Knowledge-based extraction of adverse drug events from biomedical text

Background: Many biomedical relation extraction systems are machine-learning based and have to be trained on large annotated corpora that are expensive and cumbersome to construct. We developed a knowledge-based relation extraction system that requires minimal training data, and applied the system for the extraction of adverse drug events from biomedical text. The system consists of a concept recognition module that identifies drugs and adverse effects in sentences, and a knowledg

Combined SVM-CRFs for Biological Named Entity Recognition with Maximal Bidirectional Squeezing

Biological named entity recognition, the identification of biological terms in text, is essential for biomedical information extraction. Machine learning-based approaches have been widely applied in this area. However, the recognition performance of current approaches could still be improved. Our novel approach is to combine support vector machines (SVMs) and conditional random fields (CRFs), which can complement and facilitate each other. During the hybrid process, we use SVM to separate biological terms from non-biological terms, before we use CRFs to determine the types of biological terms, which makes full use of the power of SVM as a binary-class classifier and the data-labeling capacity of CRFs. We then merge the results of SVM and CRFs. To remove any inconsistencies that might result from the merging, we develop a useful algorithm and apply two rules. To ensure biological terms with a maximum length are identified, we propose a maximal bidirectional squeezing approach that finds the longest term. We also add a positive gain to rare events to reinforce their probability and avoid bias. Our approach will also gradually extend the context so more contextual information can be included. We examined the performance of four approaches with GENIA corpus and JNLPBA04 data. The combination of SVM and CRFs improved performance. The macro-precision, macro-recall, and macro-F1 of the SVM-CRFs hybrid approach surpassed conventional SVM and CRFs. After applying the new algorithms, the macro-F1 reached 91.67% with the GENIA corpus and 84.04% with the JNLPBA04 data

Using rule-based natural language processing to improve disease normalization in biomedical text

Background and objective: In order for computers to extract useful information from unstructured text, a concept normalization system is needed to link relevant concepts in a text to sources that contain further information about the concept. Popular concept normalization tools in the biomedical field are dictionarybased. In this study we investigate the usefulness of natural language processing (NLP) as an adjunct to dictionary-based concept normalization. Methods: We compared the performance of two biomedical concept normalization systems, MetaMap and Peregrine, on the Arizona Disease Corpus, with and without the use of a rule-based NLP module. Performance was assessed for exact and inexact boundary matching of the system annotations with those of the gold standard and for concept identifier matching. Results: Without the NLP module, MetaMap and Peregrine attained F-scores of 61.0% and 63.9%, respectively, for exact boundary matching, and 55.1% and 56.9% for concept identifier matching. With the aid of the NLP module, the F-scores of MetaMap and Peregrine improved to 73.3% and 78.0% for boundary matching, and to 66.2% and 69.8% for concept identifier matching. For inexact boundary matching, performances further increased to 85.5% and 85.4%, and to 73.6% and 73.3% for concept identifier matching. Conclusions: We have shown the added value of NLP for the recognition and normalization of diseases with MetaMap and Peregrine. The NLP module is general and can be applied in combination with any concept normalization system. Whether its use for concept types other than disease is equally advantageous remains to be investigated

A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

Many researchers focus on developing protein-named entity recognition (Protein-NER) or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM) and parsing tree. PPIMiner consists of three main models: natural language processing (NLP) model, Protein-NER model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER

A pilot study in an application of text mining to learning system evaluation

Text mining concerns discovering and extracting knowledge from unstructured data. It transforms textual data into a usable, intelligible format that facilitates classifying documents, finding explicit relationships or associations between documents, and clustering documents into categories. Given a collection of survey comments evaluating the civil engineering learning system, text mining technique is applied to discover and extract knowledge from the comments. This research focuses on the study of a systematic way to apply a software tool, SAS Enterprise Miner, to the survey data. The purpose is to categorize the comments into different groups in an attempt to identify major concerns from the users or students. Each group will be associated with a set of key terms. This is able to assist the evaluators of the learning system to obtain the ideas from those summarized terms without the need of going through a potentially huge amount of data --Abstract, page iii

Statistical Methods for Semiconductor Manufacturing

In this thesis techniques for non-parametric modeling, machine learning, filtering and prediction and run-to-run control for semiconductor manufacturing are described. In particular, algorithms have been developed for two major applications area: - Virtual Metrology (VM) systems; - Predictive Maintenance (PdM) systems. Both technologies have proliferated in the past recent years in the semiconductor industries, called fabs, in order to increment productivity and decrease costs. VM systems aim of predicting quantities on the wafer, the main and basic product of the semiconductor industry, that may be physically measurable or not. These quantities are usually ’costly’ to be measured in economic or temporal terms: the prediction is based on process variables and/or logistic information on the production that, instead, are always available and that can be used for modeling without further costs. PdM systems, on the other hand, aim at predicting when a maintenance action has to be performed. This approach to maintenance management, based like VM on statistical methods and on the availability of process/logistic data, is in contrast with other classical approaches: - Run-to-Failure (R2F), where there are no interventions performed on the machine/process until a new breaking or specification violation happens in the production; - Preventive Maintenance (PvM), where the maintenances are scheduled in advance based on temporal intervals or on production iterations. Both aforementioned approaches are not optimal, because they do not assure that breakings and wasting of wafers will not happen and, in the case of PvM, they may lead to unnecessary maintenances without completely exploiting the lifetime of the machine or of the process. The main goal of this thesis is to prove through several applications and feasibility studies that the use of statistical modeling algorithms and control systems can improve the efficiency, yield and profits of a manufacturing environment like the semiconductor one, where lots of data are recorded and can be employed to build mathematical models. We present several original contributions, both in the form of applications and methods. The introduction of this thesis will be an overview on the semiconductor fabrication process: the most common practices on Advanced Process Control (APC) systems and the major issues for engineers and statisticians working in this area will be presented. Furthermore we will illustrate the methods and mathematical models used in the applications. We will then discuss in details the following applications: - A VM system for the estimation of the thickness deposited on the wafer by the Chemical Vapor Deposition (CVD) process, that exploits Fault Detection and Classification (FDC) data is presented. In this tool a new clustering algorithm based on Information Theory (IT) elements have been proposed. In addition, the Least Angle Regression (LARS) algorithm has been applied for the first time to VM problems. - A new VM module for multi-step (CVD, Etching and Litography) line is proposed, where Multi-Task Learning techniques have been employed. - A new Machine Learning algorithm based on Kernel Methods for the estimation of scalar outputs from time series inputs is illustrated. - Run-to-Run control algorithms that employ both the presence of physical measures and statistical ones (coming from a VM system) is shown; this tool is based on IT elements. - A PdM module based on filtering and prediction techniques (Kalman Filter, Monte Carlo methods) is developed for the prediction of maintenance interventions in the Epitaxy process. - A PdM system based on Elastic Nets for the maintenance predictions in Ion Implantation tool is described. Several of the aforementioned works have been developed in collaborations with major European semiconductor companies in the framework of the European project UE FP7 IMPROVE (Implementing Manufacturing science solutions to increase equiPment pROductiVity and fab pErformance); such collaborations will be specified during the thesis, underlying the practical aspects of the implementation of the proposed technologies in a real industrial environment

Um Modelo de descoberta de conhecimento inerente à evolução temporal dos relacionamentos entre elementos textuais

Tese (doutorado) - Universidade Federal de Santa Catarina, Centro Tecnológico, Programa de Pós-Graduação em Engenharia e Gestão do Conhecimento, Florianópolis, 2011Há algum tempo tem sido observado e discutido o aumento expressivo na quantidade de informação produzida e publicada pelo mundo. Se por um lado essa situação propicia muitas oportunidades de uso dessa informação para a tomada de decisão, por outro, lança muitos desafios em como armazenar, recuperar e transformar essa informação em conhecimento. Umas das formas de descoberta de conhecimento que tem atraído atenção de pesquisadores é a análise dos relacionamentos presentes nas informações disponíveis. Não obstante, devido à grande velocidade de criação de novos conteúdos a dimensão tempo torna-se uma propriedade intrínseca e relevante presente nestas fontes de informação. Assim, o objetivo é desenvolver um modelo para descoberta de conhecimento a partir de informações não estruturadas analisando a evolução dos relacionamentos entre os elementos textuais ao longo do tempo. O modelo proposto é dividido por fases, assim como os modelos tradicionais de descoberta de conhecimento. As fases deste modelo são: configuração dos temas de análise, identificação das ocorrências dos conceitos, correlação e correlação temporal, associação e associação temporal, criação do repositório de temas de análise, e tarefas intensivas em conhecimento, com ênfase nos relacionamentos diretos e indiretos entre os conceitos do domínio. A demonstração de viabilidade é realizada por meio de um protótipo baseado no modelo proposto e sua aplicação em um estudo de caso. É realizada também uma análise comparativa do modelo proposto com outros modelos de descoberta de conhecimento em textos