23957657
Terminology model discovery using natural language processing and visualization techniques
Medical terminologies are important for unambiguous encoding and exchange of clinical information. The traditional manual method of developing terminology models is time-consuming and limited in the number of phrases that a human developer can examine. In this paper, we present an automated method for developing medical terminology models based on natural language processing (NLP) and information visualization techniques. Surgical pathology reports were selected as the testing corpus for developing a pathology procedure terminology model. The use of a general NLP processor for the medical domain, MedLEE, provides an automated method for acquiring semantic structures from a free text corpus and sheds light on a new high-throughput method of medical terminology model development. The use of an information visualization technique supports the summarization and visualization of the large quantity of semantic structures generated from medical documents. We believe that a general method based on NLP and information visualization will facilitate the modeling of medical terminologies.
13024009
Building effective defect-prediction models in practice
Defective software modules cause software failures, increase development and maintenance costs, and decrease customer satisfaction. Effective defect prediction models can help developers focus quality assurance activities on defect-prone modules and thus improve software quality by using resources more efficiently. These models often use static measures obtained from source code, mainly size, coupling, cohesion, inheritance, and complexity measures, which have been associated with risk factors, such as defects and changes.
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.
208013251
Modeling the Effect of Size on Defect Proneness for Open-Source Software
Quality is becoming increasingly important with the continuous adoption of open-source software. Previous research has found that there is generally a positive relationship between module size and defect proneness. Therefore, in open-source software development, it is important to monitor module size and understand its impact on defect proneness. However, traditional approaches to quality modeling, which measure specific system snapshots and obtain future defect counts, are not well suited because open-source modules usually evolve and their size changes over time. In this study, we used Cox proportional hazards modeling with recurrent events to study the effect of class size on defect-proneness in the Mozilla product. We found that the effect of size was significant, and we quantified this effect on defect proneness.
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/.
6684027
iProLINK: an integrated protein resource for literature mining
The exponential growth of large-scale molecular sequence data and of the PubMed scientific literature has prompted active research in biological literature mining and information extraction to facilitate genome/proteome annotation and improve the quality of biological databases. Motivated by the promise of text mining methodologies, but at the same time, the lack of adequate curated data for training and benchmarking, the Protein Information Resource (PIR) has developed a resource for protein literature mining--iProLINK (integrated Protein Literature INformation and Knowledge). As PIR focuses its effort on the curation of the UniProt protein sequence database, the goal of iProLINK is to provide curated data sources that can be utilized for text mining research in the areas of bibliography mapping, annotation extraction, protein named entity recognition, and protein ontology development. The data sources for bibliography mapping and annotation extraction include mapped citations (PubMed ID to protein entry and feature line mapping) and annotation-tagged literature corpora. The latter includes several hundred abstracts and full-text articles tagged with experimentally validated post-translational modifications (PTMs) annotated in the PIR protein sequence database. The data sources for entity recognition and ontology development include a protein name dictionary, word token dictionaries, protein name-tagged literature corpora along with tagging guidelines, as well as a protein ontology based on PIRSF protein family names. iProLINK is freely accessible at http://pir.georgetown.edu/iprolink, with hypertext links for all downloadable files.
34878858
Dimensionality reduction of unsupervised data
Dimensionality reduction is an important problem for efficient handling of large databases. Many feature selection methods exist for supervised data having class information. Little work has been done for dimensionality reduction of unsupervised data in which class information is not available. Principal component analysis (PCA) is often used. However, PCA creates new features. It is difficult to obtain intuitive understanding of the data using the new features only. We are concerned with the problem of determining and choosing the important original features for unsupervised data. Our method is based on the observation that removing an irrelevant feature from the feature set may not change the underlying concept of the data, but not so otherwise. We propose an entropy measure for ranking features, and conduct extensive experiments to show that our method is able to find the important features. Also it compares well with a similar feature ranking method (Relief) that requires class information unlike our method.
17436749
Feature Transformation and Multivariate Decision Tree Induction
Univariate decision trees (UDT's) have inherent problems of replication, repetition, and fragmentation. Multivariate decision trees (MDT's) have been proposed to overcome some of the problems. Close examination of the conventional ways of building MDT's, however, reveals that the fragmentation problem still persists. A novel approach is suggested to minimize the fragmentation problem by separating hyperplane search from decision tree building. This is achieved by feature transformation. Let the initial feature vector be x, the new feature vector after feature transformation T is y, i.e., y = T(x). We can obtain an MDTb y (1) building a UDT on y; and (2) replacing new features y at each node with the combinations of initial features x. We elaborate on the advantages of this approach, the details of T, and why it is expected to perform well. Experiments are conducted in order to confirm the analysis, and results are compared to those of C4.5, OC1, and CART.
507681
A Novel Approach to Model Generation for Heterogeneous Data Classification
Ensemble methods such as bagging and boosting have been successfully applied to classification problems. Two important issues associated with an ensemble approach are: how to generate models to construct an ensemble, and how to combine them for classification. In this paper, we focus on the problem of model generation for heterogeneous data classification. If we could partition heterogeneous data into a number of homogeneous partitions, we will likely generate reliable and accurate classification models over the homogeneous partitions. We examine different ways of forming homogeneous subsets and propose a novel method that allows a data point to be assigned multiple times in order to generate homogeneous partitions for ensemble learning. We present the details of the new algorithm and empirical studies over the UCI benchmark datasets and datasets of image classification, and show that the proposed approach is effective for heterogeneous data classification.
11656540
Searching for Interacting Features
Feature interaction presents a challenge to feature selection for classification. A feature by itself may have little correlation with the target concept, but when it is combined with some other features, they can be strongly correlated with the target concept. Unintentional removal of these features can result in poor classification performance. Handling feature interaction can be computationally intractable. Recognizing the presence of feature interaction, we propose to efficiently handle feature interaction to achieve efficient feature selection and present extensive experimental results of evaluation.
10149257
Semi-supervised Feature Selection via Spectral Analysis
Feature selection is an important task in effective data mining. A new challenge to feature selection is the socalled “small labeled-sample problem” in which labeled data is small and unlabeled data is large. The paucity of labeled instances provides insufficient information about the structure of the target concept, and can cause supervised feature selection algorithms to fail. Unsupervised feature selection algorithms can work without labeled data. However, these algorithms ignore label information, which may lead to performance deterioration. In this work, we propose to use both (small) labeled and (large) unlabeled data in feature selection, which is a topic has not yet been addressed in feature selection research. We present a semi-supervised feature selection algorithm based on spectral analysis. The algorithm exploits both labeled and unlabeled data through a regularization framework, which provides an effective way to address the “small labeled-sample” problem. Experimental results demonstrated the efficacy of our approach and confirmed that small labeled samples can help feature selection with unlabeled data. Keyword: Feature Selection, Semi-supervised Learning, Machine Learning, Spectral Analysis