With the development and business adoption of knowledge graph, there is an increasing demand for extracting entities and relations of knowledge graphs from unstructured domain documents. This makes the automatic knowledge extraction for domain text quite meaningful. This paper proposes a knowledge extraction method based on BERT, which is used to extract knowledge points from unstructured specific domain texts (such as insurance clauses in the insurance industry) automatically to save manpower of knowledge graph construction. Different from the commonly used methods which are based on rules, templates or entity extraction models, this paper converts the domain knowledge points into question and answer pairs and uses the text around the answer in documents as the context. The method adopts a BERT-based model similar to BERT's SQuAD reading comprehension task. The model is fine-tuned. And it is used to directly extract knowledge points from more insurance clauses. According to the test results, the model performance is good.
In this paper, we propose Multi$^2$OIE, which performs open information extraction (open IE) by combining BERT with multi-head attention. Our model is a sequence-labeling system with an efficient and effective argument extraction method. We use a query, key, and value setting inspired by the Multimodal Transformer to replace the previously used bidirectional long short-term memory architecture with multi-head attention. Multi$^2$OIE outperforms existing sequence-labeling systems with high computational efficiency on two benchmark evaluation datasets, Re-OIE2016 and CaRB. Additionally, we apply…
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…
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.
University of Washington（华盛顿大学）；George Mason University（乔治梅森大学）
Medical imaging is critical to the diagnosis and treatment of numerous medical problems, including many forms of cancer. Medical imaging reports distill the findings and observations of radiologists, creating an unstructured textual representation of unstructured medical images. Large-scale use of this text-encoded information requires converting the unstructured text to a structured, semantic representation. We explore the extraction and normalization of anatomical information in radiology reports that is associated with radiological findings. We investigate this extraction and normalization …
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…
The web contains vast repositories of unstructured text. We investigate the opportunity for building a knowledge graph from these text sources. We generate a set of triples which can be used in knowledge gathering and integration. We define the architecture of a language compiler for processing subject-predicate-object triples using the OpenNLP parser. We implement a depth-first search traversal on the POS tagged syntactic tree appending predicate and object information. A parser enables higher precision and higher recall extractions of syntactic relationships across conjunction boundaries. We…
Loria, CNRS, Inria, Université de Lorraine（洛里亚研究所、法国国家科学研究中心、法国国家信息与自动化研究所、洛林大学）
Relation extraction (RE) consists in identifying and structuring automatically relations of interest from texts. Recently, BERT improved the top performances for several NLP tasks, including RE. However, the best way to use BERT, within a machine learning architecture, and within a transfer learning strategy is still an open question since it is highly dependent on each specific task and domain. Here, we explore various BERT-based architectures and transfer learning strategies (i.e., frozen or fine-tuned) for the task of biomedical RE on two corpora. Among tested architectures and strategies, …
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…
National Taiwan University（国立台湾大学）；National Cheng Kung University（国立成功大学）
While relation extraction is an essential task in knowledge acquisition and representation, and new-generated relations are common in the real world, less effort is made to predict unseen relations that cannot be observed at the training stage. In this paper, we formulate the zero-shot relation extraction problem by incorporating the text description of seen and unseen relations. We propose a novel multi-task learning model, zero-shot BERT (ZS-BERT), to directly predict unseen relations without hand-crafted attribute labeling and multiple pairwise classifications. Given training instances cons…
University of Delaware（特拉华大学）；Weill Cornell Medicine（威尔康奈尔医学院）
Contrastive learning has been used to learn a high-quality representation of the image in computer vision. However, contrastive learning is not widely utilized in natural language processing due to the lack of a general method of data augmentation for text data. In this work, we explore the method of employing contrastive learning to improve the text representation from the BERT model for relation extraction. The key knob of our framework is a unique contrastive pre-training step tailored for the relation extraction tasks by seamlessly integrating linguistic knowledge into the data augmentatio…
Clinical notes contain an abundance of important but not-readily accessible information about patients. Systems to automatically extract this information rely on large amounts of training data for which their exists limited resources to create. Furthermore, they are developed dis-jointly; meaning that no information can be shared amongst task-specific systems. This bottle-neck unnecessarily complicates practical application, reduces the performance capabilities of each individual solution and associates the engineering debt of managing multiple information extraction systems. We address these …
Université Paris-Saclay, INRAE, MaIAGE（巴黎-萨克雷大学，法国国家农业食品与环境研究院，应用数学与计算机科学、基因组学与环境研究单位）；Université Paris-Saclay, CNRS, Laboratoire interdisciplinaire des sciences du numérique（巴黎-萨克雷大学，法国国家科学研究中心，数字科学跨学科实验室）
Recently many studies have been conducted on the topic of relation extraction. The DrugProt track at BioCreative VII provides a manually-annotated corpus for the purpose of the development and evaluation of relation extraction systems, in which interactions between chemicals and genes are studied. We describe the ensemble system that we used for our submission, which combines predictions of fine-tuned bioBERT, sciBERT and const-bioBERT models by majority voting. We specifically tested the contribution of syntactic information to relation extraction with BERT. We observed that adding constituen…
Department of Computer and Information Science University of Delaware（特拉华大学计算机与信息科学系）；University of Delaware（特拉华大学）；Department of Computer and Information Science（计算机与信息科学系）
With the explosive growth of biomedical literature, designing automatic tools to extract information from the literature has great significance in biomedical research. Recently, transformer-based BERT models adapted to the biomedical domain have produced leading results. However, all the existing BERT models for relation classification only utilize partial knowledge from the last layer. In this paper, we will investigate the method of utilizing the entire layer in the fine-tuning process of BERT model. To the best of our knowledge, we are the first to explore this method. The experimental resu…
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…
We convert the Chinese medical text attributes extraction task into a sequence tagging or machine reading comprehension task. Based on BERT pre-trained models, we have not only tried the widely used LSTM-CRF sequence tagging model, but also other sequence models, such as CNN, UCNN, WaveNet, SelfAttention, etc, which reaches similar performance as LSTM+CRF. This sheds a light on the traditional sequence tagging models. Since the aspect of emphasis for different sequence tagging models varies substantially, ensembling these models adds diversity to the final system. By doing so, our system achie…
National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH)（美国国家生物技术信息中心（NCBI）、美国国家医学图书馆（NLM）、美国国立卫生研究院（NIH））
A biomedical relation statement is commonly expressed in multiple sentences and consists of many concepts, including gene, disease, chemical, and mutation. To automatically extract information from biomedical literature, existing biomedical text-mining approaches typically formulate the problem as a cross-sentence n-ary relation-extraction task that detects relations among n entities across multiple sentences, and use either a graph neural network (GNN) with long short-term memory (LSTM) or an attention mechanism. Recently, Transformer has been shown to outperform LSTM on many natural language…
Aristotle University of Thessaloniki（塞萨洛尼基亚里士多德大学）
Distantly-supervised relation extraction (RE) is an effective method to scale RE to large corpora but suffers from noisy labels. Existing approaches try to alleviate noise through multi-instance learning and by providing additional information, but manage to recognize mainly the top frequent relations, neglecting those in the long-tail. We propose REDSandT (Relation Extraction with Distant Supervision and Transformers), a novel distantly-supervised transformer-based RE method, that manages to capture a wider set of relations through highly informative instance and label embeddings for RE, by e…
Professionals in modern healthcare systems are increasingly burdened by documentation workloads. Documentation of the initial patient anamnesis is particularly relevant, forming the basis of successful further diagnostic measures. However, manually prepared notes are inherently unstructured and often incomplete. In this paper, we investigate the potential of modern NLP techniques to support doctors in this matter. We present a dataset of German patient monologues, and formulate a well-defined information extraction task under the constraints of real-world utility and practicality. In addition,…
Knowledge-based question answering relies on the availability of facts, the majority of which cannot be found in structured sources (e.g. Wikipedia info-boxes, Wikidata). One of the major components of extracting facts from unstructured text is Relation Extraction (RE). In this paper we propose a novel method for creating distant (weak) supervision labels for training a large-scale RE system. We also provide new evidence about the effectiveness of neural network approaches by decoupling the model architecture from the feature design of a state-of-the-art neural network system. Surprisingly, a …
Techniques for automatically extracting important content elements from business documents such as contracts, statements, and filings have the potential to make business operations more efficient. This problem can be formulated as a sequence labeling task, and we demonstrate the adaption of BERT to two types of business documents: regulatory filings and property lease agreements. There are aspects of this problem that make it easier than "standard" information extraction tasks and other aspects that make it more difficult, but on balance we find that modest amounts of annotated data (less than…
