This study investigates the use of unsupervised word embeddings and sequence features for sample representation in an active learning framework built to extract clinical concepts from clinical free text. The objective is to further reduce the manual annotation effort while achieving higher effectiveness compared to a set of baseline features. Unsupervised features are derived from skip-gram word embeddings and a sequence representation approach. The comparative performance of unsupervised features and baseline hand-crafted features in an active learning framework are investigated using a wide range of selection criteria including least confidence, information diversity, information density and diversity, and domain knowledge informativeness. Two clinical datasets are used for evaluation: the i2b2/VA 2010 NLP challenge and the ShARe/CLEF 2013 eHealth Evaluation Lab. Our results demonstrate significant improvements in terms of effectiveness as well as annotation effort savings across both datasets. Using unsupervised features along with baseline features for sample representation lead to further savings of up to 9% and 10% of the token and concept annotation rates, respectively.
Georgia Institute of Technology（佐治亚理工学院）；Google Inc（谷歌公司）；Sutter Health（萨特医疗中心）
The text of clinical notes can be a valuable source of patient information and clinical assessments. Historically, the primary approach for exploiting clinical notes has been information extraction: linking spans of text to concepts in a detailed domain ontology. However, recent work has demonstrated the potential of supervised machine learning to extract document-level codes directly from the raw text of clinical notes. We propose to bridge the gap between the two approaches with two novel syntheses: (1) treating extracted concepts as features, which are used to supplement or replace the text…
Clinical trials predicate subject eligibility on a diversity of criteria ranging from patient demographics to food allergies. Trials post their requirements as semantically complex, unstructured free-text. Formalizing trial criteria to a computer-interpretable syntax would facilitate eligibility determination. In this paper, we investigate an information extraction (IE) approach for grounding criteria from trials in ClinicalTrials(dot)gov to a shared knowledge base. We frame the problem as a novel knowledge base population task, and implement a solution combining machine learning and context f…
We submitted two systems to the SemEval-2016 Task 12: Clinical TempEval challenge, participating in Phase 1, where we identified text spans of time and event expressions in clinical notes and Phase 2, where we predicted a relation between an event and its parent document creation time. For temporal entity extraction, we find that a joint inference-based approach using structured prediction outperforms a vanilla recurrent neural network that incorporates word embeddings trained on a variety of large clinical document sets. For document creation time relations, we find that a combination of date…
MIT CSAIL（麻省理工学院计算机科学与人工智能实验室）；UMass Lowell（马萨诸塞大学洛厄尔分校）
Clinical notes often describe important aspects of a patient's stay and are therefore critical to medical research. Clinical concept extraction (CCE) of named entities - such as problems, tests, and treatments - aids in forming an understanding of notes and provides a foundation for many downstream clinical decision-making tasks. Historically, this task has been posed as a standard named entity recognition (NER) sequence tagging problem, and solved with feature-based methods using handengineered domain knowledge. Recent advances, however, have demonstrated the efficacy of LSTM-based models for…
University of Washington（华盛顿大学）；George Mason University（乔治梅森大学）
Symptom information is primarily documented in free-text clinical notes and is not directly accessible for downstream applications. To address this challenge, information extraction approaches that can handle clinical language variation across different institutions and specialties are needed. In this paper, we present domain generalization for symptom extraction using pretraining and fine-tuning data that differs from the target domain in terms of institution and/or specialty and patient population. We extract symptom events using a transformer-based joint entity and relation extraction metho…
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) …
School of Computing and Information Systems（计算与信息系统学院）；The University of Melbourne（墨尔本大学）
We investigate the incorporation of character-based word representations into a standard CNN-based relation extraction model. We experiment with two common neural architectures, CNN and LSTM, to learn word vector representations from character embeddings. Through a task on the BioCreative-V CDR corpus, extracting relationships between chemicals and diseases, we show that models exploiting the character-based word representations improve on models that do not use this information, obtaining state-of-the-art result relative to previous neural approaches.
A lot of prior work on event extraction has exploited a variety of features to represent events. Such methods have several drawbacks: 1) the features are often specific for a particular domain and do not generalize well; 2) the features are derived from various linguistic analyses and are error-prone; and 3) some features may be expensive and require domain expert. In this paper, we develop a Chinese event extraction system that uses word embedding vectors to represent language, and deep neural networks to learn the abstract feature representation in order to greatly reduce the effort of featu…
In recent years extracting relevant information from biomedical and clinical texts such as research articles, discharge summaries, or electronic health records have been a subject of many research efforts and shared challenges. Relation extraction is the process of detecting and classifying the semantic relation among entities in a given piece of texts. Existing models for this task in biomedical domain use either manually engineered features or kernel methods to create feature vector. These features are then fed to classifier for the prediction of the correct class. It turns out that the resu…
To minimize the accelerating amount of time invested in the biomedical literature search, numerous approaches for automated knowledge extraction have been proposed. Relation extraction is one such task where semantic relations between the entities are identified from the free text. In the biomedical domain, extraction of regulatory pathways, metabolic processes, adverse drug reaction or disease models necessitates knowledge from the individual relations, for example, physical or regulatory interactions between genes, proteins, drugs, chemical, disease or phenotype. In this paper, we study the …
Keyword-optimized Template Insertion for Clinical Information Extraction via Prompt-based Learning
Mount Sinai（西奈山）；Hasso Plattner Institute for Digital Health at Mount Sinai（西奈山哈索·普拉特纳数字健康研究所）；Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院）；Institute for Personalized Medicine（个性化医学研究所）
University of Southern California（南加州大学）；Information Sciences Institute（信息科学研究所）
Learning causal and temporal relationships between events is an important step towards deeper story and commonsense understanding. Though there are abundant datasets annotated with event relations for story comprehension, many have no empirical results associated with them. In this work, we establish strong baselines for event temporal relation extraction on two under-explored story narrative datasets: Richer Event Description (RED) and Causal and Temporal Relation Scheme (CaTeRS). To the best of our knowledge, these are the first results reported on these two datasets. We demonstrate that neu…
Negative medical findings are prevalent in clinical reports, yet discriminating them from positive findings remains a challenging task for information extraction. Most of the existing systems treat this task as a pipeline of two separate tasks, i.e., named entity recognition (NER) and rule-based negation detection. We consider this as a multi-task problem and present a novel end-to-end neural model to jointly extract entities and negations. We extend a standard hierarchical encoder-decoder NER model and first adopt a shared encoder followed by separate decoders for the two tasks. This architec…
HwaMei Hospital, University of Chinese Academy of Sciences（中国科学院大学华美医院）；Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences（中国科学院大学宁波生命与健康产业研究院）
Medical information extraction consists of a group of natural language processing (NLP) tasks, which collaboratively convert clinical text to pre-defined structured formats. Current state-of-the-art (SOTA) NLP models are highly integrated with deep learning techniques and thus require massive annotated linguistic data. This study presents an engineering framework of medical entity recognition, relation extraction and attribute extraction, which are unified in annotation, modeling and evaluation. Specifically, the annotation scheme is comprehensive, and compatible between tasks, especially for …
Mayo Clinic（梅奥诊所）；University of Minnesota – Twin Cities（明尼苏达大学双城分校）
Background Concept extraction, a subdomain of natural language processing (NLP) with a focus on extracting concepts of interest, has been adopted to computationally extract clinical information from text for a wide range of applications ranging from clinical decision support to care quality improvement. Objectives In this literature review, we provide a methodology review of clinical concept extraction, aiming to catalog development processes, available methods and tools, and specific considerations when developing clinical concept extraction applications. Methods Based on the Preferred Report…
German Research Center for Artificial Intelligence (DFKI)（德国人工智能研究中心）；Charité – Universitätsmedizin Berlin（柏林夏里特医学院）；Berlin Institute of Health（柏林健康研究所）
Background: In the information extraction and natural language processing domain, accessible datasets are crucial to reproduce and compare results. Publicly available implementations and tools can serve as benchmark and facilitate the development of more complex applications. However, in the context of clinical text processing the number of accessible datasets is scarce -- and so is the number of existing tools. One of the main reasons is the sensitivity of the data. This problem is even more evident for non-English languages. Approach: In order to address this situation, we introduce a workbe…
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…
Single implementing, concatenating, adding or replacing of the representations has yielded significant improvements on many NLP tasks. Mainly in Relation Extraction where static, contextualized and others representations that are capable of explaining word meanings through the linguistic features that these incorporates. In this work addresses the question of how is improved the relation extraction using different types of representations generated by pretrained language representation models. We benchmarked our approach using popular word representation models, replacing and concatenating sta…
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 …
HIORE: Leveraging High-order Interactions for Unified Entity Relation Extraction
Tencent Inc.（腾讯公司）；ByteDance AI Lab（字节跳动人工智能实验室）；East China Normal University（华东师范大学）；University of California Santa Barbara（加州大学圣巴巴拉分校）；Shanghai Jiao Tong University（上海交通大学）
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）
The clinical named entity recognition (CNER) task seeks to locate and classify clinical terminologies into predefined categories, such as diagnostic procedure, disease disorder, severity, medication, medication dosage, and sign symptom. CNER facilitates the study of side-effect on medications including identification of novel phenomena and human-focused information extraction. Existing approaches in extracting the entities of interests focus on using static word embeddings to represent each word. However, one word can have different interpretations that depend on the context of the sentences. …
The knowledge extraction task is to extract triple relations (head entity-relation-tail entity) from unstructured text data. The existing knowledge extraction methods are divided into "pipeline" method and joint extraction method. The "pipeline" method is to separate named entity recognition and entity relationship extraction and use their own modules to extract them. Although this method has better flexibility, the training speed is slow. The learning model of joint extraction is an end-to-end model implemented by neural network to realize entity recognition and relationship extraction at the…
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 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…
We report an implementation of a clinical information extraction tool that leverages deep neural network to annotate event spans and their attributes from raw clinical notes and pathology reports. Our approach uses context words and their part-of-speech tags and shape information as features. Then we hire temporal (1D) convolutional neural network to learn hidden feature representations. Finally, we use Multilayer Perceptron (MLP) to predict event spans. The empirical evaluation demonstrates that our approach significantly outperforms baselines.
Wuhan University（武汉大学）；National University of Singapore（新加坡国立大学）；University of São Paulo（圣保罗大学）
Event extraction (EE) is an essential task of information extraction, which aims to extract structured event information from unstructured text. Most prior work focuses on extracting flat events while neglecting overlapped or nested ones. A few models for overlapped and nested EE includes several successive stages to extract event triggers and arguments,which suffer from error propagation. Therefore, we design a simple yet effective tagging scheme and model to formulate EE as word-word relation recognition, called OneEE. The relations between trigger or argument words are simultaneously recogn…
In November 27, 2018, Amazon Web Services (AWS) released Amazon Comprehend Medical (ACM), a deep learning based system that automatically extracts clinical concepts (which include anatomy, medical conditions, protected health information (PH)I, test names, treatment names, and medical procedures, and medications) from clinical text notes. Uptake and trust in any new data product relies on independent validation across benchmark datasets and tools to establish and confirm expected quality of results. This work focuses on the medication extraction task, and particularly, ACM was evaluated using …
The Clinical E-Science Framework (CLEF) project was used to extract important information from medical texts by building a system for the purpose of clinical research, evidence-based healthcare and genotype-meets-phenotype informatics. The system is divided into two parts, one part concerns with the identification of relationships between clinically important entities in the text. The full parses and domain-specific grammars had been used to apply many approaches to extract the relationship. In the second part of the system, statistical machine learning (ML) approaches are applied to extract r…
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）
SIFTING: A Novel LLM-Based Framework for Structured and Transparent Information Extraction from Clinical Free-Text Reports, with Application to Tumor Staging in Lung Cancer
Axana B.V.（阿克萨纳有限公司）；University College London Hospitals NHS Foundation Trust（伦敦大学学院医院 NHS 基金会信托）；University College London（伦敦大学学院）；Mid & South Essex NHS Foundation Trust（中埃塞克斯及南埃塞克斯 NHS 基金会信托）；NHS Greater Glasgow and Clyde（大格拉斯哥及克莱德 NHS）
Northwestern University Feinberg School of Medicine（西北大学范伯格医学院）
To reduce the large amount of time spent screening, identifying, and recruiting patients into clinical trials, we need prescreening systems that are able to automate the data extraction and decision-making tasks that are typically relegated to clinical research study coordinators. However, a major obstacle is the vast amount of patient data available as unstructured free-form text in electronic health records. Here we propose an information extraction-based approach that first automatically converts unstructured text into a structured form. The structured data are then compared against a list …
University of Minnesota（明尼苏达大学）；Dartmouth College（达特茅斯学院）；Mayo Clinic（梅奥诊所）；The University of Texas Health Science Center（德克萨斯大学健康科学中心）
Our objective in this study is to investigate the behavior of Boolean operators on combining annotation output from multiple Natural Language Processing (NLP) systems across multiple corpora and to assess how filtering by aggregation of Unified Medical Language System (UMLS) Metathesaurus concepts affects system performance for Named Entity Recognition (NER) of UMLS concepts. We used three corpora annotated for UMLS concepts: 2010 i2b2 VA challenge set (31,161 annotations), Multi-source Integrated Platform for Answering Clinical Questions (MiPACQ) corpus (17,457 annotations including UMLS conc…
Nanjing Medical University（南京医科大学）；the First Affiliated Hospital（第一附属医院）
Event extraction is an important work of medical text processing. According to the complex characteristics of medical text annotation, we use the end-to-end event extraction model to enhance the output formatting information of events. Through pre training and fine-tuning, we can extract the attributes of the four dimensions of medical text: anatomical position, subject word, description word and occurrence state. On the test set, the accuracy rate was 0.4511, the recall rate was 0.3928, and the F1 value was 0.42. The method of this model is simple, and it has won the second place in the task …
Coronavirus disease 2019 (COVID-19) is a global pandemic. Although much has been learned about the novel coronavirus since its emergence, there are many open questions related to tracking its spread, describing symptomology, predicting the severity of infection, and forecasting healthcare utilization. Free-text clinical notes contain critical information for resolving these questions. Data-driven, automatic information extraction models are needed to use this text-encoded information in large-scale studies. This work presents a new clinical corpus, referred to as the COVID-19 Annotated Clinica…
University of California, Los Angeles（加州大学洛杉矶分校）；University of Southern California（南加州大学）
There has been a steady need in the medical community to precisely extract the temporal relations between clinical events. In particular, temporal information can facilitate a variety of downstream applications such as case report retrieval and medical question answering. Existing methods either require expensive feature engineering or are incapable of modeling the global relational dependencies among the events. In this paper, we propose a novel method, Clinical Temporal ReLation Exaction with Probabilistic Soft Logic Regularization and Global Inference (CTRL-PG) to tackle the problem at the …
Shanghai Jiao Tong University（上海交通大学）；University of Macau（澳门大学）
Extracting relations is critical for knowledge base completion and construction in which distant supervised methods are widely used to extract relational facts automatically with the existing knowledge bases. However, the automatically constructed datasets comprise amounts of low-quality sentences containing noisy words, which is neglected by current distant supervised methods resulting in unacceptable precisions. To mitigate this problem, we propose a novel word-level distant supervised approach for relation extraction. We first build Sub-Tree Parse(STP) to remove noisy words that are irrelev…
Google Cloud AI（谷歌云人工智能）；McGill University（麦吉尔大学）；Google Research（谷歌研究院）
Natural reading orders of words are crucial for information extraction from form-like documents. Despite recent advances in Graph Convolutional Networks (GCNs) on modeling spatial layout patterns of documents, they have limited ability to capture reading orders of given word-level node representations in a graph. We propose Reading Order Equivariant Positional Encoding (ROPE), a new positional encoding technique designed to apprehend the sequential presentation of words in documents. ROPE generates unique reading order codes for neighboring words relative to the target word given a word-level …
To make an interactive guidance mechanism for document retrieval systems, we developed a user-interface which presents users the visualized map of topics at each stage of retrieval process. Topic words are automatically extracted by frequency analysis and the strength of the relationships between topic words is measured by their co-occurrence. A major factor affecting a user's impression of a given topic word graph is the balance between common topic words and specific topic words. By using frequency classes for topic word extraction, we made it possible to select well-balanced set of topic wo…
This paper describes our submission to ICASSP 2023 MUG Challenge Track 4, Keyphrase Extraction, which aims to extract keyphrases most relevant to the conference theme from conference materials. We model the challenge as a single-class Named Entity Recognition task and developed techniques for better performance on the challenge: For the data preprocessing, we encode the split keyphrases after word segmentation. In addition, we increase the amount of input information that the model can accept at one time by fusing multiple preprocessed sentences into one segment. We replace the loss function w…
Indian Institute of Technology Patna（印度理工学院巴特那分校）；ezDI, INC（ezDI公司）
Owing to the exponential rise in the electronic medical records, information extraction in this domain is becoming an important area of research in recent years. Relation extraction between the medical concepts such as medical problem, treatment, and test etc. is also one of the most important tasks in this area. In this paper, we present an efficient relation extraction system based on the shortest dependency path (SDP) generated from the dependency parsed tree of the sentence. Instead of relying on many handcrafted features and the whole sequence of tokens present in a sentence, our system r…
Consiglio Nazionale delle Ricerche (CNR)（意大利国家研究委员会）；Politecnico di Milano（米兰理工大学）；Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milano（米兰大医院基金会）
Information extraction from narrative clinical notes is useful for patient care, as well as for secondary use of medical data, for research or clinical purposes. Many studies focused on information extraction from English clinical texts, but less dealt with clinical notes in languages other than English. This study tested the feasibility of using 'off the shelf' information extraction algorithms to identify medical concepts from Italian clinical notes. We used MetaMap to map medical concepts to the Unified Medical Language System (UMLS). The study addressed two questions: (Q1) to understand if…
University of California, San Diego（加利福尼亚大学圣地亚哥分校）；Sensetime Group Limited（商汤集团有限公司）；Beihang University（北京航空航天大学）
Forms are a common type of document in real life and carry rich information through textual contents and the organizational structure. To realize automatic processing of forms, word grouping and relation extraction are two fundamental and crucial steps after preliminary processing of optical character reader (OCR). Word grouping is to aggregate words that belong to the same semantic entity, and relation extraction is to predict the links between semantic entities. Existing works treat them as two individual tasks, but these two tasks are correlated and can reinforce each other. The grouping pr…
Efficient extraction of medication information from clinical notes: an evaluation in two languages
University hospital of Strasbourg（斯特拉斯堡大学医院）；Inria（法国国家信息与自动化研究所）；Inserm（法国国家健康与医学研究院）；Université Paris Cité（巴黎西岱大学）；HeKA；Université Paris-Saclay（巴黎萨克雷大学）；CNRS（法国国家科学研究中心）；LISN（巴黎第十一大学计算机科学实验室）
Massachusetts Institute of Technology（麻省理工学院）；Massachusetts General Hospital（麻省总医院）
Clinical studies often require understanding elements of a patient's narrative that exist only in free text clinical notes. To transform notes into structured data for downstream use, these elements are commonly extracted and normalized to medical vocabularies. In this work, we audit the performance of and indicate areas of improvement for state-of-the-art systems. We find that high task accuracies for clinical entity normalization systems on the 2019 n2c2 Shared Task are misleading, and underlying performance is still brittle. Normalization accuracy is high for common concepts (95.3%), but mu…
Document information extraction tasks performed by humans create data consisting of a PDF or document image input, and extracted string outputs. This end-to-end data is naturally consumed and produced when performing the task because it is valuable in and of itself. It is naturally available, at no additional cost. Unfortunately, state-of-the-art word classification methods for information extraction cannot use this data, instead requiring word-level labels which are expensive to create and consequently not available for many real life tasks. In this paper we propose the Attend, Copy, Parse ar…
University of Westminster（威斯敏斯特大学）；Oakland University（奥克兰大学）
Given the recent advances and progress in Natural Language Processing (NLP), extraction of semantic relationships has been at the top of the research agenda in the last few years. This work has been mainly motivated by the fact that building knowledge graphs (KG) and bases (KB), as a key ingredient of intelligent applications, is a never-ending challenge, since new knowledge needs to be harvested while old knowledge needs to be revised. Currently, approaches towards relation extraction from text are dominated by neural models practicing some sort of distant (weak) supervision in machine learni…
Current approaches for clinical information extraction are inefficient in terms of computational costs and memory consumption, hindering their application to process large-scale electronic health records (EHRs). We propose an efficient end-to-end model, the Joint-NER-RE-Fourier (JNRF), to jointly learn the tasks of named entity recognition and relation extraction for documents of variable length. The architecture uses positional encoding and unitary batch sizes to process variable length documents and uses a weight-shared Fourier network layer for low-complexity token mixing. Finally, we reach…
Relation extraction (RE) seeks to detect and classify semantic relationships between entities, which provides useful information for many NLP applications. Since the state-of-the-art RE models require large amounts of manually annotated data and language-specific resources to achieve high accuracy, it is very challenging to transfer an RE model of a resource-rich language to a resource-poor language. In this paper, we propose a new approach for cross-lingual RE model transfer based on bilingual word embedding mapping. It projects word embeddings from a target language to a source language, so …
