Mercurial > repos > rnateam > rnacommender
view model.py @ 4:a609d6dc8047 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
author | rnateam |
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date | Thu, 28 Jul 2016 05:55:25 -0400 |
parents | 8918de535391 |
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"""Recommender model.""" from __future__ import print_function import sys import numpy as np from theano import function, shared import theano.tensor as T __author__ = "Gianluca Corrado" __copyright__ = "Copyright 2016, Gianluca Corrado" __license__ = "MIT" __maintainer__ = "Gianluca Corrado" __email__ = "gianluca.corrado@unitn.it" __status__ = "Production" class Model(): """Factorization model.""" def __init__(self, sp, sr, kp, kr, irange=0.01, learning_rate=0.01, lambda_reg=0.01, verbose=True, seed=1234): """ Constructor. Parameters ---------- sp : int Number of protein features. sr : int Number of RNA features. kp : int Size of the protein latent space. kr : int Size of the RNA latent space. irange : float (default : 0.01) Initialization range for the model weights. learning_rate : float (default : 0.01) Learning rate for the weights update. lambda_reg : (default : 0.01) Lambda parameter for the regularization. verbose : bool (default : True) Print information at STDOUT. seed : int (default : 1234) Seed for random number generator. """ if verbose: print("Compiling model...", end=' ') sys.stdout.flush() self.learning_rate = learning_rate self.lambda_reg = lambda_reg np.random.seed(seed) # explictit features for proteins fp = T.matrix("Fp", dtype='float32') # explictit features for RNAs fr = T.matrix("Fr", dtype='float32') # Correct label y = T.vector("y") # projection matrix for proteins self.Ap = shared(((.5 - np.random.rand(kp, sp)) * irange).astype('float32'), name="Ap") self.bp = shared(((.5 - np.random.rand(kp)) * irange).astype('float32'), name="bp") # projection matrix for RNAs self.Ar = shared(((.5 - np.random.rand(kr, sr)) * irange).astype('float32'), name="Ar") self.br = shared(((.5 - np.random.rand(kr)) * irange).astype('float32'), name="br") # generalization matrix self.B = shared(((.5 - np.random.rand(kp, kr)) * irange).astype('float32'), name="B") # Latent space for proteins p = T.nnet.sigmoid(T.dot(fp, self.Ap.T) + self.bp) # Latent space for RNAs r = T.nnet.sigmoid(T.dot(fr, self.Ar.T) + self.br) # Predicted output y_hat = T.nnet.sigmoid(T.sum(T.dot(p, self.B) * r, axis=1)) def _regularization(): """Normalized Frobenius norm.""" norm_proteins = self.Ap.norm(2) + self.bp.norm(2) norm_rnas = self.Ar.norm(2) + self.br.norm(2) norm_b = self.B.norm(2) num_proteins = self.Ap.flatten().shape[0] + self.bp.shape[0] num_rnas = self.Ar.flatten().shape[0] + self.br.shape[0] num_b = self.B.flatten().shape[0] return (norm_proteins / num_proteins + norm_rnas / num_rnas + norm_b / num_b) / 3 # mean squared error cost_ = (T.sqr(y - y_hat)).mean() reg = lambda_reg * _regularization() cost = cost_ + reg # compute sgd updates g_Ap, g_bp, g_Ar, g_br, g_B = T.grad( cost, [self.Ap, self.bp, self.Ar, self.br, self.B]) updates = ((self.Ap, self.Ap - learning_rate * g_Ap), (self.bp, self.bp - learning_rate * g_bp), (self.Ar, self.Ar - learning_rate * g_Ar), (self.br, self.br - learning_rate * g_br), (self.B, self.B - learning_rate * g_B)) # training step self.train = function( inputs=[fp, fr, y], outputs=[y_hat, cost], updates=updates) # test self.test = function( inputs=[fp, fr, y], outputs=[y_hat, cost]) # predict self.predict = function( inputs=[fp, fr], outputs=y_hat) if verbose: print("Done.") sys.stdout.flush() def get_params(self): """Return the parameters of the model.""" return {'Ap': self.Ap.get_value(), 'bp': self.bp.get_value(), 'Ar': self.Ar.get_value(), 'br': self.br.get_value(), 'B': self.B.get_value()}