In the electronic health record, using clinical notes to identify entities such as disorders and their temporality (e.g. the order of an event relative to a time index) can inform many important analyses. However, creating training data for clinical entity tasks is time consuming and sharing labeled data is challenging due to privacy concerns. The information needs of the COVID-19 pandemic highlight the need for agile methods of training machine learning models for clinical notes. We present Trove, a framework for weakly supervised entity classification using medical ontologies and expert-generated rules. Our approach, unlike hand-labeled notes, is easy to share and modify, while offering performance comparable to learning from manually labeled training data. In this work, we validate our framework on six benchmark tasks and demonstrate Trove's ability to analyze the records of patients visiting the emergency department at Stanford Health Care for COVID-19 presenting symptoms and risk factors.
Tencent Jarvis Lab(腾讯天衍实验室);Tencent(腾讯);University of Oxford(牛津大学)
Semantic embedding has been widely investigated for aligning knowledge graph (KG) entities. Current methods have explored and utilized the graph structure, the entity names and attributes, but ignore the ontology (or ontological schema) which contains critical meta information such as classes and their membership relationships with entities. In this paper, we propose an ontology-guided entity alignment method named OntoEA, where both KGs and their ontologies are jointly embedded, and the class hierarchy and the class disjointness are utilized to avoid false mappings. Extensive experiments on s…
Allen Institute for Artificial Intelligence(艾伦人工智能研究所);University of Washington(华盛顿大学)
Ontology alignment is the task of identifying semantically equivalent entities from two given ontologies. Different ontologies have different representations of the same entity, resulting in a need to de-duplicate entities when merging ontologies. We propose a method for enriching entities in an ontology with external definition and context information, and use this additional information for ontology alignment. We develop a neural architecture capable of encoding the additional information when available, and show that the addition of external data results in an F1-score of 0.69 on the Ontolo…
Peking University(北京大学);IER Business Development Center(IER业务发展中心)
Ontology can be used for the interpretation of natural language. To construct an anti-infective drug ontology, one needs to design and deploy a methodological step to carry out the entity discovery and linking. Medical synonym resources have been an important part of medical natural language processing (NLP). However, there are problems such as low precision and low recall rate. In this study, an NLP approach is adopted to generate candidate entities. Open ontology is analyzed to extract semantic relations. Six-word vector features and word-level features are selected to perform the entity lin…
Beyond Fine-Tuning: Robust Food Entity Linking under Ontology Drift with FoodOntoRAG
Computer Systems Department, Jožef Stefan International Postgraduate School, Ljubljana, Slovenia(卢布尔雅那,斯洛文尼亚乔泽夫·斯蒂芬国际研究生学院计算机系统系);Computer Systems Department, Jožef Stefan Institute, Ljubljana, Slovenia(卢布尔雅那,斯洛文尼亚乔泽夫·斯蒂芬研究所计算机系统系)
University College London(伦敦大学学院);University of Edinburgh(爱丁堡大学)
Adverse Childhood Experiences (ACEs) are defined as a collection of highly stressful, and potentially traumatic, events or circumstances that occur throughout childhood and/or adolescence. They have been shown to be associated with increased risks of mental health diseases or other abnormal behaviours in later lives. However, the identification of ACEs from textual data with Natural Language Processing (NLP) is challenging because (a) there are no NLP ready ACE ontologies; (b) there are few resources available for machine learning, necessitating the data annotation from clinical experts; (c) c…
IBM Research(IBM研究院);IIT Guwahati(印度理工学院古瓦哈提分校);IBM Research Almaden(IBM阿尔马登研究院)
A person ontology comprising concepts, attributes and relationships of people has a number of applications in data protection, didentification, population of knowledge graphs for business intelligence and fraud prevention. While artificial neural networks have led to improvements in Entity Recognition, Entity Classification, and Relation Extraction, creating an ontology largely remains a manual process, because it requires a fixed set of semantic relations between concepts. In this work, we present a system for automatically populating a person ontology graph from unstructured data using neura…
The lack of labeled training data has limited the development of natural language processing tools, such as named entity recognition, for many languages spoken in developing countries. Techniques such as distant and weak supervision can be used to create labeled data in a (semi-) automatic way. Additionally, to alleviate some of the negative effects of the errors in automatic annotation, noise-handling methods can be integrated. Pretrained word embeddings are another key component of most neural named entity classifiers. With the advent of more complex contextual word embeddings, an interestin…
