Disease Prediction Based on Prior Knowledge

Gregoe Stiglic, Igor Pernek, Peter Kokol Facuty of Health Sciences University of Maribor Slovania Zoran Obradovic Center for Information Science and Technology, Temple University, Philadelphia, USA

ACM SIGKDD Workshop on Health Informatics (HI-KDD 2012) August 12, 2012

Outline
Background Objectives Evolution Disease networks SVM Experimental setup Class-imbalanced data Classification Experiments Stability

Background
Patient Name Michael asthma Blood Pressure 1 Prostate Cancer 0 Diabetes Heart Failure ?

Objectives
Using prior knowledge from human disease networks to lower the burden of building classifiers
Estimation of disease risk from hospital discharge data optimally Enhancing Support Vector Machine Recursive Feature Elimination(SVM-RFE) approach to Support Vector MachineReweighted Recursive Feature Elimination (SVM-RRFE)

Evolution
1. Bringing health data into digital form 2. Increasing acceptance of electronic health records (comparing patients) 3. Constructing disease related networks 4. Increasing amount of studies in the application of data mining approaches in this field

Methods of integrating network knowledge

Network centric: focuses on mapping gene/disease expression data onto a network and uses techniques from network analysis to select the important genes/diseases. Data centric: Focuses on machine learning techniques where prior knowledge from biological networks is used to bias the feature selection process toward strongly connected genes/diseases. (Such as SVMRRFE)

SVM
SVM used for classification and constructs a hyperplane or sets of hyperplanes in high dimensional space which divide data to two separate classes. Hyperplane should divide the classes with the largest distance to the nearest training data point of any class.

Two basic concepts that are used when constructing disease networks
Morbidity: Represents the support for a single diagnosis in the given population.
Co-morbidity: Represents the support for co-occurrence of two diseases.

common measures for calculating relations

Weight:
SVM-RFE

Relative Risk:

SVM-RRFE

Phi:

Experimental setup
Healthcare Cost and Utilization Project (HCUP) Agency for Healthcare Research and Quality Nationwide Inpatient Sample (NIS) 20% of US hospitals
Data for the adult population from year 2008 for network construction. Data for the adult population from year 2009 for model evaluation. 6,840,196 discharge records in 2008. 6,546,273 discharge records in 2009.

Experimental setup
Each record contains: Personal characteristics of a patient Age Gender Race Administrative information: Length of stay Discharge status Medical information: Diagnoses codes (ICD-9-CM) Surgical and nonsurgical procedures

Experimental setup
ICD-9-CM: The International Classification of Diseases, 9th Revision, Clinical modification. Uses taxonomy of 5-digit codes. First 3 digits represent the general diagnosis 2 additional digits describe more detailed subgroup of the general diagnosis.

14,000 diagnosis codes in dataset After removing the codes that were not used in data from 2009, there are 11,170 codes.

Experimental setup
Age group frequency for both 2008 and 2009

Experimental setup
Elimination of rare diagnosis with prevalence less than 1% Ranking all diagnosis codes Choosing 5 diagnosis with closest prevalence to 20, 10, 5, 2, and 1%

Class-imbalanced data
This problem occurs when we have a dataset with a small number of positive (target class) samples and a much larger number of negative samples. Solutions: Undersampling Oversampling

After balancing, classification performance increases.

Experimental setup
Repeated random subsampling: Selecting 10,000 samples randomly in each iteration for testing In the first experience in training, they use train set with balanced samples. In the second experience in training, they use train set that 75% of its samples are positive and 25% of samples are negative. Each random subsampling evaluation was repeated 10 times for all target diagnosis codes.

Experimental setup
Feature elimination: In first experience, they eliminate 10% of low impact features (those with the lowest RR measure) in each iteration. In second experience, they eliminate 50% of low impact features in each iteration.

Experimental setup
Balanced Subsampling(50% positive 50% negative) Feature elimination with 10% removal rate Feature elimination with 50% removal rate

Imbalanced subsampling(75% positive 25% negative) Feature elimination with 10% removal rate Feature elimination with 50% removal rate

dataset Subsampling (repeated 10 times)

train set

test set

Feature elimination remove 10 or 50 percent of low impact features

train SVM

sort features

yes

are features left?

no

test final model

Classification
Comparison of AUC for SVM-RRFE and SVM-RFE with 10% removal rate.

Classification
Comparison of AUC for SVM-RRFE and SVM-RFE with 50% removal rate.

Experiments
In the case of hospital discharge classification, it is crucial to use less complex and faster methods. So here the case of 50% removal rate, improves the performance of classification. In the case of 10% removal rate, the differences in AUC between RFE and RRFE is not significant, but in the case of 50% removal it is significant. Testing RRFE on another large dataset from 2000 to 2008 shows that a larger network does not produce significantly better results in classification performance. Using less complex and more recent disease network does not significantly impact the classification performance.

Stability
Frequency of disease code selection in the optimal feature sets for Hyperlipidemia (272.4) classification.

Conclusion
Adaptation of the RRFE method for feature selection in imbalanced high-dimensional hospital discharge data. Observe significant improvements of classification performance when large batches of features are eliminated.

After evaluation of classification performance of the proposed solution, it would be possible to use it in combination with another classification model.