17890414
Identifying significant genes from microarray data
Microarray technology is a recent development in experimental molecular biology which can produce quantitative expression measurements for thousands of genes in a single, cellular mRNA sample. These many gene expression measurements form a composite profile of the sample, which can be used to differentiate samples from different classes such as tissue types or treatments. However, for the gene expression profile data obtained in a specific comparison, most likely only some of the genes will, be differentially expressed between the classes, while many other genes have similar expression levels. Selecting a list of informative differential genes from these data is important for microarray data analysis. In this paper, we describe a framework for selecting informative genes, called ranking and combination analysis (RAC), which combines various existing informative gene selection methods. We conducted experiments using three data sets and six existing feature selection methods. The results show that the RAC framework is a robust and efficient approach to identify informative gene for microarray data. The combination approach on two selecting methods almost always performed better than the less efficient individual, and in many cases, better than both. More significantly, when considering all three data sets together, the combination approach, on average, outperforms each individual feature selection method. All of these indicate that RCA might be a viable and feasible approach for the microarray gene expression analysis.
267445
Biological Nomenclatures: A Source of Lexical Knowledge and Ambiguity
There has been increased work in developing automated systems that involve natural language processing (NLP) to recognize and extract genomic information from the literature. Recognition and identification of biological entities is a critical step in this process. NLP systems generally rely on nomenclatures and ontological specifications as resources for determining the names of the entities, assigning semantic categories that are consistent with the corresponding ontology, and assignment of identifiers that map to well-defined entities within a particular nomenclature. Although nomenclatures and ontologies are valuable for text processing systems, they were developed to aid researchers and are heterogeneous in structure and semantics. A uniform resource that is automatically generated from diverse resources, and that is designed for NLP purposes would be a useful tool for the field, and would further database interoperability. This paper presents work towards this goal. We have automatically created lexical resources from four model organism nomenclature systems (mouse, fly, worm, and yeast), and have studied performance of the resources within an existing NLP system, GENIES. Using nomenclatures is not straightforward because issues concerning ambiguity, synonymy, and name variations are quite challenging. In this paper we focus mainly on ambiguity. We determined that the number of ambiguous gene names within the individual nomenclatures, across the four nomenclatures, and with general English ranged from 0%-10.18%, 1.187%-20.30%, and 0%-2.49% respectively. When actually processing text, we found the rate of ambiguous occurrences (not counting ambiguities stemming from English words) to range from 2.4%-32.9% depending on the organisms considered.
2276859
Dynamically Generating a Protein Entity Dictionary Using Online Resources
With the overwhelming amount of biological knowledge stored in free text, natural language processing (NLP) has received much attention recently to make the task of managing information recorded in free text more feasible. One requirement for most NLP systems is the ability to accurately recognize biological entity terms in free text and the ability to map these terms to corresponding records in databases. Such task is called biological named entity tagging. In this paper, we present a system that automatically constructs a protein entity dictionary, which contains gene or protein names associated with UniProt identifiers using online resources. The system can run periodically to always keep up-to-date with these online resources. Using online resources that were available on Dec. 25, 2004, we obtained 4,046,733 terms for 1,640,082 entities. The dictionary can be accessed from the following website: http://biocreative.ifsm.umbc.edu/biothesaurus/.
3172606
Gene name ambiguity of eukaryotic nomenclatures
MOTIVATION
With more and more scientific literature published online, the effective management and reuse of this knowledge has become problematic. Natural language processing (NLP) may be a potential solution by extracting, structuring and organizing biomedical information in online literature in a timely manner. One essential task is to recognize and identify genomic entities in text. 'Recognition' can be accomplished using pattern matching and machine learning. But for 'identification' these techniques are not adequate. In order to identify genomic entities, NLP needs a comprehensive resource that specifies and classifies genomic entities as they occur in text and that associates them with normalized terms and also unique identifiers so that the extracted entities are well defined. Online organism databases are an excellent resource to create such a lexical resource. However, gene name ambiguity is a serious problem because it affects the appropriate identification of gene entities. In this paper, we explore the extent of the problem and suggest ways to address it.


RESULTS
We obtained gene information from 21 organisms and quantified naming ambiguities within species, across species, with English words and with medical terms. When the case (of letters) was retained, official symbols displayed negligible intra-species ambiguity (0.02%) and modest ambiguities with general English words (0.57%) and medical terms (1.01%). In contrast, the across-species ambiguity was high (14.20%). The inclusion of gene synonyms increased intra-species ambiguity substantially and full names contributed greatly to gene-medical-term ambiguity. A comprehensive lexical resource that covers gene information for the 21 organisms was then created and used to identify gene names by using a straightforward string matching program to process 45,000 abstracts associated with the mouse model organism while ignoring case and gene names that were also English words. We found that 85.1% of correctly retrieved mouse genes were ambiguous with other gene names. When gene names that were also English words were included, 233% additional 'gene' instances were retrieved, most of which were false positives. We also found that authors prefer to use synonyms (74.7%) to official symbols (17.7%) or full names (7.6%) in their publications.


