Identifying disease-related expressions in reviews using conditional random fields

As the as the volume of user-generated content in social media expands so do the potential benefits of mining social media to learn about patient conditions, drug indications, and beneficial or adverse drug reactions. In this paper, we apply Conditional Random Fields (CRF) model for extracting expressions related to diseases from patient comments. Our method utilizes hand-crafted features including contextual features, dictionaries, clusterbased and distributed word representation generated from unlabeled user posts in social media. We compare our CRF-based approach with deep recurrent neural networks and a dictionary-based approach. We examine different word embeddings generated from unlabeled user posts in social media and scientific literature. We show that CRF outperformed other methods and achieved the F1-measures of 69.1% and 79.4% on recognition of disease-related expressions in the exact and partial matching exercises, respectively. Qualitative evaluation of disease-related expressions recognized by our feature-rich CRF-based approach demonstrates the variability of reactions from patients with different health conditions

ИЗВЛЕЧЕНИЕ СВЯЗАННЫХ С ЗАБОЛЕВАНИЯМИ ВЫРАЖЕНИЙ НА ОСНОВЕ МОДЕЛИ УСЛОВНЫХ СЛУЧАЙНЫХ ПОЛЕЙ

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Text Mining for Chemical Compounds

Exploring the chemical and biological space covered by patent and journal publications is crucial in early- stage medicinal chemistry activities. The analysis provides understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents and journals through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. In this book, we addressed the lack of quality measurements for assessing the correctness of structural representation within and across chemical databases; lack of resources to build text-mining systems; lack of high performance systems to extract chemical compounds from journals and patents; and lack of automated systems to identify relevant compounds in patents. The consistency and ambiguity of chemical identifiers was analyzed within and between small- molecule databases in Chapter 2 and Chapter 3. In Chapter 4 and Chapter 7 we developed resources to enable the construction of chemical text-mining systems. In Chapter 5 and Chapter 6, we used community challenges (BioCreative V and BioCreative VI) and their corresponding resources to identify mentions of chemical compounds in journal abstracts and patents. In Chapter 7 we used our findings in previous chapters to extract chemical named entities from patent full text and to classify the relevancy of chemical compounds