Objective: Causality mining is an active research area, which requires the application of state-of-the-art natural language processing techniques. In the healthcare domain, medical experts create clinical text to overcome the limitation of well-defined and schema driven information systems. The objective of this research work is to create a framework, which can convert clinical text into causal knowledge. Methods: A practical approach based on term expansion, phrase generation, BERT based phrase embedding and semantic matching, semantic enrichment, expert verification, and model evolution has been used to construct a comprehensive causality mining framework. This active transfer learning based framework along with its supplementary services, is able to extract and enrich, causal relationships and their corresponding entities from clinical text. Results: The multi-model transfer learning technique when applied over multiple iterations, gains performance improvements in terms of its accuracy and recall while keeping the precision constant. We also present a comparative analysis of the presented techniques with their common alternatives, which demonstrate the correctness of our approach and its ability to capture most causal relationships. Conclusion: The presented framework has provided cutting-edge results in the healthcare domain. However, the framework can be tweaked to provide causality detection in other domains, as well. Significance: The presented framework is generic enough to be utilized in any domain, healthcare services can gain massive benefits due to the voluminous and various nature of its data. This causal knowledge extraction framework can be used to summarize clinical text, create personas, discover medical knowledge, and provide evidence to clinical decision making.
The main goal of this paper is to develop a spell checker module for clinical text in Russian. The described approach combines string distance measure algorithms with technics of machine learning embedding methods. Our overall precision is 0.86, lexical precision - 0.975 and error precision is 0.74. We develop spell checker as a part of medical text mining tool regarding the problems of misspelling, negation, experiencer and temporality detection.
Developing predictive modeling in medicine requires additional features from unstructured clinical texts. In Russia, there are no instruments for natural language processing to cope with problems of medical records. This paper is devoted to a module of negation detection. The corpus-free machine learning method is based on gradient boosting classifier is used to detect whether a disease is denied, not mentioned or presented in the text. The detector classifies negations for five diseases and shows average F-score from 0.81 to 0.93. The benefits of negation detection have been demonstrated by p…
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…
Mining causality from text is a complex and crucial natural language understanding task corresponding to the human cognition. Existing studies at its solution can be grouped into two primary categories: feature engineering based and neural model based methods. In this paper, we find that the former has incomplete coverage and inherent errors but provide prior knowledge; while the latter leverages context information but causal inference of which is insufficiency. To handle the limitations, we propose a novel causality detection model named MCDN to explicitly model causal reasoning process, and…
Bakar Computational Health Sciences Institute, University of California, San Francisco（加州大学旧金山分校巴卡尔计算健康科学研究所）；Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University（乌得勒支大学医学中心尤利乌斯健康科学与初级保健中心）
Objective: Text mining of clinical notes embedded in electronic medical records is increasingly used to extract patient characteristics otherwise not or only partly available, to assess their association with relevant health outcomes. As manual data labeling needed to develop text mining models is resource intensive, we investigated whether off-the-shelf text mining models developed at external institutions, together with limited within-institution labeled data, could be used to reliably extract study variables to conduct association studies. Materials and Methods: We developed multiple text m…
Given a current news event, we tackle the problem of generating plausible predictions of future events it might cause. We present a new methodology for modeling and predicting such future news events using machine learning and data mining techniques. Our Pundit algorithm generalizes examples of causality pairs to infer a causality predictor. To obtain precisely labeled causality examples, we mine 150 years of news articles and apply semantic natural language modeling techniques to headlines containing certain predefined causality patterns. For generalization, the model uses a vast number of wo…
