Medical decision rules play a key role in many clinical decision support systems (CDSS). However, these rules are conventionally constructed by medical experts, which is expensive and hard to scale up. In this study, we explore the automatic extraction of medical decision rules from text, leading to a solution to construct large-scale medical decision rules. We adopt a formulation of medical decision rules as binary trees consisting of condition/decision nodes. Such trees are referred to as medical decision trees and we introduce several generative models to extract them from text. The proposed models inherit the merit of two categories of successful natural language generation frameworks, i.e., sequence-to-sequence generation and autoregressive generation. To unleash the potential of pretrained language models, we design three styles of linearization (natural language, augmented natural language and JSON code), acting as the target sequence for our models. Our final system achieves 67% tree accuracy on a comprehensive Chinese benchmark, outperforming state-of-the-art baseline by 12%. The result demonstrates the effectiveness of generative models on explicitly modeling structural decision-making roadmaps, and shows great potential to boost the development of CDSS and explainable AI. Our code will be open-source upon acceptance.

Event co-occurrences have been proved effective for event extraction (EE) in previous studies, but have not been considered for event argument extraction (EAE) recently. In this paper, we try to fill this gap between EE research and EAE research, by highlighting the question that “Can EAE models learn better when being aware of event co-occurrences?”. To answer this question, we reformulate EAE as a problem of table generation and extend a SOTA prompt-based EAE model into a non-autoregressive generation framework, called TabEAE, which is able to extract the arguments of multiple events in parallel. Under this framework, we experiment with 3 different training-inference schemes on 4 datasets (ACE05, RAMS, WikiEvents and MLEE) and discover that via training the model to extract all events in parallel, it can better distinguish the semantic boundary of each event and its ability to extract single event gets substantially improved. Experimental results show that our method achieves new state-of-the-art performance on the 4 datasets. Our code is avilable at https://github.com/Stardust-hyx/TabEAE.

By modeling the interaction among instances and avoiding error propagation, Set Prediction Networks (SPNs) achieve state-of-the-art performance on the tasks of named entity recognition and relation triple extraction respectively. However, how to jointly extract entities and relation triples via SPNs remains an unexplored problem, where the main challenge is the maintenance of coherence between the predicted entity/relation sets during one-pass generation. In this work, we present Bipartite Set Prediction Network (BiSPN), a novel joint entity-relation extraction model that can efficiently generate entity set and relation set in parallel. To overcome the challenge of coherence, BiSPN is equipped with a novel bipartite consistency loss as well as an entity-relation linking loss during training. Experiments on three biomedical/clinical datasets and a general-domain dataset show that BiSPN achieves new state of the art in knowledge-intensive scene and performs competitively in general-domain, while being more efficient than two-stage joint extraction methods.

Measuring Semantic Textual Similarity (STS) is a fundamental task in biomedical text processing, which aims at quantifying the similarity between two input biomedical sentences. Unfortunately, the STS datasets in the biomedical domain are relatively smaller but more complex in semantics than common domain, often leading to overfitting issues and insufficient text representation even based on Pre-trained Language Models (PLMs) due to too many biomedical entities. In this paper, we propose EARA, an entity-aligned, attention-based and retrieval-augmented PLMs. Our proposed EARA first aligns the same type of fine-grained entity information in each sentence pair with an entity alignment matrix. Then, EARA regularizes the attention mechanism with an entity alignment matrix with an auxiliary loss. Finally, we add a retrieval module that retrieves similar instances to expand the scope of entity pairs and improve the model’s generalization. The comprehensive experiments reflect that EARA can achieve state-of-the-art performance on both in-domain and out-of-domain datasets. Source code is available.

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.

Recently, joint recognition of flat, nested and discontinuous entities has received increasing attention. Motivated by the observation that the target output of NER is essentially a set of sequences, we propose a novel entity set generation framework for general NER scenes in this paper. Different from sequence-to-sequence NER methods, our method does not force the entities to be generated in a predefined order and can get rid of the problem of error propagation and inefficient decoding. Distinguished from the set-prediction NER framework, our method treats each entity as a sequence and is capable of recognizing discontinuous mentions. Given an input sentence, the model first encodes the sentence in word-level and detects potential entity mentions based on the encoder’s output, then reconstructs entity mentions from the detected entity heads in parallel. To let the encoder of our model capture better right-to-left semantic structure, we also propose an auxiliary Inverse Generation Training task. Extensive experiments show that our model (w/o. Inverse Generation Training) outperforms state-of-the-art generative NER models by a large margin on two discontinuous NER datasets, two nested NER datasets and one flat NER dataset. Besides, the auxiliary Inverse Generation Training task is found to further improve the model’s performance on the five datasets.

This is the system description of the Harbin Institute of Technology Shenzhen (HITSZ) team for the first and second subtasks of the fifth Social Media Mining for Health Applications (SMM4H) shared task in 2020. The first task is automatic classification of tweets that mention medications and the second task is automatic classification of tweets in English that report adverse effects. The system we propose for these tasks is based on bidirectional encoder representations from transformers (BERT) incorporating with knowledge graph and retrieving evidence from online information. Our system achieves an F1 of 0.7553 in task 1 and an F1 of 0.5455 in task 2.

