Query-constraint-based mining of association rules for exploratory analysis of clinical datasets in the National Sleep Research Resource

Abstract

BackgroundAssociation Rule Mining (ARM) has been widely used by biomedical researchers to perform exploratory data analysis and uncover potential relationships among variables in biomedical datasets. However, when biomedical datasets are high-dimensional, performing ARM on such datasets will yield a large number of rules, many of which may be uninteresting. Especially for imbalanced datasets, performing ARM directly would result in uninteresting rules that are dominated by certain variables that capture general characteristics.MethodsWe introduce a query-constraint-based ARM (QARM) approach for exploratory analysis of multiple, diverse clinical datasets in the National Sleep Research Resource (NSRR). QARM enables rule mining on a subset of data items satisfying a query constraint. We first perform a series of data-preprocessing steps including variable selection, merging semantically similar variables, combining multiple-visit data, and data transformation. We use Top-k Non-Redundant (TNR) ARM algorithm to generate association rules. Then we remove general and subsumed rules so that unique and non-redundant rules are resulted for a particular query constraint.ResultsApplying QARM on five datasets from NSRR obtained a total of 2517 association rules with a minimum confidence of 60% (using top 100 rules for each query constraint). The results show that merging similar variables could avoid uninteresting rules. Also, removing general and subsumed rules resulted in a more concise and interesting set of rules.ConclusionsQARM shows the potential to support exploratory analysis of large biomedical datasets. It is also shown as a useful method to reduce the number of uninteresting association rules generated from imbalanced datasets. A preliminary literature-based analysis showed that some association rules have supporting evidence from biomedical literature, while others without literature-based evidence may serve as the candidates for new hypotheses to explore and investigate. Together with literature-based evidence, the association rules mined over the NSRR clinical datasets may be used to support clinical decisions for sleep-related problems.Electronic supplementary materialThe online version of this article (10.1186/s12911-018-0633-7) contains supplementary material, which is available to authorized users.

Risk Assessment for Anti-Infectives-Related Acute Kidney Injury Using the Japanese Adverse Drug Event Report Database

“…The association rule was evaluated by measures of support, con dence, and lift. The support of the rule is de ned as the percentage of transactions in T that contain both X and Y [24,25]. The support was calculated as follows:…”

TUSQ: Targeted High-Utility Sequence Querying

“…The fast and generic tool GFP-growth can determine the frequency of a given large list of itemsets, which serve as the targets, in a large dataset from an FP-tree [45] based on Target Itemset Tree. Recently, a query-constraint-based ARM model [17], [21] was developed for exploratory analysis of diverse clinical datasets integrated in the National Sleep Research Resource. It is important to consider the sequential ordering of itemsets in real-life applications.…”

“…Till now, target-oriented frequent itemset querying [14], association rule querying [15], [16], [17], and sequential pattern querying (SPQ) [18], [19], [20] have performed significant roles in querying in the database. The three target-oriented technologies can efficiently excavate patterns and rules involving a subset of certain items, such as targeted queries, and have shown significant potential in several real-life situations [21].…”

TargetUM: Targeted High-Utility Itemset Querying

“…Its motivation is that utility-driven sequential pattern mining algorithms often obtain several useless patterns owing to exhaustive results. At present, mining algorithms with target-querying constraints have been applied in various applications [19], [40].…”