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2.  Survival Association Rule Mining Towards Type 2 Diabetes Risk Assessment 
AMIA Annual Symposium Proceedings  2013;2013:1293-1302.
Type-2 Diabetes Mellitus is a growing epidemic that often leads to severe complications. Effective preventive measures exist and identifying patients at high risk of diabetes is a major health-care need.
The use of association rule mining (ARM) is advantageous, as it was specifically developed to identify associations between risk factors in an interpretable form. Unfortunately, traditional ARM is not directly applicable to survival outcomes and it lacks the ability to compensate for confounders and to incorporate dosage effects. In this work, we propose Survival Association Rule (SAR) Mining, which addresses these shortcomings.
We demonstrate on a real diabetes data set that SARs are naturally more interpretable than the traditional association rules, and predictive models built on top of these rules are very competitive relative to state of the art survival models and substantially outperform the most widely used diabetes index, the Framingham score.
PMCID: PMC3900145  PMID: 24551408
3.  Using Association Rule Mining for Phenotype Extraction from Electronic Health Records  
The increasing adoption of electronic health records (EHRs) due to Meaningful Use is providing unprecedented opportunities to enable secondary use of EHR data. Significant emphasis is being given to the development of algorithms and methods for phenotype extraction from EHRs to facilitate population-based studies for clinical and translational research. While preliminary work has shown demonstrable progress, it is becoming increasingly clear that developing, implementing and testing phenotyping algorithms is a time- and resource-intensive process. To this end, in this manuscript we propose an efficient machine learning technique—distributional associational rule mining (ARM)—for semi-automatic modeling of phenotyping algorithms. ARM provides a highly efficient and robust framework for discovering the most predictive set of phenotype definition criteria and rules from large datasets, and compared to other machine learning techniques, such as logistic regression and support vector machines, our preliminary results indicate not only significantly improved performance, but also generation of rule patterns that are amenable to human interpretation .
PMCID: PMC3845788  PMID: 24303254
4.  Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues 
PLoS ONE  2013;8(1):e52517.
MicroRNAs play a role in regulating diverse biological processes and have considerable utility as molecular markers for diagnosis and monitoring of human disease. Several technologies are available commercially for measuring microRNA expression. However, cross-platform comparisons do not necessarily correlate well, making it difficult to determine which platform most closely represents the true microRNA expression level in a tissue. To address this issue, we have analyzed RNA derived from cell lines, as well as fresh frozen and formalin-fixed paraffin embedded tissues, using Affymetrix, Agilent, and Illumina microRNA arrays, NanoString counting, and Illumina Next Generation Sequencing. We compared the performance within- and between the different platforms, and then verified these results with those of quantitative PCR data. Our results demonstrate that the within-platform reproducibility for each method is consistently high and although the gene expression profiles from each platform show unique traits, comparison of genes that were commonly detectable showed that detection of microRNA transcripts was similar across multiple platforms.
PMCID: PMC3561362  PMID: 23382819
5.  Antemortem Differential Diagnosis of Dementia Pathology using Structural MRI: Differential-STAND 
NeuroImage  2010;55(2):522-531.
The common neurodegenerative pathologies underlying dementia are Alzheimer’s disease (AD), Lewy body disease (LBD) and Frontotemporal lobar degeneration (FTLD). Our aim was to identify patterns of atrophy unique to each of these diseases using antemortem structural-MRI scans of pathologically-confirmed dementia cases and build an MRI-based differential diagnosis system. Our approach of creating atrophy maps using structural-MRI and applying them for classification of new incoming patients is labeled Differential-STAND (Differential-diagnosis based on STructural Abnormality in NeuroDegeneration). Pathologically-confirmed subjects with a single dementing pathologic diagnosis who had an MRI at the time of clinical diagnosis of dementia were identified: 48 AD, 20 LBD, 47 FTLD-TDP (pathology-confirmed FTLD with TDP-43). Gray matter density in 91 regions-of-interest was measured in each subject and adjusted for head-size and age using a database of 120 cognitively normal elderly. The atrophy patterns in each dementia type when compared to pathologically-confirmed controls mirrored known disease-specific anatomic patterns: AD-temporoparietal association cortices and medial temporal lobe; FTLD-TDP-frontal and temporal lobes and LBD-bilateral amygdalae, dorsal midbrain and inferior temporal lobes. Differential-STAND based classification of each case was done based on a mixture model generated using bisecting k-means clustering of the information from the MRI scans. Leave-one-out classification showed reasonable performance compared to the autopsy gold-standard and clinical diagnosis: AD (sensitivity:90.7%; specificity:84 %), LBD (sensitivity:78.6%; specificity:98.8%) and FTLD-TDP (sensitivity:84.4%; specificity:93.8%). The proposed approach establishes a direct a priori relationship between specific topographic patterns on MRI and “gold standard” of pathology which can then be used to predict underlying dementia pathology in new incoming patients.
PMCID: PMC3039279  PMID: 21195775
MRI; Alzheimer’s disease; Lewy body disease; Frontotemporal lobar degeneration

Results 1-5 (5)