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.
3069530
HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data
MOTIVATION
Recent studies have shown that microarray gene expression data are useful for phenotype classification of many diseases. A major problem in this classification is 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. Many approaches have been proposed for this gene selection problem. Most of the previous gene ranking methods typically select 50-200 top-ranked genes and these genes are often highly correlated. Our goal is to select a small set of non-redundant marker genes that are most relevant for the classification task.


RESULTS
To achieve this goal, we developed a novel hybrid approach that combines gene ranking and clustering analysis. In this approach, we first applied feature filtering algorithms to select a set of top-ranked genes, and then applied hierarchical clustering on these genes to generate a dendrogram. Finally, the dendrogram was analyzed by a sweep-line algorithm and marker genes are selected by collapsing dense clusters. Empirical study using three public datasets shows that our approach is capable of selecting relatively few marker genes while offering the same or better leave-one-out cross-validation accuracy compared with approaches that use top-ranked genes directly for classification.


AVAILABILITY
The HykGene software is freely available at http://www.cs.dartmouth.edu/~wyh/software.htm


CONTACT
wyh@cs.dartmouth.edu


SUPPLEMENTARY INFORMATION
Supplementary material is available from http://www.cs.dartmouth.edu/~wyh/hykgene/supplement/index.htm.
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.
12928468
Distributed goal recognition algorithms for modular robots
Modular robots are systems composed of a number of independent units that can be reconfigured to fit the task at hand. When the modules are computationally independent, they form a large distributed system with no central controller. We are concerned with the ability of such modular robots to easily recognize the achievement (or lack thereof) of a given goal configuration. We present algorithms for a class of 2D and 3D modular robots, along with correctness and running time analysis. We have successfully implemented the 2D algorithm on the second-generation Crystalline Atomic robot, a self-reconfigurable modular robot under development in our laboratory and we present implementation details and experimental results.
7477567
Design formalism for collaborative assembly design
Abstract Joints in product design are common because of the limitations of component geometric configurations and material properties, and the requirements of inspection, accessibility, repair, and portability. Collaborative product design is emerging as a viable alternative to the traditional design process. The collaborative assembly design (AsD) methodologies are needed for distributed product development. Existing AsD methodologies have limitations in capturing the non-geometric aspects of designer's intent on joining and are not efficient for a collaborative design environment. This paper introduces an AsD formalism and associated AsD tools to capture joining relations and spatial relationship implications. This AsD formalism allows the joining relations to be modeled symbolically for computer interpretation, and the model can be used for inferring mathematical and physical implications. An AsD model generated from the AsD formalism is used to exchange AsD information transparently in a collaborative AsD environment. An assembly relation model and a generic assembly relationship diagram are to capture assembly and joining information concisely and persistently. As a demonstration, the developed AsD formalism and AsD tools are applied on a connector assembly with arc weld and rivet joints.
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.
23798301
The cognitive process of comprehension
Comprehension is the action or capability of understanding. Comprehension is a higher cognitive process of the brain that searches relations between a given object or attribute and other objects, attributes, and relations in the long-term memory, and establishes a representational model for the object or attribute by connecting it to appropriate clusters of memory. It is recognized that although knowledge and information are powerful, before any information can be possessed and processed, it should be comprehended properly. This paper intends to model one of the cognitive life functions, comprehension, in cognitive informatics. The mechanism and process of comprehension are described based on the cognitive model of the brain developed by Wang. Then, real-time process algebra (RTPA) is used to formally describe the comprehension process.
17279570
Protocol Design and Optimization for Delay/Fault-Tolerant Mobile Sensor Networks
While extensive studies have been carried out in the past several years for many sensor applications, they cannot be applied to the network with extremely low and intermittent connectivity, dubbed the delay/fault-tolerant mobile sensor network (DFT-MSN). Without end-to-end connections due to sparse network density and sensor node mobility, routing in DFT-MSN becomes localized and ties closely to medium access control, which naturally calls for merging Layer 3 and Layer 2 protocols in order to reduce overhead and improve network efficiency. DFT-MSN is fundamentally an opportunistic network, where the communication links exist only with certain probabilities and become the scarcest resource. At the same time, the sensor nodes in DFT-MSN have very limited battery power like those in other sensor networks. Clearly, there is a tradeoff between link utilization and energy efficiency. To address this tradeoff, we develop a cross-layer data delivery protocol for DFT-MSN, which includes two phases, i.e., the asynchronous phase and the synchronous phase. In the first phase, the sender contacts its neighbors to identify a set of appropriate receivers. Since no central control exists, the communication in the first phase is contention-based. In the second phase, the sender gains channel control and multicasts its data message to the receivers. Furthermore, several optimization issues in these two phases are identified, with solutions provided to reduce the collision probability and to balance between link utilization and energy efficiency. Our results show that the proposed cross-layer data delivery protocol for DFT-MSN achieves a high message delivery ratio with low energy consumption and an acceptable delay.
2472095
Coarse and Reliable Geometric Alignment for Protein Docking
We present an efficient algorithm for generating a small set of coarse alignments between interacting proteins using meaningful features on their surfaces. The proteins are treated as rigid bodies, but the results are more generally useful as the produced configurations can serve as input to local improvement algorithms that allow for protein flexibility. We apply our algorithm to a diverse set of protein complexes from the Protein Data Bank, demonstrating the effectivity of our algorithm, both for bound and for unbound protein docking problems.