Composite Ontology-Based Medical Diagnosis Decision Support System Framework

Current medical decision support systems have evolved from the automation of medical decision routines to improving the quality of health care services. Knowledge-based systems, compared to conventional data-driven techniques, are promising to support medical decision making. However, knowledge acquisition is usually a bottleneck in the process of developing such systemsOne possibility for acquiring medical knowledge, particularly tacit knowledge, is to use data or cases in both syntactic and semantic ways. Case-based Reasoning (CBR) methodology provides a practical way of problem solving with recalled knowledge memory of solved cases. To reduce the difficulty of knowledge acquisition, this paper proposes a design of the system framework that utilizes the simplified medical knowledge:disease-symptom ontology for prediagnosis, given patients symptoms and signs as input. In the first stage, simple pattern matching is used to gather candidate diseases in diagnosis. Following that, case-based reasoning is used to refine diagnostic decision. The case base is structured with ontological knowledge model. The case retrieval process is based on semantic similarity. The diagnostic system uses a composite knowledge base, and will allow automated diagnosis recommendation. The system framework also aims at facilitating semantic explanations to the solution derived

Automated Transformation of Probablistic Knowledge for a Medical Diagnostic System

Conference PaperBiomedical Informatic

Machine-Learning-based Prediction of Sepsis Events from Vertical Clinical Trial Data: a Naïve Approach

Sepsis is a potentially life-threatening condition characterized by a dysregulated, disproportionate immune response to infection by which the afflicted body attacks its own tissues, sometimes to the point of organ failure, and in the worst cases, death. According to the Centers for Disease Control and Prevention (CDC) Sepsis is reported to kill upwards of 270,000 Americans annually, though this figure may be greater given certain ambiguities in the current accepted diagnostic framework of the disease. This study attempted to first establish an understanding of past definitions of sepsis, and to then recommend use of machine learning as integral in an eventual amended disease definition. Longitudinal clinical trial data (ntrials=30,915) were vectorized into a machine-readable format compatible with predictive modeling, selected and reduced in dimension, and used to predict incidences of sepsis via application of several machine learning models: logistic regression, support vector machines (SVM), naïve Bayes Classifier, decision trees, and random forests. The intent of the study was to identify possible predictive features for sepsis via comparative analysis of different machine learning models, and to recommend subsequent study of sepsis prediction using the training model on new data (non-clinical-trial-derived) in the same format. If the models can be generalized to new data, it stands to assume they could eventually become clinically useful. In referencing F1 scores and recall scores, the random forest classifier was the best performer among this cohort of models

Automated Transformation of Probabilistic Knowledge for a Medical Diagnostic System

Conference PaperBiomedical Informatic

Synergy of Physics-based Reasoning and Machine Learning in Biomedical Applications: Towards Unlimited Deep Learning with Limited Data

Technological advancements enable collecting vast data, i.e., Big Data, in science and industry including biomedical field. Increased computational power allows expedient analysis of collected data using statistical and machine-learning approaches. Historical data incompleteness problem and curse of dimensionality diminish practical value of pure data-driven approaches, especially in biomedicine. Advancements in deep learning (DL) frameworks based on deep neural networks (DNN) improved accuracy in image recognition, natural language processing, and other applications yet severe data limitations and/or absence of transfer-learning-relevant problems drastically reduce advantages of DNN-based DL. Our earlier works demonstrate that hierarchical data representation can be alternatively implemented without NN, using boosting-like algorithms for utilization of existing domain knowledge, tolerating significant data incompleteness, and boosting accuracy of low-complexity models within the classifier ensemble, as illustrated in physiological-data analysis. Beyond obvious use in initial-factor selection, existing simplified models are effectively employed for generation of realistic synthetic data for later DNN pre-training. We review existing machine learning approaches, focusing on limitations caused by training-data incompleteness. We outline our hybrid framework that leverages existing domain-expert models/knowledge, boosting-like model combination, DNN-based DL and other machine learning algorithms for drastic reduction of training-data requirements. Applying this framework is illustrated in context of analyzing physiological data