Centro de Informática, Universidade Federal de Pernambuco（伯南布哥联邦大学信息中心）；Montreal Institute for Learning Algorithms, University of Montreal（蒙特利尔大学蒙特利尔学习算法研究所）；Department of Chemical and Biological Engineering, Northwestern University（西北大学化学与生物工程系）
Relation extraction (RE) consists in categorizing the relationship between entities in a sentence. A recent paradigm to develop relation extractors is Distant Supervision (DS), which allows the automatic creation of new datasets by taking an alignment between a text corpus and a Knowledge Base (KB). KBs can sometimes also provide additional information to the RE task. One of the methods that adopt this strategy is the RESIDE model, which proposes a distantly-supervised neural relation extraction using side information from KBs. Considering that this method outperformed state-of-the-art baselin…
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…
Zhejiang University（浙江大学）；AZFT Joint Lab for Knowledge Engine（AZFT知识引擎联合实验室）；Hangzhou Innovation Center, Zhejiang University（浙江大学杭州国际科创中心）
Fine-tuning pre-trained models have achieved impressive performance on standard natural language processing benchmarks. However, the resultant model generalizability remains poorly understood. We do not know, for example, how excellent performance can lead to the perfection of generalization models. In this study, we analyze a fine-tuned BERT model from different perspectives using relation extraction. We also characterize the differences in generalization techniques according to our proposed improvements. From empirical experimentation, we find that BERT suffers a bottleneck in terms of robus…
Microsoft Research Asia（微软亚洲研究院）；Peking University（北京大学）；University of Science and Technology of China（中国科学技术大学）
Recent grid-based document representations like BERTgrid allow the simultaneous encoding of the textual and layout information of a document in a 2D feature map so that state-of-the-art image segmentation and/or object detection models can be straightforwardly leveraged to extract key information from documents. However, such methods have not achieved comparable performance to state-of-the-art sequence- and graph-based methods such as LayoutLM and PICK yet. In this paper, we propose a new multi-modal backbone network by concatenating a BERTgrid to an intermediate layer of a CNN model, where th…
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…
Huawei Turkey Research and Development Center（华为土耳其研发中心）；Ford Otosan（福特奥托桑）；Bogazici University（海峡大学）；Yildiz Technical University（伊尔迪兹技术大学）
Neural relation extraction discovers semantic relations between entities from unstructured text using deep learning methods. In this study, we present a comprehensive review of methods on neural network based relation extraction. We discuss advantageous and incompetent sides of existing studies and investigate additional research directions and improvement ideas in this field.
Shanghai University of Finance and Economics（上海财经大学）
With the rapid development of information technology, online platforms (e.g., news portals and social media) generate enormous web information every moment. Therefore, it is crucial to extract structured representations of events from social streams. Generally, existing event extraction research utilizes pattern matching, machine learning, or deep learning methods to perform event extraction tasks. However, the performance of Chinese event extraction is not as good as English due to the unique characteristics of the Chinese language. In this paper, we propose an integrated framework to perform…
University of California（加利福尼亚大学）；Diffbot（Diffbot公司）
The broad goal of information extraction is to derive structured information from unstructured data. However, most existing methods focus solely on text, ignoring other types of unstructured data such as images, video and audio which comprise an increasing portion of the information on the web. To address this shortcoming, we propose the task of multimodal attribute extraction. Given a collection of unstructured and semi-structured contextual information about an entity (such as a textual description, or visual depictions) the task is to extract the entity's underlying attributes. In this pape…
National Science Library, Chinese Academy of Science（中国科学院国家科学图书馆）；University of Chinese Academy of Science（中国科学院大学）；City University of New York（纽约城市大学）；Tsinghua University（清华大学）
Computational chemistry develops fast in recent years due to the rapid growth and breakthroughs in AI. Thanks for the progress in natural language processing, researchers can extract more fine-grained knowledge in publications to stimulate the development in computational chemistry. While the works and corpora in chemical entity extraction have been restricted in the biomedicine or life science field instead of the chemistry field, we build a new corpus in chemical bond field annotated for 7 types of entities: compound, solvent, method, bond, reaction, pKa and pKa value. This paper presents a …
University of Oxford（牛津大学）；The Alan Turing Institute（艾伦·图灵研究所）
Relying on large pretrained language models such as Bidirectional Encoder Representations from Transformers (BERT) for encoding and adding a simple prediction layer has led to impressive performance in many clinical natural language processing (NLP) tasks. In this work, we present a novel extension to the Transformer architecture, by incorporating signature transform with the self-attention model. This architecture is added between embedding and prediction layers. Experiments on a new Swedish prescription data show the proposed architecture to be superior in two of the three information extrac…
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.
Research on Information Extraction of LCSTS Dataset Based on an Improved BERTSum-LSTM Model
College of Information Science and Technology, Donghua University（东华大学信息科学与技术学院）；College of Physics, Donghua University（东华大学物理学院）；Glorious Sun School of Business & Management, Donghua University（东华大学旭日工商管理学院）；College of Medical Technology, Shanghai University of Medicine & Health Sciences（上海健康医学院医学技术学院）；College of Information Sciences and Technology, Donghua University（东华大学信息科学与技术学院）
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.
EURA NOVA（欧瑞诺瓦（EURA NOVA））；Aix Marseille Univ（艾克斯-马赛大学）；Université de Toulon（土伦大学）；CNRS（法国国家科学研究中心）
This paper explains our participation in task 1 of the CASE 2021 shared task. This task is about multilingual event extraction from news. We focused on sub-task 4, event information extraction. This sub-task has a small training dataset and we fine-tuned a multilingual BERT to solve this sub-task. We studied the instability problem on the dataset and tried to mitigate it.
In Track-1 of the BioCreative VII Challenge participants are asked to identify interactions between drugs/chemicals and proteins. In-context named entity annotations for each drug/chemical and protein are provided and one of fourteen different interactions must be automatically predicted. For this relation extraction task, we attempt both a BERT-based sentence classification approach, and a more novel text-to-text approach using a T5 model. We find that larger BERT-based models perform better in general, with our BioMegatron-based model achieving the highest scores across all metrics, achievin…
Distilling Large Language Models for Efficient Clinical Information Extraction
Poolesville High School（普尔斯维尔高中）；University of California Santa Cruz（加州大学圣克鲁兹分校）；Stanford University School of Medicine（斯坦福大学医学院）；Clinical Excellence Research Center（临床卓越研究中心）；Stanford Health Care（斯坦福医疗保健系统）
University of Florida（佛罗里达大学）；University of Florida Health Cancer Center（佛罗里达大学健康癌症中心）
The newly emerged transformer technology has a tremendous impact on NLP research. In the general English domain, transformer-based models have achieved state-of-the-art performances on various NLP benchmarks. In the clinical domain, researchers also have investigated transformer models for clinical applications. The goal of this study is to systematically explore three widely used transformer-based models (i.e., BERT, RoBERTa, and XLNet) for clinical relation extraction and develop an open-source package with clinical pre-trained transformer-based models to facilitate information extraction in…
Fetch Technologies（Fetch技术公司）；University of Southern California（南加州大学）；Information Sciences Institute（信息科学研究所）
Vast amounts of text on the Web are unstructured and ungrammatical, such as classified ads, auction listings, forum postings, etc. We call such text "posts." Despite their inconsistent structure and lack of grammar, posts are full of useful information. This paper presents work on semi-automatically building tables of relational information, called "reference sets," by analyzing such posts directly. Reference sets can be applied to a number of tasks such as ontology maintenance and information extraction. Our reference-set construction method starts with just a small amount of background knowl…
Relation extraction is the task of extracting semantic relations between entities in a sentence. It is an essential part of some natural language processing tasks such as information extraction, knowledge extraction, and knowledge base population. The main motivations of this research stem from a lack of a dataset for relation extraction in the Persian language as well as the necessity of extracting knowledge from the growing big-data in the Persian language for different applications. In this paper, we present "PERLEX" as the first Persian dataset for relation extraction, which is an expert-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…
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…
DCSE, University of Engineering and Technology, Peshawar, Pakistan（巴基斯坦白沙瓦工程与技术大学DCSE）；Abasyn University Islamabad Campus, Pakistan（巴基斯坦阿巴辛大学伊斯兰堡校区）；Department of AI, AJOU University, South Korea（韩国亚洲大学人工智能系）；Department of Computer Science, Munster Technological University, Cork, Ireland（爱尔兰科克芒斯特理工大学计算机科学系）
This paper presents our solutions for the MediaEval 2022 task on DisasterMM. The task is composed of two subtasks, namely (i) Relevance Classification of Twitter Posts (RCTP), and (ii) Location Extraction from Twitter Texts (LETT). The RCTP subtask aims at differentiating flood-related and non-relevant social posts while LETT is a Named Entity Recognition (NER) task and aims at the extraction of location information from the text. For RCTP, we proposed four different solutions based on BERT, RoBERTa, Distil BERT, and ALBERT obtaining an F1-score of 0.7934, 0.7970, 0.7613, and 0.7924, respectiv…
Adverse drug reactions / events (ADR/ADE) have a major impact on patient health and health care costs. Detecting ADR's as early as possible and sharing them with regulators, pharma companies, and healthcare providers can prevent morbidity and save many lives. While most ADR's are not reported via formal channels, they are often documented in a variety of unstructured conversations such as social media posts by patients, customer support call transcripts, or CRM notes of meetings between healthcare providers and pharma sales reps. In this paper, we propose a natural language processing (NLP) so…
CINNAMON LAB（肉桂实验室）；Hung Yen University of Technology and Education（兴安技术教育大学）；Le Quy Don Technical University（黎贵惇技术大学）
This paper presents a practical approach to fine-grained information extraction. Through plenty of experiences of authors in practically applying information extraction to business process automation, there can be found a couple of fundamental technical challenges: (i) the availability of labeled data is usually limited and (ii) highly detailed classification is required. The main idea of our proposal is to leverage the concept of transfer learning, which is to reuse the pre-trained model of deep neural networks, with a combination of common statistical classifiers to determine the class of ea…
The Australian National University (ANU)（澳大利亚国立大学）；Data61, Commonwealth Scientific and Industrial Research Organization (CSIRO)（澳大利亚联邦科学与工业研究组织Data61部门）；University of Canberra（堪培拉大学）；University of Turku（图尔库大学）
The Bidirectional Encoder Representations from Transformers (BERT) model has achieved the state-of-the-art performance for many natural language processing (NLP) tasks. Yet, limited research has been contributed to studying its effectiveness when the target domain is shifted from the pre-training corpora, for example, for biomedical or clinical NLP applications. In this paper, we applied it to a widely studied a hospital information extraction (IE) task and analyzed its performance under the transfer learning setting. Our application became the new state-of-the-art result by a clear margin, co…
Information Extraction from Clinical Notes: Are We Ready to Switch to Large Language Models?
McWilliams 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麦克威廉姆斯生物医学信息学学院）；Yale School of Medicine, Yale University（耶鲁大学医学院）
Max Planck Institute for Informatics（马克斯·普朗克信息学研究所）
This paper presents a new task of predicting the coverage of a text document for relation extraction (RE): does the document contain many relational tuples for a given entity? Coverage predictions are useful in selecting the best documents for knowledge base construction with large input corpora. To study this problem, we present a dataset of 31,366 diverse documents for 520 entities. We analyze the correlation of document coverage with features like length, entity mention frequency, Alexa rank, language complexity and information retrieval scores. Each of these features has only moderate pred…
This paper presents our participation in the AGAC Track from the 2019 BioNLP Open Shared Tasks. We provide a solution for Task 3, which aims to extract "gene - function change - disease" triples, where "gene" and "disease" are mentions of particular genes and diseases respectively and "function change" is one of four pre-defined relationship types. Our system extends BERT (Devlin et al., 2018), a state-of-the-art language model, which learns contextual language representations from a large unlabelled corpus and whose parameters can be fine-tuned to solve specific tasks with minimal additional …
University of California, Berkeley（加州大学伯克利分校）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）
Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in…
