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Artifical Neural Network for Predicting Protein Secondary Structures

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ANN-for-protien-secondary-structer


Approximately replecated methodology from ...

Using knowledge-based neural networks to improve algorithms:
Refining the Chou-Fasman algorithm for protein folding


Data Set:

Test set for study of secondary structure of globular proteins by Ning Qing and Terry Sejnowski.

There were 128 protiens in the UC-Irvine archive. Train and Test were combined into one file (with train in front). Data was split into three test sets for our version of this network: Train, Tune and Test.

Out of 128 proteins, they were broken up as follows:

  • tune: index % 5 = 0
  • train: index % 6 = 0
  • test: the rest of the proteins.

Network:

This network is implemented with:

  • Hinton's Droput
  • Momentum Term for backpropagation
  • Early Stopping

Network preforms best with the configuration found in the main method.


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Artifical Neural Network for Predicting Protein Secondary Structures

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