CONTACT
lifeng.chen@dbmi.columbia.edu
17120587
Combination methods in microarray analysis
Microarray technology and experiment can produce thousands or tens of thousands of gene expression measurements in a single cellular mRNA sample. Selecting a list of informative differential genes from these measurement data has been the central problem for microarray analysis. Many methods to identify informative genes have been proposed in the past. However, due to the complexity of biological systems, each proposed method seems to perform nicely in a particular data set or specific experiment. It remains a great challenge to come up with a selection method for a wider spectrum of experiments and a broader variety of data sets. In this paper, we take the approach of method combination using data fusion and rank-score graph which have been used successfully in other application domains such as information retrieval, pattern recognition and tracking, and molecular similarity search. Our method combination is efficient and flexible and can be extended to become a general learning system for microarray gene expression analysis.
35256277
Generalized shuffle-exchange digraphs: Hamiltonian properties
The k-ary n-dimensional shuffle-exchange directed network S(k, n) consists of k/sup n/ nodes such that each node is represented as an k-ary n-tuple vector, a/sub 1/a/sub 2/...a/sub n/, where a/sub i/ is in [0, k-1]. Node a/sub 1/a/sub 2/...a/sub n/ is adjacent to node a/sub 2/a/sub 3/...a/sub n/a/sub 1/ (one shuffle link) and k-1 other nodes a/sub 1/a/sub 2/...a/sub n-1/b, where b/spl isin/[0, k-1] and b/spl ne/a/sub n/ (k-1 exchange links). S(k, n) have been widely used as topologies for VLSI networks, parallel architectures, and communication systems. However, since S(k, n) does not exist for the number of nodes between k/sup n/ and k/sup n+1/, Liu and Hsu have recently proposed a class of digraphs GS(k, N), which generalized S(k, n) to any number N of nodes. They also showed that GS(k, N) retains all the nice properties of S(k, n). In this paper, we survey these combinatorial properties and study Hamiltonian properties of GS(k, N). In particular, we have successfully obtained a Hamiltonian circuit for GS(k, k(k+1)) for any k>2.
18200538
Mining "Hidden Phrase" Definitions from the Web
Keyword searching is the most common form of document search on the Web. Many Web publishers manually annotate the META tags and titles of their pages with frequently queried phrases in order to improve their placement and ranking. A "hidden phrase" is defined as a phrase that occurs in the META tag of a Web page but not in its body. In this paper we present an algorithm that mines the definitions of hidden phrases from the Web documents. Phrase definitions allow (i) publishers to find relevant phrases with high query frequency, and, (ii) search engines to test if the content of the body of a document matches the phrases. We use co-occurrence clustering and association rule mining algorithms to learn phrase definitions from high-dimensional data sets. We also provide experimental results.
17123515
A Probabilistic Approach to Feature Selection - A Filter Solution
Feature selection can be de ned as a problem of nding a minimum set of M relevant at tributes that describes the dataset as well as the original N attributes do where M N After examining the problems with both the exhaustive and the heuristic approach to fea ture selection this paper proposes a proba bilistic approach The theoretic analysis and the experimental study show that the pro posed approach is simple to implement and guaranteed to nd the optimal if resources permit It is also fast in obtaining results and e ective in selecting features that im prove the performance of a learning algo rithm An on site application involving huge datasets has been conducted independently It proves the e ectiveness and scalability of the proposed algorithm Discussed also are various aspects and applications of this fea ture selection algorithm
15137899
Ensembles of cascading trees
We introduce a new method, called CS4, to construct committees of decision trees for classification. The method considers different top-ranked features as the root nodes of member trees. This idea is particularly suitable for dealing with high-dimensional bio-medical data as top-ranked features in this type of data usually possess similar merits for classification. To make a decision, the committee combines the power of individual trees in a weighted manner. Unlike Bagging or Boosting which uses bootstrapped training data, our method builds all the member trees of a committee using exactly the same set of training data. We have tested these ideas on UCI data sets as well as recent bio-medical data sets of gene expression or proteomic profiles that are usually described by more than 10,000 features. All the experimental results show that our method is efficient and that the classification performance are superior to C4.5 family algorithms.
36964410
A Knowledge Object Oriented System for High Throughput Collection and Analysis of Data
7580221
Efficient Feature Selection via Analysis of Relevance and Redundancy
Feature selection is applied to reduce the number of features in many applications where data has hundreds or thousands of features. Existing feature selection methods mainly focus on finding relevant features. In this paper, we show that feature relevance alone is insufficient for efficient feature selection of high-dimensional data. We define feature redundancy and propose to perform explicit redundancy analysis in feature selection. A new framework is introduced that decouples relevance analysis and redundancy analysis. We develop a correlation-based method for relevance and redundancy analysis, and conduct an empirical study of its efficiency and effectiveness comparing with representative methods.