Gene based diagnostic prediction of cancers by using Artificial Neural Network Liya Wang ECE/CS/ME539.

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Presentation transcript:

Gene based diagnostic prediction of cancers by using Artificial Neural Network Liya Wang ECE/CS/ME539

Introduction Neuroblastoma (NB), Burkitt lymphomas (BL), Rhabdmyosarcoma (RMS) and Ewing family of tumors (EWS) are different cancers with similar appearance on routine histology. Accurate diagnosis is essential because the treatment options vary widely depending on the diagnosis. Gene-expression technique provides a new support for diagnosis.

Project Description There are 63 training samples and 20 testing samples. Each sample is expressed by 96 genes. Nature Medicine, 7(6), June 2001 Generalized Hebbian Algorithm (GHA) is used for extracting the principal components of the gene data. Multilayer Perceptron with Back-propagation learning is responsible for performing the actual classification.

Neural Network Design y1y1 y2y2 ynyn  x1x1 x2x2 xmxm x3x3    GHAMLP m  n, m=96,n=10 1

Generalized Hebbian Algorithm Initialize the weights of the network, w ji, to small random values at time k=1. Assign a small positive value to the learning-rate parameter . Calculate Increment k by 1, go to step 2, and continue until w ji reach their steady-state values.

GHA weights convergence

Multilayer Perceptron 10 input neurons, 4 output neurons, no hidden layer. Output neurons use sigmoidal active function Output from output nodes for training samples are scaled to: [ ] Use the entire training set to estimate training error # training samples = epoch size = 63

Training error

Results Testing Sample ANN TESTING RESULTS RMS NB BL EWS ANN Histological Classification Diagnosis TEST NB NB-C TEST RMS RMS-T TEST NB NB-C TEST EWS EWS-C TEST RMS RMS-T TEST BL BL-C TEST EWS EWS-T TEST RMS RMS-T TEST EWS EWS-T TEST EWS EWS TEST BL EWS-T

Results (Cont’d) Testing Sample ANN TESTING RESULTS RMS NB BL EWS ANN Histological Classification Diagnosis TEST RMS RMS-T TEST BL BL-C TEST RMS RMS-T TEST NB NB-T TEST NB NB-T TEST NB NB-T TEST NB NB-T TEST BL BL-C TEST EWS EWS