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.
Drug name extraction and their classification are one of the challenges in the Semantic Evaluation Task (SemEval 2013). The best-reported performance for this challenge was 71.5 A hybrid approach model, which combines statistical learning and dictionary based, is proposed by @cite_11 . In their study, the author utilizes word2vec representation, CRF learning model and DINTO, a drug ontology. With this word2vec representation, targeted drug is treated as a current token in a context windows which consists of three tokens on the left and three tokens in the right. Additional features are included in the data representation such as pos tags, lemma in the windows context, an orthography feature as uppercase, lowercase, and mixed cap. The author also used Wikipedia text as an additional resource to perform word2vec representation training. The best F-score value in extracting the drug name provided by the method is 0.72.
@cite_11
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This paper describes a machine learningbased approach that uses word embedding features to recognize drug names from biomedical texts. As a starting point, we developed a baseline system based on Conditional Random Field (CRF) trained with standard features used in current Named Entity Recognition (NER) systems. Then, the system was extended to incorporate new features, such as word vectors and word clusters generated by the Word2Vec tool and a lexicon feature from the DINTO ontology. We trained the Word2vec tool over two different corpus: Wikipedia and MedLine. Our main goal is to study the effectiveness of using word embeddings as features to improve performance on our baseline system, as well as to analyze whether the DINTO ontology could be a valuable complementary data source integrated in a machine learning NER system. To evaluate our approach and compare it with previous work, we conducted a series of experiments on the dataset of SemEval-2013 Task 9.1 Drug Name Recognition.