221927
The similarity metric
A new class of distances appropriate for measuring similarity relations between sequences, say one type of similarity per distance, is studied. We propose a new "normalized information distance," based on the noncomputable notion of Kolmogorov complexity, and show that it is in this class and it minorizes every computable distance in the class (that is, it is universal in that it discovers all computable similarities). We demonstrate that it is a metric and call it the similarity metric . This theory forms the foundation for a new practical tool. To evidence generality and robustness, we give two distinctive applications in widely divergent areas using standard compression programs like gzip and GenCompress. First, we compare whole mitochondrial genomes and infer their evolutionary history. This results in a first completely automatic computed whole mitochondrial phylogeny tree. Secondly, we fully automatically compute the language tree of 52 different languages.
30296056
Computational inference of regulatory pathways in microbes
We present a computational protocol for inference of regulatory and signaling pathways in a microbial cell, through mining "high-throughput" biological data of various types, literature search, and computer-assisted human inference. This protocol consists of four key components: (a) construction of template pathways for microbial genomes related to the target genome, which have either been thoroughly studied or had a significant amount of relevant experimental data, (b) inference of target pathways for the target genome, by combining the template pathway models and target genome-specific information, (c) assignment of genes of the target genome to each individual functional roles in the pathway model, and (d) validation and refinement of the pathway models using pathway-specific experimental data or other information. To demonstrate the effectiveness of this procedure, we have applied this computational protocol to the construction of the phosphorus assimilation pathways in synechococcus WH8102. In this paper, we present a model of the core component of this pathway and provide our justification in support of the predicted model.
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.
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.
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.
12374753
Efficient Method for Geometric Attribute Estimation
A new method is proposed to estimate the discrete geometric attributes, such as normal vector and curvature. The method contains two steps: points sampling and 4D Shepard interpolation. In the first step, we extract points from point cloud and estimate the attribute of the sampled points. During the second step, we interpolate a global 4D Shepard surface over these sampled points and compute the attribute of each point in point cloud. This method is very effective for using a new global surface model. It benefits many applications such as segmentation, feature extraction, data preprocessing and etc. Application examples are given to verify the proposed method.
14272026
Fully automated facial symmetry axis detection in frontal color images
We consider the problem of automatically detecting a facial symmetry axis in what we will call a standard human face image (acquired when the subject is looking directly into the camera, in front of a clean gray background under controlled illumination). Images of this kind are encountered in face recognition scenarios; this detection should facilitate more sophisticated facial image processing. The proposed method is based on GLDH (gray level difference histogram) analysis and consists of three components: (1) the face region detection stage crops an approximate face region out of the background, (2) symmetry detection discovers a vertical axis to optimally bisect the region of interest, assuming it is bilaterally symmetric, and (3) orientation adjustment aligns the angle of the symmetry axis with the orientation of the face. An implementation of the method is described, and results are presented. This detector's robust performance is evidenced by its success finding symmetry axes in more than 7,500 images collected from 600 distinct subjects. One of our method's most noteworthy contributions is that, according to our experimental results, many of the automatically detected axes are more accurate than the reference axes. Our automated detector is a powerful tool because it is not as susceptible to human error as its manual counterpart and, as the first application of its kind, it could potentially serve as a new biometric.
8954904
Modification of the AdaBoost-based Detector for Partially Occluded Faces
While face detection seems a solved problem under general conditions, most state-of-the-art systems degrade rapidly when faces are partially occluded by other objects. This paper presents a solution to detect partially occluded faces by reasonably modifying the AdaBoost-based face detector. Our basic idea is that the weak classifiers in the AdaBoost-based face detector, each corresponding to a Haar-like feature, are inherently a patch-based model. Therefore, one can divide the whole face region into multiple patches, and map those weak classifiers to the patches. The weak classifiers belonging to each patch are re-formed to be a new classifier to determine if it is a valid face patch - without occlusion. Finally, we combine all of the valid face patches by assigning the patches with different weights to make the final decision whether the input subwindow is a face. The experimental results show that the proposed method is promising for the detection of occluded faces
35009889
Tree Domination in Graphs
761547
Finite Element Surface Fitting for Bridge Management
We propose a new finite element surface fitting method which can handle very large databases. This method uses finite element discretization to find an approximation of a smooth function which minimizes a sum of data residuals and second derivatives under some constraints on data. The finite element discretization derives a large scale constrained quadratic program, which can be reformulated as a system of piecewise linear equations. We develop a preconditioned Newton method to solve the system efficiently. We apply this method to form surfaces over Aomori Region in Japan by geographic databases, such that every bridge became associated with environmental information.