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Register a new userImproving Multi-Word Entity Recognition for Biomedical Texts
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Added by
Hamada Nayel
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Biomedical Named Entity Recognition (BioNER) is a crucial step for analyzing Biomedical texts, which aims at extracting biomedical named entities from a given text. Different supervised machine learning algorithms have been applied for BioNER by various researchers. The main requirement of these approaches is an annotated dataset used for learning the parameters of machine learning algorithms. Segment Representation (SR) models comprise of different tag sets used for representing the annotated data, such as IOB2, IOE2 and IOBES. In this paper, we propose an extension of IOBES model to improve the performance of BioNER. The proposed SR model, FROBES, improves the representation of multi-word entities. We used Bidirectional Long Short-Term Memory (BiLSTM) network; an instance of Recurrent Neural Networks (RNN), to design a baseline system for BioNER and evaluated the new SR model on two datasets, i2b2/VA 2010 challenge dataset and JNLPBA 2004 shared task dataset. The proposed SR model outperforms other models for multi-word entities with length greater than two. Further, the outputs of different SR models have been combined using majority voting ensemble method which outperforms the baseline models performance.
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Named entity recognition, and other information extraction tasks, frequently use linguistic features such as part of speech tags or chunkings. For languages where word boundaries are not readily identified in text, word segmentation is a key first step to generating features for an NER system. While using word boundary tags as features are helpful, the signals that aid in identifying these boundaries may provide richer information for an NER system. New state-of-the-art word segmentation systems use neural models to learn representations for predicting word boundaries. We show that these same representations, jointly trained with an NER system, yield significant improvements in NER for Chinese social media. In our experiments, jointly training NER and word segmentation with an LSTM-CRF model yields nearly 5% absolute improvement over previously published results.
Fine-Grained Named Entity Recognition (FG-NER) is critical for many NLP applications. While classical named entity recognition (NER) has attracted a substantial amount of research, FG-NER is still an open research domain. The current state-of-the-art (SOTA) model for FG-NER relies heavily on manual efforts for building a dictionary and designing hand-crafted features. The end-to-end framework which achieved the SOTA result for NER did not get the competitive result compared to SOTA model for FG-NER. In this paper, we investigate how effective multi-task learning approaches are in an end-to-end framework for FG-NER in different aspects. Our experiments show that using multi-task learning approaches with contextualized word representation can help an end-to-end neural network model achieve SOTA results without using any additional manual effort for creating data and designing features.
Sentence embeddings have become an essential part of todays natural language processing (NLP) systems, especially together advanced deep learning methods. Although pre-trained sentence encoders are available in the general domain, none exists for biomedical texts to date. In this work, we introduce BioSentVec: the first open set of sentence embeddings trained with over 30 million documents from both scholarly articles in PubMed and clinical notes in the MIMIC-III Clinical Database. We evaluate BioSentVec embeddings in two sentence pair similarity tasks in different text genres. Our benchmarking results demonstrate that the BioSentVec embeddings can better capture sentence semantics compared to the other competitive alternatives and achieve state-of-the-art performance in both tasks. We expect BioSentVec to facilitate the research and development in biomedical text mining and to complement the existing resources in biomedical word embeddings. BioSentVec is publicly available at https://github.com/ncbi-nlp/BioSentVec
This paper presents a novel framework, MGNER, for Multi-Grained Named Entity Recognition where multiple entities or entity mentions in a sentence could be non-overlapping or totally nested. Different from traditional approaches regarding NER as a sequential labeling task and annotate entities consecutively, MGNER detects and recognizes entities on multiple granularities: it is able to recognize named entities without explicitly assuming non-overlapping or totally nested structures. MGNER consists of a Detector that examines all possible word segments and a Classifier that categorizes entities. In addition, contextual information and a self-attention mechanism are utilized throughout the framework to improve the NER performance. Experimental results show that MGNER outperforms current state-of-the-art baselines up to 4.4% in terms of the F1 score among nested/non-overlapping NER tasks.
Pre-trained language models induce dense entity representations that offer strong performance on entity-centric NLP tasks, but such representations are not immediately interpretable. This can be a barrier to model uptake in important domains such as biomedicine. There has been recent work on general interpretable representation learning (Onoe and Durrett, 2020), but these domain-agnostic representations do not readily transfer to the important domain of biomedicine. In this paper, we create a new entity type system and training set from a large corpus of biomedical texts by mapping entities to concepts in a medical ontology, and from these to Wikipedia pages whose categories are our types. From this mapping we derive Biomedical Interpretable Entity Representations(BIERs), in which dimensions correspond to fine-grained entity types, and values are predicted probabilities that a given entity is of the corresponding type. We propose a novel method that exploits BIERs final sparse and intermediate dense representations to facilitate model and entity type debugging. We show that BIERs achieve strong performance in biomedical tasks including named entity disambiguation and entity label classification, and we provide error analysis to highlight the utility of their interpretability, particularly in low-supervision settings. Finally, we provide our induced 68K biomedical type system, the corresponding 37 million triples of derived data used to train BIER models and our best performing model.
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