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

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch\u27s APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch\u27s data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch\u27s analytic tools by developing a customized plugin for OpenAI\u27s ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app

A Cloud Computing Capability Model for Large-Scale Semantic Annotation

Semantic technologies are designed to facilitate context-awareness for web content, enabling machines to understand and process them. However, this has been faced with several challenges, such as disparate nature of existing solutions and lack of scalability in proportion to web scale. With a holistic perspective to web content semantic annotation, this paper focuses on leveraging cloud computing for these challenges. To achieve this, a set of requirements towards holistic semantic annotation on the web is defined and mapped with cloud computing mechanisms to facilitate them. Technical specification for the requirements is critically reviewed and examined against each of the cloud computing mechanisms, in relation to their technical functionalities. Hence, a mapping is established if the cloud computing mechanism's functionalities proffer a solution for implementation of a requirement's technical specification. The result is a cloud computing capability model for holistic semantic annotation which presents an approach towards delivering large scale semantic annotation on the web via a cloud platform

Knowledge extraction from unstructured data and classification through distributed ontologies

The World Wide Web has changed the way humans use and share any kind of information. The Web removed several access barriers to the information published and has became an enormous space where users can easily navigate through heterogeneous resources (such as linked documents) and can easily edit, modify, or produce them. Documents implicitly enclose information and relationships among them which become only accessible to human beings. Indeed, the Web of documents evolved towards a space of data silos, linked each other only through untyped references (such as hypertext references) where only humans were able to understand. A growing desire to programmatically access to pieces of data implicitly enclosed in documents has characterized the last efforts of the Web research community. Direct access means structured data, thus enabling computing machinery to easily exploit the linking of different data sources. It has became crucial for the Web community to provide a technology stack for easing data integration at large scale, first structuring the data using standard ontologies and afterwards linking them to external data. Ontologies became the best practices to define axioms and relationships among classes and the Resource Description Framework (RDF) became the basic data model chosen to represent the ontology instances (i.e. an instance is a value of an axiom, class or attribute). Data becomes the new oil, in particular, extracting information from semi-structured textual documents on the Web is key to realize the Linked Data vision. In the literature these problems have been addressed with several proposals and standards, that mainly focus on technologies to access the data and on formats to represent the semantics of the data and their relationships. With the increasing of the volume of interconnected and serialized RDF data, RDF repositories may suffer from data overloading and may become a single point of failure for the overall Linked Data vision. One of the goals of this dissertation is to propose a thorough approach to manage the large scale RDF repositories, and to distribute them in a redundant and reliable peer-to-peer RDF architecture. The architecture consists of a logic to distribute and mine the knowledge and of a set of physical peer nodes organized in a ring topology based on a Distributed Hash Table (DHT). Each node shares the same logic and provides an entry point that enables clients to query the knowledge base using atomic, disjunctive and conjunctive SPARQL queries. The consistency of the results is increased using data redundancy algorithm that replicates each RDF triple in multiple nodes so that, in the case of peer failure, other peers can retrieve the data needed to resolve the queries. Additionally, a distributed load balancing algorithm is used to maintain a uniform distribution of the data among the participating peers by dynamically changing the key space assigned to each node in the DHT. Recently, the process of data structuring has gained more and more attention when applied to the large volume of text information spread on the Web, such as legacy data, news papers, scientific papers or (micro-)blog posts. This process mainly consists in three steps: \emph{i)} the extraction from the text of atomic pieces of information, called named entities; \emph{ii)} the classification of these pieces of information through ontologies; \emph{iii)} the disambigation of them through Uniform Resource Identifiers (URIs) identifying real world objects. As a step towards interconnecting the web to real world objects via named entities, different techniques have been proposed. The second objective of this work is to propose a comparison of these approaches in order to highlight strengths and weaknesses in different scenarios such as scientific and news papers, or user generated contents. We created the Named Entity Recognition and Disambiguation (NERD) web framework, publicly accessible on the Web (through REST API and web User Interface), which unifies several named entity extraction technologies. Moreover, we proposed the NERD ontology, a reference ontology for comparing the results of these technologies. Recently, the NERD ontology has been included in the NIF (Natural language processing Interchange Format) specification, part of the Creating Knowledge out of Interlinked Data (LOD2) project. Summarizing, this dissertation defines a framework for the extraction of knowledge from unstructured data and its classification via distributed ontologies. A detailed study of the Semantic Web and knowledge extraction fields is proposed to define the issues taken under investigation in this work. Then, it proposes an architecture to tackle the single point of failure issue introduced by the RDF repositories spread within the Web. Although the use of ontologies enables a Web where data is structured and comprehensible by computing machinery, human users may take advantage of it especially for the annotation task. Hence, this work describes an annotation tool for web editing, audio and video annotation in a web front end User Interface powered on the top of a distributed ontology. Furthermore, this dissertation details a thorough comparison of the state of the art of named entity technologies. The NERD framework is presented as technology to encompass existing solutions in the named entity extraction field and the NERD ontology is presented as reference ontology in the field. Finally, this work highlights three use cases with the purpose to reduce the amount of data silos spread within the Web: a Linked Data approach to augment the automatic classification task in a Systematic Literature Review, an application to lift educational data stored in Sharable Content Object Reference Model (SCORM) data silos to the Web of data and a scientific conference venue enhancer plug on the top of several data live collectors. Significant research efforts have been devoted to combine the efficiency of a reliable data structure and the importance of data extraction techniques. This dissertation opens different research doors which mainly join two different research communities: the Semantic Web and the Natural Language Processing community. The Web provides a considerable amount of data where NLP techniques may shed the light within it. The use of the URI as a unique identifier may provide one milestone for the materialization of entities lifted from a raw text to real world object

