One essential task in information extraction from the medical corpus is drug name recognition. Compared with text sources come from other domains, the medical text is special and has unique characteristics. In addition, the medical text mining poses more challenges, e.g., more unstructured text, the fast growing of new terms addition, a wide range of name variation for the same drug. The mining is even more challenging due to the lack of labeled dataset sources and external knowledge, as well as multiple token representations for a single drug name that is more common in the real application setting. Although many approaches have been proposed to overwhelm the task, some problems remained with poor F-score performance (less than 0.75). This paper presents a new treatment in data representation techniques to overcome some of those challenges. We propose three data representation techniques based on the characteristics of word distribution and word similarities as a result of word embedding training. The first technique is evaluated with the standard NN model, i.e., MLP (Multi-Layer Perceptrons). The second technique involves two deep network classifiers, i.e., DBN (Deep Belief Networks), and SAE (Stacked Denoising Encoders). The third technique represents the sentence as a sequence that is evaluated with a recurrent NN model, i.e., LSTM (Long Short Term Memory). In extracting the drug name entities, the third technique gives the best F-score performance compared to the state of the art, with its average F-score being 0.8645.
Another approach for discovering valuable information from clinical text data that adopts event-location extraction model was examined by J, @cite_10 . They use an SVM classifier to predict drug or non-drug entity which is applied to DrugBank dataset. The best performance achieved by their method is a 0.6 in F-score. The drawback of their approach is that it only deals with a single token drug name.
@cite_10
2251644265 2097300420 2102563561 2124479345
Several state-of-the-art event extraction systems employ models based on Support Vector Machines (SVMs) in a pipeline architecture, which fails to exploit the joint dependencies that typically exist among events and arguments. While there have been attempts to overcome this limitation using Markov Logic Networks (MLNs), it remains challenging to perform joint inference in MLNs when the model encodes many high-dimensional sophisticated features such as those essential for event extraction. In this paper, we propose a new model for event extraction that combines the power of MLNs and SVMs, dwarfing their limitations. The key idea is to reliably learn and process high-dimensional features using SVMs; encode the output of SVMs as low-dimensional, soft formulas in MLNs; and use the superior joint inferencing power of MLNs to enforce joint consistency constraints over the soft formulas. We evaluate our approach for the task of extracting biomedical events on the BioNLP 2013, 2011 and 2009 Genia shared task datasets. Our approach yields the best F1 score to date on the BioNLP’13 (53.61) and BioNLP’11 (58.07) datasets and the second-best F1 score to date on the BioNLP’09 dataset (58.16). Motivation: The abundance of biomedical literature has attracted significant interest in novel methods to automatically extract biomedical relations from the literature. Until recently, most research was focused on extracting binary relations such as protein–protein interactions and drug–disease relations. However, these binary relations cannot fully represent the original biomedical data. Therefore, there is a need for methods that can extract fine-grained and complex relations known as biomedical events. Results: In this article we propose a novel method to extract biomedical events from text. Our method consists of two phases. In the first phase, training data are mapped into structured representations. Based on that, templates are used to extract rules automatically. In the second phase, extraction methods are developed to process the obtained rules. When evaluated against the Genia event extraction abstract and full-text test datasets (Task 1), we obtain results with F-scores of 52.34 and 53.34, respectively, which are comparable to the state-of-the-art systems. Furthermore, our system achieves superior performance in terms of computational efficiency. Availability: Our source code is available for academic use at http: dl.dropbox.com u 10256952 BioEvent.zip Contact: [email protected] Nested event structures are a common occurrence in both open domain and domain specific extraction tasks, e.g., a "crime" event can cause a "investigation" event, which can lead to an "arrest" event. However, most current approaches address event extraction with highly local models that extract each event and argument independently. We propose a simple approach for the extraction of such structures by taking the tree of event-argument relations and using it directly as the representation in a reranking dependency parser. This provides a simple framework that captures global properties of both nested and flat event structures. We explore a rich feature space that models both the events to be parsed and context from the original supporting text. Our approach obtains competitive results in the extraction of biomedical events from the BioNLP'09 shared task with a F1 score of 53.5 in development and 48.6 in testing. Motivation: Knowledge of drug-drug interactions (DDIs) is crucial for healthcare professionals in order to avoid adverse effects when co-administering drugs to patients. Since most newly discovered DDIs are made available through scientific publications, automatic DDI extraction is highly relevant. Results: We propose a novel feature-based approach to extract DDIs from text. Our approach consists of three steps. First, we apply text preprocessing to convert input sentences from a given dataset into structured representations. Second, we map each candidate DDI pair from that dataset into a suitable syntactic structure. Based on that, a novel set of features is used to generate feature vectors for these candidate DDI pairs. Third, the obtained feature vectors are used to train a support vector machine (SVM) classifier. When evaluated on two DDI extraction challenge test datasets from 2011 and 2013, our system achieves F-scores of 71.1 and 83.5 , respectively, outperforming any state-of-the-art DDI extraction system. Availability: The source code is available for academic use at http: www.biosemantics.org uploads DDI.zip