A Comparison between a Relational Database and a Graph Database in the context of a Personalized Cancer Treatment Application

This paper presents a performance comparison between a relational database (implemented in MySQL) and a graph database (implemented in Neo4j). Unlike traditional benchmarks, this comparison is made in the context of a real health application which was developed in Costa Rica. The comparison encompassed twelve queries and three data size configurations.The results of the comparison indicate that MySQL performs better than Neo4j in most cases, but has a poor performance when data size is large and the queries have multiple join operations.Universidad de Costa Rica/[]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ingeniería::Centro de Investigaciones en Tecnologías de Información y Comunicación (CITIC)UCR::Vicerrectoría de Docencia::Ingeniería::Facultad de Ingeniería::Escuela de Ciencias de la Computación e Informátic

Portinari: A Data Exploration Tool to Personalize Cervical Cancer Screening

Socio-technical systems play an important role in public health screening programs to prevent cancer. Cervical cancer incidence has significantly decreased in countries that developed systems for organized screening engaging medical practitioners, laboratories and patients. The system automatically identifies individuals at risk of developing the disease and invites them for a screening exam or a follow-up exam conducted by medical professionals. A triage algorithm in the system aims to reduce unnecessary screening exams for individuals at low-risk while detecting and treating individuals at high-risk. Despite the general success of screening, the triage algorithm is a one-size-fits all approach that is not personalized to a patient. This can easily be observed in historical data from screening exams. Often patients rely on personal factors to determine that they are either at high risk or not at risk at all and take action at their own discretion. Can exploring patient trajectories help hypothesize personal factors leading to their decisions? We present Portinari, a data exploration tool to query and visualize future trajectories of patients who have undergone a specific sequence of screening exams. The web-based tool contains (a) a visual query interface (b) a backend graph database of events in patients' lives (c) trajectory visualization using sankey diagrams. We use Portinari to explore diverse trajectories of patients following the Norwegian triage algorithm. The trajectories demonstrated variable degrees of adherence to the triage algorithm and allowed epidemiologists to hypothesize about the possible causes.Comment: Conference paper published at ICSE 2017 Buenos Aires, at the Software Engineering in Society Track. 10 pages, 5 figure

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

Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

Graph4Med: a web application and a graph database for visualizing and analyzing medical databases

Background: Medical databases normally contain large amounts of data in a variety of forms. Although they grant significant insights into diagnosis and treatment, implementing data exploration into current medical databases is challenging since these are often based on a relational schema and cannot be used to easily extract information for cohort analysis and visualization. As a consequence, valuable information regarding cohort distribution or patient similarity may be missed. With the rapid advancement of biomedical technologies, new forms of data from methods such as Next Generation Sequencing (NGS) or chromosome microarray (array CGH) are constantly being generated; hence it can be expected that the amount and complexity of medical data will rise and bring relational database systems to a limit. Description: We present Graph4Med, a web application that relies on a graph database obtained by transforming a relational database. Graph4Med provides a straightforward visualization and analysis of a selected patient cohort. Our use case is a database of pediatric Acute Lymphoblastic Leukemia (ALL). Along routine patients’ health records it also contains results of latest technologies such as NGS data. We developed a suitable graph data schema to convert the relational data into a graph data structure and store it in Neo4j. We used NeoDash to build a dashboard for querying and displaying patients’ cohort analysis. This way our tool (1) quickly displays the overview of patients’ cohort information such as distributions of gender, age, mutations (fusions), diagnosis; (2) provides mutation (fusion) based similarity search and display in a maneuverable graph; (3) generates an interactive graph of any selected patient and facilitates the identification of interesting patterns among patients. Conclusion: We demonstrate the feasibility and advantages of a graph database for storing and querying medical databases. Our dashboard allows a fast and interactive analysis and visualization of complex medical data. It is especially useful for patients similarity search based on mutations (fusions), of which vast amounts of data have been generated by NGS in recent years. It can discover relationships and patterns in patients cohorts that are normally hard to grasp. Expanding Graph4Med to more medical databases will bring novel insights into diagnostic and research

Model-guided therapy for hepatocellular carcinoma: A role for information technology in predictive, preventive and personalized medicine

Predictive, preventive and personalized medicine (PPPM) may have the potential to eventually improve the nature of health care delivery. However, the tools required for a practical and comprehensive form of PPPM that is capable of handling the vast amounts of medical information that is currently available are currently lacking. This article reviews a rationale and method for combining and integrating diagnostic and therapeutic management with information technology (IT), in a manner that supports patients through their continuum of care. It is imperative that any program devised to explore and develop personalized health care delivery must be firmly rooted in clinically confirmed and accepted principles and technologies. Therefore, a use case, relating to hepatocellular carcinoma (HCC), was developed. The approach to the management of medical information we have taken is based on model theory and seeks to implement a form of model-guided therapy (MGT) that can be used as a decision support system in the treatment of patients with HCC. The IT structures to be utilized in MGT include a therapy imaging and model management system (TIMMS) and a digital patient model (DPM). The system that we propose will utilize patient modeling techniques to generate valid DPMs (which factor in age, physiologic condition, disease and co-morbidities, genetics, biomarkers and responses to previous treatments). We may, then, be able to develop a statistically valid methodology, on an individual basis, to predict certain diseases or conditions, to predict certain treatment outcomes, to prevent certain diseases or complications and to develop treatment regimens that are personalized for that particular patient. An IT system for predictive, preventive and personalized medicine (ITS-PM) for HCC is presented to provide a comprehensive system to provide unified access to general medical and patient-specific information for medical researchers and health care providers from different disciplines including hepatologists, gastroenterologists, medical and surgical oncologists, liver transplant teams, interventional radiologists and radiation oncologists. The article concludes with a review providing an outlook and recommendations for the application of MGT to enhance the medical management of HCC through PPPM

A Comparative Analysis of Graph Vs Relational Database For Instructional Module Development System

abstract: In today's data-driven world, every datum is connected to a large amount of data. Relational databases have been proving itself a pioneer in the field of data storage and manipulation since 1970s. But more recently they have been challenged by NoSQL graph databases in handling data models which have an inherent graphical representation. Graph databases with the ability to store physical relationships between two nodes and native graph processing technique have been doing exceptionally well in graph data storage and management for applications like recommendation engines, biological modeling, network modeling, social media applications, etc. Instructional Module Development System (IMODS) is a web-based software system that guides STEM instructors through the complex task of curriculum design, ensures tight alignment between various components of a course (i.e., learning objectives, content, assessments), and provides relevant information about research-based pedagogical and assessment strategies. The data model of IMODS is highly connected and has an inherent graphical representation between all its entities with numerous relationships between them. This thesis focuses on developing an algorithm to determine completeness of course design developed using IMODS. As part of this research objective, the study also analyzes the data model for best fit database to run these algorithms. As part of this thesis, two separate applications abstracting the data model of IMODS have been developed - one with Neo4j (graph database) and another with PostgreSQL (relational database). The research objectives of the thesis are as follows: (i) evaluate the performance of Neo4j and PostgreSQL in handling complex queries that will be fired throughout the life cycle of the course design process; (ii) devise an algorithm to determine the completeness of a course design developed using IMODS. This thesis presents the process of creating data model for PostgreSQL and converting it into a graph data model to be abstracted by Neo4j, creating SQL and CYPHER scripts for undertaking experiments on both platforms, testing and elaborate analysis of the results and evaluation of the databases in the context of IMODS.Dissertation/ThesisMasters Thesis Computer Science 201