Chuanqi Tan


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CBLUE: A Chinese Biomedical Language Understanding Evaluation Benchmark
Ningyu Zhang | Mosha Chen | Zhen Bi | Xiaozhuan Liang | Lei Li | Xin Shang | Kangping Yin | Chuanqi Tan | Jian Xu | Fei Huang | Luo Si | Yuan Ni | Guotong Xie | Zhifang Sui | Baobao Chang | Hui Zong | Zheng Yuan | Linfeng Li | Jun Yan | Hongying Zan | Kunli Zhang | Buzhou Tang | Qingcai Chen
Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

Artificial Intelligence (AI), along with the recent progress in biomedical language understanding, is gradually offering great promise for medical practice. With the development of biomedical language understanding benchmarks, AI applications are widely used in the medical field. However, most benchmarks are limited to English, which makes it challenging to replicate many of the successes in English for other languages. To facilitate research in this direction, we collect real-world biomedical data and present the first Chinese Biomedical Language Understanding Evaluation (CBLUE) benchmark: a collection of natural language understanding tasks including named entity recognition, information extraction, clinical diagnosis normalization, single-sentence/sentence-pair classification, and an associated online platform for model evaluation, comparison, and analysis. To establish evaluation on these tasks, we report empirical results with the current 11 pre-trained Chinese models, and experimental results show that state-of-the-art neural models perform by far worse than the human ceiling.

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Code Synonyms Do Matter: Multiple Synonyms Matching Network for Automatic ICD Coding
Zheng Yuan | Chuanqi Tan | Songfang Huang
Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers)

Automatic ICD coding is defined as assigning disease codes to electronic medical records (EMRs).Existing methods usually apply label attention with code representations to match related text snippets.Unlike these works that model the label with the code hierarchy or description, we argue that the code synonyms can provide more comprehensive knowledge based on the observation that the code expressions in EMRs vary from their descriptions in ICD. By aligning codes to concepts in UMLS, we collect synonyms of every code. Then, we propose a multiple synonyms matching network to leverage synonyms for better code representation learning, and finally help the code classification. Experiments on the MIMIC-III dataset show that our proposed method outperforms previous state-of-the-art methods.

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Fusing Heterogeneous Factors with Triaffine Mechanism for Nested Named Entity Recognition
Zheng Yuan | Chuanqi Tan | Songfang Huang | Fei Huang
Findings of the Association for Computational Linguistics: ACL 2022

Nested entities are observed in many domains due to their compositionality, which cannot be easily recognized by the widely-used sequence labeling framework.A natural solution is to treat the task as a span classification problem.To learn better span representation and increase classification performance, it is crucial to effectively integrate heterogeneous factors including inside tokens, boundaries, labels, and related spans which could be contributing to nested entities recognition.To fuse these heterogeneous factors, we propose a novel triaffine mechanism including triaffine attention and scoring.Triaffine attention uses boundaries and labels as queries and uses inside tokens and related spans as keys and values for span representations.Triaffine scoring interacts with boundaries and span representations for classification.Experiments show that our proposed method outperforms previous span-based methods, achieves the state-of-the-art F1 scores on nested NER datasets GENIA and KBP2017, and shows comparable results on ACE2004 and ACE2005.


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Improving Biomedical Pretrained Language Models with Knowledge
Zheng Yuan | Yijia Liu | Chuanqi Tan | Songfang Huang | Fei Huang
Proceedings of the 20th Workshop on Biomedical Language Processing

Pretrained language models have shown success in many natural language processing tasks. Many works explore to incorporate the knowledge into the language models. In the biomedical domain, experts have taken decades of effort on building large-scale knowledge bases. For example, UMLS contains millions of entities with their synonyms and defines hundreds of relations among entities. Leveraging this knowledge can benefit a variety of downstream tasks such as named entity recognition and relation extraction. To this end, we propose KeBioLM, a biomedical pretrained language model that explicitly leverages knowledge from the UMLS knowledge bases. Specifically, we extract entities from PubMed abstracts and link them to UMLS. We then train a knowledge-aware language model that firstly applies a text-only encoding layer to learn entity representation and then applies a text-entity fusion encoding to aggregate entity representation. In addition, we add two training objectives as entity detection and entity linking. Experiments on the named entity recognition and relation extraction tasks from the BLURB benchmark demonstrate the effectiveness of our approach. Further analysis on a collected probing dataset shows that our model has better ability to model medical knowledge.

