Association Rules Mining Based Clinical Observations

Healthcare institutes enrich the repository of patients' disease related information in an increasing manner which could have been more useful by carrying out relational analysis. Data mining algorithms are proven to be quite useful in exploring useful correlations from larger data repositories. In this paper we have implemented Association Rules mining based a novel idea for finding co-occurrences of diseases carried by a patient using the healthcare repository. We have developed a system-prototype for Clinical State Correlation Prediction (CSCP) which extracts data from patients' healthcare database, transforms the OLTP data into a Data Warehouse by generating association rules. The CSCP system helps reveal relations among the diseases. The CSCP system predicts the correlation(s) among primary disease (the disease for which the patient visits the doctor) and secondary disease/s (which is/are other associated disease/s carried by the same patient having the primary disease).Comment: 5 pages, MEDINFO 2010, C. Safran et al. (Eds.), IOS Pres

Doctor of Philosophy

dissertationDisease-specific ontologies, designed to structure and represent the medical knowledge about disease etiology, diagnosis, treatment, and prognosis, are essential for many advanced applications, such as predictive modeling, cohort identification, and clinical decision support. However, manually building disease-specific ontologies is very labor-intensive, especially in the process of knowledge acquisition. On the other hand, medical knowledge has been documented in a variety of biomedical knowledge resources, such as textbook, clinical guidelines, research articles, and clinical data repositories, which offers a great opportunity for an automated knowledge acquisition. In this dissertation, we aim to facilitate the large-scale development of disease-specific ontologies through automated extraction of disease-specific vocabularies from existing biomedical knowledge resources. Three separate studies presented in this dissertation explored both manual and automated vocabulary extraction. The first study addresses the question of whether disease-specific reference vocabularies derived from manual concept acquisition can achieve a near-saturated coverage (or near the greatest possible amount of disease-pertinent concepts) by using a small number of literature sources. Using a general-purpose, manual acquisition approach we developed, this study concludes that a small number of expert-curated biomedical literature resources can prove sufficient for acquiring near-saturated disease-specific vocabularies. The second and third studies introduce automated techniques for extracting disease-specific vocabularies from both MEDLINE citations (title and abstract) and a clinical data repository. In the second study, we developed and assessed a pipeline-based system which extracts disease-specific treatments from PubMed citations. The system has achieved a mean precision of 0.8 for the top 100 extracted treatment concepts. In the third study, we applied classification models to reduce irrelevant disease-concepts associations extracted from MEDLINE citations and electronic medical records. This study suggested the combination of measures of relevance from disparate sources to improve the identification of true-relevant concepts through classification and also demonstrated the generalizability of the studied classification model to new diseases. With the studies, we concluded that existing biomedical knowledge resources are valuable sources for extracting disease-concept associations, from which classification based on statistical measures of relevance could assist a semi-automated generation of disease-specific vocabularies

Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts

Electronic patient records remain a rather unexplored, but potentially rich data source for discovering correlations between diseases. We describe a general approach for gathering phenotypic descriptions of patients from medical records in a systematic and non-cohort dependent manner. By extracting phenotype information from the free-text in such records we demonstrate that we can extend the information contained in the structured record data, and use it for producing fine-grained patient stratification and disease co-occurrence statistics. The approach uses a dictionary based on the International Classification of Disease ontology and is therefore in principle language independent. As a use case we show how records from a Danish psychiatric hospital lead to the identification of disease correlations, which subsequently can be mapped to systems biology frameworks

COVID-19 Data Warehouse: A Systematic Literature Review

The coronavirus disease (COVID-19) affects the whole world and led clinicians to use the available knowledge to diagnose or predict the infection. Data Warehouse is one of the most crucial tools that may enhance decision-making (DW).In this paper, three main questions will be investigated according to using DW in the COVID-19 pandemic. The effect of using DW in the field of diagnosing and prediction will be investigated, besides, the most used architecture of DW will be explored. The sectors that faced a lot of researchers' attention such as diagnosing, predicting, and finding the correlations among features will be examined. The selected studies are explored where the papers that have been published between 2019-2022 in the digital libraries (ACM, IEEE, Springer, Science Direct, and Elsevier) in the field of DW that handle the COVID-19 are selected. During the research, many limitations have been detected, while some future works are presented. Enterprise DW is the most used architecture for COVID-19 DW while finding correlation among features and prediction are the sectors that had taken the researchers' attentio

Doctor of Philosophy

dissertationWith the growing national dissemination of the electronic health record (EHR), there are expectations that the public will benefit from biomedical research and discovery enabled by electronic health data. Clinical data are needed for many diseases and conditions to meet the demands of rapidly advancing genomic and proteomic research. Many biomedical research advancements require rapid access to clinical data as well as broad population coverage. A fundamental issue in the secondary use of clinical data for scientific research is the identification of study cohorts of individuals with a disease or medical condition of interest. The problem addressed in this work is the need for generalized, efficient methods to identify cohorts in the EHR for use in biomedical research. To approach this problem, an associative classification framework was designed with the goal of accurate and rapid identification of cases for biomedical research: (1) a set of exemplars for a given medical condition are presented to the framework, (2) a predictive rule set comprised of EHR attributes is generated by the framework, and (3) the rule set is applied to the EHR to identify additional patients that may have the specified condition. iv Based on this functionality, the approach was termed the ‘cohort amplification' framework. The development and evaluation of the cohort amplification framework are the subject of this dissertation. An overview of the framework design is presented. Improvements to some standard associative classification methods are described and validated. A qualitative evaluation of predictive rules to identify diabetes cases and a study of the accuracy of identification of asthma cases in the EHR using frameworkgenerated prediction rules are reported. The framework demonstrated accurate and reliable rules to identify diabetes and asthma cases in the EHR and contributed to methods for identification of biomedical research cohorts

