Disease is one of the fundamental entities in biomedical research. Recognizing such entities from biomedical text and then normalizing them to a standardized disease vocabulary offer a tremendous opportunity for many downstream applications. Previous studies have demonstrated that joint modeling of the two sub-tasks has superior performance than the pipelined counterpart. Although the neural joint model based on multi-task learning framework has achieved state-of-the-art performance, it suffers from the boundary inconsistency problem due to the separate decoding procedures. Moreover, it ignores the rich information (e.g., the text surface form) of each candidate concept in the vocabulary, which is quite essential for entity normalization. In this work, we propose a neural transition-based joint model to alleviate these two issues. We transform the end-to-end disease recognition and normalization task as an action sequence prediction task, which not only jointly learns the model with shared representations of the input, but also jointly searches the output by state transitions in one search space. Moreover, we introduce attention mechanisms to take advantage of the text surface form of each candidate concept for better normalization performance. Experimental results conducted on two publicly available datasets show the effectiveness of the proposed method.

Dual-Encoders is a promising mechanism for answer retrieval in question answering (QA) systems. Currently most conventional Dual-Encoders learn the semantic representations of questions and answers merely through matching score. Researchers proposed to introduce the QA interaction features in scoring function but at the cost of low efficiency in inference stage. To keep independent encoding of questions and answers during inference stage, variational auto-encoder is further introduced to reconstruct answers (questions) from question (answer) embeddings as an auxiliary task to enhance QA interaction in representation learning in training stage. However, the needs of text generation and answer retrieval are different, which leads to hardness in training. In this work, we propose a framework to enhance the Dual-Encoders model with question answer cross-embeddings and a novel Geometry Alignment Mechanism (GAM) to align the geometry of embeddings from Dual-Encoders with that from Cross-Encoders. Extensive experimental results show that our framework significantly improves Dual-Encoders model and outperforms the state-of-the-art method on multiple answer retrieval datasets.

This paper describes our system developed for the subtask 1c of the sixth Social Media Mining for Health Applications (SMM4H) shared task in 2021. The aim of the subtask is to recognize the adverse drug effect (ADE) mentions from tweets and normalize the identified mentions to their mapping MedDRA preferred term IDs. Our system is based on a neural transition-based joint model, which is to perform recognition and normalization simultaneously. Our final two submissions outperform the average F1 score by 1-2%.