The Biological Text Mining Unit at BSC and CNIO organized the first shared task on chemical & drug mention recognition from Spanish medical texts called PharmaCoNER (Pharmacological Substances, Compounds and proteins and Named Entity Recognition track) in 2019, which includes two tracks: one for NER offset and entity classification (track 1) and the other one for concept indexing (track 2). We developed a pipeline system based on deep learning methods for this shared task, specifically, a subsystem based on BERT (Bidirectional Encoder Representations from Transformers) for NER offset and entity classification and a subsystem based on Bpool (Bi-LSTM with max/mean pooling) for concept indexing. Evaluation conducted on the shared task data showed that our system achieves a micro-average F1-score of 0.9105 on track 1 and a micro-average F1-score of 0.8391 on track 2.

The prediction of the relationship between the disease with genes and its mutations is a very important knowledge extraction task that can potentially help drug discovery. In this paper, we present our approaches for trigger word detection (task 1) and the identification of its thematic role (task 2) in AGAC track of BioNLP Open Shared Task 2019. Task 1 can be regarded as the traditional name entity recognition (NER), which cultivates molecular phenomena related to gene mutation. Task 2 can be regarded as relation extraction which captures the thematic roles between entities. For two tasks, we exploit the pre-trained biomedical language representation model (i.e., BERT) in the pipe of information extraction for the collection of mutation-disease knowledge from PubMed. And also, we design a fine-tuning technique and extra features by using multi-task learning. The experiment results show that our proposed approaches achieve 0.60 (ranks 1) and 0.25 (ranks 2) on task 1 and task 2 respectively in terms of F₁ metric.

This is the system description of the Harbin Institute of Technology Shenzhen (HITSZ) team for the first and second subtasks of the fourth Social Media Mining for Health Applications (SMM4H) shared task in 2019. The two subtasks are automatic classification and extraction of adverse effect mentions in tweets. The systems for the two subtasks are based on bidirectional encoder representations from transformers (BERT), and achieves promising results. Among the systems we developed for subtask1, the best F1-score was 0.6457, for subtask2, the best relaxed F1-score and the best strict F1-score were 0.614 and 0.407 respectively. Our system ranks first among all systems on subtask1.

The lack of large-scale question matching corpora greatly limits the development of matching methods in question answering (QA) system, especially for non-English languages. To ameliorate this situation, in this paper, we introduce a large-scale Chinese question matching corpus (named LCQMC), which is released to the public1. LCQMC is more general than paraphrase corpus as it focuses on intent matching rather than paraphrase. How to collect a large number of question pairs in variant linguistic forms, which may present the same intent, is the key point for such corpus construction. In this paper, we first use a search engine to collect large-scale question pairs related to high-frequency words from various domains, then filter irrelevant pairs by the Wasserstein distance, and finally recruit three annotators to manually check the left pairs. After this process, a question matching corpus that contains 260,068 question pairs is constructed. In order to verify the LCQMC corpus, we split it into three parts, i.e., a training set containing 238,766 question pairs, a development set with 8,802 question pairs, and a test set with 12,500 question pairs, and test several well-known sentence matching methods on it. The experimental results not only demonstrate the good quality of LCQMC but also provide solid baseline performance for further researches on this corpus.

This paper introduces the Bank Question (BQ) corpus, a Chinese corpus for sentence semantic equivalence identification (SSEI). The BQ corpus contains 120,000 question pairs from 1-year online bank custom service logs. To efficiently process and annotate questions from such a large scale of logs, this paper proposes a clustering based annotation method to achieve questions with the same intent. First, the deduplicated questions with the same answer are clustered into stacks by the Word Mover’s Distance (WMD) based Affinity Propagation (AP) algorithm. Then, the annotators are asked to assign the clustered questions into different intent categories. Finally, the positive and negative question pairs for SSEI are selected in the same intent category and between different intent categories respectively. We also present six SSEI benchmark performance on our corpus, including state-of-the-art algorithms. As the largest manually annotated public Chinese SSEI corpus in the bank domain, the BQ corpus is not only useful for Chinese question semantic matching research, but also a significant resource for cross-lingual and cross-domain SSEI research. The corpus is available in public.

The number of word embedding models is growing every year. Most of them are based on the co-occurrence information of words and their contexts. However, it is still an open question what is the best definition of context. We provide a systematical investigation of 4 different syntactic context types and context representations for learning word embeddings. Comprehensive experiments are conducted to evaluate their effectiveness on 6 extrinsic and intrinsic tasks. We hope that this paper, along with the published code, would be helpful for choosing the best context type and representation for a given task.

In community question answering (cQA), the quality of answers are determined by the matching degree between question-answer pairs and the correlation among the answers. In this paper, we show that the dependency between the answer quality labels also plays a pivotal role. To validate the effectiveness of label dependency, we propose two neural network-based models, with different combination modes of Convolutional Neural Net-works, Long Short Term Memory and Conditional Random Fields. Extensive experi-ments are taken on the dataset released by the SemEval-2015 cQA shared task. The first model is a stacked ensemble of the networks. It achieves 58.96% on macro averaged F1, which improves the state-of-the-art neural network-based method by 2.82% and outper-forms the Top-1 system in the shared task by 1.77%. The second is a simple attention-based model whose input is the connection of the question and its corresponding answers. It produces promising results with 58.29% on overall F1 and gains the best performance on the Good and Bad categories.