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 of the note; (2) treating extracted concepts as labels, which are used to learn a better representation of the text. Unfortunately, the resulting concepts do not yield performance gains on the document-level clinical coding task. We explore possible explanations and future research directions.
LongHealth: A Question Answering Benchmark with Long Clinical Documents
Technical University of Munich（慕尼黑工业大学）；Charité – Universitätsmedizin Berlin（柏林夏里特医学院）；University Hospital Aachen（亚琛大学医院）；Kaduceo；Berliner Hochschule für Technik (BHT)（柏林工业大学）；Mass General Brigham, Harvard Medical School（麻省总医院布莱根医疗集团，哈佛医学院）；Maastricht University（马斯特里赫特大学）；University Hospital RWTH Aachen（亚琛工业大学医院）；Technical University Dresden（德累斯顿工业大学）；German Heart Center Munich（慕尼黑德国心脏中心）
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…
Traditional text classification techniques in clinical domain have heavily relied on the manually extracted textual cues. This paper proposes a generally supervised machine learning method that is equally hassle-free and does not use clinical knowledge. The employed methods were simple to implement, fast to run and yet effective. This paper proposes a novel named entity recognition (NER) based an ensemble system capable of learning the keyword features in the document. Instead of merely considering the whole sentence/paragraph for analysis, the NER based keyword features can stress the importa…
The problem of named entity recognition in the medical/clinical domain has gained increasing attention do to its vital role in a wide range of clinical decision support applications. The identification of complete and correct term span is vital for further knowledge synthesis (e.g., coding/mapping concepts thesauruses and classification standards). This paper investigates boundary adjustment by sequence labeling representations models and post-processing techniques in the problem of clinical named entity recognition (recognition of clinical events). Using current state-of-the-art sequence labe…
This paper reports on Qwant Research contribution to tasks 2 and 3 of the DEFT 2019's challenge, focusing on French clinical cases analysis. Task 2 is a task on semantic similarity between clinical cases and discussions. For this task, we propose an approach based on language models and evaluate the impact on the results of different preprocessings and matching techniques. For task 3, we have developed an information extraction system yielding very encouraging results accuracy-wise. We have experimented two different approaches, one based on the exclusive use of neural networks, the other base…
Over the past decade, there has been a steep rise in the data-driven analysis in major areas of medicine, such as clinical decision support system, survival analysis, patient similarity analysis, image analytics etc. Most of the data in the field are well-structured and available in numerical or categorical formats which can be used for experiments directly. But on the opposite end of the spectrum, there exists a wide expanse of data that is intractable for direct analysis owing to its unstructured nature which can be found in the form of discharge summaries, clinical notes, procedural notes w…
Following the global COVID-19 pandemic, the number of scientific papers studying the virus has grown massively, leading to increased interest in automated literate review. We present a clinical text mining system that improves on previous efforts in three ways. First, it can recognize over 100 different entity types including social determinants of health, anatomy, risk factors, and adverse events in addition to other commonly used clinical and biomedical entities. Second, the text processing pipeline includes assertion status detection, to distinguish between clinical facts that are present, …
ReLyfe - Medical Intelligence（ReLyfe 医疗智能公司）；Ecole Polytechnique（巴黎综合理工学院）；BeCareLink（BeCareLink 公司）
Structuring medical data in France remains a challenge mainly because of the lack of medical data due to privacy concerns and the lack of methods and approaches on processing the French language. One of these challenges is structuring drug-related information in French clinical documents. To our knowledge, over the last decade, there are less than five relevant papers that study French prescriptions. This paper proposes a new approach for extracting drug-related information from French clinical scanned documents while preserving patients' privacy. In addition, we deployed our method in a healt…
Electronic Health Records (EHR) store clinical documentation as base64 encoded attachments in FHIR DocumentReference resources, which makes semantic question answering difficult. Traditional vector database methods often miss nuanced clinical relationships. The Clinical Entity Augmented Retrieval (CLEAR) method, introduced by Lopez et al. 2025, uses entity aware retrieval and achieved improved performance with an F1 score of 0.90 versus 0.86 for embedding based retrieval, while using over 70 percent fewer tokens. We developed a Clinical Notes QA Evaluation Platform to validate CLEAR against ze…
