Medical Image Data and Datasets in the Era of Machine Learning-Whitepaper from the 2016 C-MIMI Meeting Dataset Session.

At the first annual Conference on Machine Intelligence in Medical Imaging (C-MIMI), held in September 2016, a conference session on medical image data and datasets for machine learning identified multiple issues. The common theme from attendees was that everyone participating in medical image evaluation with machine learning is data starved. There is an urgent need to find better ways to collect, annotate, and reuse medical imaging data. Unique domain issues with medical image datasets require further study, development, and dissemination of best practices and standards, and a coordinated effort among medical imaging domain experts, medical imaging informaticists, government and industry data scientists, and interested commercial, academic, and government entities. High-level attributes of reusable medical image datasets suitable to train, test, validate, verify, and regulate ML products should be better described. NIH and other government agencies should promote and, where applicable, enforce, access to medical image datasets. We should improve communication among medical imaging domain experts, medical imaging informaticists, academic clinical and basic science researchers, government and industry data scientists, and interested commercial entities

From Raw Data to FAIR Data: The FAIRification Workflow for Health Research

BackgroundFAIR (findability, accessibility, interoperability, and reusability) guidingprinciples seek the reuse of data and other digital research input, output, and objects(algorithms, tools, and workflows that led to that data) making themfindable, accessible,interoperable, and reusable. GO FAIR - a bottom-up, stakeholder driven and self-governedinitiative-defined a seven-step FAIRificationprocessfocusingondata,butalsoindicatingtherequired work for metadata. This FAIRification process aims at addressing the translation ofraw datasets into FAIR datasets in a general way, without considering specific requirementsand challenges that may arise when dealing with some particular types of data.This work was performed in the scope of FAIR4Healthproject. FAIR4Health has received funding from the European Union’s Horizon 2020 research and innovationprogramme under grant agreement number 824666

SNOMED CT standard ontology based on the ontology for general medical science

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way that will support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications

Is Normalization Indispensable for Multi-domain Federated Learning?

Federated learning (FL) enhances data privacy with collaborative in-situ training on decentralized clients. Nevertheless, FL encounters challenges due to non-independent and identically distributed (non-i.i.d) data, leading to potential performance degradation and hindered convergence. While prior studies predominantly addressed the issue of skewed label distribution, our research addresses a crucial yet frequently overlooked problem known as multi-domain FL. In this scenario, clients' data originate from diverse domains with distinct feature distributions, as opposed to label distributions. To address the multi-domain problem in FL, we propose a novel method called Federated learning Without normalizations (FedWon). FedWon draws inspiration from the observation that batch normalization (BN) faces challenges in effectively modeling the statistics of multiple domains, while alternative normalization techniques possess their own limitations. In order to address these issues, FedWon eliminates all normalizations in FL and reparameterizes convolution layers with scaled weight standardization. Through comprehensive experimentation on four datasets and four models, our results demonstrate that FedWon surpasses both FedAvg and the current state-of-the-art method (FedBN) across all experimental setups, achieving notable improvements of over 10% in certain domains. Furthermore, FedWon is versatile for both cross-silo and cross-device FL, exhibiting strong performance even with a batch size as small as 1, thereby catering to resource-constrained devices. Additionally, FedWon effectively tackles the challenge of skewed label distribution

A Learning Health System for Radiation Oncology

The proposed research aims to address the challenges faced by clinical data science researchers in radiation oncology accessing, integrating, and analyzing heterogeneous data from various sources. The research presents a scalable intelligent infrastructure, called the Health Information Gateway and Exchange (HINGE), which captures and structures data from multiple sources into a knowledge base with semantically interlinked entities. This infrastructure enables researchers to mine novel associations and gather relevant knowledge for personalized clinical outcomes. The dissertation discusses the design framework and implementation of HINGE, which abstracts structured data from treatment planning systems, treatment management systems, and electronic health records. It utilizes disease-specific smart templates for capturing clinical information in a discrete manner. HINGE performs data extraction, aggregation, and quality and outcome assessment functions automatically, connecting seamlessly with local IT/medical infrastructure. Furthermore, the research presents a knowledge graph-based approach to map radiotherapy data to an ontology-based data repository using FAIR (Findable, Accessible, Interoperable, Reusable) concepts. This approach ensures that the data is easily discoverable and accessible for clinical decision support systems. The dissertation explores the ETL (Extract, Transform, Load) process, data model frameworks, ontologies, and provides a real-world clinical use case for this data mapping. To improve the efficiency of retrieving information from large clinical datasets, a search engine based on ontology-based keyword searching and synonym-based term matching tool was developed. The hierarchical nature of ontologies is leveraged to retrieve patient records based on parent and children classes. Additionally, patient similarity analysis is conducted using vector embedding models (Word2Vec, Doc2Vec, GloVe, and FastText) to identify similar patients based on text corpus creation methods. Results from the analysis using these models are presented. The implementation of a learning health system for predicting radiation pneumonitis following stereotactic body radiotherapy is also discussed. 3D convolutional neural networks (CNNs) are utilized with radiographic and dosimetric datasets to predict the likelihood of radiation pneumonitis. DenseNet-121 and ResNet-50 models are employed for this study, along with integrated gradient techniques to identify salient regions within the input 3D image dataset. The predictive performance of the 3D CNN models is evaluated based on clinical outcomes. Overall, the proposed Learning Health System provides a comprehensive solution for capturing, integrating, and analyzing heterogeneous data in a knowledge base. It offers researchers the ability to extract valuable insights and associations from diverse sources, ultimately leading to improved clinical outcomes. This work can serve as a model for implementing LHS in other medical specialties, advancing personalized and data-driven medicine

Analyzing fluctuation of topics and public sentiment through social media data

Over the past decade years, Internet users were expending rapidly in the world. They form various online social networks through such Internet platforms as Twitter, Facebook and Instagram. These platforms provide a fast way that helps their users receive and disseminate information and express personal opinions in virtual space. When dealing with massive and chaotic social media data, how to accurately determine what events or concepts users are discussing is an interesting and important problem. This dissertation work mainly consists of two parts. First, this research pays attention to mining the hidden topics and user interest trend by analyzing real-world social media activities. Topic modeling and sentiment analysis methods are proposed to classify the social media posts into different sentiment classes and then discover the trend of sentiment based on different topics over time. The presented case study focuses on COVID-19 pandemic that started in 2019. A large amount of Twitter data is collected and used to discover the vaccine-related topics during the pre- and post-vaccine emergency use period. By using the proposed framework, 11 vaccine-related trend topics are discovered. Ultimately the discovered topics can be used to improve the readability of confusing messages about vaccines on social media and provide effective results to support policymakers in making their policy their informed decisions about public health. Second, using conventional topic models cannot deal with the sparsity problem of short text. A novel topic model, named Topic Noise based-Biterm Topic Model with FastText embeddings (TN-BTMF), is proposed to deal with this problem. Word co-occurrence patterns (i.e. biterms) are dirctly generated in BTM. A scoring method based on word co-occurrence and semantic similarity is proposed to detect noise biterms. In th