Profiling risk factors for chronic uveitis in juvenile idiopathic arthritis: a new model for EHR-based research.

BackgroundJuvenile idiopathic arthritis is the most common rheumatic disease in children. Chronic uveitis is a common and serious comorbid condition of juvenile idiopathic arthritis, with insidious presentation and potential to cause blindness. Knowledge of clinical associations will improve risk stratification. Based on clinical observation, we hypothesized that allergic conditions are associated with chronic uveitis in juvenile idiopathic arthritis patients.MethodsThis study is a retrospective cohort study using Stanford's clinical data warehouse containing data from Lucile Packard Children's Hospital from 2000-2011 to analyze patient characteristics associated with chronic uveitis in a large juvenile idiopathic arthritis cohort. Clinical notes in patients under 16 years of age were processed via a validated text analytics pipeline. Bivariate-associated variables were used in a multivariate logistic regression adjusted for age, gender, and race. Previously reported associations were evaluated to validate our methods. The main outcome measure was presence of terms indicating allergy or allergy medications use overrepresented in juvenile idiopathic arthritis patients with chronic uveitis. Residual text features were then used in unsupervised hierarchical clustering to compare clinical text similarity between patients with and without uveitis.ResultsPreviously reported associations with uveitis in juvenile idiopathic arthritis patients (earlier age at arthritis diagnosis, oligoarticular-onset disease, antinuclear antibody status, history of psoriasis) were reproduced in our study. Use of allergy medications and terms describing allergic conditions were independently associated with chronic uveitis. The association with allergy drugs when adjusted for known associations remained significant (OR 2.54, 95% CI 1.22-5.4).ConclusionsThis study shows the potential of using a validated text analytics pipeline on clinical data warehouses to examine practice-based evidence for evaluating hypotheses formed during patient care. Our study reproduces four known associations with uveitis development in juvenile idiopathic arthritis patients, and reports a new association between allergic conditions and chronic uveitis in juvenile idiopathic arthritis patients

Statistical data mining for symbol associations in genomic databases

A methodology is proposed to automatically detect significant symbol associations in genomic databases. A new statistical test is proposed to assess the significance of a group of symbols when found in several genesets of a given database. Applied to symbol pairs, the thresholded p-values of the test define a graph structure on the set of symbols. The cliques of that graph are significant symbol associations, linked to a set of genesets where they can be found. The method can be applied to any database, and is illustrated MSigDB C2 database. Many of the symbol associations detected in C2 or in non-specific selections did correspond to already known interactions. On more specific selections of C2, many previously unkown symbol associations have been detected. These associations unveal new candidates for gene or protein interactions, needing further investigation for biological evidence

Detecting Large Concept Extensions for Conceptual Analysis

When performing a conceptual analysis of a concept, philosophers are interested in all forms of expression of a concept in a text---be it direct or indirect, explicit or implicit. In this paper, we experiment with topic-based methods of automating the detection of concept expressions in order to facilitate philosophical conceptual analysis. We propose six methods based on LDA, and evaluate them on a new corpus of court decision that we had annotated by experts and non-experts. Our results indicate that these methods can yield important improvements over the keyword heuristic, which is often used as a concept detection heuristic in many contexts. While more work remains to be done, this indicates that detecting concepts through topics can serve as a general-purpose method for at least some forms of concept expression that are not captured using naive keyword approaches

Mining and analysis of audiology data to find significant factors associated with tinnitus masker

Objectives: The objective of this research is to find the factors associated with tinnitus masker from the literature, and by using the large amount of audiology data available from a large NHS (National Health Services, UK) hearing aid clinic. The factors evaluated were hearing impairment, age, gender, hearing aid type, mould and clinical comments. Design: The research includes literature survey for factors associated with tinnitus masker, and performs the analysis of audiology data using statistical and data mining techniques. Setting: This research uses a large audiology data but it also faced the problem of limited data for tinnitus. Participants: It uses 1,316 records for tinnitus and other diagnoses, and 10,437 records of clinical comments from a hearing aid clinic. Primary and secondary outcome measures: The research is looking for variables associated with tinnitus masker, and in future, these variables can be combined into a single model to develop a decision support system to predict about tinnitus masker for a patient. Results: The results demonstrated that tinnitus maskers are more likely to be fit to individuals with milder forms of hearing loss, and the factors age, gender, type of hearing aid and mould were all found significantly associated with tinnitus masker. In particular, those patients having Age<=55 years were more likely to wear a tinnitus masker, as well as those with milder forms of hearing loss. ITE (in the ear) hearing aids were also found associated with tinnitus masker. A feedback on the results of association of mould with tinnitus masker from a professional audiologist of a large NHS (National Health Services, UK) was also taken to better understand them. The results were obtained with different accuracy for different techniques. For example, the chi-squared test results were obtained with 95% accuracy, for Support and Confidence only those results were retained which had more than 1% Support and 80% Confidence. Conclusions: The variables audiograms, age, gender, hearing aid type and mould were found associated with the choice of tinnitus masker in the literature and by using statistical and data mining techniques. The further work in this research would lead to the development of a decision support system for tinnitus masker with an explanation that how that decision was obtained

Class Association Rules Mining based Rough Set Method

This paper investigates the mining of class association rules with rough set approach. In data mining, an association occurs between two set of elements when one element set happen together with another. A class association rule set (CARs) is a subset of association rules with classes specified as their consequences. We present an efficient algorithm for mining the finest class rule set inspired form Apriori algorithm, where the support and confidence are computed based on the elementary set of lower approximation included in the property of rough set theory. Our proposed approach has been shown very effective, where the rough set approach for class association discovery is much simpler than the classic association method.Comment: 10 pages, 2 figure

Buzz monitoring in word space

This paper discusses the task of tracking mentions of some topically interesting textual entity from a continuously and dynamically changing flow of text, such as a news feed, the output from an Internet crawler or a similar text source - a task sometimes referred to as buzz monitoring. Standard approaches from the field of information access for identifying salient textual entities are reviewed, and it is argued that the dynamics of buzz monitoring calls for more accomplished analysis mechanisms than the typical text analysis tools provide today. The notion of word space is introduced, and it is argued that word spaces can be used to select the most salient markers for topicality, find associations those observations engender, and that they constitute an attractive foundation for building a representation well suited for the tracking and monitoring of mentions of the entity under consideration

Social Search with Missing Data: Which Ranking Algorithm?

Online social networking tools are extremely popular, but can miss potential discoveries latent in the social 'fabric'. Matchmaking services which can do naive profile matching with old database technology are too brittle in the absence of key data, and even modern ontological markup, though powerful, can be onerous at data-input time. In this paper, we present a system called BuddyFinder which can automatically identify buddies who can best match a user's search requirements specified in a term-based query, even in the absence of stored user-profiles. We deploy and compare five statistical measures, namely, our own CORDER, mutual information (MI), phi-squared, improved MI and Z score, and two TF/IDF based baseline methods to find online users who best match the search requirements based on 'inferred profiles' of these users in the form of scavenged web pages. These measures identify statistically significant relationships between online users and a term-based query. Our user evaluation on two groups of users shows that BuddyFinder can find users highly relevant to search queries, and that CORDER achieved the best average ranking correlations among all seven algorithms and improved the performance of both baseline methods

The potential of text mining in data integration and network biology for plant research : a case study on Arabidopsis

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies