Automatic Transformation of Raw Clinical Data into Clean Data Using Decision Tree Learning

Jian Zhang

Supervised by: Karen Petrie

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Background

Cancer research has become an extremely data rich environment.

Plenty of analysis packages can be used for analyzing the data.

Data preprocessing.

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Rich data environment

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• There are some factors about breast cancer

Raw clinical data sample

Yes-No data:

yes: yes, Yes, Ye, yed, yef …

no: No, n, not …

null: don’t know, no data, waiting for lab Positive-Negative data:

Positive: +, ++, p, p++…

Negative: -, n, neg, n---…

Null: no data, ruined sample, waiting for lab

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Basic version

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Question?

Could we make the process automated?

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Introduction

Decision Tree learning Weka

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Decision Tree Learning

Decision tree learning is a method for approximating discrete-valued functions, which is one of the most popular inductive algorithms.

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Decision tree sample

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Weka

Weka (Waikato Environment for Knowledge Analysis) is a popular suite of machine learning software written in Java, which contains a collection of algorithms for data analysis and predictive modeling.

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Experiment

Data: Training dataset with 100 instances

Test dataset with 100 instances, which has 17 different values from the training dataset

Tool: weka

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Experiment

Experiment 1 : training dataset Experiment 2 : training dataset, test dataset

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Experiment 1

Name of Tree Correctly Classified Instances (%)

Testing (%) Root mean squared error

BFTree 89 99 0.0588DecisionStump 47 55 0.422

FT 87 98 0.1698J48 82 98 0.0976

J48graft 82 98 0.0976LADTree 81 90 0.2317

LMT 84 91 0.2344NBTree 80 98 0.2326

RandomForest 83 100 0.0781

RandomTree 83 100 0.0447

REPTree 82 98 0.0985SimpleCart 89 96 0.1511

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Experiment 2

Name of Tree Correctly Classified Instances(%)

Testing (%)

Root mean squared error

BFTree 89 88 0.2813

DecisionStump 47 49 0.4318

FT 87 90 0.2194

J48 82 88 0.2098

J48graft 82 88 0.2098

LADTree 81 89 0.2494

LMT 84 89 0.234

NBTree 80 88 0.2569

RandomForest 83 88 0.2095

RandomTree 83 88 0.209

REPTree 82 88 0.2098

SimpleCart 89 87 0.284814

Result

Through the results, the decision tree has a good classification and prediction for the existing entries, but for the unknown entries, the prediction is not as good as expected.

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Future work

Find and correct the incorrect prediction in the process

Automated transformation for unknown entries

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Thank you !

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