12010325
An information-based sequence distance and its application to whole mitochondrial genome phylogeny
MOTIVATION
Traditional sequence distances require an alignment and therefore are not directly applicable to the problem of whole genome phylogeny where events such as rearrangements make full length alignments impossible. We present a sequence distance that works on unaligned sequences using the information theoretical concept of Kolmogorov complexity and a program to estimate this distance.


RESULTS
We establish the mathematical foundations of our distance and illustrate its use by constructing a phylogeny of the Eutherian orders using complete unaligned mitochondrial genomes. This phylogeny is consistent with the commonly accepted one for the Eutherians. A second, larger mammalian dataset is also analyzed, yielding a phylogeny generally consistent with the commonly accepted one for the mammals.


AVAILABILITY
The program to estimate our sequence distance, is available at http://www.cs.cityu.edu.hk/~cssamk/gencomp/GenCompress1.htm. The distance matrices used to generate our phylogenies are available at http://www.math.uwaterloo.ca/~mli/distance.html.
960732
Computing the Assignment of Orthologous Genes via Genome Rearrangement
The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics. Existing methods that assign orthologs based on the similarity between DNA or protein sequences may make erroneous assignments when sequence similarity does not clearly delineate the evolutionary relationship among genes of the same families. In this paper, we present a new approach to ortholog assignment that takes into account both sequence similarity and evolutionary events at genome level, where orthologous genes are assumed to correspond to each other in the most parsimonious evolving scenario under genome rearrangement. It is then formulated as a problem of computing the signed reversal distance with duplicates between two genomes of interest, for which an efcient heuristic algorithm was given by introducing two new optimization problems, minimum common partition and maximum cycle decomposition. Following this approach, we have implemented a high-throughput system for assigning orthologs on a genome scale, called SOAR, and tested it on both simulated data and real genome sequence data. Compared to a recent ortholog assignment method based entirely on homology search (called INPARANOID), SOAR shows a marginally better performance in terms of sensitivity on the real data set because it was able to identify several correct orthologous pairs that were missed by INPARANOID. The simulation results demonstrate that SOAR in general performs better than the iterated exemplar algorithm in terms of computing the reversal distance and assigning correct orthologs.
12408696
DNACompress: fast and effective DNA sequence compression
While achieving the best compression ratios for DNA sequences, our new DNACompress program significantly improves the running time of all previous DNA compression programs.
1552680
Shared information and program plagiarism detection
A fundamental question in information theory and in computer science is how to measure similarity or the amount of shared information between two sequences. We have proposed a metric, based on Kolmogorov complexity, to answer this question and have proven it to be universal. We apply this metric in measuring the amount of shared information between two computer programs, to enable plagiarism detection. We have designed and implemented a practical system SID (Software Integrity Diagnosis system) that approximates this metric by a heuristic compression algorithm. Experimental results demonstrate that SID has clear advantages over other plagiarism detection systems. SID system server is online at http://software.bioinformatics.uwaterloo.ca/SID/.
12811258
A Parsimony Approach to Genome-Wide Ortholog Assignment
The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics, since many computational methods for solving various biological problems critically rely on bona fide orthologs as input. While it is usually done using sequence similarity search, we recently proposed a new combinatorial approach that combines sequence similarity and genome rearrangement. This paper continues the development of the approach and unites genome rearrangement events and (post-speciation) duplication events in a single framework under the parsimony principle. In this framework, orthologous genes are assumed to correspond to each other in the most parsimonious evolutionary scenario involving both genome rearrangement and (post-speciation) gene duplication. Besides several original algorithmic contributions, the enhanced method allows for the detection of inparalogs. Following this approach, we have implemented a high-throughput system for ortholog assignment on a genome scale, called MSOAR, and applied it to the genomes of human and mouse. As the result will show, MSOAR is able to find 99 more true orthologs than the INPARANOID program did. We have also compared MSOAR with the iterated exemplar algorithm on simulated data and found that MSOAR performed very well in terms of assignment accuracy. These test results indiate that our approach is very promising for genome-wide ortholog assignment.
8099146
A new compression scheme for color-quantized images
An efficient compression scheme for color-quantized images based on progressive coding of color information has been developed. Instead of sorting color indexes into a linear list struc- ture, a binary-tree structure of color indexes is proposed. With this structure, the new algorithm can progressively recover an image from two colors to all of the colors contained in the original image, i.e., a lossless recovery is achieved. Experimental results showed that it can efficiently compress images in both lossy and lossless cases. Typically for color-quantized Lena image with 256 colors, the algorithm achieved 0.5 bpp below state-of-the-art lossless com- pression methods while preserving the efficient lossy compression. Such a compression scheme is very attractive to many applications that require the ability of fast browsing or progressive transmis- sion, and if necessary, to exactly recover the original image. Index Terms—Color-quantized images, data compression, index sorting, progressive refinement.
2743837
A hybrid classifier approach for Web retrieved documents classification
The paper presents a hybrid technique for the classification of Web returned hits into concept hierarchies. The technique involves a combination of manual and automatic classifiers. At first, all Web returned documents are assigned to human defined categories using manual classifiers, and then automatic classifiers are used to generate a concept hierarchy for each of these categories. The results of the evaluation reveal the following: (a) for polysemous queries, our system is able to generate meaningful categories corresponding to (but not limited to), the different semantic facets of the queries; (b) as expected, for non-polysemous queries the system generates fewer categories; (c) the hierarchy precision of the concept hierarchies generated for polysemous queries is found to be significantly better when compared to the one obtained using a baseline system.
2587881
Isomap Based on the Image Euclidean Distance
Scientists find that the human perception is based on the similarity on the manifold of data set. Isometric feature mapping (isomap) is one of the representative techniques of manifold. It is intuitive, well understood and produces reasonable mapping results. However, if the input data for manifold learning are corrupted with noises, the isomap algorithm is topologically unstable. In this paper, we present an improved manifold learning method when the input data are images - the image Euclidean distance based isomap (imisomap), in which we use a new distance for images called image Euclidean distance (IMED). Experimental results demonstrate a consistent performance improvement of the algorithm imisomap over the traditional isomap based on Euclidean distance
3223686
Personalized Knowledge Discovery: Mining Novel Association Rules from Text
This paper presents a methodology for personalized knowledge discovery from text. It derives a user’s background knowledge from his/her background documents, and exploits such knowledge to evaluate the novelty of discovered knowledge in the form of association rules by measuring the semantic distance between the antecedent and the consequent of a rule in the background knowledge. The experiment results show that the proposed user-oriented novelty measure is highly correlated with the human subjective rule novelty and usefulness ratings. It outperforms seven major objective interestingness measures and the WordNet novelty measure for identifying novel and useful rules.
3226359
Segmentation, Registration, and Deformation Analysis of 3D MR Images of Mice
We demonstrate our mouse MR image and shape analysis pipeline. The long term goal of our work is the description of structural shape variations in normal, genetically identical mice and the subsequent detection of pathological phenotypes in genetically modified mice. The pipeline begins with the acquisition and reconstruction of high resolution MR images of mice. Regions of the images containing organs under study are enhanced via edge-preserving smoothing and mouse organs are segmented using a deformable mesh model. Images are registered using a multi-resolution approach and displacement fields are used to calculate local volume changes. Detailed descriptions and results for each step of the pipeline are presented.
41168099
A note on Roman domination in graphs
Let G=(V,E) be a simple graph. A subset [email protected]?V is a dominating set of G, if for any vertex [email protected]?V-S, there exists a vertex [email protected]?S such that [email protected]?E. The domination number of G, @c(G), equals the minimum cardinality of a dominating set. A Roman dominating function on graph G=(V,E) is a function f:V->{0,1,2} satisfying the condition that every vertex v for which f(v)=0 is adjacent to at least one vertex u for which f(u)=2. The weight of a Roman dominating function is the value f(V)[email protected]?"v"@?"Vf(v). The Roman domination number of a graph G, denoted by @c"R(G), equals the minimum weight of a Roman dominating function on G. In this paper, for any integer k(2=