Zenan Zhai


2019

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A Bag-of-concepts Model Improves Relation Extraction in a Narrow Knowledge Domain with Limited Data
Jiyu Chen | Karin Verspoor | Zenan Zhai
Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Student Research Workshop

This paper focuses on a traditional relation extraction task in the context of limited annotated data and a narrow knowledge domain. We explore this task with a clinical corpus consisting of 200 breast cancer follow-up treatment letters in which 16 distinct types of relations are annotated. We experiment with an approach to extracting typed relations called window-bounded co-occurrence (WBC), which uses an adjustable context window around entity mentions of a relevant type, and compare its performance with a more typical intra-sentential co-occurrence baseline. We further introduce a new bag-of-concepts (BoC) approach to feature engineering based on the state-of-the-art word embeddings and word synonyms. We demonstrate the competitiveness of BoC by comparing with methods of higher complexity, and explore its effectiveness on this small dataset.

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Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings
Zenan Zhai | Dat Quoc Nguyen | Saber Akhondi | Camilo Thorne | Christian Druckenbrodt | Trevor Cohn | Michelle Gregory | Karin Verspoor
Proceedings of the 18th BioNLP Workshop and Shared Task

Chemical patents are an important resource for chemical information. However, few chemical Named Entity Recognition (NER) systems have been evaluated on patent documents, due in part to their structural and linguistic complexity. In this paper, we explore the NER performance of a BiLSTM-CRF model utilising pre-trained word embeddings, character-level word representations and contextualized ELMo word representations for chemical patents. We compare word embeddings pre-trained on biomedical and chemical patent corpora. The effect of tokenizers optimized for the chemical domain on NER performance in chemical patents is also explored. The results on two patent corpora show that contextualized word representations generated from ELMo substantially improve chemical NER performance w.r.t. the current state-of-the-art. We also show that domain-specific resources such as word embeddings trained on chemical patents and chemical-specific tokenizers, have a positive impact on NER performance.

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Detecting Chemical Reactions in Patents
Hiyori Yoshikawa | Dat Quoc Nguyen | Zenan Zhai | Christian Druckenbrodt | Camilo Thorne | Saber A. Akhondi | Timothy Baldwin | Karin Verspoor
Proceedings of the The 17th Annual Workshop of the Australasian Language Technology Association

Extracting chemical reactions from patents is a crucial task for chemists working on chemical exploration. In this paper we introduce the novel task of detecting the textual spans that describe or refer to chemical reactions within patents. We formulate this task as a paragraph-level sequence tagging problem, where the system is required to return a sequence of paragraphs which contain a description of a reaction. To address this new task, we construct an annotated dataset from an existing proprietary database of chemical reactions manually extracted from patents. We introduce several baseline methods for the task and evaluate them over our dataset. Through error analysis, we discuss what makes the task complex and challenging, and suggest possible directions for future research.

2018

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Comparing CNN and LSTM character-level embeddings in BiLSTM-CRF models for chemical and disease named entity recognition
Zenan Zhai | Dat Quoc Nguyen | Karin Verspoor
Proceedings of the Ninth International Workshop on Health Text Mining and Information Analysis

We compare the use of LSTM-based and CNN-based character-level word embeddings in BiLSTM-CRF models to approach chemical and disease named entity recognition (NER) tasks. Empirical results over the BioCreative V CDR corpus show that the use of either type of character-level word embeddings in conjunction with the BiLSTM-CRF models leads to comparable state-of-the-art performance. However, the models using CNN-based character-level word embeddings have a computational performance advantage, increasing training time over word-based models by 25% while the LSTM-based character-level word embeddings more than double the required training time.