University of Bristol（布里斯托大学）；University of Sussex（萨塞克斯大学）
This research on data extraction methods applies recent advances in natural language processing to evidence synthesis based on medical texts. Texts of interest include abstracts of clinical trials in English and in multilingual contexts. The main focus is on information characterized via the Population, Intervention, Comparator, and Outcome (PICO) framework, but data extraction is not limited to these fields. Recent neural network architectures based on transformers show capacities for transfer learning and increased performance on downstream natural language processing tasks such as universal…
RDMA: Cost Effective Agent-Driven Rare Disease Mining from Electronic Health Records
Department of Computer Science, University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校计算机科学系）；Department of Pediatrics, University of Illinois College of Medicine Peoria（伊利诺伊大学皮奥里亚医学院儿科系）
National Center for Biotechnology Information（国家生物技术信息中心）；National Library of Medicine, National Institutes of Health（美国国立卫生研究院国家医学图书馆）
Multi-task learning (MTL) has achieved remarkable success in natural language processing applications. In this work, we study a multi-task learning model with multiple decoders on varieties of biomedical and clinical natural language processing tasks such as text similarity, relation extraction, named entity recognition, and text inference. Our empirical results demonstrate that the MTL fine-tuned models outperform state-of-the-art transformer models (e.g., BERT and its variants) by 2.0% and 1.3% in biomedical and clinical domains, respectively. Pairwise MTL further demonstrates more details a…
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…
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 …
Mining Social Determinants of Health for Heart Failure Patient 30-Day Readmission via Large Language Model
Department of Computer Science, Emory University（计算机科学系，埃默里大学）；Nell Hodgson Woodruff School of Nursing, Emory University（Nell Hodgson Woodruff护理学院，埃默里大学）
Quantitative Evidence Mining for Plausibility-Aware Biomedical AI: A Narrative Review and Conceptual Framework
Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)（弗劳恩霍夫算法与科学计算研究所（SCAI））；Kairntech SAS（Kairntech公司）；Bonn-Aachen International Center for Information Technology (b-it), University of Bonn（波恩大学波恩-亚琛国际信息技术中心（b-it））
Responsible Integration of AI in Cancer Genomics: Barriers, Risks, and Pathways to Trustworthy Clinical Translation
Robert Koch Institute（罗伯特·科赫研究所）；European Commission（欧洲委员会）；Deree-The American College of Greece（希腊 Deree 美国学院）；Åbo Akademi University（奥布学术大学）；Arcada University of Applied Sciences（阿卡达应用科学大学）；University of Münster（明斯特大学）
Exploration of Attention Mechanism-Enhanced Deep Learning Models in the Mining of Medical Textual Data
University of California San Diego（加州大学圣迭戈分校）；Columbia University（哥伦比亚大学）；Brandeis University（布兰迪斯大学）；New York University（纽约大学）；North Carolina State University（北卡罗来纳州立大学）
A foundation model for human-AI collaboration in medical literature mining
University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；National Library of Medicine, National Institutes of Health（美国国立卫生研究院国家医学图书馆）；National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health（美国国立卫生研究院国家糖尿病、消化和肾脏疾病研究所）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；National Eye Institute, National Institutes of Health（美国国立卫生研究院国家眼科研究所）；Northwestern University Feinberg School of Medicine（西北大学费恩伯格医学院）；Chungbuk National University Hospital（忠北国立大学医院）；Chungbuk National University College of Medicine（忠北国立大学医学院）；University of Pittsburgh Medical Center（匹兹堡大学医学中心）；Weill Cornell Medicine（威尔康奈尔医学院）；UT Southwestern Medical Center（德克萨斯大学西南医学中心）；University of Washington（华盛顿大学）；NYU Langone Health（纽约大学朗格尼健康中心）；OSF HealthCare Illinois Neurological Institute（OSF医疗保健伊利诺伊神经研究所）
Emory University（埃默里大学）；Mayo Clinic（妙佑医疗国际）；Indian Institute of Technology (IIT)（印度理工学院）；Arizona State University（亚利桑那州立大学）
Pathology text mining is a challenging task given the reporting variability and constant new findings in cancer sub-type definitions. However, successful text mining of a large pathology database can play a critical role to advance 'big data' cancer research like similarity-based treatment selection, case identification, prognostication, surveillance, clinical trial screening, risk stratification, and many others. While there is a growing interest in developing language models for more specific clinical domains, no pathology-specific language space exist to support the rapid data-mining develo…
