Information Extraction from Biomedical Text Using Machine Learning

Inadequate drug experimental data and the use of unlicensed drugs may cause adverse drug reactions, especially in pediatric populations. Every year the U.S. Food and Drug Administration approves human prescription drugs for marketing. The labels associated with these drugs include information about clinical trials and drug response in pediatric population. In order for doctors to make an informed decision about the safety and effectiveness of these drugs for children, there is a need to analyze complex and often unstructured drug labels. In this work, first, an exploratory analysis of drug labels using a Natural Language Processing pipeline is performed. Second, Machine Learning algorithms have been employed to build baseline binary classification models to identify pediatric text in unstructured drug labels. Third, a series of experiments have been executed to evaluate the accuracy of the model. The prototype is able to classify pediatrics-related text with a recall of 0.93 and precision of 0.86

New Resources and Perspectives for Biomedical Event Extraction

Event extraction is a major focus of recent work in biomedical information extraction. Despite substantial advances, many challenges still remain for reliable automatic extraction of events from text. We introduce a new biomedical event extraction resource consisting of analyses automatically created by systems participating in the recent BioNLP Shared Task (ST) 2011. In providing for the first time the outputs of a broad set of state-ofthe-art event extraction systems, this resource opens many new opportunities for studying aspects of event extraction, from the identification of common errors to the study of effective approaches to combining the strengths of systems. We demonstrate these opportunities through a multi-system analysis on three BioNLP ST 2011 main tasks, focusing on events that none of the systems can successfully extract. We further argue for new perspectives to the performance evaluation of domain event extraction systems, considering a document-level, “off-the-page ” representation and evaluation to complement the mentionlevel evaluations pursued in most recent work.

Application of Biomedical Text Mining

With the enormous volume of biological literature, increasing growth phenomenon due to the high rate of new publications is one of the most common motivations for the biomedical text mining. Aiming at this massive literature to process, it could extract more biological information for mining biomedical knowledge. Using the information will help understand the mechanism of disease generation, promote the development of disease diagnosis technology, and promote the development of new drugs in the field of biomedical research. Based on the background, this chapter introduces the rise of biomedical text mining. Then, it describes the biomedical text-mining technology, namely natural language processing, including the several components. This chapter emphasizes the two aspects in biomedical text mining involving static biomedical information recognization and dynamic biomedical information extraction using instance analysis from our previous works. The aim is to provide a way to quickly understand biomedical text mining for some researchers

Enhancing Biomedical Text Summarization Using Semantic Relation Extraction

Automatic text summarization for a biomedical concept can help researchers to get the key points of a certain topic from large amount of biomedical literature efficiently. In this paper, we present a method for generating text summary for a given biomedical concept, e.g., H1N1 disease, from multiple documents based on semantic relation extraction. Our approach includes three stages: 1) We extract semantic relations in each sentence using the semantic knowledge representation tool SemRep. 2) We develop a relation-level retrieval method to select the relations most relevant to each query concept and visualize them in a graphic representation. 3) For relations in the relevant set, we extract informative sentences that can interpret them from the document collection to generate text summary using an information retrieval based method. Our major focus in this work is to investigate the contribution of semantic relation extraction to the task of biomedical text summarization. The experimental results on summarization for a set of diseases show that the introduction of semantic knowledge improves the performance and our results are better than the MEAD system, a well-known tool for text summarization

Ontology-based knowledge representation of experiment metadata in biological data mining

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes