1876538
PSoL: a positive sample only learning algorithm for finding non-coding RNA genes
MOTIVATION
Small non-coding RNA (ncRNA) genes play important regulatory roles in a variety of cellular processes. However, detection of ncRNA genes is a great challenge to both experimental and computational approaches. In this study, we describe a new approach called positive sample only learning (PSoL) to predict ncRNA genes in the Escherichia coli genome. Although PSoL is a machine learning method for classification, it requires no negative training data, which, in general, is hard to define properly and affects the performance of machine learning dramatically. In addition, using the support vector machine (SVM) as the core learning algorithm, PSoL can integrate many different kinds of information to improve the accuracy of prediction. Besides the application of PSoL for predicting ncRNAs, PSoL is applicable to many other bioinformatics problems as well.


RESULTS
The PSoL method is assessed by 5-fold cross-validation experiments which show that PSoL can achieve about 80% accuracy in recovery of known ncRNAs. We compared PSoL predictions with five previously published results. The PSoL method has the highest percentage of predictions overlapping with those from other methods.
12184758
Integrating program component executables on distributed memory architectures via MPH
Summary form only given. A growing trend in developing large and complex applications on today's Teraflop computers is to integrate stand-alone and/or semiindependent program components into a comprehensive simulation package. One example is the climate system model, which consists of atmosphere, ocean, land-surface and sea-ice. Each component is semiindependent and has been developed at different institutions. We study how this multicomponent multiexecutable application can run effectively on distributed memory architectures. We identify five effective execution modes and develop the MPH library to support application developments utilizing these modes. MPH performs component-name registration, resource allocation and initial component handshaking in a flexible way.
4990172
Structure search and stability enhancement of Bayesian networks
Learning Bayesian network structure from large-scale data sets, without any expert-specified ordering of variables, remains a difficult problem. We propose systematic improvements to automatically learn Bayesian network structure from data. (1) We propose a linear parent search method to generate candidate graph. (2) We propose a comprehensive approach to eliminate cycles using minimal likelihood loss, a short cycle first heuristic, and a cut-edge repairing. (3) We propose structure perturbation to assess the stability of the network and a stability-improvement method to refine the network structure. The algorithms are easy to implement and efficient for large networks. Experimental results on two data sets show that our new approach outperforms existing methods.
17669185
Unsupervised Learning: Self-aggregation in Scaled Principal Component Space
We demonstrate that data clustering amounts to a dynamic process of self-aggregation in which data objects move towards each other to form clusters, revealing the inherent pattern of similarity. Self-aggregation is governed by connectivity and occurs in a space obtained by a nonlinear scaling of principal component analysis (PCA). The method combines dimensionality reduction with clustering into a single framework. It can apply to both square similarity matrices and rectangular association matrices.
30201789
Term norm distribution and its effects on Latent Semantic Indexing
Latent Semantic Indexing (LSI) uses the singular value decomposition to reduce noisy dimensions and improve the performance of text retrieval systems. Preliminary results have shown modest improvements in retrieval accuracy and recall, but these have mainly explored small collections. In this paper we investigate text retrieval on a larger document collection (TREC) and focus on distribution of word norm (magnitude). Our results indicate the inadequacy of word representations in LSI space on large collections. We emphasize the query expansion interpretation of LSI and propose an LSI term normalization that achieves better performance on larger collections.
45840953
Dynamic Cluster Formation Using Level Set Methods
Density-based clustering has the advantages for (i) allowing arbitrary shape of cluster and (ii) not requiring the number of clusters as input. However, when clusters touch each other, both the cluster centers and cluster boundaries (as the peaks and valleys of the density distribution) become fuzzy and difficult to determine. In higher dimension, the boundaries become wiggly and over-fitting often occurs. We introduce the notion of cluster intensity function (CIF) which captures the important characteristics of clusters. When clusters are well-separated, CIFs are similar to density functions. But as clusters touch each other, CIFs still clearly reveal cluster centers, cluster boundaries, and, degree of membership of each data point to the cluster that it belongs. Clustering through bump hunting and valley seeking based on these functions are more robust than that based on kernel density functions which are often oscillatory or over-smoothed. These problems of kernel density estimation are resolved using Level Set Methods and related techniques. Comparisons with two existing density-based methods, valley seeking and DBSCAN, are presented to illustrate the advantages of our approach.
1490908
Word segmentation and recognition for web document framework
It is observed that a better approach to Web information understanding is to base on its document framework, which is mainly consisted of (i) the title and the URL name of the page, (ii) the titles and the URL names of the Web pages that it points to, (iii) the alternative information source for the embedded Web objects, and (iv) its linkage to other Web pages of the same document. Investigation reveals that a high percentage of words inside the document framework are “compound words” which cannot be understood by ordinary dictionaries. They might be abbreviations or acronyms, or concatenations of several (partial) words. To recover the content hierarchy of Web documents, we propose a new word segmentation and recognition mechanism to understand the information derived from the Web document framework. A maximal bi-directional matching algorithm with heuristic rules is used to resolve ambiguous segmentation and meaning in compound words. An adaptive training process is further employed to build a dictionary of recognisable abbreviations and acronyms. Empirical results show that over 75% of the compound words found in the Web document framework can be understood by our mechanism. With the training process, the success rate of recognising compound words can be increased to about 90%.
13552447
Reverse mapping of referral links from storage hierarchy for Web documents
Due to the lack of back-pointers, information about the referral parent(s) of a given Web page is not usually available to Web surfers. This significantly reduces the effectiveness of Web surfing and information discovery. We propose a mechanism to locate the referral parent(s) for a given fragment of a Web document (in terms of an URL address) from the client side. The basic idea is to explore the hierarchical hyperlink structure of a Web document fragment from its storage path directory information that is embedded in its URL. Two mechanisms were proposed: exhaustibility first search (EFS) and generalization first search (GFS). Results showed that through direct mapping of the storage hierarchy path to the URL address and then performing reverse tracing along the hyperlink structure, the chance of discovering a referral parent ranged from 41% to 51%. Compared to EFS, GFS was found to reduce the average search space from 26 pages to 4 pages.
13344452
Context query in information retrieval
There is an important query requirement missing for search engines. With the wide variation of domain knowledge and user interest, a user would like to retrieve documents in which one query term is discussed in the context of another. Based on existing query mechanisms, what can be specified at most is the co-occurrence of multiple terms in a query. This is insufficient because the co-occurrence of two terms does not necessarily mean that one is discussed in the context of the other. In this paper we propose the context query for Web searching. A new query operator, called the 'in' operator, is used to specify context inclusion between two terms. Heuristic rules to identify context inclusion are suggested and implementation of the 'in' operator in search engines is proposed. Results show that both the precision and ranking relevance of Web searching are improved significantly.
209398610
Beyond the traditional query operators.
15395970
Towards an adaptive and task-specific ranking mechanism in Web searching (poster session)
A baler has a preservative applicator assembly with an improved nozzle array for applying a volatile crop treating fluid to crop material as the crop material is being formed into a bale. The nozzle has a centrally disposed passageway which has a cross-sectional area greater than the minimum sum of the cross-sectional areas of a plurality of fluid dispensing openings in the end of the nozzle. Each of the openings includes a throat and a lip outwardly diverging from the throat. The nozzle array maintains the fluid under high pressure and aids in dispersing the fluid with a high velocity to enhance the retention of the fluid as a liquid while in the nozzle and to promote wide and uniform dispersing of the fluid throughout the crop material during the application.