Ishani Mondal


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Extracting Semantic Aspects for Structured Representation of Clinical Trial Eligibility Criteria
Tirthankar Dasgupta | Ishani Mondal | Abir Naskar | Lipika Dey
Proceedings of the 3rd Clinical Natural Language Processing Workshop

Eligibility criteria in the clinical trials specify the characteristics that a patient must or must not possess in order to be treated according to a standard clinical care guideline. As the process of manual eligibility determination is time-consuming, automatic structuring of the eligibility criteria into various semantic categories or aspects is the need of the hour. Existing methods use hand-crafted rules and feature-based statistical machine learning methods to dynamically induce semantic aspects. However, in order to deal with paucity of aspect-annotated clinical trials data, we propose a novel weakly-supervised co-training based method which can exploit a large pool of unlabeled criteria sentences to augment the limited supervised training data, and consequently enhance the performance. Experiments with 0.2M criteria sentences show that the proposed approach outperforms the competitive supervised baselines by 12% in terms of micro-averaged F1 score for all the aspects. Probing deeper into analysis, we observe domain-specific information boosts up the performance by a significant margin.


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Medical Entity Linking using Triplet Network
Ishani Mondal | Sukannya Purkayastha | Sudeshna Sarkar | Pawan Goyal | Jitesh Pillai | Amitava Bhattacharyya | Mahanandeeshwar Gattu
Proceedings of the 2nd Clinical Natural Language Processing Workshop

Entity linking (or Normalization) is an essential task in text mining that maps the entity mentions in the medical text to standard entities in a given Knowledge Base (KB). This task is of great importance in the medical domain. It can also be used for merging different medical and clinical ontologies. In this paper, we center around the problem of disease linking or normalization. This task is executed in two phases: candidate generation and candidate scoring. In this paper, we present an approach to rank the candidate Knowledge Base entries based on their similarity with disease mention. We make use of the Triplet Network for candidate ranking. While the existing methods have used carefully generated sieves and external resources for candidate generation, we introduce a robust and portable candidate generation scheme that does not make use of the hand-crafted rules. Experimental results on the standard benchmark NCBI disease dataset demonstrate that our system outperforms the prior methods by a significant margin.