Research Center for Social Computing and Information Retrieval(社会计算与信息检索研究中心);Harbin Institute of Technology, China(哈尔滨工业大学(中国))
Attribute acquisition for classes is a key step in ontology construction, which is often achieved by community members manually. This paper investigates an attention-based automatic paradigm called TransATT for attribute acquisition, by learning the representation of hierarchical classes and attributes in Chinese ontology. The attributes of an entity can be acquired by merely inspecting its classes, because the entity can be regard as the instance of its classes and inherit their attributes. For explicitly describing of the class of an entity unambiguously, we propose class-path to represent t…
Tsinghua University(清华大学);Bosch Center for AI(博世人工智能中心)
Entity alignment, aiming to identify equivalent entities across different knowledge graphs (KGs), is a fundamental problem for constructing Web-scale KGs. Over the course of its development, the label supervision has been considered necessary for accurate alignments. Inspired by the recent progress of self-supervised learning, we explore the extent to which we can get rid of supervision for entity alignment. Commonly, the label information (positive entity pairs) is used to supervise the process of pulling the aligned entities in each positive pair closer. However, our theoretical analysis sug…
Google AI(谷歌人工智能);Google Research(谷歌研究院);The University of Austin at Texas(得克萨斯大学奥斯汀分校)
We focus on the problem of capturing declarative knowledge about entities in the learned parameters of a language model. We introduce a new model - Entities as Experts (EAE) - that can access distinct memories of the entities mentioned in a piece of text. Unlike previous efforts to integrate entity knowledge into sequence models, EAE's entity representations are learned directly from text. We show that EAE's learned representations capture sufficient knowledge to answer TriviaQA questions such as "Which Dr. Who villain has been played by Roger Delgado, Anthony Ainley, Eric Roberts?", outperfor…
In a large-scale knowledge graph (KG), an entity is often described by a large number of triple-structured facts. Many applications require abridged versions of entity descriptions, called entity summaries. Existing solutions to entity summarization are mainly unsupervised. In this paper, we present a supervised approach NEST that is based on our novel neural model to jointly encode graph structure and text in KGs and generate high-quality diversified summaries. Since it is costly to obtain manually labeled summaries for training, our supervision is weak as we train with programmatically label…
A growing number of applications users daily interact with have to operate in (near) real-time: chatbots, digital companions, knowledge work support systems -- just to name a few. To perform the services desired by the user, these systems have to analyze user activity logs or explicit user input extremely fast. In particular, text content (e.g. in form of text snippets) needs to be processed in an information extraction task. Regarding the aforementioned temporal requirements, this has to be accomplished in just a few milliseconds, which limits the number of methods that can be applied. Practi…
Johns Hopkins University(约翰斯·霍普金斯大学);University of Rochester(罗切斯特大学)
We present LOME, a system for performing multilingual information extraction. Given a text document as input, our core system identifies spans of textual entity and event mentions with a FrameNet (Baker et al., 1998) parser. It subsequently performs coreference resolution, fine-grained entity typing, and temporal relation prediction between events. By doing so, the system constructs an event and entity focused knowledge graph. We can further apply third-party modules for other types of annotation, like relation extraction. Our (multilingual) first-party modules either outperform or are competi…
Cross-lingual Entity Linking (XEL) aims to ground entity mentions written in any language to an English Knowledge Base (KB), such as Wikipedia. XEL for most languages is challenging, owing to limited availability of resources as supervision. We address this challenge by developing the first XEL approach that combines supervision from multiple languages jointly. This enables our approach to: (a) augment the limited supervision in the target language with additional supervision from a high-resource language (like English), and (b) train a single entity linking model for multiple languages, impro…
Entity-Augmented Neuroscience Knowledge Retrieval Using Ontology and Semantic Understanding Capability of LLM
Sudha Gopalakrishnan Brain Centre, Indian Institute of Technology, Madras(印度理工学院马德拉斯分校苏达·戈帕拉克里希南脑科学中心);Department of Electrical Engineering, Indian Institute of Technology, Madras(印度理工学院马德拉斯分校电气工程系)
Structured representations of entity names are useful for many entity-related tasks such as entity normalization and variant generation. Learning the implicit structured representations of entity names without context and external knowledge is particularly challenging. In this paper, we present a novel learning framework that combines active learning and weak supervision to solve this problem. Our experimental evaluation show that this framework enables the learning of high-quality models from merely a dozen or so labeled examples.
