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Added Usability of Local Alignment Scores
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HarshitGupta11
GitHub
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1 changed files with 76 additions and 59 deletions
135
model.py
135
model.py
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@ -1,12 +1,14 @@
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dim=30
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dim=10
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n=3
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fl=2*n+1
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import tensorflow as tf
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import tensorflow as tf
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def create_model():
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def create_model():
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tf.reset_default_graph()
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tf.reset_default_graph()
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g=tf.Graph()
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g=tf.Graph()
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with g.as_default():
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with g.as_default():
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synm=tf.placeholder(dtype=tf.float64,shape=(None,5,5,2),name="Synteny_matrix_placeholder")
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synmg=tf.placeholder(dtype=tf.float64,shape=(None,2*n+1,2*n+1,2),name="Synteny_matrix_placeholder_Global")
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synml=tf.placeholder(dtype=tf.float64,shape=(None,2*n+1,2*n+1,2),name="Synteny_matrix_placeholder_Local")
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bls=tf.placeholder(dtype=tf.float64,shape=(None,21),name="Species_Branch_Length_Placeholder")
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bls=tf.placeholder(dtype=tf.float64,shape=(None,21),name="Species_Branch_Length_Placeholder")
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blhs=tf.placeholder(dtype=tf.float64,shape=(None,21),name="Homology_Species_Branch_Length_Placeholder")
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blhs=tf.placeholder(dtype=tf.float64,shape=(None,21),name="Homology_Species_Branch_Length_Placeholder")
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gl=tf.placeholder(dtype=tf.float64,shape=(None,1),name="Mean_gene_length")
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gl=tf.placeholder(dtype=tf.float64,shape=(None,1),name="Mean_gene_length")
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@ -22,93 +24,108 @@ def create_model():
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#dphs=tf.expand_dims(dphs,-1)
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#dphs=tf.expand_dims(dphs,-1)
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#dis=tf.expand_dims(dis,-1)
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#dis=tf.expand_dims(dis,-1)
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x=tf.concat([gl,dps,dphs,dis],1,name="Create_train_vector")
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x=tf.concat([gl,dps-dphs,dis],1,name="Create_train_vector")
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print(synm,"\n",bls,"\n",blhs,"\n",gl,"\n",dps,"\n",dphs,"\n",dis,"\n",x)
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print(synmg,"\n",synml,"\n",bls,"\n",blhs,"\n",gl,"\n",dps,"\n",dphs,"\n",dis,"\n",x)
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reg=tf.contrib.layers.l2_regularizer(0.01)
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reg_l2=tf.contrib.layers.l2_regularizer(0.001)
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reg_l1 = tf.contrib.layers.l1_regularizer(scale=0.005, scope=None)
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def get_variable_by_shape(shape,name):
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def get_variable_by_shape(shape,name):
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f=tf.get_variable(name,shape=shape,initializer=tf.glorot_uniform_initializer(),dtype=tf.float64,regularizer=reg)
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f=tf.get_variable(name,shape=shape,initializer=tf.glorot_uniform_initializer(),dtype=tf.float64,regularizer=reg_l2)
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return f
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return f
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with tf.variable_scope("Synteny_Aligner",reuse=tf.AUTO_REUSE):
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def create_synteny_aligner(name,synm):
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with tf.variable_scope(name+"Synteny_Aligner",reuse=tf.AUTO_REUSE):
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fconv=get_variable_by_shape((2,2,2,dim),"fconv")
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fconv=get_variable_by_shape((2,2,2,dim),"fconv")
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conv=tf.nn.conv2d(synm,fconv,(1,1,1,1),padding="VALID",name="Conv_aligner")
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conv=tf.nn.conv2d(synm,fconv,(1,1,1,1),padding="VALID",name="Conv_aligner")
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fconv_1=get_variable_by_shape((2,2,dim,dim*2),"fconv_1")
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fconv_1=get_variable_by_shape((2,2,dim,dim*2),"fconv_1")
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conv_1=tf.nn.conv2d(conv,fconv_1,(1,1,1,1),padding="VALID",name="Conv_aligner_1")
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conv_1=tf.nn.conv2d(conv,fconv_1,(1,1,1,1),padding="VALID",name="Conv_aligner_1")
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print(conv)
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print(conv)
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print(conv_1)
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print(conv_1)
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#fxconv=get_variable_by_shape((1,5,2,dim),"fxconv")
