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.
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
14024342
A Semantic Approach for Mining Hidden Links from Complementary and Non-interactive Biomedical Literature
Two complementary and non-interactive literature sets of articles, when they are considered together, can reveal useful information of scientific interest not apparent in either of the two sets alone. Swanson called the existence of such hidden links as undiscovered public knowledge (UPK). The novel connection between Raynaud disease and fish oils was uncovered from complementary and non-interactive biomedical literature by Swanson in 1986. Since then, there have been many approaches to uncover UPK by mining the biomedical literature. These earlier works, however, required substantial manual intervention to reduce the number of possible connections. This paper proposes a semantic-based mining model for undiscovered public knowledge using the biomedical literature. Our method replaces manual ad-hoc pruning by using semantic knowledge from the biomedical ontologies. Using the semantic types and semantic relationships of the biomedical concepts, our prototype system can identify the relevant concepts collected from Medline and generate the novel hypothesis between these concepts. The system successfully replicates Swanson’s two famous discoveries: Raynaud disease/fish oils and migraine/magnesium. Compared with previous approaches such as LSI-based and traditional association rule-based methods, our method generates much fewer but more relevant novel hypotheses, and requires much less human intervention in the discovery procedure
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.
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.
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.
8353152
An Efficient Algorithm for Mining Coherent Patterns from Heterogeneous Microarrays
DNA microarray techniques present a novel way for geneticists to monitor interactions among tens of thousands of genes simultaneously, and have become standard lab routines in gene discovery, disease diagnosis, and drug design. There has been extensive research on coherent subspace clustering of gene expressions measured under consistent experimental settings. This implies that all experiments are run using the same batch of microarray chips with similar characteristics of noise. Algorithms developed under this assumption may not be applicable for analyzing data collected from heterogeneous settings, where the set of genes being monitored may be different and expression levels may be not directly comparable even for the same gene. In this paper, we propose a model, F-cluster, for mining subspace coherent patterns from heterogeneous gene expression data, which is shown effective for revealing truthful patterns and reducing spurious ones. We also develop an efficient and scalable hybrid approach that combines gene-pair based and sample-pair based pruning to generate F-clusters from multiple gene expression matrices simultaneously. The experimental results demonstrate that our model can discover significant clusters that may not be identified by previous models.
13935393
Lossy to lossless image compression using allpass filters
In this paper, an effective implementation of the allpass-based orthonormal symmetric wavelets is proposed for image compression. Since the orthonormal symmetric wavelets are used, it can be expected to get better compression performance than biorthogonal wavelets. Firstly, the implementation of irreversible real-to-real wavelets is presented and its decomposition process is shown by using allpass filters. Then, the realization of the reversible integer-to-integer wavelets is given by utilizing the invertible implementation of allpass filters. Finally, the coding performance of the orthonormal symmetric wavelets is evaluated and compared with the D-9/7 and D-5/3 wavelets. It is shown from the experimental results that the allpass-based orthonormal symmetric wavelets can achieve better compression performance than the D-9/7 and D-5/3 wavelets.
17630030
Prediction of Protein Complexes Based on Protein Interaction Data and Functional Annotation Data Using Kernel Methods
Prediction of protein complexes is a crucial problem in computational biology. The increasing amount of available genomic data can enhance the identification of protein complexes. Here we describe an approach for predicting protein complexes based on integration of protein-protein interaction (PPI) data and protein functional annotation data. The basic idea is that proteins in protein complexes often interact with each other and protein complexes exhibit high functional consistency/even multiple functional consistency. We create a protein-protein relationship network (PPRN) via a kernel-based integration of these two genomic data. Then we apply the MCODE algorithm on PPRN to detect network clusters as numerically determined protein complexes. We present the results of the approach to yeast Sacchromyces cerevisiae. Comparison with well-known experimentally derived complexes and results of other methods verifies the effectiveness of our approach.
6465422
CAEP: Classification by Aggregating Emerging Patterns
Emerging patterns (EPs) are itemsets whose supports change significantly from one dataset to another; they were recently proposed to capture multi-attribute contrasts between data classes, or trends over time. In this paper we propose a new classifier, CAEP, using the following main ideas based on EPs: (i) Each EP can sharply differentiate the class membership of a (possibly small) fraction of instances containing the EP, due to the big difference between its supports in the opposing classes; we define the differentiating power of the EP in terms of the supports and their ratio, on instances containing the EP. (ii) For each instance t, by aggregating the differentiating power of a fixed, automatically selected set of EPs, a score is obtained for each class. The scores for all classes are normalized and the largest score determines t’s class. CAEP is suitable for many applications, even those with large volumes of high (e.g. 45) dimensional data; it does not depend on dimension reduction on data; and it is usually equally accurate on all classes even if their populations are unbalanced. Experiments show that CAEP has consistent good predictive accuracy, and it almost always outperforms C4.5 and CBA. By using efficient, border-based algorithms (developed elsewhere) to discover EPs, CAEP scales up on data volume and dimensionality. Observing that accuracy on the whole dataset is too coarse description of classifiers, we also used a more accurate measure, sensitivity and precision, to better characterize the performance of classifiers. CAEP is also very good under this measure.
8152868
A web-enabled video indexing system
Video parsing and indexing is an important early stage of content-based video analysis. In this paper, we present a new web-enabled video indexing system that integrates Synchronized Multimedia Integration Language (SMIL) standard. New algorithms are proposed for video temporal segmentation. Sharp transition detection is achieved by an enhanced histogram-based method that is robust to illumination changes. For gradual transition detection, new features are introduced for dissolve detection. The proposed dissolve detector is based on a combined analysis of mean-variance-skewness of intensity. Compared with existing variance-based approaches, the introduced new features improve the discrimination ability on shot boundaries. We also describe methods for eliminating false positives. Experimental results show that the proposed algorithms can effectively detect shot boundaries. Detected scenes and other cinematic attributes are structured and organized by integrating HTML and SMIL. For each video file, the system generates a table-of-contents indexing file. The user-friendly interface provides web-based interaction, browsing and previewing of video content