Multilingual biomedical entity linking (MBEL) aims to map language-specific mentions in the biomedical text to standardized concepts in a multilingual knowledge base (KB) such as Unified Medical Language System (UMLS). In this paper, we propose Con2GEN, a prompt-based controllable contrastive generation framework for MBEL, which summarizes multidimensional information of the UMLS concept mentioned in biomedical text into a natural sentence following a predefined template. Instead of tackling the MBEL problem with a discriminative classifier, we formulate it as a sequence-to-sequence generation task, which better exploits the shared dependencies between source mentions and target entities. Moreover, Con2GEN matches against UMLS concepts in as many languages and types as possible, hence facilitating cross-information disambiguation. Extensive experiments show that our model achieves promising performance improvements compared with several state-of-the-art techniques on the XL-BEL and the Mantra GSC datasets spanning 12 typologically diverse languages.
Feature attribution methods highlight the important input tokens as explanations to model predictions, which have been widely applied to deep neural networks towards trustworthy AI. However, recent works show that explanations provided by these methods face challenges of being faithful and robust. In this paper, we propose a method with Robustness improvement and Explanation Guided training towards more faithful EXplanations (REGEX) for text classification. First, we improve model robustness by input gradient regularization technique and virtual adversarial training. Secondly, we use salient ranking to mask noisy tokens and maximize the similarity between model attention and feature attribution, which can be seen as a self-training procedure without importing other external information. We conduct extensive experiments on six datasets with five attribution methods, and also evaluate the faithfulness in the out-of-domain setting. The results show that REGEX improves fidelity metrics of explanations in all settings and further achieves consistent gains based on two randomization tests. Moreover, we show that using highlight explanations produced by REGEX to train select-then-predict models results in comparable task performance to the end-to-end method.
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.
Calibration strengthens the trustworthiness of black-box models by producing better accurate confidence estimates on given examples. However, little is known about if model explanations can help confidence calibration. Intuitively, humans look at important features attributions and decide whether the model is trustworthy. Similarly, the explanations may tell us when the model might know and when it does not. Inspired by this, we propose a method named CME that leverages model explanations to make the model less confident with non-inductive attributions. The idea is that when the model is not highly confident, it is difficult to identify strong indications of any class, and the tokens accordingly do not have high attribution scores for any class and vice versa. We conduct extensive experiments on six datasets with two popular pre-trained language models in the in-domain and out-of-domain settings. The results show that CME improves calibration performance in all settings. The expected calibration errors are further reduced when combined with temperature scaling. Our findings highlight that model explanations can help calibrate posterior estimates.
Pre-trained Language Models (PLMs) have been applied in NLP tasks and achieve promising results. Nevertheless, the fine-tuning procedure needs labeled data of the target domain, making it difficult to learn in low-resource and non-trivial labeled scenarios. To address these challenges, we propose Prompt-based Text Entailment (PTE) for low-resource named entity recognition, which better leverages knowledge in the PLMs. We first reformulate named entity recognition as the text entailment task. The original sentence with entity type-specific prompts is fed into PLMs to get entailment scores for each candidate. The entity type with the top score is then selected as final label. Then, we inject tagging labels into prompts and treat words as basic units instead of n-gram spans to reduce time complexity in generating candidates by n-grams enumeration. Experimental results demonstrate that the proposed method PTE achieves competitive performance on the CoNLL03 dataset, and better than fine-tuned counterparts on the MIT Movie and Few-NERD dataset in low-resource settings.
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.
Graph convolutional network (GCN) has become popular in various natural language processing (NLP) tasks with its superiority in long-term and non-consecutive word interactions. However, existing single-hop graph reasoning in GCN may miss some important non-consecutive dependencies. In this study, we define the spectral graph convolutional network with the high-order dynamic Chebyshev approximation (HDGCN), which augments the multi-hop graph reasoning by fusing messages aggregated from direct and long-term dependencies into one convolutional layer. To alleviate the over-smoothing in high-order Chebyshev approximation, a multi-vote-based cross-attention (MVCAttn) with linear computation complexity is also proposed. The empirical results on four transductive and inductive NLP tasks and the ablation study verify the efficacy of the proposed model.
Integrating knowledge into text is a promising way to enrich text representation, especially in the medical field. However, undifferentiated knowledge not only confuses the text representation but also imports unexpected noises. In this paper, to alleviate this problem, we propose leveraging capsule routing to associate knowledge with medical literature hierarchically (called HiCapsRKL). Firstly, HiCapsRKL extracts two empirically designed text fragments from medical literature and encodes them into fragment representations respectively. Secondly, the capsule routing algorithm is applied to two fragment representations. Through the capsule computing and dynamic routing, each representation is processed into a new representation (denoted as caps-representation), and we integrate the caps-representations as information gain to associate knowledge with medical literature hierarchically. Finally, HiCapsRKL are validated on relevance prediction and medical literature retrieval test sets. The experimental results and analyses show that HiCapsRKLcan more accurately associate knowledge with medical literature than mainstream methods. In summary, HiCapsRKL can efficiently help selecting the most relevant knowledge to the medical literature, which may be an alternative attempt to improve knowledge-based text representation. Source code is released on GitHub.
Machine reading comprehension (MRC) has achieved significant progress on the open domain in recent years, mainly due to large-scale pre-trained language models. However, it performs much worse in specific domains such as the medical field due to the lack of extensive training data and professional structural knowledge neglect. As an effort, we first collect a large scale medical multi-choice question dataset (more than 21k instances) for the National Licensed Pharmacist Examination in China. It is a challenging medical examination with a passing rate of less than 14.2% in 2018. Then we propose a novel reading comprehension model KMQA, which can fully exploit the structural medical knowledge (i.e., medical knowledge graph) and the reference medical plain text (i.e., text snippets retrieved from reference books). The experimental results indicate that the KMQA outperforms existing competitive models with a large margin and passes the exam with 61.8% accuracy rate on the test set.
To exploit the domain knowledge to guarantee the correctness of generated text has been a hot topic in recent years, especially for high professional domains such as medical. However, most of recent works only consider the information of unstructured text rather than structured information of the knowledge graph. In this paper, we focus on the medical topic-to-text generation task and adapt a knowledge-aware text generation model to the medical domain, named MedWriter, which not only introduces the specific knowledge from the external MKG but also is capable of learning graph-level representation. We conduct experiments on a medical literature dataset collected from medical journals, each of which has a set of topic words, an abstract of medical literature and a corresponding knowledge graph from CMeKG. Experimental results demonstrate incorporating knowledge graph into generation model can improve the quality of the generated text and has robust superiority over the competitor methods.
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 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 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.
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.