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fxconv=get_variable_by_shape((5,2,dim*2),"fxconv")
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#fxconv=get_variable_by_shape((1,5,2,dim),"fxconv")
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x_conv=tf.reshape(synm,(-1,25,2))
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fxconv=get_variable_by_shape((fl,2,dim*2),"fxconv")
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x_conv=tf.nn.conv1d(x_conv,fxconv,stride=5,padding="SAME",name="row_aligner")
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x_conv=tf.reshape(synm,(-1,fl*fl,2))
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print(x_conv)
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x_conv=tf.nn.conv1d(x_conv,fxconv,stride=fl,padding="SAME",name="row_aligner")
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#fyconv=get_variable_by_shape((5,1,2,dim),"fyconv")
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print(x_conv)
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#y_conv=tf.nn.conv2d(synm,fyconv,(1,1,1,1),padding="SAME",name="column_aligner")
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y_conv=tf.reshape(tf.transpose(synm,(0,2,1,3)),(-1,25,2))
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print(y_conv)
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#fyconv=get_variable_by_shape((5,1,2,dim),"fyconv")
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fyconv=get_variable_by_shape((5,2,dim*2),"fyconv")
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#y_conv=tf.nn.conv2d(synm,fyconv,(1,1,1,1),padding="SAME",name="column_aligner")
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y_conv=tf.nn.conv1d(y_conv,fyconv,stride=5,padding="SAME",name="column_aligner")
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y_conv=tf.reshape(tf.transpose(synm,(0,2,1,3)),(-1,fl*fl,2))
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print(y_conv)
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print(y_conv)
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fyconv=get_variable_by_shape((fl,2,dim*2),"fyconv")
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conv_1=tf.reshape(conv_1,(-1,9,dim*2))
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y_conv=tf.nn.conv1d(y_conv,fyconv,stride=fl,padding="SAME",name="column_aligner")
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print(conv)
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print(y_conv)
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x_conv=tf.reshape(x_conv,(-1,5,dim*2))
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print(x_conv)
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y_conv=tf.reshape(y_conv,(-1,5,dim*2))
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wconv=get_variable_by_shape((fl,fl,2,dim*2*10),"wconv")
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print(y_conv)
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w_conv=tf.nn.conv2d(synm,wconv,(1,1,1,1),padding="VALID",name="Global_Aligner_1")
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conv_final=tf.concat([conv_1,x_conv,y_conv],1,name="Concatenate_All_Alignments")
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print(w_conv)
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print(conv_final)
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conv_1=tf.reshape(conv_1,(-1,25,dim*2))
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W=get_variable_by_shape((5,5,2),"W")
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print(conv)
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print(W)
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x_conv=tf.reshape(x_conv,(-1,fl,dim*2))
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W=W*synm
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print(x_conv)
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print(W)
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y_conv=tf.reshape(y_conv,(-1,fl,dim*2))
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#W=tf.reduce_sum(W,[1,2,3])
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print(y_conv)
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#W=tf.reshape(W,(-1,1))
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w_conv=tf.reshape(w_conv,(-1,10,dim*2))
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#print(W)
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print(wconv)
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conv_final=tf.concat([conv_1,x_conv,y_conv,w_conv],1,name="Concatenate_All_Alignments")
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print(conv_final)
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return conv_final
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conv_final_g=create_synteny_aligner("Global",synmg)
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conv_final_l=create_synteny_aligner("Local",synml)
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final=tf.concat([conv_final_g,conv_final_l],1)
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with tf.variable_scope("Combine_Renormalize",reuse=tf.AUTO_REUSE):
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with tf.variable_scope("Combine_Renormalize",reuse=tf.AUTO_REUSE):
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bl=tf.concat([bls,blhs],1)
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bl=tf.concat([bls,blhs],1)
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theta_bl=get_variable_by_shape((42,1),"theta_bl")
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#bl=bls-blhs
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theta_bl=get_variable_by_shape((21*2,1),"theta_bl")
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theta_bl=tf.matmul(bl,theta_bl)
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theta_bl=tf.matmul(bl,theta_bl)
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x=tf.concat([x,theta_bl],1)
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x=tf.concat([x,theta_bl],1)
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theta=get_variable_by_shape((5,19),"theta")
