Traditional biomedical version of embeddings obtained from pre-trained language models have recently shown state-of-the-art results for relation extraction (RE) tasks in the medical domain. In this paper, we explore how to incorporate domain knowledge, available in the form of molecular structure of drugs, for predicting Drug-Drug Interaction from textual corpus. We propose a method, BERTChem-DDI, to efficiently combine drug embeddings obtained from the rich chemical structure of drugs along with off-the-shelf domain-specific BioBERT embedding-based RE architecture. Experiments conducted on the DDIExtraction 2013 corpus clearly indicate that this strategy improves other strong baselines architectures by 3.4\% macro F1-score.
Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language understanding tasks (NLU) in the biomedical domain. Relation Classification (RC) falls into one of the most critical tasks. In this paper, we explore how to incorporate domain knowledge of the biomedical entities (such as drug, disease, genes), obtained from Knowledge Graph (KG) Embeddings, for predicting Drug-Drug Interaction from textual corpus. We propose a new meth…
ColdDDI: Evaluating Knowledge Utilization in Cold-Start Drug-Drug Interaction Prediction
William & Mary（威廉与玛丽学院）；Baylor University（贝勒大学）；Southwest University（西南大学）；Hefei University of Technology（合肥工业大学）；Florida Atlantic University（佛罗里达大西洋大学）
City University of Hong Kong（香港城市大学）；Hong Kong Institute for Data Science, City University of Hong Kong（香港城市大学香港数据科学研究院）；Jilin University（吉林大学）
The rapid growth in literature accumulates diverse and yet comprehensive biomedical knowledge hidden to be mined such as drug interactions. However, it is difficult to extract the heterogeneous knowledge to retrieve or even discover the latest and novel knowledge in an efficient manner. To address such a problem, we propose EGFI for extracting and consolidating drug interactions from large-scale medical literature text data. Specifically, EGFI consists of two parts: classification and generation. In the classification part, EGFI encompasses the language model BioBERT which has been comprehensi…
Large language models management of medications: three performance analyses
University of Colorado School of Medicine（科罗拉多大学医学院）；University of Georgia（佐治亚大学）；University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences（科罗拉多大学斯卡格斯药学院）；Mayo Clinic（梅奥诊所）；University of Georgia College of Pharmacy（佐治亚大学药学院）；Cleveland Clinic（克利夫兰诊所）
Drug-drug interaction (DDI) is a vital information when physicians and pharmacists intend to co-administer two or more drugs. Thus, several DDI databases are constructed to avoid mistakenly combined use. In recent years, automatically extracting DDIs from biomedical text has drawn researchers' attention. However, the existing work utilize either complex feature engineering or NLP tools, both of which are insufficient for sentence comprehension. Inspired by the deep learning approaches in natural language processing, we propose a recur- rent neural network model with multiple attention layers f…
Learning to Describe for Predicting Zero-shot Drug-Drug Interactions
Harbin Institute of Technology, Shenzhen（哈尔滨工业大学（深圳））；Paradigm Inc.（第四范式公司）；Hong Kong University of Science and Technology (GZ)（香港科技大学（广州））；Peng Cheng Laboratory（鹏城实验室）
We propose a novel neural method to extract drug-drug interactions (DDIs) from texts using external drug molecular structure information. We encode textual drug pairs with convolutional neural networks and their molecular pairs with graph convolutional networks (GCNs), and then we concatenate the outputs of these two networks. In the experiments, we show that GCNs can predict DDIs from the molecular structures of drugs in high accuracy and the molecular information can enhance text-based DDI extraction by 2.39 percent points in the F-score on the DDIExtraction 2013 shared task data set.
