10593169
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs
ProMiR is a web-based service for the prediction of potential microRNAs (miRNAs) in a query sequence of 60–150 nt, using a probabilistic colearning model. Identification of miRNAs requires a computational method to predict clustered and nonclustered, conserved and nonconserved miRNAs in various species. Here we present an improved version of ProMiR for identifying new clusters near known or unknown miRNAs. This new version, ProMiR II, integrates additional evidence, such as free energy data, G/C ratio, conservation score and entropy of candidate sequences, for more controllable prediction of miRNAs in mouse and human genomes. It also provides a wider range of services, e.g. the prediction of miRNA genes in long nonrelated sequences such as viral genomes. Importantly, we have validated this method using several case studies. All data used in ProMiR II are structured in the MySQL database for efficient analysis. The ProMiR II web server is available at .
9400771
Identification of biochemical networks by S-tree based genetic programming
MOTIVATION
Most previous approaches to model biochemical networks have focused either on the characterization of a network structure with a number of components or on the estimation of kinetic parameters of a network with a relatively small number of components. For system-level understanding, however, we should examine both the interactions among the components and the dynamic behaviors of the components. A key obstacle to this simultaneous identification of the structure and parameters is the lack of data compared with the relatively large number of parameters to be estimated. Hence, there are many plausible networks for the given data, but most of them are not likely to exist in the real system.


RESULTS
We propose a new representation named S-trees for both the structural and dynamical modeling of a biochemical network within a unified scheme. We further present S-tree based genetic programming to identify the structure of a biochemical network and to estimate the corresponding parameter values at the same time. While other evolutionary algorithms require additional techniques for sparse structure identification, our approach can automatically assemble the sparse primitives of a biochemical network in an efficient way. We evaluate our algorithm on the dynamic profiles of an artificial genetic network. In 20 trials for four settings, we obtain the true structure and their relative squared errors are <5% regardless of releasing constraints about structural sparseness. In addition, we confirm that the proposed algorithm is robust within +/-10% noise ratio. Furthermore, the proposed approach ensures a reasonable estimate of a real yeast fermentation pathway. The comparatively less important connections with non-zero parameters can be detected even though their orders are below 10(-2). To demonstrate the usefulness of the proposed algorithm for real experimental biological data, we provide an additional example on the transcriptional network of SOS response to DNA damage in Escherichia coli. We confirm that the proposed algorithm can successfully identify the true structure except only one relation.
9456425
Adaptive Sampling for Estimating a Scalar Field using a Robotic Boat and a Sensor Network
This paper introduces an adaptive sampling algorithm for a mobile sensor network to estimate a scalar field. The sensor network consists of static nodes and one mobile robot. The static nodes are able to take sensor readings continuously in place, while the mobile robot is able to move and sample at multiple locations. The measurements from the robot and the static nodes are used to reconstruct an underlying scalar field. The algorithm presented in this paper accepts the measurements made by the static nodes as inputs and computes a path for the mobile robot which minimizes the integrated mean square error of the reconstructed field subject to the constraint that the robot has limited energy. We assume that the field does not change when robot is taking samples. In addition to simulations, we have validated the algorithm on a robotic boat and a system of static buoys operating in a lake over several km of traversed distance while reconstructing the temperature field of the lake surface
58797822
Discriminatory power of handwritten words for writer recognition
Analysis of allographs (characters) and allograph combinations (words) is the key for the identification/verification of a writer's handwriting. While allographs are usually part of words and the segmentation of a word into allographs is a subjective process, analysis of handwritten words is a natural option, complementary to allograph and document-level analysis. We consider four different types of features obtained using both segmentation-based and segmentation-free approaches: (i) GSC (gradient, structural and concavity) features that are extracted from the cells of a grid superimposed on the word image (ii) WMR (word model recognizer) features, extracted from the cells of superimposed grids on the segmented characters (iii) SC (shape curvature) features that describe characters by the distribution of curvature values on their contours and (iv) SCON (shape context) features that measure the similarity between character contour shapes. Their individual and accumulated performance is evaluated for the writer identification and verification tasks on over 75000 words images, written by more than 1000 writers. Experimental results show that handwritten words are very effective in discriminating handwriting and that both segmentation-free and segmentation-based approaches are valid.
9623784
Multi-type Features Based Web Document Clustering
Clustering has been demonstrated as a feasible way to explore the contents of document collection and organize search engine results. For this task, many features of Web page, such as content, anchor text, URL, hyperlink etc, can be exploited and different results can be obtained. We expect to provide a unified and even better result for end users. Some work have studied how to use several types of features together to perform clustering. Most of them focus on ensemble method or combination of similarity. In this paper, we propose a novel algorithm: Multi-type Features based Reinforcement Clustering (MFRC). This algorithm does not use a unique combine score for all feature spaces, but uses the intermediate clustering result in one feature space as additional information to gradually enhance clustering in other spaces. Finally a consensus can be achieved by such mutual reinforcement. And the experimental results show that MFRC also provides some performance improvement.
1777247
Web-page classification through summarization
Web-page classification is much more difficult than pure-text classification due to a large variety of noisy information embedded in Web pages. In this paper, we propose a new Web-page classification algorithm based on Web summarization for improving the accuracy. We first give empirical evidence that ideal Web-page summaries generated by human editors can indeed improve the performance of Web-page classification algorithms. We then propose a new Web summarization-based classification algorithm and evaluate it along with several other state-of-the-art text summarization algorithms on the LookSmart Web directory. Experimental results show that our proposed summarization-based classification algorithm achieves an approximately 8.8% improvement as compared to pure-text-based classification algorithm. We further introduce an ensemble classifier using the improved summarization algorithm and show that it achieves about 12.9% improvement over pure-text based methods.
16669804
An effective region-based image retrieval framework
We present a region-based image retrieval framework that integrates efficient region-based representation in terms of storage and retrieval and effective on-line learning capability. The framework consists of methods for image segmentation and grouping, indexing using modified inverted file, relevance feedback, and continuous learning. By exploiting a vector quantization method, a compact region-based image representation is achieved. Based on this representation, an indexing scheme similar to the inverted file technology is proposed. In addition, it supports relevance feedback based on the vector model with a weighting scheme. A continuous learning strategy is also proposed to enable the system to self improve. Experimental results on a database of 10,000 general-purposed images demonstrate the efficiency and effectiveness of the proposed framework.