在Bircocrive VII的Track-1中，要求参与者识别药物/化学品和蛋白质之间的相互作用。提供每个药物/化学和蛋白质的内部名称实体注释，必须自动预测14个不同的相互作用中的一种。对于此关系提取任务，我们尝试两种基于BERT的句子分类方法，以及使用T5模型的更新文本到文本方法。我们发现基于BERT的模型一般表现更好，我们的生物综太基模型实现了所有指标的最高分，实现了0.74 F1得分。虽然我们的小说T5文本到文本方法没有表现出基于BERT的大多数模型，但它表现出在类似数据上培训的那些，呈现出有希望的结果，实现0.65 F1得分。我们认为，与关系提取的文本文本方法有一些竞争优势，并且有很多研究进步的空间。

生物重建VII Track-2挑战包括命名实体识别，实体链接（或实体 - 归一化），主题索引任务 - 与实体和主题限制为这项挑战的化学品。命名实体识别是一个完善的问题，我们通过基于Bert的生物群体模型实现了我们的最佳性能。我们将基于BERT的方法扩展到实体链接任务。在预先预订Biobert的第二阶段，通过称为自对准预先训练（SAP）的度量学习损失策略，我们将基于其SAP-Biobert Word Embeddings之间的余弦相似性链接实体。尽管我们的命名实体识别实验取得了成功，但我们发现化学指数任务一般更具挑战性。除了传统的NER方法之外，我们还尝试使用基于新颖的文本或“提示”方法的命名实体识别和实体链接，该方法使用生成语言模型，例如T5和GPT。我们通过这种新方法实现了令人鼓舞的结果。

生物医学研究正在以这种指数速度增长，科学家，研究人员和从业者不再能够应对该领域发表的文献的数量。文献中提出的知识需要以这种方式系统化，可以轻松找到声明和假设，访问和验证。知识图可以为文献提供这样的语义知识表示框架。然而，为了构建知识图形，有必要以生物医学实体之间的关系形式提取知识并使两个实体和关系类型进行正常化。在本文中，我们展示并比较了少数基于规则和基于机器学习的（天真的贝叶斯，随机森林作为传统机器学习方法和T5基础的示例，作为现代深层学习的示例）可扩展关系从生物医学中提取的方法集成到知识图中的文献。我们研究了如何为不平衡和相当小的数据集进行弹性，显示T5模型，由于其在大型C4数据集以及不平衡数据上进行预培训，因此T5模型处理得好的小型数据集。最佳执行模型是T5模型在平衡数据上进行微调，报告F1分数为0.88。

Motivation: Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora. Results: We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts.

在这项研究中，我们展示了我们的工作参与BioCreative VII挑战的药物支持。药物靶靶相互作用（DTI）对于药物发现和重新施加至关重要，其通常从实验制品中手动提取。有关PubMed的32M生物医学文章和手动提取来自这种巨大的知识库的DTI是具有挑战性的。为了解决这个问题，我们为赛道1提供了一种解决方案，旨在提取药物和蛋白质实体之间的10种类型的相互作用。我们应用了一个组合生物向罗伯塔，艺术语言模型的艺术状态的集合类模型，卷积神经网络（CNN）来提取这些关系。尽管Biocreative VII药物测试语料库中的阶级失衡，但我们的模型与挑战中其他提交的平均值相比实现了良好的性能，微F1分数为55.67％（生物重建VI Chemprot测试语料库）。结果表明，深入学习在提取各种类型的DTIS方面的潜力。

社交媒体帖子包含有关医疗条件和与健康相关行为的潜在有价值的信息。生物重建VII任务3专注于通过识别推文中的药物和膳食补充剂的提及来挖掘这些信息。我们通过精细调整多个BERT样式语言模型来执行此任务以执行令牌级分类，并将它们组合成集合以生成最终预测。我们最好的系统由五个Megatron-Bert-345M型号组成，在看不见的测试数据上实现了0.764的严格F1得分。

Triplet extraction aims to extract entities and their corresponding relations in unstructured text. Most existing methods train an extraction model on high-quality training data, and hence are incapable of extracting relations that were not observed during training. Generalizing the model to unseen relations typically requires fine-tuning on synthetic training data which is often noisy and unreliable. In this paper, we argue that reducing triplet extraction to a template filling task over a pre-trained language model can equip the model with zero-shot learning capabilities and enable it to leverage the implicit knowledge in the language model. Embodying these ideas, we propose a novel framework, ZETT (ZEro-shot Triplet extraction by Template infilling), that is based on end-to-end generative transformers. Our experiments show that without any data augmentation or pipeline systems, ZETT can outperform previous state-of-the-art models with 25% less parameters. We further show that ZETT is more robust in detecting entities and can be incorporated with automatically generated templates for relations.

There is an increasing interest in developing artificial intelligence (AI) systems to process and interpret electronic health records (EHRs). Natural language processing (NLP) powered by pretrained language models is the key technology for medical AI systems utilizing clinical narratives. However, there are few clinical language models, the largest of which trained in the clinical domain is comparatively small at 110 million parameters (compared with billions of parameters in the general domain). It is not clear how large clinical language models with billions of parameters can help medical AI systems utilize unstructured EHRs. In this study, we develop from scratch a large clinical language model - GatorTron - using >90 billion words of text (including >82 billion words of de-identified clinical text) and systematically evaluate it on 5 clinical NLP tasks including clinical concept extraction, medical relation extraction, semantic textual similarity, natural language inference (NLI), and medical question answering (MQA). We examine how (1) scaling up the number of parameters and (2) scaling up the size of the training data could benefit these NLP tasks. GatorTron models scale up the clinical language model from 110 million to 8.9 billion parameters and improve 5 clinical NLP tasks (e.g., 9.6% and 9.5% improvement in accuracy for NLI and MQA), which can be applied to medical AI systems to improve healthcare delivery. The GatorTron models are publicly available at: https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/models/gatortron_og.

We introduce a new language representation model called BERT, which stands for Bidirectional Encoder Representations from Transformers. Unlike recent language representation models (Peters et al., 2018a;Radford et al., 2018), BERT is designed to pretrain deep bidirectional representations from unlabeled text by jointly conditioning on both left and right context in all layers. As a result, the pre-trained BERT model can be finetuned with just one additional output layer to create state-of-the-art models for a wide range of tasks, such as question answering and language inference, without substantial taskspecific architecture modifications.BERT is conceptually simple and empirically powerful. It obtains new state-of-the-art results on eleven natural language processing tasks, including pushing the GLUE score to 80.5% (7.7% point absolute improvement), MultiNLI accuracy to 86.7% (4.6% absolute improvement), SQuAD v1.1 question answering Test F1 to 93.2 (1.5 point absolute improvement) and SQuAD v2.0 Test F1 to 83.1 (5.1 point absolute improvement).

The strong few-shot in-context learning capability of large pre-trained language models (PLMs) such as GPT-3 is highly appealing for application domains such as biomedicine, which feature high and diverse demands of language technologies but also high data annotation costs. In this paper, we present the first systematic and comprehensive study to compare the few-shot performance of GPT-3 in-context learning with fine-tuning smaller (i.e., BERT-sized) PLMs on two highly representative biomedical information extraction tasks, named entity recognition and relation extraction. We follow the true few-shot setting to avoid overestimating models' few-shot performance by model selection over a large validation set. We also optimize GPT-3's performance with known techniques such as contextual calibration and dynamic in-context example retrieval. However, our results show that GPT-3 still significantly underperforms compared to simply fine-tuning a smaller PLM. In addition, GPT-3 in-context learning also yields smaller gains in accuracy when more training data becomes available. Our in-depth analyses further reveal issues of the in-context learning setting that may be detrimental to information extraction tasks in general. Given the high cost of experimenting with GPT-3, we hope our study provides guidance for biomedical researchers and practitioners towards more promising directions such as fine-tuning small PLMs.

我们提出了一个新的框架，在增强的自然语言（TANL）之间的翻译，解决了许多结构化预测语言任务，包括联合实体和关系提取，嵌套命名实体识别，关系分类，语义角色标记，事件提取，COREREFED分辨率和对话状态追踪。通过培训特定于特定于任务的鉴别分类器来说，我们将其作为一种在增强的自然语言之间的翻译任务，而不是通过培训问题，而不是解决问题，而是可以轻松提取任务相关信息。我们的方法可以匹配或优于所有任务的特定于任务特定模型，特别是在联合实体和关系提取（Conll04，Ade，NYT和ACE2005数据集）上实现了新的最先进的结果，与关系分类（偶尔和默示）和语义角色标签（Conll-2005和Conll-2012）。我们在使用相同的架构和超参数的同时为所有任务使用相同的架构和超级参数，甚至在培训单个模型时同时解决所有任务（多任务学习）。最后，我们表明，由于更好地利用标签语义，我们的框架也可以显着提高低资源制度的性能。

生物医学文献中的自动关系提取（RE）对于研究和现实世界中的许多下游文本挖掘应用至关重要。但是，用于生物医学的大多数现有基准测试数据集仅关注句子级别的单一类型（例如蛋白质 - 蛋白质相互作用）的关系，从而极大地限制了生物医学中RE系统的开发。在这项工作中，我们首先审查了常用的名称实体识别（NER）和RE数据集。然后，我们提出了Biored，这是一种具有多种实体类型（例如，基因/蛋白质，疾病，化学）和关系对（例如，基因 - 疾病；化学化学化学化学）的首个生物医学RE语料库，在文档水平上，在一组600个PubMed摘要中。此外，我们将每个关系标记为描述一种新颖的发现或先前已知的背景知识，使自动化算法能够区分新颖和背景信息。我们通过基准在NER和RE任务上对几种现有的最新方法（包括基于BERT的模型）进行基准测试来评估Biored的实用性。我们的结果表明，尽管现有方法可以在NER任务上达到高性能（F-评分为89.3％），但重新任务的改进空间很大，尤其是在提取新颖的关系时（F-评分为47.7％）。我们的实验还表明，如此丰富的数据集可以成功地促进生物医学更准确，高效和健壮的RE系统的开发。 Biored数据集和注释指南可在https://ftp.ncbi.nlm.nih.gov/pub/lu/biored/中免费获得。

与伯特（Bert）等语言模型相比，已证明知识增强语言表示的预培训模型在知识基础构建任务（即〜关系提取）中更有效。这些知识增强的语言模型将知识纳入预训练中，以生成实体或关系的表示。但是，现有方法通常用单独的嵌入表示每个实体。结果，这些方法难以代表播出的实体和大量参数，在其基础代币模型之上（即〜变压器），必须使用，并且可以处理的实体数量为由于内存限制，实践限制。此外，现有模型仍然难以同时代表实体和关系。为了解决这些问题，我们提出了一个新的预培训模型，该模型分别从图书中学习实体和关系的表示形式，并分别在文本中跨越跨度。通过使用SPAN模块有效地编码跨度，我们的模型可以代表实体及其关系，但所需的参数比现有模型更少。我们通过从Wikipedia中提取的知识图对我们的模型进行了预训练，并在广泛的监督和无监督的信息提取任务上进行了测试。结果表明，我们的模型比基线学习对实体和关系的表现更好，而在监督的设置中，微调我们的模型始终优于罗伯塔，并在信息提取任务上取得了竞争成果。

Two key obstacles in biomedical relation extraction (RE) are the scarcity of annotations and the prevalence of instances without explicitly pre-defined labels due to low annotation coverage. Existing approaches, which treat biomedical RE as a multi-class classification task, often result in poor generalization in low-resource settings and do not have the ability to make selective prediction on unknown cases but give a guess from seen relations, hindering the applicability of those approaches. We present NBR, which converts biomedical RE as natural language inference formulation through indirect supervision. By converting relations to natural language hypotheses, NBR is capable of exploiting semantic cues to alleviate annotation scarcity. By incorporating a ranking-based loss that implicitly calibrates abstinent instances, NBR learns a clearer decision boundary and is instructed to abstain on uncertain instances. Extensive experiments on three widely-used biomedical RE benchmarks, namely ChemProt, DDI and GAD, verify the effectiveness of NBR in both full-set and low-resource regimes. Our analysis demonstrates that indirect supervision benefits biomedical RE even when a domain gap exists, and combining NLI knowledge with biomedical knowledge leads to the best performance gains.

In this work, we explore "prompt tuning," a simple yet effective mechanism for learning "soft prompts" to condition frozen language models to perform specific downstream tasks. Unlike the discrete text prompts used by GPT-3, soft prompts are learned through backpropagation and can be tuned to incorporate signals from any number of labeled examples. Our end-to-end learned approach outperforms GPT-3's few-shot learning by a large margin. More remarkably, through ablations on model size using T5, we show that prompt tuning becomes more competitive with scale: as models exceed billions of parameters, our method "closes the gap" and matches the strong performance of model tuning (where all model weights are tuned). This finding is especially relevant because large models are costly to share and serve and the ability to reuse one frozen model for multiple downstream tasks can ease this burden. Our method can be seen as a simplification of the recently proposed "prefix tuning" of Li and Liang (2021) and we provide a comparison to this and other similar approaches. Finally, we show that conditioning a frozen model with soft prompts confers benefits in robustness to domain transfer and enables efficient "prompt ensembling." * Work done as a Google AI Resident.

本文是关于我们的系统提交给生物重建VII轨道2挑战的化学识别任务的技术报告。这一挑战的主要特点是数据包括全文文章，而当前数据集通常由只有标题和摘要组成。为了有效解决该问题，我们的目的是使用各种方法改进标记一致性和实体覆盖，例如在与命名实体识别（ner）的相同文章中的多数投票和组合字典和神经模型进行归一化的混合方法。在NLM-Chem数据集的实验中，我们表明我们的方法改善了模型的性能，特别是在召回方面。最后，在对挑战的官方评估中，我们的系统通过大幅表现出基线模型和来自16支队伍的超过80个提交来排名第一。

我们提供了从文本到文本变换器（T5）的第一次探索句子嵌入式。句子嵌入式广泛适用于语言处理任务。虽然T5在作为序列到序列映射问题的语言任务上实现令人印象深刻的性能，但目前尚不清楚如何从编码器解码器模型生成陈列嵌入的句子。我们调查三种方法提取T5句子嵌入方法：两个仅利用T5编码器，一个使用全T5编码器解码器模型。为了支持我们的调查，我们建立了一个新的句子代表转移基准，SentGlue，它将Senteval Toolkit扩展到粘合基准的九个任务。我们的编码器的型号优于Senteval和SentGlue传输任务的句子 - BERT和SIMCSE句子嵌入，包括语义文本相似性（STS）。发现从数百万到数十亿参数的缩放T5产生一致的进一步改进。最后，我们的编码器 - 解码器方法在使用句子嵌入时在STS上实现了新的最先进的。我们的模型在https://tfhub.dev/google/collections/sentence-t5/1发布。

Powerful generative models have led to recent progress in question generation (QG). However, it is difficult to measure advances in QG research since there are no standardized resources that allow a uniform comparison among approaches. In this paper, we introduce QG-Bench, a multilingual and multidomain benchmark for QG that unifies existing question answering datasets by converting them to a standard QG setting. It includes general-purpose datasets such as SQuAD for English, datasets from ten domains and two styles, as well as datasets in eight different languages. Using QG-Bench as a reference, we perform an extensive analysis of the capabilities of language models for the task. First, we propose robust QG baselines based on fine-tuning generative language models. Then, we complement automatic evaluation based on standard metrics with an extensive manual evaluation, which in turn sheds light on the difficulty of evaluating QG models. Finally, we analyse both the domain adaptability of these models as well as the effectiveness of multilingual models in languages other than English. QG-Bench is released along with the fine-tuned models presented in the paper https://github.com/asahi417/lm-question-generation, which are also available as a demo https://autoqg.net/.

问题答案（QA）是自然语言处理中最具挑战性的最具挑战性的问题之一（NLP）。问答（QA）系统试图为给定问题产生答案。这些答案可以从非结构化或结构化文本生成。因此，QA被认为是可以用于评估文本了解系统的重要研究区域。大量的QA研究致力于英语语言，调查最先进的技术和实现最先进的结果。然而，由于阿拉伯QA中的研究努力和缺乏大型基准数据集，在阿拉伯语问答进展中的研究努力得到了很大速度的速度。最近许多预先接受的语言模型在许多阿拉伯语NLP问题中提供了高性能。在这项工作中，我们使用四个阅读理解数据集来评估阿拉伯QA的最先进的接种变压器模型，它是阿拉伯语 - 队，ArcD，AQAD和TYDIQA-GoldP数据集。我们微调并比较了Arabertv2基础模型，ArabertV0.2大型型号和ARAElectra模型的性能。在最后，我们提供了一个分析，了解和解释某些型号获得的低绩效结果。

预先训练的语言模型（LMS）通常逻辑地扭转或以组成方式概括。最近的工作表明，结合外部实体知识可以提高LMS的能力和推广。然而，明确提供实体抽象的效果仍然不清楚，特别是在最近的研究表明，预先训练的LMS已经在其参数中编码了一些知识。我们研究将实体型抽象的实用程序融入预先训练的变压器，并在需要不同形式的逻辑推理的四个NLP任务上测试这些方法：（1）与基于文本的关系推理（CLUTRR）的组成语言理解，（2）绑架推理（校对者），（3）多跳问题应答（HotpotQA），和（4）会话问题应答（COQA）。我们提出并经验探索了三种方法来添加此类抽象：（i）作为附加输入嵌入式，（ii）作为编码的单独序列，（iii）作为模型的辅助预测任务。总体而言，我们的分析表明，具有抽象实体知识的模型比没有它更好。然而，我们的实验还表明，强烈的益处取决于所使用的技术和手头的任务。与基线模型相比，最佳抽象意识模型分别达到了88.8％和91.8％的总精度，分别在CLUTRR和校对者上实现了62.3％和89.8％。此外，抽象感知模型在插值和外推设置中显示出改善的组成概括。然而，对于热杆菌和CoQA，我们发现F1分数平均仅提高0.5％。我们的结果表明，明确抽象的好处在正式定义的逻辑推理设置中需要许多推理跳跃，但指向它对具有较少正式逻辑结构的NLP任务不利的概念。