University of Kentucky（肯塔基大学）；Lister Hill National Center for Biomedical Communications, National Library of Medicine（国家医学图书馆利斯特·希尔国家生物医学传播中心）
Preventable adverse drug reactions as a result of medical errors present a growing concern in modern medicine. As drug-drug interactions (DDIs) may cause adverse reactions, being able to extracting DDIs from drug labels into machine-readable form is an important effort in effectively deploying drug safety information. The DDI track of TAC 2018 introduces two large hand-annotated test sets for the task of extracting DDIs from structured product labels with linkage to standard terminologies. Herein, we describe our approach to tackling tasks one and two of the DDI track, which corresponds to nam…
Zhejiang University（浙江大学）；Hikvision（海康威视）；University of Southern California（南加州大学）
When patients need to take medicine, particularly taking more than one kind of drug simultaneously, they should be alarmed that there possibly exists drug-drug interaction. Interaction between drugs may have a negative impact on patients or even cause death. Generally, drugs that conflict with a specific drug (or label drug) are usually described in its drug label or package insert. Since more and more new drug products come into the market, it is difficult to collect such information by manual. We take part in the Drug-Drug Interaction (DDI) Extraction from Drug Labels challenge of Text Analy…
University of Kentucky（肯塔基大学）；National Library of Medicine（美国国家医学图书馆）
Preventable adverse events as a result of medical errors present a growing concern in the healthcare system. As drug-drug interactions (DDIs) may lead to preventable adverse events, being able to extract DDIs from drug labels into a machine-processable form is an important step toward effective dissemination of drug safety information. In this study, we tackle the problem of jointly extracting drugs and their interactions, including interaction outcome, from drug labels. Our deep learning approach entails composing various intermediate representations including sequence and graph based context…
Simultaneous administration of multiple drugs can have synergistic or antagonistic effects as one drug can affect activities of other drugs. Synergistic effects lead to improved therapeutic outcomes, whereas, antagonistic effects can be life-threatening, may lead to increased healthcare cost, or may even cause death. Thus identification of unknown drug-drug interaction (DDI) is an important concern for efficient and effective healthcare. Although multiple resources for DDI exist, they are often unable to keep pace with rich amount of information available in fast growing biomedical texts. Most…
Georgia Institute of Technology（佐治亚理工学院）；Harvard T.H. Chan School of Public Health（哈佛大学陈曾熙公共卫生学院）；IQVIA（艾昆纬）
Thanks to the increasing availability of drug-drug interactions (DDI) datasets and large biomedical knowledge graphs (KGs), accurate detection of adverse DDI using machine learning models becomes possible. However, it remains largely an open problem how to effectively utilize large and noisy biomedical KG for DDI detection. Due to its sheer size and amount of noise in KGs, it is often less beneficial to directly integrate KGs with other smaller but higher quality data (e.g., experimental data). Most of the existing approaches ignore KGs altogether. Some try to directly integrate KGs with other…
Dietary supplements are used by a large portion of the population, but information on their pharmacologic interactions is incomplete. To address this challenge, we present SUPP.AI, an application for browsing evidence of supplement-drug interactions (SDIs) extracted from the biomedical literature. We train a model to automatically extract supplement information and identify such interactions from the scientific literature. To address the lack of labeled data for SDI identification, we use labels of the closely related task of identifying drug-drug interactions (DDIs) for supervision. We fine-t…
MUDI: A Multimodal Biomedical Dataset for Understanding Pharmacodynamic Drug-Drug Interactions
VNU University of Engineering and Technology (VNU-UET)（越南工程技术大学）；Lausanne University Hospital (CHUV)（洛桑大学医院）；University of Lausanne (UNIL)（洛桑大学）；Hanoi Medical University（河内医学院）；National Geriatric Hospital, Hanoi（河内国立老年医院）
The Joint Entity-Relation Extraction Model Based on Span and Interactive Fusion Representation for Chinese Medical Texts with Complex Semantics
School of Computer and Artificial Intelligence, Zhengzhou University（郑州大学计算机与人工智能学院）；Cooperative Innovation Center of Internet Healthcare, Zhengzhou University（郑州大学互联网医疗协同创新中心）；Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College（中国医学科学院北京协和医学院国家心血管病中心阜外医院）；Department of Geriatrics, Beijing Friendship Hospital, Capital Medical University（首都医科大学附属北京友谊医院老年医学科）
Congestive Heart Failure, or CHF, is a serious medical condition that can result in fluid buildup in the body as a result of a weak heart. When the heart can't pump enough blood to efficiently deliver nutrients and oxygen to the body, kidney function may be impaired, resulting in fluid retention. CHF patients require a broad drug regimen to maintain the delicate system balance, particularly between their heart and kidneys. These drugs include ACE inhibitors and Beta Blockers to control blood pressure, anticoagulants to prevent blood clots, and diuretics to reduce fluid overload. Many of these …
The development of deep neural networks has improved representation learning in various domains, including textual, graph structural, and relational triple representations. This development opened the door to new relation extraction beyond the traditional text-oriented relation extraction. However, research on the effectiveness of considering multiple heterogeneous domain information simultaneously is still under exploration, and if a model can take an advantage of integrating heterogeneous information, it is expected to exhibit a significant contribution to many problems in the world. This th…
University of Technology Sydney（悉尼科技大学）；Capital Markets Cooperative Research Center（资本市场合作研究中心）
Background. Previous state-of-the-art systems on Drug Name Recognition (DNR) and Clinical Concept Extraction (CCE) have focused on a combination of text "feature engineering" and conventional machine learning algorithms such as conditional random fields and support vector machines. However, developing good features is inherently heavily time-consuming. Conversely, more modern machine learning approaches such as recurrent neural networks (RNNs) have proved capable of automatically learning effective features from either random assignments or automated word "embeddings". Objectives. (i) To creat…