CHORUS Deliverable 2.2: Second report - identification of multi-disciplinary key issues for gap analysis toward EU multimedia search engines roadmap

After addressing the state-of-the-art during the first year of Chorus and establishing the existing landscape in multimedia search engines, we have identified and analyzed gaps within European research effort during our second year. In this period we focused on three directions, notably technological issues, user-centred issues and use-cases and socio- economic and legal aspects. These were assessed by two central studies: firstly, a concerted vision of functional breakdown of generic multimedia search engine, and secondly, a representative use-cases descriptions with the related discussion on requirement for technological challenges. Both studies have been carried out in cooperation and consultation with the community at large through EC concertation meetings (multimedia search engines cluster), several meetings with our Think-Tank, presentations in international conferences, and surveys addressed to EU projects coordinators as well as National initiatives coordinators. Based on the obtained feedback we identified two types of gaps, namely core technological gaps that involve research challenges, and “enablers”, which are not necessarily technical research challenges, but have impact on innovation progress. New socio-economic trends are presented as well as emerging legal challenges

Semantic multimedia analysis using knowledge and context

PhDThe difficulty of semantic multimedia analysis can be attributed to the extended diversity in form and appearance exhibited by the majority of semantic concepts and the difficulty to express them using a finite number of patterns. In meeting this challenge there has been a scientific debate on whether the problem should be addressed from the perspective of using overwhelming amounts of training data to capture all possible instantiations of a concept, or from the perspective of using explicit knowledge about the concepts’ relations to infer their presence. In this thesis we address three problems of pattern recognition and propose solutions that combine the knowledge extracted implicitly from training data with the knowledge provided explicitly in structured form. First, we propose a BNs modeling approach that defines a conceptual space where both domain related evi- dence and evidence derived from content analysis can be jointly considered to support or disprove a hypothesis. The use of this space leads to sig- nificant gains in performance compared to analysis methods that can not handle combined knowledge. Then, we present an unsupervised method that exploits the collective nature of social media to automatically obtain large amounts of annotated image regions. By proving that the quality of the obtained samples can be almost as good as manually annotated images when working with large datasets, we significantly contribute towards scal- able object detection. Finally, we introduce a method that treats images, visual features and tags as the three observable variables of an aspect model and extracts a set of latent topics that incorporates the semantics of both visual and tag information space. By showing that the cross-modal depen- dencies of tagged images can be exploited to increase the semantic capacity of the resulting space, we advocate the use of all existing information facets in the semantic analysis of social media

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues