External knowledge is often useful for natural language understanding tasks. We introduce a contextual text representation model called Conceptual-Contextual (CC) embeddings, which incorporates structured knowledge into text representations. Unlike entity embedding methods, our approach encodes a knowledge graph into a context model. CC embeddings can be easily reused for a wide range of tasks just like pre-trained language models. Our model effectively encodes the huge UMLS database by leveraging semantic generalizability. Experiments on electronic health records (EHRs) and medical text processing benchmarks showed our model gives a major boost to the performance of supervised medical NLP tasks.
Event Ontology Expansion via LLM-Based Conceptualization
State Key Laboratory of AI Safety（人工智能安全国家重点实验室）；Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；School of Computer Science and Technology, University of Chinese Academy of Sciences（中国科学院大学计算机科学与技术学院）
Contextual Evaluation of Large Language Models for Classifying Tropical and Infectious Diseases
Google Research（谷歌研究院）；Google DeepMind（谷歌DeepMind）；University of Michigan（密歇根大学）；Gear Health（吉尔健康）；Ministry of Health, Sierra Leone（塞拉利昂卫生部）；Nigerian Center for Disease Control（尼日利亚疾病控制中心）；Kenyatta University（肯雅塔大学）
Beyond the Parameters: A Technical Survey of Contextual Enrichment in Large Language Models: From In-Context Prompting to Causal Retrieval-Augmented Generation
Huawei Noah’s Ark Lab（华为诺亚方舟实验室）；Huawei Cloud & AI（华为云与AI）；School of Computer Science, University of Science and Technology of China（中国科学技术大学计算机科学学院）
Complex node interactions are common in knowledge graphs, and these interactions also contain rich knowledge information. However, traditional methods usually treat a triple as a training unit during the knowledge representation learning (KRL) procedure, neglecting contextualized information of the nodes in knowledge graphs (KGs). We generalize the modeling object to a very general form, which theoretically supports any subgraph extracted from the knowledge graph, and these subgraphs are fed into a novel transformer-based model to learn the knowledge embeddings. To broaden usage scenarios of k…
UMass Amherst（马萨诸塞大学阿默斯特分校）；UMass Lowell（马萨诸塞大学洛厄尔分校）；UMass Medical School（马萨诸塞大学医学院）；U.S. Department of Veterans Affairs（美国退伍军人事务部）
This paper proposes a new natural language processing (NLP) application for identifying medical jargon terms potentially difficult for patients to comprehend from electronic health record (EHR) notes. We first present a novel and publicly available dataset with expert-annotated medical jargon terms from 18K+ EHR note sentences ($MedJ$). Then, we introduce a novel medical jargon extraction ($MedJEx$) model which has been shown to outperform existing state-of-the-art NLP models. First, MedJEx improved the overall performance when it was trained on an auxiliary Wikipedia hyperlink span dataset, w…
Biomedical text mining is becoming increasingly important as the number of biomedical documents and web data rapidly grows. Recently, word representation models such as BERT has gained popularity among researchers. However, it is difficult to estimate their performance on datasets containing biomedical texts as the word distributions of general and biomedical corpora are quite different. Moreover, the medical domain has long-tail concepts and terminologies that are difficult to be learned via language models. For the Chinese biomedical text, it is more difficult due to its complex structure an…
Clinical word embeddings are extensively used in various Bio-NLP problems as a state-of-the-art feature vector representation. Although they are quite successful at the semantic representation of words, due to the dataset - which potentially carries statistical and societal bias - on which they are trained, they might exhibit gender stereotypes. This study analyses gender bias of clinical embeddings on three medical categories: mental disorders, sexually transmitted diseases, and personality traits. To this extent, we analyze two different pre-trained embeddings namely (contextualized) clinica…
In this paper, we investigate a new approach to Population, Intervention and Outcome (PIO) element detection, a common task in Evidence Based Medicine (EBM). The purpose of this study is two-fold: to build a training dataset for PIO element detection with minimum redundancy and ambiguity and to investigate possible options in utilizing state of the art embedding methods for the task of PIO element detection. For the former purpose, we build a new and improved dataset by investigating the shortcomings of previously released datasets. For the latter purpose, we leverage the state of the art text…
College of Computing, UNC Charlotte（北卡罗来纳大学夏洛特分校计算学院）；School of Data Science, UNC Charlotte（北卡罗来纳大学夏洛特分校数据科学学院）；Departments of Philosophy & Medical Education, U. of Central Florida（中佛罗里达大学哲学与医学教育系）
Using natural language processing tools, we investigate the differences of recommendations in medical guidelines for the same decision problem -- breast cancer screening. We show that these differences arise from knowledge brought to the problem by different medical societies, as reflected in the conceptual vocabularies used by the different groups of authors.The computational models we build and analyze agree with the near-peer epistemic model of expert disagreement proposed by Garbayo. Even though the article is a case study focused on one set of guidelines, the proposed methodology is broad…
