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.
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.
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.
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.
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/.
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
15165209
A PCA-Based Vehicle Classification Framework
Due to its great practical importance, Intelligent Transportation System has been an active research area in recent years. In this paper, we present a framework that incorporates various aspects of an intelligent transportation system with its ultimate goal being vehicle classification. Given a traffic video sequence, the proposed system first proceeds to segment individual vehicles. Then the extracted vehicle objects are normalized so that all vehicles are aligned along the same direction and measured at the same scale. Following the preprocessing step, two classification algorithms - Eigenvehicle and PCA-SVM, are proposed and implemented to classify vehicle objects into trucks, passenger cars, vans, and pick-ups. These two methods exploit the distinguishing power of Principal Component Analysis (PCA) at different granularities with different learning mechanisms. Experiments are conducted to compare these two methods and the results demonstrate the effectiveness of the proposed framework.
3210423
Verification Approach of Metropolis Design Framework for Embedded Systems
In this paper, we focus on the verification approach of Metropolis, an integrated design framework for heterogeneous embedded systems. The verification approach is based on the formal properties specified in Linear Temporal Logic (LTL) or Logic of Constraints (LOC). Designs may be refined due to synthesis or be abstracted for verification. An automatic abstraction propagation algorithm is used to simplify the design for specific properties. A user-defined starting point may also be used with automatic propagation. Two main verification techniques are implemented in Metropolis the formal verification utilizing the model checker Spin and the simulation trace checking with automatic generated checkers. Translation algorithms from specification models to verification models, as well as algorithms of generated checkers are discussed. We use several case studies to demonstrate our approach for verification of system level designs at multiple levels of abstraction.
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.
62212743
Resampling for face detection by self-adaptive genetic algorithm
Over the past ten years, face detection has been thoroughly studied in computer vision research for its interesting applications. However, all of the state-of-the-art statistical methods suffer from the data collection for training a classifier. This paper presents a self-adaptive genetic algorithm (GA)-based method to swell face database through re-sampling from the existing faces. The basic idea is that a face is composed of a limited components set, and the GA can simulate the procedure of heredity. This simulation can also cover the variations of faces in different lighting conditions, poses, accessories, and quality conditions. To verify the generalization capability of the proposed method, we also use the expanded database to train an Adaboost-based face detector and test it on the MIT+CMU frontal face test set. The experimental results show that the data collection can be efficiently speeded up by the proposed methods.