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Register a new userMedical Synonym Extraction with Concept Space Models
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Added by
Liangliang Cao
Publication date
2015
fields
Informatics Engineering
and research's language is
English
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In this paper, we present a novel approach for medical synonym extraction. We aim to integrate the term embedding with the medical domain knowledge for healthcare applications. One advantage of our method is that it is very scalable. Experiments on a dataset with more than 1M term pairs show that the proposed approach outperforms the baseline approaches by a large margin.
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Synonym extraction is an important task in natural language processing and often used as a submodule in query expansion, question answering and other applications. Automatic synonym extractor is highly preferred for large scale applications. Previous studies in synonym extraction are most limited to small scale datasets. In this paper, we build a large dataset with 3.4 million synonym/non-synonym pairs to capture the challenges in real world scenarios. We proposed (1) a new cost function to accommodate the unbalanced learning problem, and (2) a feature learning based deep neural network to model the complicated relationships in synonym pairs. We compare several different approaches based on SVMs and neural networks, and find out a novel feature learning based neural network outperforms the methods with hand-assigned features. Specifically, the best performance of our model surpasses the SVM baseline with a significant 97% relative improvement.
Biomedical named entities often play important roles in many biomedical text mining tools. However, due to the incompleteness of provided synonyms and numerous variations in their surface forms, normalization of biomedical entities is very challenging. In this paper, we focus on learning representations of biomedical entities solely based on the synonyms of entities. To learn from the incomplete synonyms, we use a model-based candidate selection and maximize the marginal likelihood of the synonyms present in top candidates. Our model-based candidates are iteratively updated to contain more difficult negative samples as our model evolves. In this way, we avoid the explicit pre-selection of negative samples from more than 400K candidates. On four biomedical entity normalization datasets having three different entity types (disease, chemical, adverse reaction), our model BioSyn consistently outperforms previous state-of-the-art models almost reaching the upper bound on each dataset.
We convert the Chinese medical text attributes extraction task into a sequence tagging or machine reading comprehension task. Based on BERT pre-trained models, we have not only tried the widely used LSTM-CRF sequence tagging model, but also other sequence models, such as CNN, UCNN, WaveNet, SelfAttention, etc, which reaches similar performance as LSTM+CRF. This sheds a light on the traditional sequence tagging models. Since the aspect of emphasis for different sequence tagging models varies substantially, ensembling these models adds diversity to the final system. By doing so, our system achieves good performance on the task of Chinese medical text attributes extraction (subtask 2 of CCKS 2019 task 1).
In longitudinal electronic health records (EHRs), the event records of a patient are distributed over a long period of time and the temporal relations between the events reflect sufficient domain knowledge to benefit prediction tasks such as the rate of inpatient mortality. Medical concept embedding as a feature extraction method that transforms a set of medical concepts with a specific time stamp into a vector, which will be fed into a supervised learning algorithm. The quality of the embedding significantly determines the learning performance over the medical data. In this paper, we propose a medical concept embedding method based on applying a self-attention mechanism to represent each medical concept. We propose a novel attention mechanism which captures the contextual information and temporal relationships between medical concepts. A light-weight neural net, Temporal Self-Attention Network (TeSAN), is then proposed to learn medical concept embedding based solely on the proposed attention mechanism. To test the effectiveness of our proposed methods, we have conducted clustering and prediction tasks on two public EHRs datasets comparing TeSAN against five state-of-the-art embedding methods. The experimental results demonstrate that the proposed TeSAN model is superior to all the compared methods. To the best of our knowledge, this work is the first to exploit temporal self-attentive relations between medical events.
Few-shot relation extraction (FSRE) is of great importance in long-tail distribution problem, especially in special domain with low-resource data. Most existing FSRE algorithms fail to accurately classify the relations merely based on the information of the sentences together with the recognized entity pairs, due to limited samples and lack of knowledge. To address this problem, in this paper, we proposed a novel entity CONCEPT-enhanced FEw-shot Relation Extraction scheme (ConceptFERE), which introduces the inherent concepts of entities to provide clues for relation prediction and boost the relations classification performance. Firstly, a concept-sentence attention module is developed to select the most appropriate concept from multiple concepts of each entity by calculating the semantic similarity between sentences and concepts. Secondly, a self-attention based fusion module is presented to bridge the gap of concept embedding and sentence embedding from different semantic spaces. Extensive experiments on the FSRE benchmark dataset FewRel have demonstrated the effectiveness and the superiority of the proposed ConceptFERE scheme as compared to the state-of-the-art baselines. Code is available at https://github.com/LittleGuoKe/ConceptFERE.
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