Saarland University(萨尔兰大学);Bosch Center for Artificial Intelligence(博世人工智能中心)
Distant supervision allows obtaining labeled training corpora for low-resource settings where only limited hand-annotated data exists. However, to be used effectively, the distant supervision must be easy to gather. In this work, we present ANEA, a tool to automatically annotate named entities in texts based on entity lists. It spans the whole pipeline from obtaining the lists to analyzing the errors of the distant supervision. A tuning step allows the user to improve the automatic annotation with their linguistic insights without labelling or checking all tokens manually. In six low-resource …
Entity-based semantic search has been widely adopted in modern search engines to improve search accuracy by understanding users' intent. In e-commerce, an accurate and complete product type (PT) ontology is essential for recognizing product entities in queries and retrieving relevant products from catalog. However, finding product types (PTs) to construct such an ontology is usually expensive due to the considerable amount of human efforts it may involve. In this work, we propose an active learning framework that efficiently utilizes domain experts' knowledge for PT discovery. We also show the…
Recently, there is an effort to extend fine-grained entity typing by using a richer and ultra-fine set of types, and labeling noun phrases including pronouns and nominal nouns instead of just named entity mentions. A key challenge for this ultra-fine entity typing task is that human annotated data are extremely scarce, and the annotation ability of existing distant or weak supervision approaches is very limited. To remedy this problem, in this paper, we propose to obtain training data for ultra-fine entity typing by using a BERT Masked Language Model (MLM). Given a mention in a sentence, our a…
OEMA: Ontology-Enhanced Multi-Agent Collaboration Framework for Zero-Shot Clinical Named Entity Recognition
Department of Artificial Intelligence, Beijing Key Lab of Traffic Data Analysis;Mining , School of Computer Science \& Technology, Beijing Jiaotong University , Beijing , 100044 , China
Distant supervision (DS) has been widely used to automatically construct (noisy) labeled data for relation extraction (RE). Given two entities, distant supervision exploits sentences that directly mention them for predicting their semantic relation. We refer to this strategy as 1-hop DS, which unfortunately may not work well for long-tail entities with few supporting sentences. In this paper, we introduce a new strategy named 2-hop DS to enhance distantly supervised RE, based on the observation that there exist a large number of relational tables on the Web which contain entity pairs that shar…
University of California, Los Angeles(加利福尼亚大学洛杉矶分校)
We study the problem of entity-relation extraction in the presence of symbolic domain knowledge. Such knowledge takes the form of an ontology defining relations and their permissible arguments. Previous approaches set out to integrate such knowledge in their learning approaches either through self-training, or through approximations that lose the precise meaning of the logical expressions. By contrast, our approach employs semantic loss which captures the precise meaning of a logical sentence through maintaining a probability distribution over all possible states, and guiding the model to solu…
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…
Norwegian Computing Center(挪威计算中心);University of Oslo(奥斯陆大学)
Named Entity Recognition (NER) performance often degrades rapidly when applied to target domains that differ from the texts observed during training. When in-domain labelled data is available, transfer learning techniques can be used to adapt existing NER models to the target domain. But what should one do when there is no hand-labelled data for the target domain? This paper presents a simple but powerful approach to learn NER models in the absence of labelled data through weak supervision. The approach relies on a broad spectrum of labelling functions to automatically annotate texts from the …
