Accepted for presentation and inclusion in CADL 2020 (International Workshop on Computational Aspects of Deep Learning) , organized in conjunction with ICPR 2020, the 25th International Conference on Pattern Recognition
Named entity recognition (NER) is a widely applicable natural language processing task and building block of question answering, topic modeling, information retrieval, etc. In the medical domain, NER plays a crucial role by extracting meaningful chunks from clinical notes and reports, which are then fed to downstream tasks like assertion status detection, entity resolution, relation extraction, and de-identification. Reimplementing a Bi-LSTM-CNN-Char deep learning architecture on top of Apache Spark, we present a single trainable NER model that obtains new state-of-the-art results on seven public biomedical benchmarks without using heavy contextual embeddings like BERT. This includes improving BC4CHEMD to 93.72% (4.1% gain), Species800 to 80.91% (4.6% gain), and JNLPBA to 81.29% (5.2% gain). In addition, this model is freely available within a production-grade code base as part of the open-source Spark NLP library; can scale up for training and inference in any Spark cluster; has GPU support and libraries for popular programming languages such as Python, R, Scala and Java; and can be extended to support other human languages with no code changes.
University of Cambridge（剑桥大学）；Monash University（莫纳什大学）；Amazon Alexa（亚马逊Alexa）
Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for entity-level tasks such as entity linking where the ability to model entity relations (especially synonymy) is pivotal. To address this challenge, we propose SapBERT, a pretraining scheme that self-aligns the representation space of biomedical entities. We design a scalable metric learning framework that can leverage UMLS, a massive collection of biomedical ontologi…
Developing high-performing systems for detecting biomedical named entities has major implications. State-of-the-art deep-learning based solutions for entity recognition often require large annotated datasets, which is not available in the biomedical domain. Transfer learning and multi-task learning have been shown to improve performance for low-resource domains. However, the applications of these methods are relatively scarce in the biomedical domain, and a theoretical understanding of why these methods improve the performance is lacking. In this study, we performed an extensive analysis to un…
Partial Annotation Learning for Biomedical Entity Recognition
University of Chinese Academy of Sciences（中国科学院大学）；National Science Library, Chinese Academy of Sciences（中国科学院国家科学图书馆）；Institute for Logic, Language and Computation (ILLC), University of Amsterdam（阿姆斯特丹大学逻辑、语言与计算研究所）
Nara Institute of Science and Technology（奈良先端科学技术大学院大学）；Megagon Labs（Megagon实验室）
We introduce BioCoM, a contrastive learning framework for biomedical entity linking that uses only two resources: a small-sized dictionary and a large number of raw biomedical articles. Specifically, we build the training instances from raw PubMed articles by dictionary matching and use them to train a context-aware entity linking model with contrastive learning. We predict the normalized biomedical entity at inference time through a nearest-neighbor search. Results found that BioCoM substantially outperforms state-of-the-art models, especially in low-resource settings, by effectively using th…
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…
Korea University（高丽大学）；AIRS Company, Hyundai Motor Group（现代汽车集团AIRS公司）；AIGEN Sciences（AIGEN科学公司）
In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing biomedical literature. In this article, we present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by employing a multi-task NER model and neural network-based NEN models to achieve much faster and more accurate inference. We hope that our tool can help annotate large-scale biomedical…
Background: Finding biomedical named entities is one of the most essential tasks in biomedical text mining. Recently, deep learning-based approaches have been applied to biomedical named entity recognition (BioNER) and showed promising results. However, as deep learning approaches need an abundant amount of training data, a lack of data can hinder performance. BioNER datasets are scarce resources and each dataset covers only a small subset of entity types. Furthermore, many bio entities are polysemous, which is one of the major obstacles in named entity recognition. Results: To address the lac…
