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The Coronavirus disease 2019 (COVID-19) global pandemic has transformed almost every facet of human society throughout the world. Against an emerging, highly transmissible disease, governments worldwide have implemented non-pharmaceutical interventions (NPIs) to slow the spread of the virus. Examples of such interventions include community actions, such as school closures or restrictions on mass gatherings, individual actions including mask wearing and self-quarantine, and environmental actions such as cleaning public facilities. We present the Worldwide Non-pharmaceutical Interventions Tracker for COVID-19 (WNTRAC), a comprehensive dataset consisting of over 6,000 NPIs implemented worldwide since the start of the pandemic. WNTRAC covers NPIs implemented across 261 countries and territories, and classifies NPIs into a taxonomy of 16 NPI types. NPIs are automatically extracted daily from Wikipedia articles using natural language processing techniques and then manually validated to ensure accuracy and veracity. We hope that the dataset will prove valuable for policymakers, public health leaders, and researchers in modeling and analysis efforts to control the spread of COVID-19. Measurement(s) Preventive Intervention • Public Health Technology Type(s) natural language processing objective • Artificial Intelligence Sample Characteristic - Environment anthropogenic environment Sample Characteristic - Location Global Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.13999484

An adverse drug event (ADE) is commonly defined as \"an injury resulting from medical intervention related to a drug\". Providing information related to ADEs and alerting caregivers at the point-of-care can reduce the risk of prescription and diagnosis errors, and improve health outcomes. ADEs captured in Electronic Health Records (EHR) structured data, as either coded problems or allergies, are often incomplete leading to underreporting. It is therefore important to develop capabilities to process unstructured EHR data in the form of clinical notes, which contain richer documentation of a patient's adverse drug events. Several natural language processing (NLP) systems were previously proposed to automatically extract information related to ADEs. However, the results from these systems showed that significant improvement is still required for automatic extraction of ADEs from clinical notes. The objective of this study is to improve automatic extraction of ADEs and related information such as drugs and their reason for administration from patient clinical notes. This research was conducted using discharge summaries from the MIMIC-III database obtained through the 2018 National NLP Clinical Challenges (n2c2) annotated with Drugs, drug attributes (Strength, Form, Frequency, Route, Dosage, Duration), Adverse Drug Events, Reasons, and relations between drugs and other entities. We developed a deep learning-based system for extracting these drug-centric concepts and relations simultaneously using a joint method enhanced with contextualized embeddings, a position-attention mechanism, and knowledge representations. The joint method generated different sentence representations with respect to each drug, which were then used to extract related concepts and relations simultaneously. Contextualized representations trained on the MIMIC-III database were used to capture context-sensitive meanings of words. The position-attention mechanism amplified benefits of the joint method by generating sentence representations that capture long-distance relations. Knowledge representations were obtained from graph embeddings created using the FAERS database to improve relation extraction, especially when contextual clues are insufficient. Our system achieved new state-of-the-art results on the n2c2 dataset, with significant improvements in recognizing the crucial Drug-->Reason (F1 0.650 vs 0.579) and Drug-->ADE (0.490 vs 0.476) relations. We present a system for extracting drug-centric concepts and relations that outperformed current state-of-the-art results. We show that contextualized embeddings, position-attention mechanism and knowledge graph embeddings effectively improve deep learning-based concept and relation extraction. This study demonstrates the further potential for deep learning-based methods to help extract real world evidence from unstructured patient data for drug safety surveillance.

Although electronic health records (EHRs) have been widely adopted in health care, effective use of EHR data is often limited because of redundant information in clinical notes introduced by the use of templates and copy-paste during note generation. Thus, it is imperative to develop solutions that can condense information while retaining its value. A step in this direction is measuring the semantic similarity between clinical text snippets. To address this problem, we participated in the 2019 National NLP Clinical Challenges (n2c2)/Open Health Natural Language Processing Consortium (OHNLP) clinical semantic textual similarity (ClinicalSTS) shared task. This study aims to improve the performance and robustness of semantic textual similarity in the clinical domain by leveraging manually labeled data from related tasks and contextualized embeddings from pretrained transformer-based language models. The ClinicalSTS data set consists of 1642 pairs of deidentified clinical text snippets annotated in a continuous scale of 0-5, indicating degrees of semantic similarity. We developed an iterative intermediate training approach using multi-task learning (IIT-MTL), a multi-task training approach that employs iterative data set selection. We applied this process to bidirectional encoder representations from transformers on clinical text mining (ClinicalBERT), a pretrained domain-specific transformer-based language model, and fine-tuned the resulting model on the target ClinicalSTS task. We incrementally ensembled the output from applying IIT-MTL on ClinicalBERT with the output of other language models (bidirectional encoder representations from transformers for biomedical text mining [BioBERT], multi-task deep neural networks [MT-DNN], and robustly optimized BERT approach [RoBERTa]) and handcrafted features using regression-based learning algorithms. On the basis of these experiments, we adopted the top-performing configurations as our official submissions. Our system ranked first out of 87 submitted systems in the 2019 n2c2/OHNLP ClinicalSTS challenge, achieving state-of-the-art results with a Pearson correlation coefficient of 0.9010. This winning system was an ensembled model leveraging the output of IIT-MTL on ClinicalBERT with BioBERT, MT-DNN, and handcrafted medication features. This study demonstrates that IIT-MTL is an effective way to leverage annotated data from related tasks to improve performance on a target task with a limited data set. This contribution opens new avenues of exploration for optimized data set selection to generate more robust and universal contextual representations of text in the clinical domain.

The Coronavirus disease 2019 (COVID-19) global pandemic has transformed almost every facet of human society throughout the world. Against an emerging, highly transmissible disease with no definitive treatment or vaccine, governments worldwide have implemented non-pharmaceutical intervention (NPI) to slow the spread of the virus. Examples of such interventions include community actions (e.g. school closures, restrictions on mass gatherings), individual actions (e.g. mask wearing, self-quarantine), and environmental actions (e.g. public facility cleaning). We present the Worldwide Non-pharmaceutical Interventions Tracker for COVID-19 (WNTRAC), a comprehensive dataset consisting of over 6,000 NPIs implemented worldwide since the start of the pandemic. WNTRAC covers NPIs implemented across 261 countries and territories, and classifies NPI measures into a taxonomy of sixteen NPI types. NPI measures are automatically extracted daily from Wikipedia articles using natural language processing techniques and manually validated to ensure accuracy and veracity. We hope that the dataset is valuable for policymakers, public health leaders, and researchers in modeling and analysis efforts for controlling the spread of COVID-19.

The evolution of AI is advancing rapidly, creating both challenges and opportunities for industry-community collaboration. In this work, we present a novel methodology aiming to facilitate this collaboration through crowdsourcing of AI models. Concretely, we have implemented a system and a process that any organization can easily adopt to host AI competitions. The system allows them to automatically harvest and evaluate the submitted models against in-house proprietary data and also to incorporate them as reusable services in a product.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task multi-align foundation model that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

In this work we introduce Disease Progression Modeling workbench 360 (DPM360) opensource clinical informatics framework for collaborative research and delivery of healthcare AI. DPM360, when fully developed, will manage the entire modeling life cycle, from data analysis (e.g., cohort identification) to machine learning algorithm development and prototyping. DPM360 augments the advantages of data model standardization and tooling (OMOP-CDM, Athena, ATLAS) provided by the widely-adopted OHDSI initiative with a powerful machine learning training framework, and a mechanism for rapid prototyping through automatic deployment of models as containerized services to a cloud environment.

Many institutions within the healthcare ecosystem are making significant investments in AI technologies to optimize their business operations at lower cost with improved patient outcomes. Despite the hype with AI, the full realization of this potential is seriously hindered by several systemic problems, including data privacy, security, bias, fairness, and explainability. In this paper, we propose a novel canonical architecture for the development of AI models in healthcare that addresses these challenges. This system enables the creation and management of AI predictive models throughout all the phases of their life cycle, including data ingestion, model building, and model promotion in production environments. This paper describes this architecture in detail, along with a qualitative evaluation of our experience of using it on real world problems.