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 ($\…
University of Massachusetts, Amherst(马萨诸塞大学阿默斯特分校);Google Research(谷歌研究院)
Understanding the meaning of text often involves reasoning about entities and their relationships. This requires identifying textual mentions of entities, linking them to a canonical concept, and discerning their relationships. These tasks are nearly always viewed as separate components within a pipeline, each requiring a distinct model and training data. While relation extraction can often be trained with readily available weak or distant supervision, entity linkers typically require expensive mention-level supervision -- which is not available in many domains. Instead, we propose a model whi…
Data and Web Science Group(数据与网络科学组);LATTICE Lab (ENS, CNRS, Paris 3)(LATTICE实验室(巴黎高等师范学院、法国国家科学研究中心、巴黎第三大学));University of Mannheim(曼海姆大学);PSL Research Univ, Sorbonne Paris Cité(巴黎文理研究大学,索邦巴黎西岱大学)
In order to create a corpus exploration method providing topics that are easier to interpret than standard LDA topic models, here we propose combining two techniques called Entity linking and Labeled LDA. Our method identifies in an ontology a series of descriptive labels for each document in a corpus. Then it generates a specific topic for each label. Having a direct relation between topics and labels makes interpretation easier; using an ontology as background knowledge limits label ambiguity. As our topics are described with a limited number of clear-cut labels, they promote interpretabilit…
Paul G. Allen School of Computer Science & Engineering, University of Washington(华盛顿大学保罗·G·艾伦计算机科学与工程学院);Allen Institute for Artificial Intelligence(艾伦人工智能研究所)
We introduce a new entity typing task: given a sentence with an entity mention, the goal is to predict a set of free-form phrases (e.g. skyscraper, songwriter, or criminal) that describe appropriate types for the target entity. This formulation allows us to use a new type of distant supervision at large scale: head words, which indicate the type of the noun phrases they appear in. We show that these ultra-fine types can be crowd-sourced, and introduce new evaluation sets that are much more diverse and fine-grained than existing benchmarks. We present a model that can predict open types, and is…
Entity alignment, aiming to identify equivalent entities across different knowledge graphs (KGs), is a fundamental problem for constructing large-scale KGs. Over the course of its development, supervision has been considered necessary for accurate alignments. Inspired by the recent progress of self-supervised learning, we explore the extent to which we can get rid of supervision for entity alignment. Existing supervised methods for this task focus on pulling each pair of positive (labeled) entities close to each other. However, our analysis suggests that the learning of entity alignment can ac…
Much research effort has been put to multilingual knowledge graph (KG) embedding methods to address the entity alignment task, which seeks to match entities in different languagespecific KGs that refer to the same real-world object. Such methods are often hindered by the insufficiency of seed alignment provided between KGs. Therefore, we propose an incidentally supervised model, JEANS , which jointly represents multilingual KGs and text corpora in a shared embedding scheme, and seeks to improve entity alignment with incidental supervision signals from text. JEANS first deploys an entity ground…
We propose a novel method for hierarchical entity classification that embraces ontological structure at both training and during prediction. At training, our novel multi-level learning-to-rank loss compares positive types against negative siblings according to the type tree. During prediction, we define a coarse-to-fine decoder that restricts viable candidates at each level of the ontology based on already predicted parent type(s). We achieve state-of-the-art across multiple datasets, particularly with respect to strict accuracy.
The distribution gap between training datasets and data encountered in production is well acknowledged. Training datasets are often constructed over a fixed period of time and by carefully curating the data to be labeled. Thus, training datasets may not contain all possible variations of data that could be encountered in real-world production environments. Tasked with building an entity resolution system - a model that identifies and consolidates data points that represent the same person - our first model exhibited a clear training-production performance gap. In this case study, we discuss ou…
Indian Institute of Science(印度科学研究所);University of British Columbia(英属哥伦比亚大学)
Relation extraction is the problem of classifying the relationship between two entities in a given sentence. Distant Supervision (DS) is a popular technique for developing relation extractors starting with limited supervision. We note that most of the sentences in the distant supervision relation extraction setting are very long and may benefit from word attention for better sentence representation. Our contributions in this paper are threefold. Firstly, we propose two novel word attention models for distantly- supervised relation extraction: (1) a Bi-directional Gated Recurrent Unit (Bi-GRU) …
University of Massachusetts, Amherst(马萨诸塞大学阿默斯特分校);Columbia University(哥伦比亚大学)
This paper describes an approach for automatic construction of dictionaries for Named Entity Recognition (NER) using large amounts of unlabeled data and a few seed examples. We use Canonical Correlation Analysis (CCA) to obtain lower dimensional embeddings (representations) for candidate phrases and classify these phrases using a small number of labeled examples. Our method achieves 16.5% and 11.3% F-1 score improvement over co-training on disease and virus NER respectively. We also show that by adding candidate phrase embeddings as features in a sequence tagger gives better performance compar…
L3S Research Center, Leibniz University of Hannover(莱布尼茨汉诺威大学L3S研究中心);GESIS - Leibniz Institute for the Social Sciences(GESIS——莱布尼茨社会科学研究所)
Entity Linking (EL) is the task of automatically identifying entity mentions in a piece of text and resolving them to a corresponding entity in a reference knowledge base like Wikipedia. There is a large number of EL tools available for different types of documents and domains, yet EL remains a challenging task where the lack of precision on particularly ambiguous mentions often spoils the usefulness of automated disambiguation results in real applications. A priori approximations of the difficulty to link a particular entity mention can facilitate flagging of critical cases as part of semi-au…
Entity linking is an indispensable operation of populating knowledge repositories for information extraction. It studies on aligning a textual entity mention to its corresponding disambiguated entry in a knowledge repository. In this paper, we propose a new paradigm named distantly supervised entity linking (DSEL), in the sense that the disambiguated entities that belong to a huge knowledge repository (Freebase) are automatically aligned to the corresponding descriptive webpages (Wiki pages). In this way, a large scale of weakly labeled data can be generated without manual annotation and fed t…
The University of Texas at Austin(德克萨斯大学奥斯汀分校);Indian Institute of Science(印度科学理工学院)
Distant Supervision for Relation Extraction uses heuristically aligned text data with an existing knowledge base as training data. The unsupervised nature of this technique allows it to scale to web-scale relation extraction tasks, at the expense of noise in the training data. Previous work has explored relationships among instances of the same entity-pair to reduce this noise, but relationships among instances across entity-pairs have not been fully exploited. We explore the use of inter-instance couplings based on verb-phrase and entity type similarities. We propose a novel technique, CANDiS…
University of Illinois at Urbana-Champaign(伊利诺伊大学厄巴纳-香槟分校)
We created this CORD-NER dataset with comprehensive named entity recognition (NER) on the COVID-19 Open Research Dataset Challenge (CORD-19) corpus (2020-03-13). This CORD-NER dataset covers 75 fine-grained entity types: In addition to the common biomedical entity types (e.g., genes, chemicals and diseases), it covers many new entity types related explicitly to the COVID-19 studies (e.g., coronaviruses, viral proteins, evolution, materials, substrates and immune responses), which may benefit research on COVID-19 related virus, spreading mechanisms, and potential vaccines. CORD-NER annotation i…
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);CooTek Inc.(触宝公司)
Recent advances in deep neural models allow us to build reliable named entity recognition (NER) systems without handcrafting features. However, such methods require large amounts of manually-labeled training data. There have been efforts on replacing human annotations with distant supervision (in conjunction with external dictionaries), but the generated noisy labels pose significant challenges on learning effective neural models. Here we propose two neural models to suit noisy distant supervision from the dictionary. First, under the traditional sequence labeling framework, we propose a revis…
Distant supervision uses triple facts in knowledge graphs to label a corpus for relation extraction, leading to wrong labeling and long-tail problems. Some works use the hierarchy of relations for knowledge transfer to long-tail relations. However, a coarse-grained relation often implies only an attribute (e.g., domain or topic) of the distant fact, making it hard to discriminate relations based solely on sentence semantics. One solution is resorting to entity types, but open questions remain about how to fully leverage the information of entity types and how to align multi-granular entity typ…
Institute of Computing Technology, Chinese Academy of Sciences(中国科学院计算技术研究所);School of Computer Science, University of Massachusetts Amherst(马萨诸塞大学阿默斯特分校计算机科学学院)
Fine-grained entity typing aims to assign entity mentions in the free text with types arranged in a hierarchical structure. Traditional distant supervision based methods employ a structured data source as a weak supervision and do not need hand-labeled data, but they neglect the label noise in the automatically labeled training corpus. Although recent studies use many features to prune wrong data ahead of training, they suffer from error propagation and bring much complexity. In this paper, we propose an end-to-end typing model, called the path-based attention neural model (PAN), to learn a no…
University of Southern California(南加利福尼亚大学);Temple University(天普大学);University of Illinois at Urbana-Champaign(伊利诺伊大学厄巴纳-香槟分校)
The task of ultra-fine entity typing (UFET) seeks to predict diverse and free-form words or phrases that describe the appropriate types of entities mentioned in sentences. A key challenge for this task lies in the large amount of types and the scarcity of annotated data per type. Existing systems formulate the task as a multi-way classification problem and train directly or distantly supervised classifiers. This causes two issues: (i) the classifiers do not capture the type semantics since types are often converted into indices; (ii) systems developed in this way are limited to predicting with…
Sberbank(俄罗斯联邦储蓄银行);Higher School of Economics(高等经济大学)
Named Entity Recognition (NER) is a fundamental task in the fields of natural language processing and information extraction. NER has been widely used as a standalone tool or an essential component in a variety of applications such as question answering, dialogue assistants and knowledge graphs development. However, training reliable NER models requires a large amount of labelled data which is expensive to obtain, particularly in specialized domains. This paper describes a method to learn a domain-specific NER model for an arbitrary set of named entities when domain-specific supervision is not…
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…
Few-Shot Domain Adaptation for Named-Entity Recognition via Joint Constrained k-Means and Subspace Selection
Université de Brest(布雷斯特大学);Université Paris-Saclay(巴黎萨克雷大学);Data Analytics Solutions, SCOR(SCOR数据分析解决方案部);INSA Rennes(雷恩国立应用科学学院);IRISA(IRISA研究所);Inria(法国国家信息与自动化研究所);CNRS(法国国家科学研究中心);Université de Rennes(雷恩大学)
University of Illinois Urbana-Champaign(伊利诺伊大学香槟分校)
We study the problem of training named entity recognition (NER) models using only distantly-labeled data, which can be automatically obtained by matching entity mentions in the raw text with entity types in a knowledge base. The biggest challenge of distantly-supervised NER is that the distant supervision may induce incomplete and noisy labels, rendering the straightforward application of supervised learning ineffective. In this paper, we propose (1) a noise-robust learning scheme comprised of a new loss function and a noisy label removal step, for training NER models on distantly-labeled data…
Studio Ousia(Ousia工作室);The University of Tokyo(东京大学);RIKEN AIP(理化学研究所AIP);National Institute of Informatics(国立信息学研究所)
We present EASE, a novel method for learning sentence embeddings via contrastive learning between sentences and their related entities. The advantage of using entity supervision is twofold: (1) entities have been shown to be a strong indicator of text semantics and thus should provide rich training signals for sentence embeddings; (2) entities are defined independently of languages and thus offer useful cross-lingual alignment supervision. We evaluate EASE against other unsupervised models both in monolingual and multilingual settings. We show that EASE exhibits competitive or better performan…
Ontology-Driven and Weakly Supervised Rare Disease Identification from Clinical Notes
University of Edinburgh(爱丁堡大学);Health Data Research UK(英国健康数据研究所);University of Oxford(牛津大学);University College London(伦敦大学学院);The University of Manchester(曼彻斯特大学)