7847880
Context-sensitive semantic smoothing for the language modeling approach to genomic IR
Semantic smoothing, which incorporates synonym and sense information into the language models, is effective and potentially significant to improve retrieval performance. The implemented semantic smoothing models, such as the translation model which statistically maps document terms to query terms, and a number of works that have followed have shown good experimental results. However, these models are unable to incorporate contextual information. Thus, the resulting translation might be mixed and fairly general. To overcome this limitation, we propose a novel context-sensitive semantic smoothing method that decomposes a document or a query into a set of weighted context-sensitive topic signatures and then translate those topic signatures into query terms. In detail, we solve this problem through (1) choosing concept pairs as topic signatures and adopting an ontology-based approach to extract concept pairs; (2) estimating the translation model for each topic signature using the EM algorithm; and (3) expanding document and query models based on topic signature translations. The new smoothing method is evaluated on TREC 2004/05 Genomics Track collections and significant improvements are obtained. The MAP (mean average precision) achieves a 33.6% maximal gain over the simple language model, as well as a 7.8% gain over the language model with context-insensitive semantic smoothing.
117458795
Semantic Smoothing of Document Models for Agglomerative Clustering
In this paper, we argue that the agglomerative clustering with vector cosine similarity measure performs poorly due to two reasons. First, the nearest neighbors of a document belong to different classes in many cases since any pair of documents shares lots of "general" words. Second, the sparsity of class-specific "core" words leads to grouping documents with the same class labels into different clusters. Both problems can be resolved by suitable smoothing of document model and using Kullback-Leibler divergence of two smoothed models as pairwise document distances. Inspired by the recent work in information retrieval, we propose a novel context-sensitive semantic smoothing method that can automatically identifies multiword phrases in a document and then statistically map phrases to individual document terms. We evaluate the new model-based similarity measure on three datasets using complete linkage criterion for agglomerative clustering and find out it significantly improves the clustering quality over the traditional vector cosine measure.
6359793
Integration of cluster ensemble and EM based text mining for microarray gene cluster identification and annotation
In this paper, we design and develop a unified system GE-Miner (Gene Expression Miner) to integrate cluster ensemble, text clustering and multi document summarization and provide an environment for comprehensive gene expression data analysis. We present a novel cluster ensemble approach to generate high quality gene cluster. In our text summarization module, given a gene cluster, our Expectation Maximization (EM) based algorithm can automatically identify subtopics and extract most probable terms for each topic. Then, the extracted top k topical terms from each subtopic are combined to form the biological explanation of each gene cluster. Experimental results demonstrate that our system can obtain high quality clusters and provide informative key terms for the gene clusters.
14856827
Relation-Based Document Retrieval for Biomedical IR
In this paper, we explore the use of term relations in information retrieval for precision-focused biomedical literature search. A relation is defined as a pair of two terms which are semantically and syntactically related to each other. Unlike the traditional “bag-of-word” model for documents, our model represents a document by a set of sense-disambiguated terms and their binary relations. Since document level co-occurrence of two terms, in many cases, does not mean this document addresses their relationships, the direct use of relation may improve the precision of very specific search, e.g. searching documents that mention genes regulated by Smad4. For this purpose, we develop a generic ontology-based approach to extract terms and their relations, and present a betweenness centrality based approach to rank retrieved documents. A prototyped IR system supporting relation-based search is then built for Medline abstract search. We use this novel IR system to improve the retrieval result of all official runs in TREC-2004 Genomics Track. The experiment shows promising performance of relation-based IR. The average P@100 (the precision of top 100 documents) for 50 topics is significantly raised from 26.37 %( the P@100 of the best run is 42.10%) to 53.69% while the MAP (mean average precision) is kept at an above-average level of 26.59%. The experiment also shows the expressiveness of relations for the representation of information needs, especially in the area of biomedical literature full of various biological relations.
9003534
A Language Modeling Text Mining Approach to the Annotation of Protein Community
This paper discusses an ontology based language modeling text mining approach to the annotation of protein community. Communities appear to play an important role in the functional properties of complex networks. Being able to annotate the identified the community structure in a biological network can help us to understand better the structure and dynamics of biological systems. Traditional method such as gene ontology (GO) provides information about the functionality of gene products, but they are not enough to annotate community as for only limited number of proteins in the database, limited protein properties available for annotation and the inability to annotate a group of gene products as a whole. Thus, we present an ontology based mixture language model approach to annotate protein community. Compared to traditional method, we have the following three advantages. First, biomedical literature mining brings much richer information than existed gene databases. Second, the mixture language model can help "purify" the document by eliminating some background noise. Third, using domain ontology, we extract biological concept and concept pairs from abstracts. Biological concept is more meaningful than word or multi-word phrases. Moreover, using concept pairs can deliver much more information and serve as evidence of annotation results. We test our approach on four communities SAGA-SRB, CCR-NOT, RFC and ARP2/3, detected from dataset of interactions for Saccharomyces cerevisae from the general repository for interaction datasets (GRID). Annotation results provide a very coherent indication of functionality of each community
5785584
Semantic Smoothing for Model-based Document Clustering
A document is often full of class-independent "general" words and short of class-specific "core " words, which leads to the difficulty of document clustering. We argue that both problems will be relieved after suitable smoothing of document models in agglomerative approaches and of cluster models in partitional approaches, and hence improve clustering quality. To the best of our knowledge, most model-based clustering approaches use Laplacian smoothing to prevent zero probability while most similarity-based approaches employ the heuristic TF*IDF scheme to discount the effect of "general" words. Inspired by a series of statistical translation language model for text retrieval, we propose in this paper a novel smoothing method referred to as context-sensitive semantic smoothing for document clustering purpose. The comparative experiment on three datasets shows that model-based clustering approaches with semantic smoothing is effective in improving cluster quality.
