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.

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.

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.

Multimodal named entity recognition and relation extraction (MNER and MRE) is a fundamental and crucial branch in information extraction. However, existing approaches for MNER and MRE usually suffer from error sensitivity when irrelevant object images incorporated in texts.To deal with these issues, we propose a novel Hierarchical Visual Prefix fusion NeTwork (HVPNeT) for visual-enhanced entity and relation extraction, aiming to achieve more effective and robust performance. Specifically, we regard visual representation as pluggable visual prefix to guide the textual representation for error insensitive forecasting decision. We further propose a dynamic gated aggregation strategy to achieve hierarchical multi-scaled visual features as visual prefix for fusion. Extensive experiments on three benchmark datasets demonstrate the effectiveness of our method, and achieve state-of-the-art performance.

Prompt-based fine-tuning has boosted the performance of Pre-trained Language Models (PLMs) on few-shot text classification by employing task-specific prompts. Yet, PLMs are unfamiliar with prompt-style expressions during pre-training, which limits the few-shot learning performance on downstream tasks.It would be desirable if the models can acquire some prompting knowledge before adapting to specific NLP tasks. We present the Unified Prompt Tuning (UPT) framework, leading to better few-shot text classification for BERT-style models by explicitly capturing prompting semantics from non-target NLP datasets. In UPT, a novel paradigm Prompt-Options-Verbalizer is proposed for joint prompt learning across different NLP tasks, forcing PLMs to capture task-invariant prompting knowledge. We further design a self-supervised task named Knowledge-enhanced Selective Masked Language Modeling to improve the PLM’s generalization abilities for accurate adaptation to previously unseen tasks. After multi-task learning across multiple tasks, the PLM can be better prompt-tuned towards any dissimilar target tasks in low-resourced settings. Experiments over a variety of NLP tasks show that UPT consistently outperforms state-of-the-arts for prompt-based fine-tuning.

Pretrained language models can be effectively stimulated by textual prompts or demonstrations, especially in low-data scenarios. Recent works have focused on automatically searching discrete or continuous prompts or optimized verbalizers, yet studies for the demonstration are still limited. Concretely, the demonstration examples are crucial for an excellent final performance of prompt-tuning. In this paper, we propose a novel pluggable, extensible, and efficient approach named contrastive demonstration tuning, which is free of demonstration sampling. Furthermore, the proposed approach can be: (i) Plugged into any previous prompt-tuning approaches; (ii) Extended to widespread classification tasks with a large number of categories. Experimental results on 16 datasets illustrate that our method integrated with previous approaches LM-BFF and P-tuning can yield better performance. Code is available in https://github.com/zjunlp/PromptKG/tree/main/research/Demo-Tuning.

Few-shot Named Entity Recognition (NER) aims to identify named entities with very little annotated data. Previous methods solve this problem based on token-wise classification, which ignores the information of entity boundaries, and inevitably the performance is affected by the massive non-entity tokens. To this end, we propose a seminal span-based prototypical network (SpanProto) that tackles few-shot NER via a two-stage approach, including span extraction and mention classification. In the span extraction stage, we transform the sequential tags into a global boundary matrix, enabling the model to focus on the explicit boundary information. For mention classification, we leverage prototypical learning to capture the semantic representations for each labeled span and make the model better adapt to novel-class entities. To further improve the model performance, we split out the false positives generated by the span extractor but not labeled in the current episode set, and then present a margin-based loss to separate them from each prototype region. Experiments over multiple benchmarks demonstrate that our model outperforms strong baselines by a large margin.

Most NER methods rely on extensive labeled data for model training, which struggles in the low-resource scenarios with limited training data. Existing dominant approaches usually suffer from the challenge that the target domain has different label sets compared with a resource-rich source domain, which can be concluded as class transfer and domain transfer. In this paper, we propose a lightweight tuning paradigm for low-resource NER via pluggable prompting (LightNER). Specifically, we construct the unified learnable verbalizer of entity categories to generate the entity span sequence and entity categories without any label-specific classifiers, thus addressing the class transfer issue. We further propose a pluggable guidance module by incorporating learnable parameters into the self-attention layer as guidance, which can re-modulate the attention and adapt pre-trained weights. Note that we only tune those inserted module with the whole parameter of the pre-trained language model fixed, thus, making our approach lightweight and flexible for low-resource scenarios and can better transfer knowledge across domains. Experimental results show that LightNER can obtain comparable performance in the standard supervised setting and outperform strong baselines in low-resource settings.

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.

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.

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.

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.

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.