An Ontology-Based Interpretable Fuzzy Decision Support System for Diabetes Diagnosis

Diabetes is a serious chronic disease. The importance of clinical decision support systems (CDSSs) to diagnose diabetes has led to extensive research efforts to improve the accuracy, applicability, interpretability, and interoperability of these systems. However, this problem continues to require optimization. Fuzzy rule-based systems are suitable for the medical domain, where interpretability is a main concern. The medical domain is data-intensive, and using electronic health record data to build the FRBS knowledge base and fuzzy sets is critical. Multiple variables are frequently required to determine a correct and personalized diagnosis, which usually makes it difficult to arrive at accurate and timely decisions. In this paper, we propose and implement a new semantically interpretable FRBS framework for diabetes diagnosis. The framework uses multiple aspects of knowledge-fuzzy inference, ontology reasoning, and a fuzzy analytical hierarchy process (FAHP) to provide a more intuitive and accurate design. First, we build a two-layered hierarchical and interpretable FRBS; then, we improve this by integrating an ontology reasoning process based on SNOMED CT standard ontology. We incorporate FAHP to determine the relative medical importance of each sub-FRBS. The proposed system offers numerous unique and critical improvements regarding the implementation of an accurate, dynamic, semantically intelligent, and interpretable CDSS. The designed system considers the ontology semantic similarity of diabetes complications and symptoms concepts in the fuzzy rules' evaluation process. The framework was tested using a real data set, and the results indicate how the proposed system helps physicians and patients to accurately diagnose diabetes mellitusThis work was supported by National Research Foundation of Korea-Grant funded by the Korean Government (Ministry of Science, ICT and Future Planning)-NRF-2017R1A2B2012337)S

An interactive retrieval system for clinical trial studies with context-dependent protocol elements.

A well-defined protocol for a clinical trial guarantees a successful outcome report. When designing the protocol, most researchers refer to electronic databases and extract protocol elements using a keyword search. However, state-of-the-art database systems only offer text-based searches for user-entered keywords. In this study, we present a database system with a context-dependent and protocol-element-selection function for successfully designing a clinical trial protocol. To do this, we first introduce a database for a protocol retrieval system constructed from individual protocol data extracted from 184,634 clinical trials and 13,210 frame structures of clinical trial protocols. The database contains a variety of semantic information that allows the filtering of protocols during the search operation. Based on the database, we developed a web application called the clinical trial protocol database system (CLIPS; available at https://corus.kaist.edu/clips). This system enables an interactive search by utilizing protocol elements. To enable an interactive search for combinations of protocol elements, CLIPS provides optional next element selection according to the previous element in the form of a connected tree. The validation results show that our method achieves better performance than that of existing databases in predicting phenotypic features

Linking social media, medical literature, and clinical notes using deep learning.

Researchers analyze data, information, and knowledge through many sources, formats, and methods. The dominant data format includes text and images. In the healthcare industry, professionals generate a large quantity of unstructured data. The complexity of this data and the lack of computational power causes delays in analysis. However, with emerging deep learning algorithms and access to computational powers such as graphics processing unit (GPU) and tensor processing units (TPUs), processing text and images is becoming more accessible. Deep learning algorithms achieve remarkable results in natural language processing (NLP) and computer vision. In this study, we focus on NLP in the healthcare industry and collect data not only from electronic medical records (EMRs) but also medical literature and social media. We propose a framework for linking social media, medical literature, and EMRs clinical notes using deep learning algorithms. Connecting data sources requires defining a link between them, and our key is finding concepts in the medical text. The National Library of Medicine (NLM) introduces a Unified Medical Language System (UMLS) and we use this system as the foundation of our own system. We recognize social media’s dynamic nature and apply supervised and semi-supervised methodologies to generate concepts. Named entity recognition (NER) allows efficient extraction of information, or entities, from medical literature, and we extend the model to process the EMRs’ clinical notes via transfer learning. The results include an integrated, end-to-end, web-based system solution that unifies social media, literature, and clinical notes, and improves access to medical knowledge for the public and experts