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theta=get_variable_by_shape((4,49*2),"theta")
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bias=get_variable_by_shape((1,19),"b")
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bias=get_variable_by_shape((1,49*2),"b")
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theta_2=tf.matmul(x,theta)+bias
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theta_2=tf.matmul(x,theta)+bias
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print(theta_2)
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print(theta_2)
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theta_2=tf.reshape(theta_2,(-1,19,1))
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theta_2=tf.reshape(theta_2,(-1,49*2,1))
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theta_2=tf.tile(theta_2,[1,1,dim*2])
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theta_2=tf.tile(theta_2,[1,1,dim*2])
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print(theta_2)
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print(theta_2)
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conv_final=conv_final*theta_2
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final=final*theta_2
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print(conv_final)
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print(final)
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flat=tf.layers.flatten(conv_final)
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flat=tf.layers.flatten(final)
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flat_w=tf.layers.flatten(W)
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#flat_w=tf.layers.flatten(W)
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flat=tf.concat([flat,flat_w],1)
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#flat=tf.concat([flat,flat_w],1)
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print(flat)
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print(flat)
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dense=tf.layers.dense(flat,2048,kernel_regularizer=reg,bias_regularizer=reg)
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dense=tf.layers.dense(flat,2048,kernel_regularizer=reg_l2,bias_regularizer=reg_l2)
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dense_2=tf.layers.dense(dense,1024,kernel_regularizer=reg,bias_regularizer=reg)
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dense_2=tf.layers.dense(dense,1024,kernel_regularizer=reg_l2,bias_regularizer=reg_l2)
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dense_3=tf.layers.dense(dense_2,512,kernel_regularizer=reg,bias_regularizer=reg)
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dense_3=tf.layers.dense(dense_2,512,kernel_regularizer=reg_l2,bias_regularizer=reg_l2)
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logits_pred=tf.layers.dense(dense_3,5,name="Predictions")
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logits_pred=tf.layers.dense(dense_3,4,name="Predictions")
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entropy=tf.nn.sparse_softmax_cross_entropy_with_logits(logits=logits_pred,labels=y)
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entropy=tf.nn.sparse_softmax_cross_entropy_with_logits(logits=logits_pred,labels=y)
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print(entropy)
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print(entropy)
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#weights = tf.trainable_variables() # all vars of your graph
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#regl1 = tf.contrib.layers.apply_regularization(reg_l1, weights)
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reg_losses = tf.get_collection(tf.GraphKeys.REGULARIZATION_LOSSES)
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reg_losses = tf.get_collection(tf.GraphKeys.REGULARIZATION_LOSSES)
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reg_constant = 0.0001
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reg_constant =0.00000001
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loss=tf.reduce_mean(entropy)+reg_constant * sum(reg_losses)
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loss=tf.reduce_mean(entropy)+reg_constant * sum(reg_losses)
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#loss=tf.reduce_mean(entropy)
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optimizer=tf.train.RMSPropOptimizer(lr)
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optimizer=tf.train.RMSPropOptimizer(lr)
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#optimizer=tf.train.AdamOptimizer()
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t_op=optimizer.minimize(loss)
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t_op=optimizer.minimize(loss)
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acc=tf.math.in_top_k(tf.cast(logits_pred,tf.float32),y,1)
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acc=tf.math.in_top_k(tf.cast(logits_pred,tf.float32),y,1)
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accuracy=tf.reduce_mean(tf.cast(acc,tf.float32))
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accuracy=tf.reduce_mean(tf.cast(acc,tf.float32))
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init=tf.global_variables_initializer()
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init=tf.global_variables_initializer()
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saver=tf.train.Saver()
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saver=tf.train.Saver()
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for node in (synm,bls,blhs,gl,dps,dphs,dis,lr,y):
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for node in (synmg,synml,bls,blhs,gl,dps,dphs,dis,lr,y):
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g.add_to_collection("input_nodes",node)
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g.add_to_collection("input_nodes",node)
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for node in (loss,t_op,accuracy,init):
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for node in (loss,t_op,accuracy,init):
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