Extracting relationships and interactions between different biological entities is still an extremely challenging problem but has not received much attention as much as extraction in other generic domains. In addition to the lack of annotated data, low benchmarking is still a major reason for slow progress. In order to fill this gap, we compare multiple existing entity and relation extraction models over a recently introduced public dataset, BioRelEx of sentences annotated with biological entities and relations. Our straightforward benchmarking shows that span-based multi-task architectures like DYGIE show 4.9% and 6% absolute improvements in entity tagging and relation extraction respectively over the previous state-of-art and that incorporating domain-specific information like embeddings pre-trained over related domains boosts performance.
University of Illinois at Urbana-Champaign(伊利诺伊大学厄巴纳-香槟分校);Adobe Research(Adobe研究院)
Compared to the general news domain, information extraction (IE) from biomedical text requires much broader domain knowledge. However, many previous IE methods do not utilize any external knowledge during inference. Due to the exponential growth of biomedical publications, models that do not go beyond their fixed set of parameters will likely fall behind. Inspired by how humans look up relevant information to comprehend a scientific text, we present a novel framework that utilizes external knowledge for joint entity and relation extraction named KECI (Knowledge-Enhanced Collective Inference). …
Korea University(高丽大学);University of California, San Diego(加州大学圣迭戈分校)
This paper is a technical report on our system submitted to the chemical identification task of the BioCreative VII Track 2 challenge. The main feature of this challenge is that the data consists of full-text articles, while current datasets usually consist of only titles and abstracts. To effectively address the problem, we aim to improve tagging consistency and entity coverage using various methods such as majority voting within the same articles for named entity recognition (NER) and a hybrid approach that combines a dictionary and a neural model for normalization. In the experiments on the…
INESC TEC;FCUP(波尔图大学理学院);ICMC-USP(圣保罗大学圣卡洛斯数学与计算机科学研究所);University of São Paulo(圣保罗大学);FEP(波尔图大学经济学院)
This paper deals with the entity extraction task (named entity recognition) of a text mining process that aims at unveiling non-trivial semantic structures, such as relationships and interaction between entities or communities. In this paper we present a simple and efficient named entity extraction algorithm. The method, named PAMPO (PAttern Matching and POs tagging based algorithm for NER), relies on flexible pattern matching, part-of-speech tagging and lexical-based rules. It was developed to process texts written in Portuguese, however it is potentially applicable to other languages as well…
To enhance research on multimodal knowledge base and multimodal information processing, we propose a new task called multimodal entity tagging (MET) with a multimodal knowledge base (MKB). We also develop a dataset for the problem using an existing MKB. In an MKB, there are entities and their associated texts and images. In MET, given a text-image pair, one uses the information in the MKB to automatically identify the related entity in the text-image pair. We solve the task by using the information retrieval paradigm and implement several baselines using state-of-the-art methods in NLP and CV.…
Demiroren Teknoloji A.S.(德米罗伦技术公司);Istanbul Technical University(伊斯坦布尔理工大学);MEF University(MEF大学)
Named entity recognition (NER) is an extensively studied task that extracts and classifies named entities in a text. NER is crucial not only in downstream language processing applications such as relation extraction and question answering but also in large scale big data operations such as real-time analysis of online digital media content. Recent research efforts on Turkish, a less studied language with morphologically rich nature, have demonstrated the effectiveness of neural architectures on well-formed texts and yielded state-of-the art results by formulating the task as a sequence tagging…
Named Entity Recognition and Relation Extraction for Chinese literature text is regarded as the highly difficult problem, partially because of the lack of tagging sets. In this paper, we build a discourse-level dataset from hundreds of Chinese literature articles for improving this task. To build a high quality dataset, we propose two tagging methods to solve the problem of data inconsistency, including a heuristic tagging method and a machine auxiliary tagging method. Based on this corpus, we also introduce several widely used models to conduct experiments. Experimental results not only show …
Contextualized embeddings, which capture appropriate word meaning depending on context, have recently been proposed. We evaluate two meth ods for precomputing such embeddings, BERT and Flair, on four Czech text processing tasks: part-of-speech (POS) tagging, lemmatization, dependency pars ing and named entity recognition (NER). The first three tasks, POS tagging, lemmatization and dependency parsing, are evaluated on two corpora: the Prague Dependency Treebank 3.5 and the Universal Dependencies 2.3. The named entity recognition (NER) is evaluated on the Czech Named Entity Corpus 1.1 and 2.0. W…