Named Entity Recognition is an information extraction task that serves as a preprocessing step for other natural language processing tasks, such as machine translation, information retrieval, and question answering. Named entity recognition enables the identification of proper names as well as temporal and numeric expressions in an open domain text. For Semitic languages such as Arabic, Amharic, and Hebrew, the named entity recognition task is more challenging due to the heavily inflected structure of these languages. In this paper, we present an Amharic named entity recognition system based o…
Named entity recognition (NER) is a fundamental part of extracting information from documents in biomedical applications. A notable advantage of NER is its consistency in extracting biomedical entities in a document context. Although existing document NER models show consistent predictions, they still do not meet our expectations. We investigated whether the adjectives and prepositions within an entity cause a low label consistency, which results in inconsistent predictions. In this paper, we present our method, ConNER, which enhances the label dependency of modifiers (e.g., adjectives and pre…
Entity linking is the task of linking mentions of named entities in natural language text, to entities in a curated knowledge-base. This is of significant importance in the biomedical domain, where it could be used to semantically annotate a large volume of clinical records and biomedical literature, to standardized concepts described in an ontology such as Unified Medical Language System (UMLS). We observe that with precise type information, entity disambiguation becomes a straightforward task. However, fine-grained type information is usually not available in biomedical domain. Thus, we prop…
Institut Polytechnique de Paris（巴黎综合理工学院）；Inria（法国国家信息与自动化研究所）；CEA（法国原子能和替代能源委员会）
Biomedical entity linking aims to map biomedical mentions, such as diseases and drugs, to standard entities in a given knowledge base. The specific challenge in this context is that the same biomedical entity can have a wide range of names, including synonyms, morphological variations, and names with different word orderings. Recently, BERT-based methods have advanced the state-of-the-art by allowing for rich representations of word sequences. However, they often have hundreds of millions of parameters and require heavy computing resources, which limits their applications in resource-limited s…
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…
College of Information and Computer Sciences University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校信息与计算机科学学院）；Chan Zuckerberg Initiative（陈-扎克伯格倡议）
Due to large number of entities in biomedical knowledge bases, only a small fraction of entities have corresponding labelled training data. This necessitates entity linking models which are able to link mentions of unseen entities using learned representations of entities. Previous approaches link each mention independently, ignoring the relationships within and across documents between the entity mentions. These relations can be very useful for linking mentions in biomedical text where linking decisions are often difficult due mentions having a generic or a highly specialized form. In this pa…
Information Sciences Institute（信息科学研究所）；University of Southern California（南加州大学）
We present a weakly-supervised data augmentation approach to improve Named Entity Recognition (NER) in a challenging domain: extracting biomedical entities (e.g., proteins) from the scientific literature. First, we train a neural NER (NNER) model over a small seed of fully-labeled examples. Second, we use a reference set of entity names (e.g., proteins in UniProt) to identify entity mentions with high precision, but low recall, on an unlabeled corpus. Third, we use the NNER model to assign weak labels to the corpus. Finally, we retrain our NNER model iteratively over the augmented training set…
Analysing Lightweight Large Language Models for Biomedical Named Entity Recognition on Diverse Ouput Formats
Inria, Inserm, Université Paris Cité, HeKA, UMR 1346, Paris, France（法国国家科学研究中心（Inria）、法国国家医学研究院（Inserm）、巴黎城市大学（Université Paris Cité）、HeKA、法国国家科研机构（UMR 1346）、巴黎）；Télécom Paris, Institut Polytechnique de Paris, France（巴黎电信学院（Télécom Paris）、巴黎理工学院（Institut Polytechnique de Paris）、法国）
We present SwellShark, a framework for building biomedical named entity recognition (NER) systems quickly and without hand-labeled data. Our approach views biomedical resources like lexicons as function primitives for autogenerating weak supervision. We then use a generative model to unify and denoise this supervision and construct large-scale, probabilistically labeled datasets for training high-accuracy NER taggers. In three biomedical NER tasks, SwellShark achieves competitive scores with state-of-the-art supervised benchmarks using no hand-labeled training data. In a drug name extraction t…
In this work, we formulate the NER task as a multi-answer knowledge guided QA task (KGQA) which helps to predict entities only by assigning B, I and O tags without associating entity types with the tags. We provide different knowledge contexts, such as, entity types, questions, definitions and examples along with the text and train on a combined dataset of 18 biomedical corpora. This formulation (a) enables systems to jointly learn NER specific features from varied NER datasets, (b) can use knowledge-text attention to identify words having higher similarity to provided knowledge, improving per…
A Unified Biomedical Named Entity Recognition Framework with Large Language Models
College of Computer Science and Technology, Dalian University of Technology（大连理工大学计算机科学与技术学院）；Air Force Communications NCO Academy（空军通信NCO学院）；Department of Pharmacy, Second Affiliated Hospital of Dalian Medical University（大连医科大学第二附属医院药学部）
Traditional language models are unable to efficiently model entity names observed in text. All but the most popular named entities appear infrequently in text providing insufficient context. Recent efforts have recognized that context can be generalized between entity names that share the same type (e.g., \emph{person} or \emph{location}) and have equipped language models with access to an external knowledge base (KB). Our Knowledge-Augmented Language Model (KALM) continues this line of work by augmenting a traditional model with a KB. Unlike previous methods, however, we train with an end-to-…
The number of biomedical literature on new biomedical concepts is rapidly increasing, which necessitates a reliable biomedical named entity recognition (BioNER) model for identifying new and unseen entity mentions. However, it is questionable whether existing models can effectively handle them. In this work, we systematically analyze the three types of recognition abilities of BioNER models: memorization, synonym generalization, and concept generalization. We find that although current best models achieve state-of-the-art performance on benchmarks based on overall performance, they have limita…
AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning
National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH)（美国国立卫生研究院国家医学图书馆国家生物技术信息中心）；School of Computer Science and Technology, Dalian University of Technology（大连理工大学计算机科学与技术学院）
Entities lie in the heart of biomedical natural language understanding, and the biomedical entity linking (EL) task remains challenging due to the fine-grained and diversiform concept names. Generative methods achieve remarkable performances in general domain EL with less memory usage while requiring expensive pre-training. Previous biomedical EL methods leverage synonyms from knowledge bases (KB) which is not trivial to inject into a generative method. In this work, we use a generative approach to model biomedical EL and propose to inject synonyms knowledge in it. We propose KB-guided pre-tra…
Nara Institute of Science and Technology（奈良先端科学技术大学院大学）；Megagon Labs（Megagon实验室）
Disease name recognition and normalization, which is generally called biomedical entity linking, is a fundamental process in biomedical text mining. Recently, neural joint learning of both tasks has been proposed to utilize the mutual benefits. While this approach achieves high performance, disease concepts that do not appear in the training dataset cannot be accurately predicted. This study introduces a novel end-to-end approach that combines span representations with dictionary-matching features to address this problem. Our model handles unseen concepts by referring to a dictionary while mai…
Microsoft Research（微软研究院）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot effectively handle unseen entities. Zero-shot entity linking has emerged as a promising direction for generalizing to new entities, but it still requires example gold entity mentions during training and canonical descriptions for all entities, both of which are rarely available outside of Wikipedia. In this paper, we explore Knowledge-RIch Self-Supervision ($\…
BioMNER: A Dataset for Biomedical Method Entity Recognition
University of Surrey（萨里大学）；The University of Manchester（曼彻斯特大学）；University of Pittsburgh（匹兹堡大学）；Chinese Academy of Sciences（中国科学院）；Durham University（杜伦大学）
Humboldt-Universität zu Berlin（柏林洪堡大学）；GFZ German Research Centre for Geosciences（德国地学研究中心）
Summary: Named Entity Recognition (NER) is an important step in biomedical information extraction pipelines. Tools for NER should be easy to use, cover multiple entity types, highly accurate, and robust towards variations in text genre and style. To this end, we propose HunFlair, an NER tagger covering multiple entity types integrated into the widely used NLP framework Flair. HunFlair outperforms other state-of-the-art standalone NER tools with an average gain of 7.26 pp over the next best tool, can be installed with a single command and is applied with only four lines of code. Availability: H…
Automated entity relation extraction (RE) from literature provides an important source for constructing biomedical database, which is more efficient and extensible than manual curation. However, existing RE models usually ignore the information contained in sentence structures and target entities. In this paper, we propose BERE, a deep learning based model which uses Gumbel Tree-GRU to learn sentence structures and joint embedding to incorporate entity information. It also employs word-level attention for improved relation extraction and sentence-level attention to suit the distantly supervise…
Soochow University（苏州大学）；The Hong Kong Polytechnic University（香港理工大学）
Causal relation extraction of biomedical entities is one of the most complex tasks in biomedical text mining, which involves two kinds of information: entity relations and entity functions. One feasible approach is to take relation extraction and function detection as two independent sub-tasks. However, this separate learning method ignores the intrinsic correlation between them and leads to unsatisfactory performance. In this paper, we propose a joint learning model, which combines entity relation extraction and entity function detection to exploit their commonality and capture their inter-re…
Retrieval augmented generation based dynamic prompting for few-shot biomedical named entity recognition using large language models
Department of Biomedical Informatics, School of Medicine, Emory University（生物医学信息学系，医学院，埃默里大学）；Department of Computer Science, Emory University（计算机科学系，埃默里大学）；National Library of Medicine, National Institutes of Health（国家医学图书馆，国立卫生研究院）；Department of Biomedical Engineering, Georgia Institute of Technology and Emory University（生物医学工程系，佐治亚理工学院和埃默里大学）
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；University of Southern California（南加州大学）；Stanford University（斯坦福大学）
Motivation: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network models for BioNER to free experts from manual feature engineering, the performance remains limited by the available training data for each entity type. Results: We propose a multi-task learning framework for BioNER to collectively use the training data of different types of entities and improve the performance on each of them. In experiments on 15 benchmark …
In biomedical literature, it is common for entity boundaries to not align with word boundaries. Therefore, effective identification of entity spans requires approaches capable of considering tokens that are smaller than words. We introduce a novel, subword approach for named entity recognition (NER) that uses byte-pair encodings (BPE) in combination with convolutional and recurrent neural networks to produce byte-level tags of entities. We present experimental results on several standard biomedical datasets, namely the BioCreative VI Bio-ID, JNLPBA, and GENETAG datasets. We demonstrate competi…
This paper presents the formal release of MedMentions, a new manually annotated resource for the recognition of biomedical concepts. What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts and over 350,000 linked mentions), as well as the size of the concept ontology (over 3 million concepts from UMLS 2017) and its broad coverage of biomedical disciplines. In addition to the full corpus, a sub-corpus of MedMentions is also presented, comprising annotations for a subset of UMLS 2017 targeted towards document retrieval. To encourage research in Bi…
MedPath: Multi-Domain Cross-Vocabulary Hierarchical Paths for Biomedical Entity Linking
Department of Medical Informatics, Amsterdam UMC, University of Amsterdam, The Netherlands（阿姆斯特丹大学医学信息学系，阿姆斯特丹大学医学中心，荷兰）；Amsterdam Public Health, Methodology, Amsterdam, The Netherlands（阿姆斯特丹公共卫生，方法学，阿姆斯特丹，荷兰）；ILLC, University of Amsterdam, The Netherlands（阿姆斯特丹大学ILLC，荷兰）
Hybrid X-Linker: Automated Data Generation and Extreme Multi-label Ranking for Biomedical Entity Linking
LASIGE, Faculdade de Ciências, Universidade de Lisboa（里斯本大学理学院LASIGE实验室）；Universidad de Málaga（马拉加大学）；Research Institute of Multilingual Language Technologies, Universidad de Málaga（马拉加大学多语言语言技术研究院）
EkStep Foundation（EkStep基金会）；Thoughtworks Technologies India Pvt Ltd.（Thoughtworks技术印度私人有限公司）；Agami
Identification of named entities from legal texts is an essential building block for developing other legal Artificial Intelligence applications. Named Entities in legal texts are slightly different and more fine-grained than commonly used named entities like Person, Organization, Location etc. In this paper, we introduce a new corpus of 46545 annotated legal named entities mapped to 14 legal entity types. The Baseline model for extracting legal named entities from judgment text is also developed.
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 …
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…
