46267544
Neighboring Feature Clustering
In spectral datasets, such as those consisting of MR spectral data derived from MS lesions, neighboring features tend to be highly correlated, suggesting the data lie on some low-dimensional space. Naturally, finding such low-dimensional space is of interest. Based on this real-life problem, this paper extracts an abstract problem, neighboring feature clustering (NFC). Noticeably different from traditional clustering schemes where the order of features doesn't matter, NFC requires that a cluster consist of neighboring features, that is features that are adjacent in the original feature ordering. NFC is then reduced to a piece-wise linear approximation problem. We use minimum description length (MDL) method to solve this reduced problem. The algorithm we proposed works well on synthetic datasets. NFC is an abstract problem. With minor changes, it can be applied to other fields where the problem of finding piece-wise neighboring groupings in a set of unlabeled data arises.
27423282
Visualization of DNA/RNA Structure using Temporal CGRs
We present a new DNA/RNA sequence visualization technique, Temporal Chaos Game Representation (TCGR), which is an extension of Frequency Chaos Game Representation (FCGR). Unlike earlier CGR variants, TCGR illustrates the distribution of nucleotide sub-patterns at different positions within a sequence, and it can be applied to sets of sequences as well as individual sequences. TCGRs are suitable for short or long sequences. Preliminary experiments examining patterns of nucleotide occurrences in micro-RNA data illustrate not only the informative nature of the images, but clearly indicate the variability of distributions based on position, and the similarity and differences of distributions across various species
15617422
R*-Histograms: efficient representation of spatial relations between objects of arbitrary topology
Representation of relative spatial relations between objects is often required in many multimedia database applications because spatial relations between objects in an image convey important information about the image. Quantitative representation of spatial relations taking into account shape, size, orientation and distance is often required. The R-Histogram is such a quantitative representation of spatial relations between two objects. However, this method only considers pixels on the object boundary, assuming that the objects are homeomorphic to a 2-ball. For objects with more complicated topology, we propose in this paper the R*-Histogram, a new extension to the R-Histogram. The R*-Histogram generalizes the R-Histogram by taking into account all the pixels in the objects. We also introduce an efficient O(kN log N) time algorithm to compute the R*-Histogram, which is asymptotically faster than the original O(N<sup>2</sup>) time algorithm for the R-Histogram even when k=O(n). Here, N=n<sup>2</sup> denotes the number of pixels in the processed n x n image and k is the number of different directions considered. The effectiveness of the R*-Histogram is evaluated empirically with a Query By Example (QBE) system on a database of 2000 synthetic images containing objects with complicated shape and topology. Experiments have shown that the similarly search results match human intuition very well.
10936975
Quantifying Evolving Processes in Multimodal 3D Medical Images
Quantitative measurements of changes in evolving brain pathology, such as multiple sclerosis lesions and brain tumors, are important for clinicians to perform pertinent diagnoses and to help in patient follow-up. Lesions or tumors can vary over time in size, shape, location and composition because of natural pathological processes or the effect of a drug treatment or therapy. In the past, people have used as a quantitative measurement the change in total or regional lesion/tumor volume. In this paper we propose a new model to quantify changes in evolving processes in multimodal 3D medical images. We believe this model reflects changes in pathology more accurately because it simultaneously takes into account information in multiple imaging modalities and the location of lesion/tumor voxels. We demonstrate the effectiveness of this model with experiments on synthetic lesion data.
15514608
Application of Relief-F feature filtering algorithm to selecting informative genes for cancer classification using microarray data
Numerous recent studies have shown that microarray gene expression data is useful for cancer classification. Classification based on microarray data is very different from previous classification problems in that the number of features (genes) greatly exceeds the number of instances (tissue samples). It has been shown that selecting a small set of informative genes can lead to improved classification accuracy. It is thus important to first apply feature selection methods prior to classification. In the machine learning field, one of the most successful feature filtering algorithms is the Relief-F algorithm. In this work, we empirically evaluate its performance on three published cancer classification data sets. We use the linear SVM and the k-NN as classifiers in the experiments, and compare the performance of Relief-F with other feature filtering methods, including Information Gain, Gain Ratio, and /spl chi//sup 2/-statistic. Using the leave-one-out cross validation, experimental results show that the performance of Relief-F is comparable with other methods.
8343773
A spatio-temporal multi-modal data management and analysis environment for tracking MS lesions
We describe the development of a system that automates data collection, metadata extraction and analysis of spatio-temporal multi-modal data, combining data management and data analysis to provide an efficient resource for clinicians. Though the system is extensible to many applications, the current focus is on managing Multiple Sclerosis (MS) lesion data, which are disparate streams of image, numeric, and text data. In order to discover patterns of MS pathology and plan early and effective treatment, multispectral magnetic resonance (MR) image streams collected over time need to be correlated efficiently with each other and with patient performance and clinical data streams.