We present the first multi-task learning model -- named PhoNLP -- for joint Vietnamese part-of-speech (POS) tagging, named entity recognition (NER) and dependency parsing. Experiments on Vietnamese benchmark datasets show that PhoNLP produces state-of-the-art results, outperforming a single-task learning approach that fine-tunes the pre-trained Vietnamese language model PhoBERT (Nguyen and Nguyen, 2020) for each task independently. We publicly release PhoNLP as an open-source toolkit under the Apache License 2.0. Although we specify PhoNLP for Vietnamese, our PhoNLP training and evaluation com…
South China University of Technology(华南理工大学);The Peng Cheng Laboratory(鹏城实验室);Yunnan University(云南大学);The Hong Kong Polytechnic University(香港理工大学)
Multimodal named entity recognition (MNER) and multimodal relation extraction (MRE) are two fundamental subtasks in the multimodal knowledge graph construction task. However, the existing methods usually handle two tasks independently, which ignores the bidirectional interaction between them. This paper is the first to propose jointly performing MNER and MRE as a joint multimodal entity-relation extraction task (JMERE). Besides, the current MNER and MRE models only consider aligning the visual objects with textual entities in visual and textual graphs but ignore the entity-entity relationships…
Span-based joint extraction simultaneously conducts named entity recognition (NER) and relation extraction (RE) in text span form. However, since previous span-based models rely on span-level classifications, they cannot benefit from token-level label information, which has been proven advantageous for the task. In this paper, we propose a Sequence Tagging augmented Span-based Network (STSN), a span-based joint model that can make use of token-level label information. In STSN, we construct a core neural architecture by deep stacking multiple attention layers, each of which consists of three ba…
Span-based joint extraction simultaneously conducts named entity recognition (NER) and relation extraction (RE) in text span form. Recent studies have shown that token labels can convey crucial task-specific information and enrich token semantics. However, as far as we know, due to completely abstain from sequence tagging mechanism, all prior span-based work fails to use token label in-formation. To solve this problem, we pro-pose Sequence Tagging enhanced Span-based Network (STSN), a span-based joint extrac-tion network that is enhanced by token BIO label information derived from sequence tag…
We describe a named entity tagging system that requires minimal linguistic knowledge and can be applied to more target languages without substantial changes. The system is based on the ideas of the Brill's tagger which makes it really simple. Using supervised machine learning, we construct a series of automatons (or transducers) in order to tag a given text. The final model is composed entirely of automatons and it requires a lineal time for tagging. It was tested with the Spanish data set provided in the CoNLL-$2002$ attaining an overall $F_{β= 1}$ measure of $60\%.$ Also, we present an algor…
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,…
Many language tasks (e.g., Named Entity Recognition, Part-of-Speech tagging, and Semantic Role Labeling) are naturally framed as sequence tagging problems. However, there has been comparatively little work on interpretability methods for sequence tagging models. In this paper, we extend influence functions - which aim to trace predictions back to the training points that informed them - to sequence tagging tasks. We define the influence of a training instance segment as the effect that perturbing the labels within this segment has on a test segment level prediction. We provide an efficient app…
FPT Technology Research Institute(FPT技术研究院);FPT University(FPT大学);Vietnam National University(越南国家大学)
This paper describes our study on using mutilingual BERT embeddings and some new neural models for improving sequence tagging tasks for the Vietnamese language. We propose new model architectures and evaluate them extensively on two named entity recognition datasets of VLSP 2016 and VLSP 2018, and on two part-of-speech tagging datasets of VLSP 2010 and VLSP 2013. Our proposed models outperform existing methods and achieve new state-of-the-art results. In particular, we have pushed the accuracy of part-of-speech tagging to 95.40% on the VLSP 2010 corpus, to 96.77% on the VLSP 2013 corpus; and t…
Azure Text Analytics, Microsoft Cloud & AI(微软云与人工智能部门Azure文本分析团队);Microsoft Dynamics 365 AI(微软Dynamics 365人工智能团队);Alexa AI, Amazon(亚马逊Alexa人工智能团队)
Conversational agents such as Cortana, Alexa and Siri are continuously working on increasing their capabilities by adding new domains. The support of a new domain includes the design and development of a number of NLU components for domain classification, intents classification and slots tagging (including named entity recognition). Each component only performs well when trained on a large amount of labeled data. Second, these components are deployed on limited-memory devices which requires some model compression. Third, for some domains such as the health domain, it is hard to find a single t…
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…
University of Southern California(南加州大学);Amazon(亚马逊)
