6184920
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
MOTIVATION
Information from fully sequenced genomes makes it possible to reconstruct strain-specific global metabolic network for structural and functional studies. These networks are often very large and complex. To properly understand and analyze the global properties of metabolic networks, methods for rationally representing and quantitatively analyzing their structure are needed.


RESULTS
In this work, the metabolic networks of 80 fully sequenced organisms are in silico reconstructed from genome data and an extensively revised bioreaction database. The networks are represented as directed graphs and analyzed by using the 'breadth first searching algorithm to identify the shortest pathway (path length) between any pair of the metabolites. The average path length of the networks are then calculated and compared for all the organisms. Different from previous studies the connections through current metabolites and cofactors are deleted to make the path length analysis physiologically more meaningful. The distribution of the connection degree of these networks is shown to follow the power law, indicating that the overall structure of all the metabolic networks has the characteristics of a small world network. However, clear differences exist in the network structure of the three domains of organisms. Eukaryotes and archaea have a longer average path length than bacteria.


AVAILABILITY
The reaction database in excel format and the programs in VBA (Visual Basic for Applications) are available upon request.


SUPPLEMENTARY MATERIAL
Bioinformatics Online.
6752301
The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks
MOTIVATION
Structural and functional analysis of genome-based large-scale metabolic networks is important for understanding the design principles and regulation of the metabolism at a system level. The metabolic network is conventionally considered to be highly integrated and very complex. A rational reduction of the metabolic network to its core structure and a deeper understanding of its functional modules are important.


RESULTS
In this work, we show that the metabolites in a metabolic network are far from fully connected. A connectivity structure consisting of four major subsets of metabolites and reactions, i.e. a fully connected sub-network, a substrate subset, a product subset and an isolated subset is found to exist in metabolic networks of 65 fully sequenced organisms. The largest fully connected part of a metabolic network, called 'the giant strong component (GSC)', represents the most complicated part and the core of the network and has the feature of scale-free networks. The average path length of the whole network is primarily determined by that of the GSC. For most of the organisms, GSC normally contains less than one-third of the nodes of the network. This connectivity structure is very similar to the 'bow-tie' structure of World Wide Web. Our results indicate that the bow-tie structure may be common for large-scale directed networks. More importantly, the uncovered structure feature makes a structural and functional analysis of large-scale metabolic network more amenable. As shown in this work, comparing the closeness centrality of the nodes in the GSC can identify the most central metabolites of a metabolic network. To quantitatively characterize the overall connection structure of the GSC we introduced the term 'overall closeness centralization index (OCCI)'. OCCI correlates well with the average path length of the GSC and is a useful parameter for a system-level comparison of metabolic networks of different organisms.


SUPPLEMENTARY INFORMATION
http://genome.gbf.de/bioinformatics/
62221666
Adaptive word style classification using a Gaussian mixture model
We present a new approach to detect bold and italic words in scanned documents. Under the assumption that OCR results are available, features used for classification are selected automatically using feature selection. For each scanned page, a Gaussian mixture model is constructed for characters with the same character code, and word styles are determined using a weighted majority vote. We applied this method to a variety of documents and compared the results with current commercial OCR software that provides style information. The experimental results show that our method performs better.
14752983
Gabor filter based multi-class classifier for scanned document images
When scanning documents with a large number of pagessuch as books, it is often feasible to provide a minimalnumber of training samples to personalize the system tocompensate for global shifts in how the document wascreated or in scanning parameters. In this paper, wepresent a supervised multi-class classifier based onGabor filters that is used to classify the scripts, font-faces,and font-styles (bold, italic, normal etc.) in anapplication where the classes are known. Classificationis performed at the word level (glyphs separated by whitespace) given training samples of each class. This methodwas applied to a variety of bilingual dictionaries toidentify different scripts, and simultaneously, to classifyRoman scripts into bold, italic and normal font-styles.Experimental results show the effectiveness of thisapproach in increasing performance over classifierstrained for general documents.
8710639
Adaptive Hindi OCR using generalized Hausdorff image comparison
We present an adaptive Hindi OCR implemented as part of a rapidly retargetable language tool effort. The system includes: script identification, character segmentation, training sample creation, and character recognition. In script identification, Hindi words are identified from bilingual or multilingual documents based on features of the Devanagari script or using Support Vector Machines. Identified words are then segmented into individual characters in the next step, where the composite characters are identified and further segmented based on the structural properties of the script and statistical information. Segmented characters are recognized using generalized Hausdorff image comparison (GHIC) and postprocessing is applied to improve the performance. The OCR system, which was designed and implemented in one month, was applied to a complete Hindi--English bilingual dictionary and a set of ideal images extracted from Hindi documents in PDF format. Experimental results show the recognition accuracy can reach 88% for noisy images and 95% for ideal images. The presented method can also be extended to design OCR systems for different scripts.
13908911
Adaptive OCR with limited user feedback
A methodology is proposed for processing noisy printed documents with limited user feedback. Without the support of ground truth, a specific collection of scanned documents can be processed to extract character templates. The adaptiveness of this approach lies in that the extracted templates are used to train an OCR classifier quickly and with limited user feedback. Experimental results show that this approach is extremely useful for the processing of noisy documents with many touching characters.