18101194
The Real-Time Process Algebra (RTPA)
The real-time process algebra (RTPA) is a set of new mathematical notations for formally describing system architectures, and static and dynamic behaviors. It is recognized that the specification of software behaviors is a three-dimensional problem known as: (i) mathematical operations, (ii) event/process timing, and (iii) memory manipulations. Conventional formal methods in software engineering were designed to describe the 1-D (type (i)) or 2-D (types (i) and (iii)) static behaviors of software systems via logic, set and type theories. However, they are inadequate to address the 3-D problems in real-time systems. A new notation system that is capable to describe and specify the 3-D real-time behaviors, the real-time process algebra (RTPA), is developed in this paper to meet the fundamental requirements in software engineering.RTPA is designed as a coherent software engineering notation system and a formal engineering method for addressing the 3-D problems in software system specification, refinement, and implementation, particularly for real-time and embedded systems. In this paper, the RTPA meta-processes, algebraic relations, system architectural notations, and a set of fundamental primary and abstract data types are described. On the basis of the RTPA notations, a system specification method and a refinement scheme of RTPA are developed. Then, a case study on a telephone switching system is provided, which demonstrates the expressive power of RTPA on formal specification of both software system architectures and behaviors. RTPA elicits and models 32 algebraic notations, which are the common core of existing formal methods and modern programming languages. The extremely small set of formal notations has been proven sufficient for modeling and specifying real-time systems, their architecture, and static/dynamic behaviors in real-world software engineering environment.
16121104
3D Surface Matching with Mutual Information and Riemann Surface Structures
Many medical imaging applications require the computation of dense correspondence vector fields that match one surface with another. Surface-based registration is useful for tracking brain change, registering functional imaging data from multiple subjects, and for creating statistical shape models of anatomy. To avoid the need for a large set of manually-defined landmarks to constrain these surface correspondences, we developed an algorithm to automate the matching of surface features. It extends the mutual information method to automatically match general 3D surfaces (including surfaces with a branching topology). We use diffeomorphic flows to optimally align the Riemann surface structures of two surfaces. First, we use holomorphic 1-forms to induce consistent conformal grids on both surfaces. High genus surfaces are mapped to a set of rectangles in the Euclidean plane, and closed genus-zero surfaces are mapped to the sphere. Next, we compute stable geometric features (mean curvature and the conformal factor) and pull them back as scalar fields onto the 2D parameter domains. Mutual information is used as a cost functional to drive a fluid flow in the parameter domain that optimally aligns these surface features. A diffeomorphic surface-tosurface mapping is then recovered that matches anatomy in 3D. Lastly, we present a spectral method that ensures that the grids induced on the target surface remain conformal when pulled through the correspondence field. Using the chain rule, we express the gradient of the mutual information between surfaces in the conformal basis of the source surface. This finite-dimensional linear space generates all conformal reparameterizations of the surface. Illustrative experiments show the method applied to hippocampal surface registration, a key step in subcortical shape analysis in Alzheimer’s disease and schizophrenia.
5267319
Volumetric harmonic brain mapping
We developed two different techniques to study volume mapping problem in Computer Graphics. The first one is to find a harmonic map from a 3 manifold to a 3D solid sphere and the second is a sphere carving algorithm which calculates the simplicial decomposition of volume adapted to surfaces. In this paper, we apply these two techniques to brain mapping problem. We use a tetrahedral mesh to represent the brain volume. The experimental results on both synthetic and brain volume data are reported. We suggest that 3D harmonic mapping of brain volumes to a solid sphere can provide a canonical coordinate system for feature identification and segmentation, as well as anatomical normalization.
14524485
Boundary finding with correspondence using statistical shape models
We propose an approach for boundary finding where the correspondence of a subset of boundary points to a model is simultaneously determined. Global shape parameters derived from the statistical variation of object boundary points in a training set are used to model the object. A Bayesian formulation, based on this prior knowledge and the edge information of the input image, is employed to find the object boundary with its subset points in correspondence with boundaries in the training set or the mean boundary. We compared the use of a generic smoothness prior and a uniform independent prior with the training set prior in order to demonstrate the power of this statistical information. A number of experiments were performed on both synthetic and real medical images of the brain and heart to evaluate the approach, including the validation of the dependence of the method on image quality, different initialization and prior information.
27410689
On cognitive informatics
Information is the third essence in modeling the natural world. This paper attempts to explore an emerging discipline know as cognitive informatics. Cognitive Informatics is a profound interdisciplinary research area that tackles the common root problems of modern informatics, computation, software engineering, artificial intelligence (AI), neural psychology, and cognitive science. Cognitive informatics studies the internal information processing mechanisms and natural intelligence of the brain. This paper describes historical development of informatics from the classical information theory, contemporary informatics, to cognitive informatics. The domain of cognitive informatics and its interdisciplinary nature are explored. Foundations of cognitive informatics, particularly the brain vs. the mind, the acquired life functions vs. the inherited ones, and generic relationships between information, matter and energy are investigated. The potential engineering applications of cognitive informatics and perspectives on future research are discussed. It is expected that the investigation into cognitive informatics will result in fundamental findings towards the development of next generation IT and software technologies, such as neural computers, bioinformatics, quantum information processing, new software development approaches, and new architectures of information systems.