Training neural models for named entity recognition (NER) in a new domain often requires additional human annotations (e.g., tens of thousands of labeled instances) that are usually expensive and time-consuming to collect. Thus, a crucial research question is how to obtain supervision in a cost-effective way. In this paper, we introduce "entity triggers," an effective proxy of human explanations for facilitating label-efficient learning of NER models. An entity trigger is defined as a group of words in a sentence that helps to explain why humans would recognize an entity in the sentence. We cr…
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 …
CRC for Innovative Dairy Products(创新乳制品合作研究中心);The University of Melbourne(墨尔本大学);Victorian Bioinformatics Consortium(维多利亚生物信息学联盟);Monash University(莫纳什大学)
A recent study reported development of Muscorian, a generic text processing tool for extracting protein-protein interactions from text that achieved comparable performance to biomedical-specific text processing tools. This result was unexpected since potential errors from a series of text analysis processes is likely to adversely affect the outcome of the entire process. Most biomedical entity relationship extraction tools have used biomedical-specific parts-of-speech (POS) tagger as errors in POS tagging and are likely to affect subsequent semantic analysis of the text, such as shallow parsin…
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 addresses the problem of extracting keyphrases from scientific articles and categorizing them as corresponding to a task, process, or material. We cast the problem as sequence tagging and introduce semi-supervised methods to a neural tagging model, which builds on recent advances in named entity recognition. Since annotated training data is scarce in this domain, we introduce a graph-based semi-supervised algorithm together with a data selection scheme to leverage unannotated articles. Both inductive and transductive semi-supervised learning strategies outperform state-of-the-art in…
Current methods for sequence tagging, a core task in NLP, are data hungry, which motivates the use of crowdsourcing as a cheap way to obtain labelled data. However, annotators are often unreliable and current aggregation methods cannot capture common types of span annotation errors. To address this, we propose a Bayesian method for aggregating sequence tags that reduces errors by modelling sequential dependencies between the annotations as well as the ground-truth labels. By taking a Bayesian approach, we account for uncertainty in the model due to both annotator errors and the lack of data fo…
In this work, we present new state-of-the-art results of 93.59,% and 79.59,% for Turkish and Czech named entity recognition based on the model of (Lample et al., 2016). We contribute by proposing several schemes for representing the morphological analysis of a word in the context of named entity recognition. We show that a concatenation of this representation with the word and character embeddings improves the performance. The effect of these representation schemes on the tagging performance is also investigated.
Hanoi Univ of Science and Technology(河内科技大学);VCCorp(VCCorp公司)
This paper presents a neural architecture for Vietnamese sequence labeling tasks including part-of-speech (POS) tagging and named entity recognition (NER). We applied the model described in \cite{lample-EtAl:2016:N16-1} that is a combination of bidirectional Long-Short Term Memory and Conditional Random Fields, which rely on two sources of information about words: character-based word representations learned from the supervised corpus and pre-trained word embeddings learned from other unannotated corpora. Experiments on benchmark datasets show that this work achieves state-of-the-art performan…
Named Entity Recognition (NER) or the extraction of concepts from clinical text is the task of identifying entities in text and slotting them into categories such as problems, treatments, tests, clinical departments, occurrences (such as admission and discharge) and others. NER forms a critical component of processing and leveraging unstructured data from Electronic Health Records (EHR). While identifying the spans and categories of concepts is itself a challenging task, these entities could also have attributes such as negation that pivot their meanings implied to the consumers of the named e…
Shanghai Jiao Tong University(上海交通大学);Microsoft Research Asia(微软亚洲研究院);Educational Testing Service Research(教育考试服务中心研究院)
Bidirectional Long Short-Term Memory Recurrent Neural Network (BLSTM-RNN) has been shown to be very effective for modeling and predicting sequential data, e.g. speech utterances or handwritten documents. In this study, we propose to use BLSTM-RNN for a unified tagging solution that can be applied to various tagging tasks including part-of-speech tagging, chunking and named entity recognition. Instead of exploiting specific features carefully optimized for each task, our solution only uses one set of task-independent features and internal representations learnt from unlabeled text for all tasks…
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…
This paper proposes a machine learning approach to part-of-speech tagging and named entity recognition for Greek, focusing on the extraction of morphological features and classification of tokens into a small set of classes for named entities. The architecture model that was used is introduced. The greek version of the spaCy platform was added into the source code, a feature that did not exist before our contribution, and was used for building the models. Additionally, a part of speech tagger was trained that can detect the morphology of the tokens and performs higher than the state-of-the-art…
