizing mutual information among gene clusters. Simulated annealing is employed to solve the optimization problem. Bootstrap techniques are employed to get more accurate estimates of mutual information when the data sample size is small. Moreover, we propose to combine the mutual information criterion and traditional distance criteria such as the Euclidean distance and the fuzzy membership metric in designing the clustering algorithm. The performances of the new clustering methods are compared with those of some existing methods, using both synthesized data and experimental data. It is seen that the clustering algorithm based on a combined metric of mutual information and fuzzy membership achieves the best performance. The supplemental material is available at www.gspsnap.tamu.edu/gspweb/zxb/glioma_zxb.

Accurate classification of protein structural families using coherent subgraph analysis.

Protein structural annotation and classification is an important problem in bioinformatics. We report on the development of an efficient subgraph mining technique and its application to finding characteristic substructural patterns within protein structural families. In our method, protein structures are represented by graphs where the nodes are residues and the edges connect residues found within certain distance from each other. Application of subgraph mining to proteins is challenging for a number reasons: (1) protein graphs are large and complex, (2) current protein databases are large and continue to grow rapidly, and (3) only a small fraction of the frequent subgraphs among the huge pool of all possible subgraphs could be significant in the context of protein classification. To address these challenges, we have developed an information theoretic model called coherent subgraph mining. From information theory, the entropy of a random variable X measures the information content carried by X and the Mutual Information (MI) between two random variables X and Y measures the correlation between X and Y. We define a subgraph X as coherent if it is strongly correlated with every sufficiently large sub-subgraph Y embedded in it. Based on the MI metric, we have designed a search scheme that only reports coherent subgraphs. To determine the significance of coherent protein subgraphs, we have conducted an experimental study in which all coherent subgraphs were identified in several protein structural families annotated in the SCOP database (Murzin et al, 1995). The Support Vector Machine algorithm was used to classify proteins from different families under the binary classification scheme. We find that this approach identifies spatial motifs unique to individual SCOP families and affords excellent discrimination between families.

Evaluation of word confidence for speech recognition systems

Confidence measures enable us to assess the output of a speech recognition system. The confidence measure provides us with an estimate of the probability that a word in the recognizer output is either correct or incorrect. In this paper we discuss ways in which to quantify the performance of confidence measures in terms of their discrimination power and bias. In particular, we analyze two different performance metrics: the classification equal error rate and the normalized mutual information metric. We then report experimental results of using these metrics to compare four different confidence measure estimation schemes. We also discuss the relationship between these metrics and the operating point of the speech recognition system and develop an approach to the robust estimation of normalized mutual information.