17670948
A General Framework for Biclustering Gene Expression Data
A large number of biclustering methods have been proposed to detect patterns in gene expression data. All these methods try to find some type of biclusters but no one can discover all the types of patterns in the data. Furthermore, researchers have to design new algorithms in order to find new types of biclusters/patterns that interest biologists. In this paper, we propose a novel approach for biclustering that, in general, can be used to discover all computable patterns in gene expression data. The method is based on the theory of Kolmogorov complexity. More precisely, we use Kolmogorov complexity to measure the randomness of submatrices as the merit of biclusters because randomness naturally consists in a lack of regularity, which is a common property of all types of patterns. On the basis of algorithmic probability measure, we develop a Markov Chain Monte Carlo algorithm to search for biclusters. Our method can also be easily extended to solve the problems of conventional clustering and checkerboard type biclustering. The preliminary experiments on simulated as well as real data show that our approach is very versatile and promising.
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.
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.
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.
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.
902904
Automatic Generation of Simulation Monitors from Quantitative Constraint Formula
System design methodology is poised to become the next big enabler for highly sophisticated electronic products. Design verification continues to be a major challenge and simulation will remain an important tool for making sure that implementations perform as they should. In this paper we present algorithms to automatically generate C++ checkers from any formula written in the formal quantitative constraint language, Logic Of Constraints (LOC). The executable can then be used to analyze the simulation traces for constraint violation and output debugging information. Different checkers can be generated for fast analysis under different memory limitations. LOC is particularly suitable for specification of system level quantitative constraints where relative coordination of instances of events, not lower level interaction, is of paramount concern. We illustrate the usefulness and efficiency of our automatic trace analysis methodology with case studies on large simulation traces from various system level designs.
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
7180811
Calibrating pan-tilt cameras in wide-area surveillance networks
Pan-tilt cameras are often used as components of wide-area surveillance systems. It is necessary to calibrate these cameras in relation to one another in order to obtain a consistent representation of the entire space. Existing methods for calibrating pan-tilt cameras have assumed an idealized model of camera mechanics. In addition, most methods have been calibrated using only a small range of camera motion. We present a method for calibrating pan-tilt cameras that introduces a more complete model of camera motion. Pan and tilt rotations are modeled as occurring around arbitrary axes in space. In addition, the wide area surveillance system itself is used to build a large virtual calibration object, resulting in better calibration than would be possible with a single small calibration target. Finally, the proposed enhancements are validated experimentally, with comparisons showing the improvement provided over more traditional methods.
1385145
Simulation based deadlock analysis for system level designs
In the design of highly complex, heterogeneous, and concurrent systems, deadlock detection and resolution remains an important issue. In this paper, we systematically analyze the synchronization dependencies in concurrent systems modeled in the Metropolis design environment, where system functions, high level architectures and function-architecture mappings can be modeled and simulated. We propose a data structure called the dynamic synchronization dependency graph, which captures the runtime (blocking) dependencies. A loop-detection algorithm is then used to detect deadlocks and help designers quickly isolate and identify modeling errors that cause the deadlock problems. We demonstrate our approach through a real world design example, which is a complex functional model for video processing and a high level model of function-architecture mapping.
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.