Relation Extraction (RE) refers to extracting the relation triples in the input text. Existing neural work based systems for RE rely heavily on manually labeled training data, but there are still a lot of domains where sufficient labeled data does not exist. Inspired by the distance-based few-shot named entity recognition methods, we put forward the definition of the few-shot RE task based on the sequence tagging joint extraction approaches, and propose a few-shot RE framework for the task. Besides, we apply two actual sequence tagging models to our framework (called Few-shot TPLinker and Few-…
IBM Research(IBM研究院);Universidade Federal Fluminense(弗鲁米嫩塞联邦大学)
Most state-of-the-art named entity recognition (NER) systems rely on handcrafted features and on the output of other NLP tasks such as part-of-speech (POS) tagging and text chunking. In this work we propose a language-independent NER system that uses automatically learned features only. Our approach is based on the CharWNN deep neural network, which uses word-level and character-level representations (embeddings) to perform sequential classification. We perform an extensive number of experiments using two annotated corpora in two different languages: HAREM I corpus, which contains texts in Por…
In this paper, we discuss a method for identifying a seed word that would best represent a class of named entities in a graphical representation of words and their similarities. Word networks, or word graphs, are representations of vectorized text where nodes are the words encountered in a corpus, and the weighted edges incident on the nodes represent how similar the words are to each other. We intend to build a bilingual word graph and identify seed words through community analysis that would be best used to segment a graph according to its named entities, therefore providing an unsupervised …
University of Zurich(苏黎世大学);Dalle Molle Institute for Artificial Intelligence Research (IDSIA)(达勒·莫勒人工智能研究所);Swiss Institute of Bioinformatics(瑞士生物信息学研究所)
Background: Named Entity Recognition (NER) and Normalisation (NEN) are core components of any text-mining system for biomedical texts. In a traditional concept-recognition pipeline, these tasks are combined in a serial way, which is inherently prone to error propagation from NER to NEN. We propose a parallel architecture, where both NER and NEN are modeled as a sequence-labeling task, operating directly on the source text. We examine different harmonisation strategies for merging the predictions of the two classifiers into a single output sequence. Results: We test our approach on the recent V…
This paper reports on the evaluation of Deep Learning (DL) transformer architecture models for Named-Entity Recognition (NER) on ten low-resourced South African (SA) languages. In addition, these DL transformer models were compared to other Neural Network and Machine Learning (ML) NER models. The findings show that transformer models substantially improve performance when applying discrete fine-tuning parameters per language. Furthermore, fine-tuned transformer models outperform other neural network and machine learning models on NER with the low-resourced SA languages. For example, the transf…
This study improves the performance of neural named entity recognition by a margin of up to 11% in F-score on the example of a low-resource language like German, thereby outperforming existing baselines and establishing a new state-of-the-art on each single open-source dataset. Rather than designing deeper and wider hybrid neural architectures, we gather all available resources and perform a detailed optimization and grammar-dependent morphological processing consisting of lemmatization and part-of-speech tagging prior to exposing the raw data to any training process. We test our approach in a…
Usually, entity relation recognition systems either use a pipe-lined model that treats the entity tagging and relation identification as separate tasks or a joint model that simultaneously identifies the relation and entities. This paper compares these two general approaches for the entity relation recognition. State-of-the-art entity relation recognition systems are built using deep recurrent neural networks which often does not capture the symbolic knowledge or the logical constraints in the problem. The main contribution of this paper is an end-to-end neural model for joint entity relation …
Extraction of missing attribute values is to find values describing an attribute of interest from a free text input. Most past related work on extraction of missing attribute values work with a closed world assumption with the possible set of values known beforehand, or use dictionaries of values and hand-crafted features. How can we discover new attribute values that we have never seen before? Can we do this with limited human annotation or supervision? We study this problem in the context of product catalogs that often have missing values for many attributes of interest. In this work, we lev…
RIKEN AIP(理化学研究所先进智能项目中心);Tohoku University(东北大学);Heidelberg Institute for Theoretical Studies gGmbH(海德堡理论研究所)
Pretrained contextual and non-contextual subword embeddings have become available in over 250 languages, allowing massively multilingual NLP. However, while there is no dearth of pretrained embeddings, the distinct lack of systematic evaluations makes it difficult for practitioners to choose between them. In this work, we conduct an extensive evaluation comparing non-contextual subword embeddings, namely FastText and BPEmb, and a contextual representation method, namely BERT, on multilingual named entity recognition and part-of-speech tagging. We find that overall, a combination of BERT, BPEmb…
Lucerne University of Applied Sciences and Arts(卢塞恩应用科学与艺术大学)
Entity Recognition (ER) within a text is a fundamental exercise in Natural Language Processing, enabling further depending tasks such as Knowledge Extraction, Text Summarisation, or Keyphrase Extraction. An entity consists of single words or of a consecutive sequence of terms, constituting the basic building blocks for communication. Mainstream ER approaches are mainly limited to flat structures, concentrating on the outermost entities while ignoring the inner ones. This paper introduces a partly-layered network architecture that deals with the complexity of overlapping and nested cases. The p…
Columbia University(哥伦比亚大学);Google Research(谷歌研究院)
We study learning named entity recognizers in the presence of missing entity annotations. We approach this setting as tagging with latent variables and propose a novel loss, the Expected Entity Ratio, to learn models in the presence of systematically missing tags. We show that our approach is both theoretically sound and empirically useful. Experimentally, we find that it meets or exceeds performance of strong and state-of-the-art baselines across a variety of languages, annotation scenarios, and amounts of labeled data. In particular, we find that it significantly outperforms the previous sta…
We propose a unified neural network architecture and learning algorithm that can be applied to various natural language processing tasks including: part-of-speech tagging, chunking, named entity recognition, and semantic role labeling. This versatility is achieved by trying to avoid task-specific engineering and therefore disregarding a lot of prior knowledge. Instead of exploiting man-made input features carefully optimized for each task, our system learns internal representations on the basis of vast amounts of mostly unlabeled training data. This work is then used as a basis for building a …
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…
Recent studies have shown that neural models can achieve high performance on several sequence labelling/tagging problems without the explicit use of linguistic features such as part-of-speech (POS) tags. These models are trained only using the character-level and the word embedding vectors as inputs. Others have shown that linguistic features can improve the performance of neural models on tasks such as chunking and named entity recognition (NER). However, the change in performance depends on the degree of semantic relatedness between the linguistic features and the target task; in some instan…
Allen Institute for Artificial Intelligence(艾伦人工智能研究院)
Pre-trained word embeddings learned from unlabeled text have become a standard component of neural network architectures for NLP tasks. However, in most cases, the recurrent network that operates on word-level representations to produce context sensitive representations is trained on relatively little labeled data. In this paper, we demonstrate a general semi-supervised approach for adding pre- trained context embeddings from bidirectional language models to NLP systems and apply it to sequence labeling tasks. We evaluate our model on two standard datasets for named entity recognition (NER) an…
Hanoi University of Science and Technology(河内理工大学);Vietnam Academy of Science and Technology(越南科学技术研究院)
Named entity recognition (NER) plays an important role in text-based information retrieval. In this paper, we combine Bidirectional Long Short-Term Memory (Bi-LSTM) \cite{hochreiter1997,schuster1997} with Conditional Random Field (CRF) \cite{lafferty2001} to create a novel deep learning model for the NER problem. Each word as input of the deep learning model is represented by a Word2vec-trained vector. A word embedding set trained from about one million articles in 2018 collected through a Vietnamese news portal (baomoi.com). In addition, we concatenate a Word2Vec\cite{mikolov2013}-trained vec…
Information Extraction from scientific literature can be challenging due to the highly specialised nature of such text. We describe our entity recognition methods developed as part of the DEAL (Detecting Entities in the Astrophysics Literature) shared task. The aim of the task is to build a system that can identify Named Entities in a dataset composed by scholarly articles from astrophysics literature. We planned our participation such that it enables us to conduct an empirical comparison between word-based tagging and span-based classification methods. When evaluated on two hidden test sets p…
Nanyang Technological University(南洋理工大学);DAMO Academy, Alibaba Group(阿里巴巴集团达摩院);National Institute of Informatics(国立信息学研究所)
Data augmentation techniques have been widely used to improve machine learning performance as they enhance the generalization capability of models. In this work, to generate high quality synthetic data for low-resource tagging tasks, we propose a novel augmentation method with language models trained on the linearized labeled sentences. Our method is applicable to both supervised and semi-supervised settings. For the supervised settings, we conduct extensive experiments on named entity recognition (NER), part of speech (POS) tagging and end-to-end target based sentiment analysis (E2E-TBSA) tas…