This paper presents the submissions by Team Dr.Quad to the ACL-BioNLP 2019 shared task on Textual Inference and Question Entailment in the Medical Domain. Our system is based on the prior work Liu et al. (2019) which uses a multi-task objective function for textual entailment. In this work, we explore different strategies for generalizing state-of-the-art language understanding models to the specialized medical domain. Our results on the shared task demonstrate that incorporating domain knowledge through data augmentation is a powerful strategy for addressing challenges posed by specialized do…
University of Amsterdam（阿姆斯特丹大学）；Georgia Institute of Technology（佐治亚理工学院）
Medical image captioning automatically generates a medical description to describe the content of a given medical image. A traditional medical image captioning model creates a medical description only based on a single medical image input. Hence, an abstract medical description or concept is hard to be generated based on the traditional approach. Such a method limits the effectiveness of medical image captioning. Multi-modal medical image captioning is one of the approaches utilized to address this problem. In multi-modal medical image captioning, textual input, e.g., expert-defined keywords, …
Biomedical association studies are increasingly done using clinical concepts, and in particular diagnostic codes from clinical data repositories as phenotypes. Clinical concepts can be represented in a meaningful, vector space using word embedding models. These embeddings allow for comparison between clinical concepts or for straightforward input to machine learning models. Using traditional approaches, good representations require high dimensionality, making downstream tasks such as visualization more difficult. We applied Poincaré embeddings in a 2-dimensional hyperbolic space to a large-sca…
Contextual word embedding models, such as BioBERT and Bio_ClinicalBERT, have achieved state-of-the-art results in biomedical natural language processing tasks by focusing their pre-training process on domain-specific corpora. However, such models do not take into consideration expert domain knowledge. In this work, we introduced UmlsBERT, a contextual embedding model that integrates domain knowledge during the pre-training process via a novel knowledge augmentation strategy. More specifically, the augmentation on UmlsBERT with the Unified Medical Language System (UMLS) Metathesaurus was perfor…
One Patient, Many Contexts: Scaling Medical AI with Contextual Intelligence
Harvard Medical School（哈佛医学院）；Clalit Research Institute（Clalit研究所）；Boston Children’s Hospital（波士顿儿童医院）；Harvard Data Science Initiative（哈佛数据科学计划）；Beth Israel Deaconess Medical Center（贝斯以色列女执事医疗中心）；Harvard T.H. Chan School of Public Health（哈佛大学陈曾熙公共卫生学院）；Clalit Health Services（Clalit医疗服务集团）；Ben Gurion University（本-古里安大学）；Ben Gurion University of the Negev（内盖夫本-古里安大学）；Brigham and Women’s Hospital（布莱根妇女医院）；Harvard University（哈佛大学）；Broad Institute of MIT and Harvard（麻省理工学院与哈佛大学布罗德研究所）
University of Notre Dame（圣母大学）；Florida International University（佛罗里达国际大学）
Medication errors most commonly occur at the ordering or prescribing stage, potentially leading to medical complications and poor health outcomes. While it is possible to catch these errors using different techniques; the focus of this work is on textual and contextual analysis of prescription information to detect and prevent potential medication errors. In this paper, we demonstrate how to use BERT-based contextual language models to detect anomalies in written or spoken text based on a data set extracted from real-world medical data of thousands of patient records. The proposed models are a…
RGAR: Recurrence Generation-augmented Retrieval for Factual-aware Medical Question Answering
King’s College London（伦敦国王学院）；School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University（上海交通大学电子信息与电气工程学院）；School of Electrical and Computer Engineering, Carnegie Mellon University（卡内基梅隆大学电气与计算机工程学院）
Despite the great success of word embedding, sentence embedding remains a not-well-solved problem. In this paper, we present a supervised learning framework to exploit sentence embedding for the medical question answering task. The learning framework consists of two main parts: 1) a sentence embedding producing module, and 2) a scoring module. The former is developed with contextual self-attention and multi-scale techniques to encode a sentence into an embedding tensor. This module is shortly called Contextual self-Attention Multi-scale Sentence Embedding (CAMSE). The latter employs two scorin…
King’s College London（伦敦国王学院）；University of Pennsylvania（宾夕法尼亚大学）；Northeastern University（东北大学）；Rutgers University-Camden（罗格斯大学卡姆登分校）；Google Inc.（谷歌公司）
Medical professionals search the published literature by specifying the type of patients, the medical intervention(s) and the outcome measure(s) of interest. In this paper we demonstrate how features encoding syntactic patterns improve the performance of state-of-the-art sequence tagging models (both linear and neural) for information extraction of these medically relevant categories. We present an analysis of the type of patterns exploited, and the semantic space induced for these, i.e., the distributed representations learned for identified multi-token patterns. We show that these learned re…
Tsinghua University（清华大学）；Chinese Academy of Medical Sciences / Peking Union Medical College（中国医学科学院/北京协和医学院）；Cornell University（康奈尔大学）
This paper proposes CODER: contrastive learning on knowledge graphs for cross-lingual medical term representation. CODER is designed for medical term normalization by providing close vector representations for different terms that represent the same or similar medical concepts with cross-lingual support. We train CODER via contrastive learning on a medical knowledge graph (KG) named the Unified Medical Language System, where similarities are calculated utilizing both terms and relation triplets from KG. Training with relations injects medical knowledge into embeddings and aims to provide poten…
Unsupervised pretraining is an integral part of many natural language processing systems, and transfer learning with language models has achieved remarkable results in many downstream tasks. In the clinical application of medical code assignment, diagnosis and procedure codes are inferred from lengthy clinical notes such as hospital discharge summaries. However, it is not clear if pretrained models are useful for medical code prediction without further architecture engineering. This paper conducts a comprehensive quantitative analysis of various contextualized language models' performance, pre…
Systematic Comparative Analysis of Large Pretrained Language Models on Contextualized Medication Event Extraction
Center of Excellence in Research and Education for Big Military Data Intelligence (CREDIT Center)（大数据智能卓越研究中心（CREDIT中心））；Department of Electrical and Computer Engineering（电气与计算机工程系）；Prairie View A&M University（普拉提维大学）；Texas A&M University System（德克萨斯A&M大学系统）
Massachusetts Institute of Technology（麻省理工学院）；Beth Israel Deaconess Medical Center（贝斯以色列女执事医疗中心）
We present a system that uses a learned autocompletion mechanism to facilitate rapid creation of semi-structured clinical documentation. We dynamically suggest relevant clinical concepts as a doctor drafts a note by leveraging features from both unstructured and structured medical data. By constraining our architecture to shallow neural networks, we are able to make these suggestions in real time. Furthermore, as our algorithm is used to write a note, we can automatically annotate the documentation with clean labels of clinical concepts drawn from medical vocabularies, making notes more struct…
National Research Council Canada（加拿大国家研究委员会）；Privacy Analytics Inc.（隐私分析公司）
Entity recognition is a critical first step to a number of clinical NLP applications, such as entity linking and relation extraction. We present the first attempt to apply state-of-the-art entity recognition approaches on a newly released dataset, MedMentions. This dataset contains over 4000 biomedical abstracts, annotated for UMLS semantic types. In comparison to existing datasets, MedMentions contains a far greater number of entity types, and thus represents a more challenging but realistic scenario in a real-world setting. We explore a number of relevant dimensions, including the use of con…
A large number of embeddings trained on medical data have emerged, but it remains unclear how well they represent medical terminology, in particular whether the close relationship of semantically similar medical terms is encoded in these embeddings. To date, only small datasets for testing medical term similarity are available, not allowing to draw conclusions about the generalisability of embeddings to the enormous amount of medical terms used by doctors. We present multiple automatically created large-scale medical term similarity datasets and confirm their high quality in an annotation stud…
Hainan University（海南大学）；Institute of Automation, Chinese Academy of Sciences（中国科学院自动化研究所）
This study presents three deidentified large medical text datasets, named DISCHARGE, ECHO and RADIOLOGY, which contain 50K, 16K and 378K pairs of report and summary that are derived from MIMIC-III, respectively. We implement convincing baselines of automated abstractive summarization on the proposed datasets with pre-trained encoder-decoder language models, including BERT2BERT, T5-large and BART. Further, based on the BART model, we leverage the sampled summaries from the train set as prior knowledge guidance, for encoding additional contextual representations of the guidance with the encoder …
Knowledge Graph has been proven effective in modeling structured information and conceptual knowledge, especially in the medical domain. However, the lack of high-quality annotated corpora remains a crucial problem for advancing the research and applications on this task. In order to accelerate the research for domain-specific knowledge graphs in the medical domain, we introduce DiaKG, a high-quality Chinese dataset for Diabetes knowledge graph, which contains 22,050 entities and 6,890 relations in total. We implement recent typical methods for Named Entity Recognition and Relation Extraction …
Word embeddings play a significant role in today's Natural Language Processing tasks and applications. While pre-trained models may be directly employed and integrated into existing pipelines, they are often fine-tuned to better fit with specific languages or domains. In this paper, we attempt to improve available embeddings in the uncovered niche of the Italian medical domain through the combination of Contrastive Learning (CL) and Knowledge Graph Embedding (KGE). The main objective is to improve the accuracy of semantic similarity between medical terms, which is also used as an evaluation ta…
MedCLM: Learning to Localize and Reason via a CoT-Curriculum in Medical Vision-Language Models
A.I.MATICS Inc（A.I.MATICS公司）；Boston University（波士顿大学）；University of Southern California（南加州大学）；Heuron（Heuron公司）；MODULABS, Open Neural Networks Research Lab（MODULABS，开放神经网络研究实验室）