Semantic textual similarity (STS) in the clinical domain helps improve diagnostic efficiency and produce concise texts for downstream data mining tasks. However, given the high degree of domain knowledge involved in clinic text, it remains challenging for general language models to infer implicit medical relationships behind clinical sentences and output similarities correctly. In this paper, we present a graph-augmented cyclic learning framework for similarity estimation in the clinical domain. The framework can be conveniently implemented on a state-of-art backbone language model, and improv…
Advancing Chinese biomedical text mining with community challenges
Sichuan University（四川大学）；West China Hospital（华西医院）；Tongji University（同济大学）；Shanghai Business School（上海商学院）；Takeda Co. Ltd.（武田制药有限公司）；Harbin Institute of Technology（哈尔滨工业大学）
University of Manchester（曼彻斯特大学）；AstraZeneca plc（阿斯利康公司）
The scientific literature is growing exponentially, and professionals are no more able to cope with the current amount of publications. Text mining provided in the past methods to retrieve and extract information from text; however, most of these approaches ignored tables and figures. The research done in mining table data still does not have an integrated approach for mining that would consider all complexities and challenges of a table. Our research is examining the methods for extracting numerical (number of patients, age, gender distribution) and textual (adverse reactions) information fro…
National University of Singapore（新加坡国立大学）；Koc University（科奇大学）；Rijksuniversiteit Groningen（格罗宁根大学）；Radboud University（拉德堡德大学）；National Institute of Japanese Literature（日本文学研究所）；Birmingham City University（伯明翰城市大学）；Instituto Politécnico Nacional（国立理工学院）；Mersin University（梅尔辛大学）；University of East Anglia（东英吉利大学）；ETH Zürich（苏黎世联邦理工学院）
Despite the importance of understanding causality, corpora addressing causal relations are limited. There is a discrepancy between existing annotation guidelines of event causality and conventional causality corpora that focus more on linguistics. Many guidelines restrict themselves to include only explicit relations or clause-based arguments. Therefore, we propose an annotation schema for event causality that addresses these concerns. We annotated 3,559 event sentences from protest event news with labels on whether it contains causal relations or not. Our corpus is known as the Causal News Co…
Causality knowledge is vital to building robust AI systems. Deep learning models often perform poorly on tasks that require causal reasoning, which is often derived using some form of commonsense knowledge not immediately available in the input but implicitly inferred by humans. Prior work has unraveled spurious observational biases that models fall prey to in the absence of causality. While language representation models preserve contextual knowledge within learned embeddings, they do not factor in causal relationships during training. By blending causal relationships with the input features …
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…
Causaly（Causaly公司）；Athens University of Economics and Business（雅典经济与商业大学）
We consider the task of detecting sentences that express causality, as a step towards mining causal relations from texts. To bypass the scarcity of causal instances in relation extraction datasets, we exploit transfer learning, namely ELMO and BERT, using a bidirectional GRU with self-attention (BIGRUATT) as a baseline. We experiment with both generic public relation extraction datasets and a new biomedical causal sentence detection dataset, a subset of which we make publicly available. We find that transfer learning helps only in very small datasets. With larger datasets, BIGRUATT reaches a p…
Diachronic text mining has frequently been applied to long-term linguistic surveys of word meaning and usage shifts over time. In this paper we apply short-term diachronic text mining to a rapidly growing corpus of scientific publications on COVID-19 captured in the CORD-19 dataset in order to identify co-occurrences and analyze the behavior of potential candidate treatments. We used a data set associated with a COVID-19 drug re-purposing study from Oak Ridge National Laboratory. This study identified existing candidate coronavirus treatments, including drugs and approved compounds, which had …
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, …
