30030780
Headwords and Suffixes in Biomedical Names
Natural Language Processing (NLP) techniques have been used for the task of extracting and mining knowledge from biomedical literature. One of the critical steps of such a task is biomedical named entity tagging (BNER) which usually contains two steps: the first step is the identification of biomedical names in text and the second is the assignment of semantic classes predefined to names identified by the first step. Headwords and suffixes have been used frequently by BNER systems as features for the assignment of semantic classes to names in text. However, there are few studies to evaluate the performance of headwords and suffixes in predicting semantic classes of biomedical terms utilizing knowledge sources in an unsupervised way. We conducted a study to evaluate the performance of headwords and suffixes using names in the Unified Medical Language System (UMLS) where the semantic classes associated with these names were obtained by modifying an existing UMLS semantic group system and incorporating the GENIA ontology. We define headwords and suffixes that are significantly associated with a specific semantic class as semantic suffixes. The performance of semantic assignment using semantic suffixes achieved an F-measure of 86.4% with a precision of 91.6% and a recall of 81.7%. When applying these semantic suffixes obtained using the UMLS to names extracted from the GENIA corpus, the system achieved an F-measure of 73.4% with a precision of 84.2% and a recall of 65.1% where these performance measures could be improved dramatically when limited to names associated with classes that have the corresponding GENIA types.
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.
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.
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.
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.
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.
16551486
Feature Extraction for Image Mining
Due to the digitization of data and advances in technology, it has become extremely easy to obtain and store large quantities of data, particularly Multimedia data. Fields ranging from Commercial to Military need to analyze these data in an efficient and fast manner. Presently, tools for mining images are few and require human intervention. Feature selection and extraction is the pre-processing step of Image Mining. Obviously this is a critical step in the entire scenario of Image Mining. Our approach to mine from Images – to extract patterns and derive knowledge from large collections of images, deals mainly with identification and extraction of unique features for a particular domain. Though there are various features available, the aim is to identify the best features and thereby extract relevant information from the images. We have tried various methods for extraction; the features extracted and the techniques used are evaluated for their contribution to solving the problem. Experimental results show that the features used are sufficient to identify the patterns from the Images. The extracted features were evaluated for goodness and tested on test images. An interactive system was developed which allows the user to define new features and to resolve uncertain regions.
24079642
Detecting outliers in irregularly distributed spatial data sets by locally adaptive and robust statistical analysis and GIS
In this paper, we propose a new method for detecting outliers in an irregularly distributed spatial data set. Our method has two desirable properties. First, it is functionally effective due to the introduction of sensitive outlier indices and locally adaptive and robust statistical criteria. Second, it is computationally efficient because of the use of super-block based spatial data sorting and searching scheme. Our method has been implemented using the C programming language and integrated with the Arc/Info GIS system. The integration leads to a powerful exploratory data analysis tool for checking and analysing anomalous values in a GIS environment. Local outliers can be automatically labeled with our method, subject to some user-defined parameters. Outliers represent anomalous or suspicious values in a statistical sense, which may not necessarily be erroneous values. Instead of being simply discarded, statistical outliers should be investigated further using prior qualitative knowledge or in association with other GIS data layers.
207156949
Design and implementation of a single system image operating system for ad hoc networks
In this paper, we describe the design and implementation of a distributed operating system for ad hoc networks. Our system simplifies the programming of ad hoc networks and extends total system lifetime by making the entire network appear as a single virtual machine. It automatically and transparently partitions applications into components and dynamically finds them a placement on nodes within the network to reduce energy consumption and to increase system longevity. This paper describes our programming model, outlines the design and implementation of our system and examines the energy efficiency of our approach through extensive simulations as well as validation of a deployment on a physical testbed. We evaluate practical, power-aware, general-purpose algorithms for component placement and migration, and demonstrate that they can significantly increase system longevity by effectively distributing energy consumption and avoiding hotspots.
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
2204750
A model of textual affect sensing using real-world knowledge
This paper presents a novel way for assessing the affective qualities of natural language and a scenario for its use. Previous approaches to textual affect sensing have employed keyword spotting, lexical affinity, statistical methods, and hand-crafted models. This paper demonstrates a new approach, using large-scale real-world knowledge about the inherent affective nature of everyday situations (such as "getting into a car accident") to classify sentences into "basic" emotion categories. This commonsense approach has new robustness implications.Open Mind Commonsense was used as a real world corpus of 400,000 facts about the everyday world. Four linguistic models are combined for robustness as a society of commonsense-based affect recognition. These models cooperate and compete to classify the affect of text. Such a system that analyzes affective qualities sentence by sentence is of practical value when people want to evaluate the text they are writing. As such, the system is tested in an email writing application. The results suggest that the approach is robust enough to enable plausible affective text user interfaces.