26181940
Efficiently Computing Iceberg Cubes with Complex Constraints through Bounding
Data cubes facilitate fast On-Line Analytical Processing (OLAP). Iceberg cubes are special cubes comprise only the multi-dimensional groups satisfying some user-specified constraints. Previous algorithms have focused on iceberg cubes defined by relatively simple constraints such as "COUNT(*) ≥ δ" and "COUNT(*) ≥ δ AND AVG(Profit) ≥ α". We propose an algorithm I-Cubing that computes iceberg cubes defined by complex constraints involving multiple predicates of aggregates such as "COUNT(*) ≥ δ AND (AVG(Profit) ≥ α OR AVG(profit) ≤ β)". State-of-the-art iceberg cubing algorithms: BUC cannot handle such cases whereas H-Cubing has to incur extra cost. Our proposed bounding technique can prune for all the given constraints at once without extra cost. Experiments show that bounding has superior pruning power and I-Cubing is twice as fast as H-Cubing. Furthermore, I-Cubing performs equally well with more complex constraints.
8738797
Applying database support for large scale data driven science in distributed environments
There is a rapidly growing set of applications, referred to as data driven applications, in which analysis of large amounts of data drives the next steps taken by the scientist, e.g., running new simulations, doing additional measurements, extending the analysis to larger data collections. Critical steps in data analysis are to extract the data of interest from large and potentially distributed datasets and to move it from storage clusters to compute clusters for processing. We have developed a middleware framework, called GridDB-Lite, that is designed to efficiently support these two steps. We describe the application of GridDB-Lite in large scale oil reservoir simulation studies and experimentally evaluate several optimizations that can be employed in the GridDB-Lite runtime system.
18526893
Scaling and parallelizing a scientific feature mining application using a cluster middleware
Summary form only given. As scientific simulations are generating large amounts of data, analyzing this data to gain insights into scientific phenomenon is increasingly becoming a challenge. We present a case study on the use of a cluster middleware for rapidly creating a scalable and parallel implementation of a scientific data analysis application. Using FREERIDE (framework for rapid implementation of data mining engines), we parallelize as well as scale to disk-resident datasets a feature extraction algorithm. We have developed a parallel algorithm for this problem which matches the communication and computation structure supported by the FREERIDE system. The main observations from our experimental results are as follows: 1) the overhead of using the middleware is quite small in most cases, 2) there is an overhead associated with breaking the datasets into more partitions or chunks, and 3) if the dataset is partitioned into the same number of chunks, the execution time stays proportional to the size of the dataset and inversely proportional to the number of nodes, i.e. the overhead of communication or reading disk-resident datasets is very small.
17933107
Safety analysis of usage control authorization models
The usage control (UCON) model was introduced as a unified approach to capture a number of extensions for traditional access control models. While the policy specification flexibility and expressive power of this model have been studied in previous work, as a related and fundamental problem, the safety analysis of UCON has not been explored. This paper presents two fundamental safety results for UCONA, a sub-model of UCON only considering authorizations. In UCONA, an access control decision is based on the subject and/or the object attributes, which can be changed as the side-effects of using the access right, resulting in possible changes to future access control decisions. Hence the safety question in UCONA is all the more pressing since every access can potentially enable additional permissions due to the mutability of attributes in UCON. In this paper, first we show that the safety problem is in general undecidable. Then, we show that a restricted form of UCONA with finite attribute value domains and acyclic attribute creation relation has a decidable safety property. The decidable model maintains good expressive power as shown by specifying an RBAC system with a specific user-role assignment scheme and a DRM application with consumable rights.
40769679
Content-based image retrieval using a Gaussian mixture model in the wavelet domain
The research on Content-based Image Retrieval (CBIR) has been very active in recent years. The performance of a CBIR system can be significantly improved by selecting a good indexing feature space to represent image characteristics. In this paper, we introduce a statistical-model based technique for analyzing and extracting image features in the wavelet domain. The images are decomposed into a set of wavelet subspaces in the wavelet domain and for each wavelet subspace, a two component Gaussian mixture model is developed to describe the statistical characteristics of the wavelet coefficients. The model parameters, which are a good reflection of image features in the wavelet subspaces, are obtained by an EM (Expectation-Maximization) algorithm and employed to construct the indexing feature space for a CBIR system. We apply the new method on the Brodatz image database to demonstrate its performance. The experimental results indicate that our indexing feature space is very effective in representing image characteristics and provides a high retrieval rate in the CBIR system. When compared with some other conventional feature extraction methods, the new method achieves comparable retrieval performance with less number of features in the feature space, which means it is more computationally efficient.