Sivanesan Sangeetha


2020

pdf bib
Want to Identify, Extract and Normalize Adverse Drug Reactions in Tweets? Use RoBERTa
Katikapalli Subramanyam Kalyan | Sivanesan Sangeetha
Proceedings of the Fifth Social Media Mining for Health Applications Workshop & Shared Task

This paper presents our approach for task 2 and task 3 of Social Media Mining for Health (SMM4H) 2020 shared tasks. In task 2, we have to differentiate adverse drug reaction (ADR) tweets from nonADR tweets and is treated as binary classification. Task 3 involves extracting ADR mentions and then mapping them to MedDRA codes. Extracting ADR mentions is treated as sequence labeling and normalizing ADR mentions is treated as multi-class classification. Our system is based on pre-trained language model RoBERTa and it achieves a) F1-score of 58% in task 2 which is 12% more than the average score b) relaxed F1-score of 70.1% in ADR extraction of task 3 which is 13.7% more than the average score and relaxed F1-score of 35% in ADR extraction + normalization of task 3 which is 5.8% more than the average score. Overall, our models achieve promising results in both the tasks with significant improvements over average scores.

pdf bib
Target Concept Guided Medical Concept Normalization in Noisy User-Generated Texts
Katikapalli Subramanyam Kalyan | Sivanesan Sangeetha
Proceedings of Deep Learning Inside Out (DeeLIO): The First Workshop on Knowledge Extraction and Integration for Deep Learning Architectures

Medical concept normalization (MCN) i.e., mapping of colloquial medical phrases to standard concepts is an essential step in analysis of medical social media text. The main drawback in existing state-of-the-art approach (Kalyan and Sangeetha, 2020b) is learning target concept vector representations from scratch which requires more number of training instances. Our model is based on RoBERTa and target concept embeddings. In our model, we integrate a) target concept information in the form of target concept vectors generated by encoding target concept descriptions using SRoBERTa, state-of-the-art RoBERTa based sentence embedding model and b) domain lexicon knowledge by enriching target concept vectors with synonym relationship knowledge using retrofitting algorithm. It is the first attempt in MCN to exploit both target concept information as well as domain lexicon knowledge in the form of retrofitted target concept vectors. Our model outperforms all the existing models with an accuracy improvement up to 1.36% on three standard datasets. Further, our model when trained only on mapping lexicon synonyms achieves up to 4.87% improvement in accuracy.

pdf bib
Social Media Medical Concept Normalization using RoBERTa in Ontology Enriched Text Similarity Framework
Katikapalli Subramanyam Kalyan | Sivanesan Sangeetha
Proceedings of Knowledgeable NLP: the First Workshop on Integrating Structured Knowledge and Neural Networks for NLP

Pattisapu et al. (2020) formulate medical concept normalization (MCN) as text similarity problem and propose a model based on RoBERTa and graph embedding based target concept vectors. However, graph embedding techniques ignore valuable information available in the clinical ontology like concept description and synonyms. In this work, we enhance the model of Pattisapu et al. (2020) with two novel changes. First, we use retrofitted target concept vectors instead of graph embedding based vectors. It is the first work to leverage both concept description and synonyms to represent concepts in the form of retrofitted target concept vectors in text similarity framework based social media MCN. Second, we generate both concept and concept mention vectors with same size which eliminates the need of dense layers to project concept mention vectors into the target concept embedding space. Our model outperforms existing methods with improvements up to 3.75% on two standard datasets. Further when trained only on mapping lexicon synonyms, our model outperforms existing methods with significant improvements up to 14.61%. We attribute these significant improvements to the two novel changes introduced.

pdf bib
Medical Concept Normalization in User-Generated Texts by Learning Target Concept Embeddings
Katikapalli Subramanyam Kalyan | Sivanesan Sangeetha
Proceedings of the 11th International Workshop on Health Text Mining and Information Analysis

Medical concept normalization helps in discovering standard concepts in free-form text i.e., maps health-related mentions to standard concepts in a clinical knowledge base. It is much beyond simple string matching and requires a deep semantic understanding of concept mentions. Recent research approach concept normalization as either text classification or text similarity. The main drawback in existing a) text classification approach is ignoring valuable target concepts information in learning input concept mention representation b) text similarity approach is the need to separately generate target concept embeddings which is time and resource consuming. Our proposed model overcomes these drawbacks by jointly learning the representations of input concept mention and target concepts. First, we learn input concept mention representation using RoBERTa. Second, we find cosine similarity between embeddings of input concept mention and all the target concepts. Here, embeddings of target concepts are randomly initialized and then updated during training. Finally, the target concept with maximum cosine similarity is assigned to the input concept mention. Our model surpasses all the existing methods across three standard datasets by improving accuracy up to 2.31%.