The surging amount of biomedical literature & digital clinical records presents a growing need for text mining techniques that can not only identify but also semantically relate entities in unstructured data. In this paper we propose a text mining framework comprising of Named Entity Recognition (NER) and Relation Extraction (RE) models, which expands on previous work in three main ways. First, we introduce two new RE model architectures -- an accuracy-optimized one based on BioBERT and a speed-optimized one utilizing crafted features over a Fully Connected Neural Network (FCNN). Second, we ev…
Infusing clinical knowledge into tokenisers for language models
The UCL Institute of Health Informatics（伦敦大学学院健康信息学研究所）；Advanced Care Research Centre（高级护理研究中心）；The Usher Institute（乌舍研究所）；College of Medicine and Veterinary Medicine（医学与兽医学院）；University of Edinburgh（爱丁堡大学）；School of Literatures, Languages and Cultures（文学、语言与文化学院）；Edinburgh Futures Institute（爱丁堡未来研究所）
Centro de Tecnología Biomédica, Universidad Politécnica de Madrid（马德里理工大学生物医学技术中心）；Universidad Politécnica de Madrid（马德里理工大学）；ETS de Ingenieros Informáticos, Universidad Politécnica de Madrid（马德里理工大学计算机工程高等技术学院）
Recent rapid increase in the generation of clinical data and rapid development of computational science make us able to extract new insights from massive datasets in healthcare industry. Oncological clinical notes are creating rich databases for documenting patients history and they potentially contain lots of patterns that could help in better management of the disease. However, these patterns are locked within free text (unstructured) portions of clinical documents and consequence in limiting health professionals to extract useful information from them and to finally perform Query and Answer…
University of Arizona（亚利桑那大学）；Boston Children’s Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）；University of Wisconsin–Madison（威斯康星大学麦迪逊分校）；Loyola University Chicago（芝加哥洛约拉大学）
Automatic phenotyping is a task of identifying cohorts of patients that match a predefined set of criteria. Phenotyping typically involves classifying long clinical documents that contain thousands of tokens. At the same time, recent state-of-art transformer-based pre-trained language models limit the input to a few hundred tokens (e.g. 512 tokens for BERT). We evaluate several strategies for incorporating pre-trained sentence encoders into document-level representations of clinical text, and find that hierarchical transformers without pre-training are competitive with task pre-trained models.
Sorbonne Université（索邦大学）；Inserm（法国国家健康与医学研究院）；Université Sorbonne Paris Nord（索邦巴黎北大学）；Assistance Publique-Hôpitaux de Paris（巴黎公立医院援助联盟）
The objective of this study is to address the critical issue of de-identification of clinical reports in order to allow access to data for research purposes, while ensuring patient privacy. The study highlights the difficulties faced in sharing tools and resources in this domain and presents the experience of the Greater Paris University Hospitals (AP-HP) in implementing a systematic pseudonymization of text documents from its Clinical Data Warehouse. We annotated a corpus of clinical documents according to 12 types of identifying entities, and built a hybrid system, merging the results of a d…
University of Edinburgh（爱丁堡大学）；University College London（伦敦大学学院）；Edinburgh Futures Institute（爱丁堡未来学院）；Epic Systems Corporation（Epic系统公司）；University College London Hospitals NHS Foundation Trust（伦敦大学学院医院NHS基金会信托）；Aalto University（阿尔托大学）；University of Oxford（牛津大学）
Clinical coding is the task of transforming medical information in a patient's health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on th…
Semantic Analysis of SNOMED CT Concept Co-occurrences in Clinical Documentation using MIMIC-IV
Informatics and Analytics, University of North Carolina Greensboro, Greensboro, NC（信息学与分析，北卡罗来纳大学格林斯伯罗分校）；Department of Computer Science, University of Nebraska Omaha, Omaha, NE（计算机科学系，内布拉斯加大学奥马哈分校）
Univ of Maryland, College Park（马里兰大学帕克分校）；M Health Information Systems（3M健康信息系统公司）
The vast majority of research in computer assisted medical coding focuses on coding at the document level, but a substantial proportion of medical coding in the real world involves coding at the level of clinical encounters, each of which is typically represented by a potentially large set of documents. We introduce encounter-level document attention networks, which use hierarchical attention to explicitly take the hierarchical structure of encounter documentation into account. Experimental evaluation demonstrates improvements in coding accuracy as well as facilitation of human reviewers in th…
Imperial College London（伦敦帝国理工学院）；Transformative AI（变革性人工智能公司）