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Raise a Child in Large Language Model: Towards Effective and Generalizable Fine-tuning
Runxin Xu | Fuli Luo | Zhiyuan Zhang | Chuanqi Tan | Baobao Chang | Songfang Huang | Fei Huang
Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing

Recent pretrained language models extend from millions to billions of parameters. Thus the need to fine-tune an extremely large pretrained model with a limited training corpus arises in various downstream tasks. In this paper, we propose a straightforward yet effective fine-tuning technique, Child-Tuning, which updates a subset of parameters (called child network) of large pretrained models via strategically masking out the gradients of the non-child network during the backward process. Experiments on various downstream tasks in GLUE benchmark show that Child-Tuning consistently outperforms the vanilla fine-tuning by 1.5 8.6 average score among four different pretrained models, and surpasses the prior fine-tuning techniques by 0.6 1.3 points. Furthermore, empirical results on domain transfer and task transfer show that Child-Tuning can obtain better generalization performance by large margins.

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Noisy-Labeled NER with Confidence Estimation
Kun Liu | Yao Fu | Chuanqi Tan | Mosha Chen | Ningyu Zhang | Songfang Huang | Sheng Gao
Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

Recent studies in deep learning have shown significant progress in named entity recognition (NER). However, most existing works assume clean data annotation, while real-world scenarios typically involve a large amount of noises from a variety of sources (e.g., pseudo, weak, or distant annotations). This work studies NER under a noisy labeled setting with calibrated confidence estimation. Based on empirical observations of different training dynamics of noisy and clean labels, we propose strategies for estimating confidence scores based on local and global independence assumptions. We partially marginalize out labels of low confidence with a CRF model. We further propose a calibration method for confidence scores based on the structure of entity labels. We integrate our approach into a self-training framework for boosting performance. Experiments in general noisy settings with four languages and distantly labeled settings demonstrate the effectiveness of our method.


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Predicting Clinical Trial Results by Implicit Evidence Integration
Qiao Jin | Chuanqi Tan | Mosha Chen | Xiaozhong Liu | Songfang Huang
Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP)

Clinical trials provide essential guidance for practicing Evidence-Based Medicine, though often accompanying with unendurable costs and risks. To optimize the design of clinical trials, we introduce a novel Clinical Trial Result Prediction (CTRP) task. In the CTRP framework, a model takes a PICO-formatted clinical trial proposal with its background as input and predicts the result, i.e. how the Intervention group compares with the Comparison group in terms of the measured Outcome in the studied Population. While structured clinical evidence is prohibitively expensive for manual collection, we exploit large-scale unstructured sentences from medical literature that implicitly contain PICOs and results as evidence. Specifically, we pre-train a model to predict the disentangled results from such implicit evidence and fine-tune the model with limited data on the downstream datasets. Experiments on the benchmark Evidence Integration dataset show that the proposed model outperforms the baselines by large margins, e.g., with a 10.7% relative gain over BioBERT in macro-F1. Moreover, the performance improvement is also validated on another dataset composed of clinical trials related to COVID-19.


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Entity Linking for Queries by Searching Wikipedia Sentences
Chuanqi Tan | Furu Wei | Pengjie Ren | Weifeng Lv | Ming Zhou
Proceedings of the 2017 Conference on Empirical Methods in Natural Language Processing

We present a simple yet effective approach for linking entities in queries. The key idea is to search sentences similar to a query from Wikipedia articles and directly use the human-annotated entities in the similar sentences as candidate entities for the query. Then, we employ a rich set of features, such as link-probability, context-matching, word embeddings, and relatedness among candidate entities as well as their related entities, to rank the candidates under a regression based framework. The advantages of our approach lie in two aspects, which contribute to the ranking process and final linking result. First, it can greatly reduce the number of candidate entities by filtering out irrelevant entities with the words in the query. Second, we can obtain the query sensitive prior probability in addition to the static link-probability derived from all Wikipedia articles. We conduct experiments on two benchmark datasets on entity linking for queries, namely the ERD14 dataset and the GERDAQ dataset. Experimental results show that our method outperforms state-of-the-art systems and yields 75.0% in F1 on the ERD14 dataset and 56.9% on the GERDAQ dataset.

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SuperAgent: A Customer Service Chatbot for E-commerce Websites
Lei Cui | Shaohan Huang | Furu Wei | Chuanqi Tan | Chaoqun Duan | Ming Zhou
Proceedings of ACL 2017, System Demonstrations


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Solving and Generating Chinese Character Riddles
Chuanqi Tan | Furu Wei | Li Dong | Weifeng Lv | Ming Zhou
Proceedings of the 2016 Conference on Empirical Methods in Natural Language Processing


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Adaptive Recursive Neural Network for Target-dependent Twitter Sentiment Classification
Li Dong | Furu Wei | Chuanqi Tan | Duyu Tang | Ming Zhou | Ke Xu
Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers)