We evaluate named entity representations of BERT-based NLP models by investigating their robustness to replacements from the same typed class in the input. We highlight that on several tasks while such perturbations are natural, state of the art trained models are surprisingly brittle. The brittleness continues even with the recent entity-aware BERT models. We also try to discern the cause of this non-robustness, considering factors such as tokenization and frequency of occurrence. Then we provide a simple method that ensembles predictions from multiple replacements while jointly modeling the uncertainty of type annotations and label predictions. Experiments on three NLP tasks show that our method enhances robustness and increases accuracy on both natural and adversarial datasets.
A typical architecture for end-to-end entity linking systems consists of three steps: mention detection, candidate generation and entity disambiguation. In this study we investigate the following questions: (a) Can all those steps be learned jointly with a model for contextualized text-representations, i.e. BERT (Devlin et al., 2019)? (b) How much entity knowledge is already contained in pretrained BERT? (c) Does additional entity knowledge improve BERT's performance in downstream tasks? To this end, we propose an extreme simplification of the entity linking setup that works surprisingly well:…
We propose a global entity disambiguation (ED) model based on BERT. To capture global contextual information for ED, our model treats not only words but also entities as input tokens, and solves the task by sequentially resolving mentions to their referent entities and using resolved entities as inputs at each step. We train the model using a large entity-annotated corpus obtained from Wikipedia. We achieve new state-of-the-art results on five standard ED datasets: AIDA-CoNLL, MSNBC, AQUAINT, ACE2004, and WNED-WIKI. The source code and model checkpoint are available at https://github.com/studi…
Xian Jiaotong University（西安交通大学）；The University of Manchester（曼彻斯特大学）；East China University of Science and Technology（华东理工大学）；Zhejiang University（浙江大学）
Automatic or semi-automatic conversion of protocols specifying steps in performing a lab procedure into machine-readable format benefits biological research a lot. These noisy, dense, and domain-specific lab protocols processing draws more and more interests with the development of deep learning. This paper presents our teamwork on WNUT 2020 shared task-1: wet lab entity extract, that we conducted studies in several models, including a BiLSTM CRF model and a Bert case model which can be used to complete wet lab entity extraction. And we mainly discussed the performance differences of \textbf{B…
NLP Research Laboratory（自然语言处理研究实验室）；Shahid Beheshti University（沙希德贝赫什提大学）
Named entity recognition is a natural language processing task to recognize and extract spans of text associated with named entities and classify them in semantic Categories. Google BERT is a deep bidirectional language model, pre-trained on large corpora that can be fine-tuned to solve many NLP tasks such as question answering, named entity recognition, part of speech tagging and etc. In this paper, we use the pre-trained deep bidirectional network, BERT, to make a model for named entity recognition in Persian. We also compare the results of our model with the previous state of the art result…
Center for Information and Language Processing, LMU Munich（慕尼黑大学信息与语言处理中心）；Siemens AG（西门子股份公司）
We present a novel way of injecting factual knowledge about entities into the pretrained BERT model (Devlin et al., 2019): We align Wikipedia2Vec entity vectors (Yamada et al., 2016) with BERT's native wordpiece vector space and use the aligned entity vectors as if they were wordpiece vectors. The resulting entity-enhanced version of BERT (called E-BERT) is similar in spirit to ERNIE (Zhang et al., 2019) and KnowBert (Peters et al., 2019), but it requires no expensive further pretraining of the BERT encoder. We evaluate E-BERT on unsupervised question answering (QA), supervised relation classi…
The use of BERT, one of the most popular language models, has led to improvements in many Natural Language Processing (NLP) tasks. One such task is Named Entity Recognition (NER) i.e. automatic identification of named entities such as location, person, organization, etc. from a given text. It is also an important base step for many NLP tasks such as information extraction and argumentation mining. Even though there is much research done on NER using BERT and other popular language models, the same is not explored in detail when it comes to Legal NLP or Legal Tech. Legal NLP applies various NLP…
School of Biomedical Informatics, The University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心生物医学信息学院）
Developing high-performance entity normalization algorithms that can alleviate the term variation problem is of great interest to the biomedical community. Although deep learning-based methods have been successfully applied to biomedical entity normalization, they often depend on traditional context-independent word embeddings. Bidirectional Encoder Representations from Transformers (BERT), BERT for Biomedical Text Mining (BioBERT) and BERT for Clinical Text Mining (ClinicalBERT) were recently introduced to pre-train contextualized word representation models using bidirectional Transformers, a…
Pune Institute of Computer Technology（浦那计算机技术学院）；L3Cube；Indian Institute of Technology Madras（印度理工学院马德拉斯分校）
Named entity recognition (NER) is the process of recognising and classifying important information (entities) in text. Proper nouns, such as a person's name, an organization's name, or a location's name, are examples of entities. The NER is one of the important modules in applications like human resources, customer support, search engines, content classification, and academia. In this work, we consider NER for low-resource Indian languages like Hindi and Marathi. The transformer-based models have been widely used for NER tasks. We consider different variations of BERT like base-BERT, RoBERTa, …
Pre-trained language models such as BERT have been a key ingredient to achieve state-of-the-art results on a variety of tasks in natural language processing and, more recently, also in information retrieval.Recent research even claims that BERT is able to capture factual knowledge about entity relations and properties, the information that is commonly obtained from knowledge graphs. This paper investigates the following question: Do BERT-based entity retrieval models benefit from additional entity information stored in knowledge graphs? To address this research question, we map entity embeddin…
Pune Institute of Computer Technology（浦那计算机技术学院）；L3Cube Pune（L3Cube浦那）；Indian Institute of Technology Madras（印度理工学院马德拉斯分校）
Named Entity Recognition (NER) is a basic NLP task and finds major applications in conversational and search systems. It helps us identify key entities in a sentence used for the downstream application. NER or similar slot filling systems for popular languages have been heavily used in commercial applications. In this work, we focus on Marathi, an Indian language, spoken prominently by the people of Maharashtra state. Marathi is a low resource language and still lacks useful NER resources. We present L3Cube-MahaNER, the first major gold standard named entity recognition dataset in Marathi. We …
University of Campinas（坎皮纳斯大学）；NeuralMind Inteligência Artificial（NeuralMind 人工智能）；New York University（纽约大学）
Recent advances in language representation using neural networks have made it viable to transfer the learned internal states of a trained model to downstream natural language processing tasks, such as named entity recognition (NER) and question answering. It has been shown that the leverage of pre-trained language models improves the overall performance on many tasks and is highly beneficial when labeled data is scarce. In this work, we train Portuguese BERT models and employ a BERT-CRF architecture to the NER task on the Portuguese language, combining the transfer capabilities of BERT with th…
In this paper, we report our method for the Information Extraction task in 2019 Language and Intelligence Challenge. We incorporate BERT into the multi-head selection framework for joint entity-relation extraction. This model extends existing approaches from three perspectives. First, BERT is adopted as a feature extraction layer at the bottom of the multi-head selection framework. We further optimize BERT by introducing a semantic-enhanced task during BERT pre-training. Second, we introduce a large-scale Baidu Baike corpus for entity recognition pre-training, which is of weekly supervised lea…
This report describes the methods employed by the Democritus University of Thrace (DUTH) team for participating in SemEval-2020 Task 11: Detection of Propaganda Techniques in News Articles. Our team dealt with Subtask 2: Technique Classification. We used shallow Natural Language Processing (NLP) preprocessing techniques to reduce the noise in the dataset, feature selection methods, and common supervised machine learning algorithms. Our final model is based on using the BERT system with entity mapping. To improve our model's accuracy, we mapped certain words into five distinct categories by emp…
Fraunhofer IAIS（弗劳恩霍夫智能分析与信息系统研究所）；University of Bonn（波恩大学）；PricewaterhouseCoopers GmbH（普华永道有限责任公司）
We present KPI-BERT, a system which employs novel methods of named entity recognition (NER) and relation extraction (RE) to extract and link key performance indicators (KPIs), e.g. "revenue" or "interest expenses", of companies from real-world German financial documents. Specifically, we introduce an end-to-end trainable architecture that is based on Bidirectional Encoder Representations from Transformers (BERT) combining a recurrent neural network (RNN) with conditional label masking to sequentially tag entities before it classifies their relations. Our model also introduces a learnable RNN-b…
University of Chinese Academy of Sciences（中国科学院大学）；The Institute of Software, Chinese Academy of Sciences（中国科学院软件研究所）；Sichuan University（四川大学）；Beijing Jiaotong University（北京交通大学）
Pre-trained models such as BERT are widely used in NLP tasks and are fine-tuned to improve the performance of various NLP tasks consistently. Nevertheless, the fine-tuned BERT model trained on our protocol corpus still has a weak performance on the Entity Linking (EL) task. In this paper, we propose a model that joints a fine-tuned language model with an RFC Domain Model. Firstly, we design a Protocol Knowledge Base as the guideline for protocol EL. Secondly, we propose a novel model, PEL-BERT, to link named entities in protocols to categories in Protocol Knowledge Base. Finally, we conduct a …
Zhejiang Informatization Development Institute, Hangzhou Dianzi University（杭州电子科技大学浙江信息化发展研究院）
We propose a new Named entity recognition (NER) method to effectively make use of the results of Part-of-speech (POS) tagging, Chinese word segmentation (CWS) and parsing while avoiding NER error caused by POS tagging error. This paper first uses Stanford natural language process (NLP) tool to annotate large-scale untagged data so as to reduce the dependence on the tagged data; then a new NLP model, g-BERT model, is designed to compress Bidirectional Encoder Representations from Transformers (BERT) model in order to reduce calculation quantity; finally, the model is evaluated based on Chinese …
The emergence and rapid progress of the Internet have brought ever-increasing impact on financial domain. How to rapidly and accurately mine the key information from the massive negative financial texts has become one of the key issues for investors and decision makers. Aiming at the issue, we propose a sentiment analysis and key entity detection approach based on BERT, which is applied in online financial text mining and public opinion analysis in social media. By using pre-train model, we first study sentiment analysis, and then we consider key entity detection as a sentence matching or Mach…
The Biocreative VII Track-2 challenge consists of named entity recognition, entity-linking (or entity-normalization), and topic indexing tasks -- with entities and topics limited to chemicals for this challenge. Named entity recognition is a well-established problem and we achieve our best performance with BERT-based BioMegatron models. We extend our BERT-based approach to the entity linking task. After the second stage of pretraining BioBERT with a metric-learning loss strategy called self-alignment pretraining (SAP), we link entities based on the cosine similarity between their SAP-BioBERT w…
Leiden Institute of Advanced Computer Science, Leiden University（莱顿大学高级计算机科学研究所）
Both generic and domain-specific BERT models are widely used for natural language processing (NLP) tasks. In this paper we investigate the vulnerability of BERT models to variation in input data for Named Entity Recognition (NER) through adversarial attack. Experimental results show that BERT models are vulnerable to variation in the entity context with 20.2 to 45.0% of entities predicted completely wrong and another 29.3 to 53.3% of entities predicted wrong partially. BERT models seem most vulnerable to changes in the local context of entities and often a single change is sufficient to fool t…
Indian Institute of Technology, Kharagpur（印度理工学院卡拉格普尔分校）
Supervised models trained to predict properties from representations have been achieving high accuracy on a variety of tasks. For instance, the BERT family seems to work exceptionally well on the downstream task from NER tagging to the range of other linguistic tasks. But the vocabulary used in the medical field contains a lot of different tokens used only in the medical industry such as the name of different diseases, devices, organisms, medicines, etc. that makes it difficult for traditional BERT model to create contextualized embedding. In this paper, we are going to illustrate the System f…
This paper presents Wojood, a corpus for Arabic nested Named Entity Recognition (NER). Nested entities occur when one entity mention is embedded inside another entity mention. Wojood consists of about 550K Modern Standard Arabic (MSA) and dialect tokens that are manually annotated with 21 entity types including person, organization, location, event and date. More importantly, the corpus is annotated with nested entities instead of the more common flat annotations. The data contains about 75K entities and 22.5% of which are nested. The inter-annotator evaluation of the corpus demonstrated a str…
East China University of Science and Technology（华东理工大学）；Shanghai Hospital Development Center（上海医院发展中心）
Entity and relation extraction is the necessary step in structuring medical text. However, the feature extraction ability of the bidirectional long short term memory network in the existing model does not achieve the best effect. At the same time, the language model has achieved excellent results in more and more natural language processing tasks. In this paper, we present a focused attention model for the joint entity and relation extraction task. Our model integrates well-known BERT language model into joint learning through dynamic range attention mechanism, thus improving the feature repre…
University of Udine（乌迪内大学）；University of Naples Federico II（那不勒斯费德里科二世大学）；The Hong Kong Polytechnic University（香港理工大学）；Bayer Pharmaceuticals（拜耳制药）
This paper describes the models developed by the AILAB-Udine team for the SMM4H 22 Shared Task. We explored the limits of Transformer based models on text classification, entity extraction and entity normalization, tackling Tasks 1, 2, 5, 6 and 10. The main take-aways we got from participating in different tasks are: the overwhelming positive effects of combining different architectures when using ensemble learning, and the great potential of generative models for term normalization.
RheinMain University of Applied Sciences（莱茵美因应用科学大学）
Entity linking, the task of mapping textual mentions to known entities, has recently been tackled using contextualized neural networks. We address the question whether these results -- reported for large, high-quality datasets such as Wikipedia -- transfer to practical business use cases, where labels are scarce, text is low-quality, and terminology is highly domain-specific. Using an entity linking model based on BERT, a popular transformer network in natural language processing, we show that a neural approach outperforms and complements hand-coded heuristics, with improvements of about 20% t…
The Hong Kong University of Science and Technology（香港科技大学）；Alibaba Group（阿里巴巴集团）
Named entity recognition (NER) models generally perform poorly when large training datasets are unavailable for low-resource domains. Recently, pre-training a large-scale language model has become a promising direction for coping with the data scarcity issue. However, the underlying discrepancies between the language modeling and NER task could limit the models' performance, and pre-training for the NER task has rarely been studied since the collected NER datasets are generally small or large but with low quality. In this paper, we construct a massive NER corpus with a relatively high quality,…
RheinMain University of Applied Sciences（莱茵美因应用科学大学）
We introduce SpERT, an attention model for span-based joint entity and relation extraction. Our key contribution is a light-weight reasoning on BERT embeddings, which features entity recognition and filtering, as well as relation classification with a localized, marker-free context representation. The model is trained using strong within-sentence negative samples, which are efficiently extracted in a single BERT pass. These aspects facilitate a search over all spans in the sentence. In ablation studies, we demonstrate the benefits of pre-training, strong negative sampling and localized context…
University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Biomedical entity linking is the task of linking entity mentions in a biomedical document to referent entities in a knowledge base. Recently, many BERT-based models have been introduced for the task. While these models have achieved competitive results on many datasets, they are computationally expensive and contain about 110M parameters. Little is known about the factors contributing to their impressive performance and whether the over-parameterization is needed. In this work, we shed some light on the inner working mechanisms of these large BERT-based models. Through a set of probing experim…
We study the open-domain named entity recognition (NER) problem under distant supervision. The distant supervision, though does not require large amounts of manual annotations, yields highly incomplete and noisy distant labels via external knowledge bases. To address this challenge, we propose a new computational framework -- BOND, which leverages the power of pre-trained language models (e.g., BERT and RoBERTa) to improve the prediction performance of NER models. Specifically, we propose a two-stage training algorithm: In the first stage, we adapt the pre-trained language model to the NER tas…
Pre-trained language models (LMs) like BERT have shown to store factual knowledge about the world. This knowledge can be used to augment the information present in Knowledge Bases, which tend to be incomplete. However, prior attempts at using BERT for task of Knowledge Base Completion (KBC) resulted in performance worse than embedding based techniques that rely only on the graph structure. In this work we develop a novel model, Cross-Entity Aware Reranker (CEAR), that uses BERT to re-rank the output of existing KBC models with cross-entity attention. Unlike prior work that scores each entity i…
Data Science and AI, Novartis（诺华数据科学与人工智能部门）；Global Drug Development, Novartis Pharma AG（诺华制药全球药物开发部）
Natural language processing (NLP) of clinical trial documents can be useful in new trial design. Here we identify entity types relevant to clinical trial design and propose a framework called CT-BERT for information extraction from clinical trial text. We trained named entity recognition (NER) models to extract eligibility criteria entities by fine-tuning a set of pre-trained BERT models. We then compared the performance of CT-BERT with recent baseline methods including attention-based BiLSTM and Criteria2Query. The results demonstrate the superiority of CT-BERT in clinical trial NLP.
Georgia Institute of Technology（佐治亚理工学院）；Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
We study the problem of learning a named entity recognition (NER) tagger using noisy labels from multiple weak supervision sources. Though cheap to obtain, the labels from weak supervision sources are often incomplete, inaccurate, and contradictory, making it difficult to learn an accurate NER model. To address this challenge, we propose a conditional hidden Markov model (CHMM), which can effectively infer true labels from multi-source noisy labels in an unsupervised way. CHMM enhances the classic hidden Markov model with the contextual representation power of pre-trained language models. Spec…
Comparative Study of Pre-Trained BERT and Large Language Models for Code-Mixed Named Entity Recognition
Dept. of Computer Engineering, Pune Institute of Computer Technology, Pune, India（计算机工程系，普那计算机技术研究所，普那，印度）；Indian Institute of Technology Madras, Chennai, India（印度理工学院马德拉斯学院，钦奈，印度）；L3Cube Labs, Pune, Maharashtra, India（L3Cube实验室，普那，马哈拉施特拉邦，印度）
School of Management, University of Science and Technology of China（中国科学技术大学管理学院）
Financial named entity recognition (FinNER) from literature is a challenging task in the field of financial text information extraction, which aims to extract a large amount of financial knowledge from unstructured texts. It is widely accepted to use sequence tagging frameworks to implement FinNER tasks. However, such sequence tagging models cannot fully take advantage of the semantic information in the texts. Instead, we formulate the FinNER task as a machine reading comprehension (MRC) problem and propose a new model termed FinBERT-MRC. This formulation introduces significant prior informati…
Named entity recognition (NER) is frequently addressed as a sequence classification task where each input consists of one sentence of text. It is nevertheless clear that useful information for the task can often be found outside of the scope of a single-sentence context. Recently proposed self-attention models such as BERT can both efficiently capture long-distance relationships in input as well as represent inputs consisting of several sentences, creating new opportunitites for approaches that incorporate cross-sentence information in natural language processing tasks. In this paper, we prese…
There is an increasing interest in studying natural language and computer code together, as large corpora of programming texts become readily available on the Internet. For example, StackOverflow currently has over 15 million programming related questions written by 8.5 million users. Meanwhile, there is still a lack of fundamental NLP techniques for identifying code tokens or software-related named entities that appear within natural language sentences. In this paper, we introduce a new named entity recognition (NER) corpus for the computer programming domain, consisting of 15,372 sentences a…
Information extraction is an important task in NLP, enabling the automatic extraction of data for relational database filling. Historically, research and data was produced for English text, followed in subsequent years by datasets in Arabic, Chinese (ACE/OntoNotes), Dutch, Spanish, German (CoNLL evaluations), and many others. The natural tendency has been to treat each language as a different dataset and build optimized models for each. In this paper we investigate a single Named Entity Recognition model, based on a multilingual BERT, that is trained jointly on many languages simultaneously, a…
In this paper, we present an empirical study of using pre-trained BERT models for the relation extraction task at the VLSP 2020 Evaluation Campaign. We applied two state-of-the-art BERT-based models: R-BERT and BERT model with entity starts. For each model, we compared two pre-trained BERT models: FPTAI/vibert and NlpHUST/vibert4news. We found that NlpHUST/vibert4news model significantly outperforms FPTAI/vibert for the Vietnamese relation extraction task. Finally, we proposed an ensemble model that combines R-BERT and BERT with entity starts. Our proposed ensemble model slightly improved agai…
Rutgers University–New Brunswick（罗格斯大学新伯朗士威校区）；Hasso Plattner Institute（哈索·普拉特纳研究所）；University of Potsdam（波茨坦大学）
Biomedical entity linking is the task of identifying mentions of biomedical concepts in text documents and mapping them to canonical entities in a target thesaurus. Recent advancements in entity linking using BERT-based models follow a retrieve and rerank paradigm, where the candidate entities are first selected using a retriever model, and then the retrieved candidates are ranked by a reranker model. While this paradigm produces state-of-the-art results, they are slow both at training and test time as they can process only one mention at a time. To mitigate these issues, we propose a BERT-bas…
University of Massachusetts, Amherst（马萨诸塞大学阿默斯特分校）；Google Research（谷歌研究院）
This paper considers the problem of zero-shot entity linking, in which a link in the test time may not present in training. Following the prevailing BERT-based research efforts, we find a simple yet effective way is to expand the long-range sequence modeling. Unlike many previous methods, our method does not require expensive pre-training of BERT with long position embedding. Instead, we propose an efficient position embeddings initialization method called Embedding-repeat, which initializes larger position embeddings based on BERT-Base. On Wikia's zero-shot EL dataset, our method improves the…
Clinical named entity recognition in the Portuguese language: a benchmark of modern BERT models and LLMs
Spesia；Faculdade de Medicina, Universidade de São Paulo（圣保罗大学医学院）；Pontifícia Universidade Católica do Paraná (PUCPR)（巴拉那天主教大学）；Florida Atlantic University（佛罗里达大西洋大学）；Universidade Federal do Paraná (UFPR)（巴拉那联邦大学）
In this work, we propose a two-stage method for named entity recognition (NER), especially for nested NER. We borrowed the idea from the two-stage Object Detection in computer vision and the way how they construct the loss function. First, a region proposal network generates region candidates and then a second-stage model discriminates and classifies the entity and makes the final prediction. We also designed a special loss function for the second-stage training that predicts the entityness and entity type at the same time. The model is built on top of pretrained BERT encoders, and we tried bo…
Contextualized entity representations learned by state-of-the-art transformer-based language models (TLMs) like BERT, GPT, T5, etc., leverage the attention mechanism to learn the data context from training data corpus. However, these models do not use the knowledge context. Knowledge context can be understood as semantics about entities and their relationship with neighboring entities in knowledge graphs. We propose a novel and effective technique to infuse knowledge context from multiple knowledge graphs for conceptual and ambiguous entities into TLMs during fine-tuning. It projects knowledge…
The amount of archaeological literature is growing rapidly. Until recently, these data were only accessible through metadata search. We implemented a text retrieval engine for a large archaeological text collection ($\sim 658$ Million words). In archaeological IR, domain-specific entities such as locations, time periods, and artefacts, play a central role. This motivated the development of a named entity recognition (NER) model to annotate the full collection with archaeological named entities. In this paper, we present ArcheoBERTje, a BERT model pre-trained on Dutch archaeological texts. We c…
Dalian University of Technology（大连理工大学）；Beijing Institute of Health Administration and Medical Information（北京卫生健康经济研究和医学信息研究所）
Recognition of biomedical entities from literature is a challenging research focus, which is the foundation for extracting a large amount of biomedical knowledge existing in unstructured texts into structured formats. Using the sequence labeling framework to implement biomedical named entity recognition (BioNER) is currently a conventional method. This method, however, often cannot take full advantage of the semantic information in the dataset, and the performance is not always satisfactory. In this work, instead of treating the BioNER task as a sequence labeling problem, we formulate it as a …
ANCHOLIK-NER: A Benchmark Dataset for Bangla Regional Named Entity Recognition
Department of Computer Science and Engineering（计算机科学与工程系）；Southeast University（东南大学）；Ahsanullah University of Science and Technology（阿沙努尔大学科学与技术学院）；Bangladesh University of Engineering and Technology（孟加拉工程与技术大学）
Named Entity Recognition task is one of the core tasks of information extraction. Word ambiguity and word abbreviation are important reasons for the low recognition rate of named entities. In this paper, we propose a novel named entity recognition model WCL-BBCD (Word Contrastive Learning with BERT-BiLSTM-CRF-DBpedia), which incorporates the idea of contrastive learning. The model first trains the sentence pairs in the text, calculate similarity between sentence pairs, and fine-tunes BERT used for the named entity recognition task according to the similarity, so as to alleviate word ambiguity.…
Social media posts contain potentially valuable information about medical conditions and health-related behavior. Biocreative VII Task 3 focuses on mining this information by recognizing mentions of medications and dietary supplements in tweets. We approach this task by fine tuning multiple BERT-style language models to perform token-level classification, and combining them into ensembles to generate final predictions. Our best system consists of five Megatron-BERT-345M models and achieves a strict F1 score of 0.764 on unseen test data.