Past studies on the ICD coding problem focus on predicting clinical codes primarily based on the discharge summary. This covers only a small fraction of the notes generated during each hospital stay and leaves potential for improving performance by analysing all the available clinical notes. We propose a hierarchical transformer architecture that uses text across the entire sequence of clinical notes in each hospital stay for ICD coding, and incorporates embeddings for text metadata such as their position, time, and type of note. While using all clinical notes increases the quantity of data su…
KREL: Automatic Medical Coding via Knowledge-Guided Reasoning over Clinical Evidence with LLMs
The University of New South Wales（新南威尔士大学）；University of Göttingen（哥廷根大学）；Macquarie University（麦考瑞大学）；Beijing Intelligent Decision Medical Technology Co. Ltd（北京智决医疗科技有限公司）
Objective. Natural language processing methods for medical auto-coding, or automatic generation of medical billing codes from electronic health records, generally assign each code independently of the others. They may thus assign codes for closely related procedures or diagnoses to the same document, even when they do not tend to occur together in practice, simply because the right choice can be difficult to infer from the clinical narrative. Materials and Methods. We propose a method that injects awareness of the propensities for code co-occurrence into this process. First, a model is trained…
Clinical Document Corpora -- Real Ones, Translated and Synthetic Substitutes, and Assorted Domain Proxies: A Survey of Diversity in Corpus Design, with Focus on German Text Data
Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig（莱比锡大学医学信息学、统计学与流行病学研究所）
Large language models are vulnerable to incidental information in clinical documentation and reasoning
NYU Langone Health（纽约大学朗格尼健康中心）；Johns Hopkins University School of Medicine（约翰霍普金斯大学医学院）；Washington University School of Medicine in St. Louis（圣路易斯华盛顿大学医学院）；University of Alabama at Birmingham Heersink School of Medicine（阿拉巴马大学伯明翰分校希尔斯金医学院）；Perelman School of Medicine at the University of Pennsylvania（宾夕法尼亚大学佩雷尔曼医学院）；New York University（纽约大学）
From Documents to Spans: Span-Centric Learning for LLM-based Explainable Medical Coding
School of Biomedical Engineering, Division of Life Sciences and Medicine, USTC（生物医学工程学院，生命科学与医学系，中国科学技术大学）；MIRACLE Center, Suzhou Institute for Advance Research, USTC（MIRACLE中心，苏州先进研究院，中国科学技术大学）；Jiangsu Provincial Key Laboratory of Multimodal Digital Twin Technology（江苏省多模态数字孪生技术重点实验室）；State Key Laboratory of Precision and Intelligent Chemistry, USTC（精密与智能化学国家重点实验室）
Detecting automatically the layout of clinical documents to enhance the performances of downstream natural language processing
Sorbonne Université（索邦大学）；Inserm（法国国家健康与医学研究院）；Institut Pierre-Louis d'Epidémiologie et de Santé Publique（皮埃尔-路易流行病学与公共卫生研究所）；Assistance Publique-Hôpitaux de Paris（巴黎公共医疗集团）；LIMICS（医学信息学与信号处理实验室）
Transformer models have achieved great success across many NLP problems. However, previous studies in automated ICD coding concluded that these models fail to outperform some of the earlier solutions such as CNN-based models. In this paper we challenge this conclusion. We present a simple and scalable method to process long text with the existing transformer models such as BERT. We show that this method significantly improves the previous results reported for transformer models in ICD coding, and is able to outperform one of the prominent CNN-based methods.
MaLei at MultiClinSUM: Summarisation of Clinical Documents using Perspective-Aware Iterative Self-Prompting with LLMs
University of Manchester, UK（曼彻斯特大学）；Modul University Vienna, Austria（维也纳Modul大学）；Leiden Institute of Advanced Computer Science (LIACS), Leiden University, The Netherlands（莱顿先进计算机科学研究所（LIACS）、莱顿大学）；Leiden University Medical Center, The Netherlands（莱顿大学医学中心）
School of Biomedical Informatics, The University of Texas Health Science Center（德克萨斯大学健康科学中心生物医学信息学院）
We present a Three-level Hierarchical Transformer Network (3-level-HTN) for modeling long-term dependencies across clinical notes for the purpose of patient-level prediction. The network is equipped with three levels of Transformer-based encoders to learn progressively from words to sentences, sentences to notes, and finally notes to patients. The first level from word to sentence directly applies a pre-trained BERT model as a fully trainable component. While the second and third levels both implement a stack of transformer-based encoders, before the final patient representation is fed into a …
InformGen: An AI Copilot for Accurate and Compliant Clinical Research Consent Document Generation
University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；University of Edinburgh（爱丁堡大学）；Carle Illinois College of Medicine（卡尔伊利诺伊医学院）；Seoul National University Bundang Hospital（首尔大学盆唐医院）
DART: A Structured Dataset of Regulatory Drug Documents in Italian for Clinical NLP
University of Naples Federico II, Department of Electrical Engineering（那不勒斯费德里科二世大学电气工程系）；Consorzio Interuniversitario Nazionale per l'Informatica (CINI) - ITEM National Lab, Complesso Universitario Monte S.Angelo, Naples, Italy（国家信息计算联合研究所（CINI）- ITEM国家实验室，那不勒斯意大利大学综合体）；Northwestern University, Department of Computer Science, McCormick School of Engineering（西北大学计算机科学系，麦科姆工程学院）