A survey on utilization of data mining approaches for dermatological (skin) diseases prediction

Due to recent technology advances, large volumes of medical data is obtained. These data contain valuable information. Therefore data mining techniques can be used to extract useful patterns. This paper is intended to introduce data mining and its various techniques and a survey of the available literature on medical data mining. We emphasize mainly on the application of data mining on skin diseases. A categorization has been provided based on the different data mining techniques. The utility of the various data mining methodologies is highlighted. Generally association mining is suitable for extracting rules. It has been used especially in cancer diagnosis. Classification is a robust method in medical mining. In this paper, we have summarized the different uses of classification in dermatology. It is one of the most important methods for diagnosis of erythemato-squamous diseases. There are different methods like Neural Networks, Genetic Algorithms and fuzzy classifiaction in this topic. Clustering is a useful method in medical images mining. The purpose of clustering techniques is to find a structure for the given data by finding similarities between data according to data characteristics. Clustering has some applications in dermatology. Besides introducing different mining methods, we have investigated some challenges which exist in mining skin data

CLINICAL DATA WAREHOUSE: A REVIEW

Clinical decisions are crucial because they are related to human lives. Thus, managers and decision makers inthe clinical environment seek new solutions that can support their decisions. A clinical data warehouse (CDW) is animportant solution that is used to achieve clinical stakeholders’ goals by merging heterogeneous data sources in a centralrepository and using this repository to find answers related to the strategic clinical domain, thereby supporting clinicaldecisions. CDW implementation faces numerous obstacles, starting with the data sources and ending with the tools thatview the clinical information. This paper presents a systematic overview of purpose of CDWs as well as the characteristics;requirements; data sources; extract, transform and load (ETL) process; security and privacy concerns; design approach;architecture; and challenges and difficulties related to implementing a successful CDW. PubMed and Google Scholarare used to find papers related to CDW. Among the total of 784 papers, only 42 are included in the literature review. Thesepapers are classified based on five perspectives, namely methodology, data, system, ETL tool and purpose, to findinsights related to aspects of CDW. This review can contribute answers to questions related to CDW and providerecommendations for implementing a successful CDW

Contextual Analysis of Large-Scale Biomedical Associations for the Elucidation and Prioritization of Genes and their Roles in Complex Disease

Vast amounts of biomedical associations are easily accessible in public resources, spanning gene-disease associations, tissue-specific gene expression, gene function and pathway annotations, and many other data types. Despite this mass of data, information most relevant to the study of a particular disease remains loosely coupled and difficult to incorporate into ongoing research. Current public databases are difficult to navigate and do not interoperate well due to the plethora of interfaces and varying biomedical concept identifiers used. Because no coherent display of data within a specific problem domain is available, finding the latent relationships associated with a disease of interest is impractical. This research describes a method for extracting the contextual relationships embedded within associations relevant to a disease of interest. After applying the method to a small test data set, a large-scale integrated association network is constructed for application of a network propagation technique that helps uncover more distant latent relationships. Together these methods are adept at uncovering highly relevant relationships without any a priori knowledge of the disease of interest. The combined contextual search and relevance methods power a tool which makes pertinent biomedical associations easier to find, easier to assimilate into ongoing work, and more prominent than currently available databases. Increasing the accessibility of current information is an important component to understanding high-throughput experimental results and surviving the data deluge

An application of association rule mining to extract risk pattern for type 2 diabetes using tehran lipid and glucose study database

Background: Type 2 diabetes, common and serious global health concern, had an estimated worldwide prevalence of 366 million in 2011, which is expected to rise to 552 million people, by 2030, unless urgent action is taken. Objectives: The aim of this study was to identify risk patterns for type 2 diabetes incidence using association rule mining (ARM). Patients and Methods: A population of 6647 individuals without diabetes, aged � 20 years at inclusion, was followed for 10-12 years, to analyze risk patterns for diabetes occurrence. Study variables included demographic and anthropometric characteristics, smoking status, medical and drug history and laboratory measures. Results: In the case of women, the results showed that impaired fasting glucose (IFG) and impaired glucose tolerance (IGT), in combination with body mass index (BMI) � 30 kg/m2, family history of diabetes, wrist circumference > 16.5 cm and waist to height � 0.5 can increase the risk for developing diabetes. For men, a combination of IGT, IFG, length of stay in the city (> 40 years), central obesity, total cholesterol to high density lipoprotein ratio � 5.3, low physical activity, chronic kidney disease and wrist circumference > 18.5 cm were identified as risk patterns for diabetes occurrence. Conclusions: Our study showed that ARM is a useful approach in determining which combinations of variables or predictors occur together frequently, in people who will develop diabetes. The ARM focuses on joint exposure to different combinations of risk factors, and not the predictors alone. © 2015, Research Institute For Endocrine Sciences and Iran Endocrine Society