Virginia Commonwealth University（弗吉尼亚联邦大学）；Johns Hopkins University（约翰斯·霍普金斯大学）
Clinical notes contain an extensive record of a patient's health status, such as smoking status or the presence of heart conditions. However, this detail is not replicated within the structured data of electronic health systems. Phenotyping, the extraction of patient conditions from free clinical text, is a critical task which supports avariety of downstream applications such as decision support and secondary use of medical records. Previous work has resulted in systems which are high performing but require hand engineering, often of rules. Recent work in pretrained contextualized language mod…
Australian e-Health Research Centre, CSIRO（澳大利亚电子健康研究中心，澳大利亚联邦科学与工业研究组织）；VinAI Research（VinAI研究院）
ICD coding is a process of assigning the International Classification of Disease diagnosis codes to clinical/medical notes documented by health professionals (e.g. clinicians). This process requires significant human resources, and thus is costly and prone to error. To handle the problem, machine learning has been utilized for automatic ICD coding. Previous state-of-the-art models were based on convolutional neural networks, using a single/several fixed window sizes. However, the lengths and interdependence between text fragments related to ICD codes in clinical text vary significantly, leadin…
Clinical Document Metadata Extraction: A Scoping Review
University of Minnesota（明尼苏达大学）；Mayo Clinic（妙佑医疗国际）；University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心）；Oregon Health & Science University（俄勒冈健康与科学大学）
University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Clinical trials are essential for drug development but are extremely expensive and time-consuming to conduct. It is beneficial to study similar historical trials when designing a clinical trial. However, lengthy trial documents and lack of labeled data make trial similarity search difficult. We propose a zero-shot clinical trial retrieval method, Trial2Vec, which learns through self-supervision without annotating similar clinical trials. Specifically, the meta-structure of trial documents (e.g., title, eligibility criteria, target disease) along with clinical knowledge (e.g., UMLS knowledge ba…
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…
Automated clinical coding using off-the-shelf large language models
Canon Medical Research Europe（佳能医疗研究欧洲）；Queen Mary University of London（伦敦玛丽女王大学）；University of Edinburgh（爱丁堡大学）；Anglia Ruskin University（安格利亚鲁斯金大学）；The Alan Turing Institute（艾伦·图灵研究所）；University of Warwick（华威大学）
The Ohio State University（俄亥俄州立大学）；National Institutes of Health（美国国立卫生研究院）
Natural language processing techniques are being applied to increasingly diverse types of electronic health records, and can benefit from in-depth understanding of the distinguishing characteristics of medical document types. We present a method for characterizing the usage patterns of clinical concepts among different document types, in order to capture semantic differences beyond the lexical level. By training concept embeddings on clinical documents of different types and measuring the differences in their nearest neighborhood structures, we are able to measure divergences in concept usage …
Stanford University（斯坦福大学）；Colorado State University（科罗拉多州立大学）；Chan-Zuckerberg Biohub（陈-扎克伯格生物中心）
Large scale veterinary clinical records can become a powerful resource for patient care and research. However, clinicians lack the time and resource to annotate patient records with standard medical diagnostic codes and most veterinary visits are captured in free text notes. The lack of standard coding makes it challenging to use the clinical data to improve patient care. It is also a major impediment to cross-species translational research, which relies on the ability to accurately identify patient cohorts with specific diagnostic criteria in humans and animals. In order to reduce the coding …
Coding-Free and Privacy-Preserving Agentic Framework for Data-Driven Clinical Research
Infmedix, Co., Ltd.（Infmedix公司）；Department of Transdisciplinary Studies, Seoul National University（首尔国立大学跨学科研究系）；Healthcare AI Research Institute, Seoul National University Hospital（首尔国立大学医院医疗人工智能研究所）；Department of Medicine, Seoul National University College of Medicine（首尔国立大学医学院医学系）；Department of Transdisciplinary Medicine, Seoul National University Hospital（首尔国立大学医院跨学科医学系）；Department of Radiology, Massachusetts General Hospital and Harvard Medical School（麻省总医院放射科及哈佛医学院）
Artificial intelligence to improve clinical coding practice in Scandinavia: a crossover randomized controlled trial
Norwegian Centre for E-health Research（挪威电子健康研究中心）；UiT The Arctic University of Norway（挪威北极大学）；University Hospital of North Norway（北挪威大学医院）；The Norwegian Centre for Clinical Artificial Intelligence（挪威临床人工智能中心）
