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Load organism: Bacillus
('./fasta/Bacillus_neg.fa', './fasta/Bacillus_pos.fa')
Input Shapes
X: (1373, 51) | y: (1373,)
>>> Testing PARTITION 1
(1235, 51)
(1235,)
__________________________________________________________________________________________________
Layer (type) Output Shape Param # Connected to
==================================================================================================
input_1 (InputLayer) (None, 51) 0
__________________________________________________________________________________________________
embedding_1 (Embedding) (None, 51, 9) 36 input_1[0][0]
__________________________________________________________________________________________________
conv1 (Conv1D) (None, 43, 256) 20992 embedding_1[0][0]
__________________________________________________________________________________________________
dropout_1 (Dropout) (None, 43, 256) 0 conv1[0][0]
__________________________________________________________________________________________________
conv1d_1 (Conv1D) (None, 18, 256) 590080 dropout_1[0][0]
__________________________________________________________________________________________________
reshape_1 (Reshape) (None, 576, 8) 0 conv1d_1[0][0]
__________________________________________________________________________________________________
lambda_1 (Lambda) (None, 576, 8) 0 reshape_1[0][0]
__________________________________________________________________________________________________
digitcaps (CapsuleLayer) (None, 1, 16) 74304 lambda_1[0][0]
__________________________________________________________________________________________________
input_2 (InputLayer) (None, 1) 0
__________________________________________________________________________________________________
mask_1 (Mask) (None, 16) 0 digitcaps[0][0]
input_2[0][0]
__________________________________________________________________________________________________
dense_1 (Dense) (None, 512) 8704 mask_1[0][0]
__________________________________________________________________________________________________
dense_2 (Dense) (None, 1024) 525312 dense_1[0][0]
__________________________________________________________________________________________________
out_caps (Length) (None, 1) 0 digitcaps[0][0]
__________________________________________________________________________________________________
dense_3 (Dense) (None, 51) 52275 dense_2[0][0]
==================================================================================================
Total params: 1,271,703
Trainable params: 1,271,127
Non-trainable params: 576
__________________________________________________________________________________________________
0 Train on SEED 23
Epoch 00001: val_loss improved from inf to 0.04778, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_0-weights.h5
Epoch 00002: val_loss improved from 0.04778 to 0.03384, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_0-weights.h5
Epoch 00003: val_loss improved from 0.03384 to 0.00405, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_0-weights.h5
Epoch 00004: val_loss did not improve
Epoch 00005: val_loss did not improve
Epoch 00006: val_loss did not improve
Epoch 00007: val_loss did not improve
Epoch 00008: val_loss did not improve
Epoch 00009: val_loss did not improve
Epoch 00010: val_loss did not improve
Epoch 00011: val_loss did not improve
Epoch 00012: val_loss did not improve
Epoch 00013: val_loss did not improve
1 Train on SEED 29
Epoch 00001: val_loss improved from inf to 0.00396, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_1-weights.h5
Epoch 00002: val_loss improved from 0.00396 to 0.00273, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_1-weights.h5
Epoch 00003: val_loss did not improve
Epoch 00004: val_loss did not improve
Epoch 00005: val_loss improved from 0.00273 to 0.00240, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_1-weights.h5
Epoch 00006: val_loss improved from 0.00240 to 0.00188, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_1-weights.h5
Epoch 00007: val_loss did not improve
Epoch 00008: val_loss did not improve
Epoch 00009: val_loss did not improve
Epoch 00010: val_loss did not improve
Epoch 00011: val_loss did not improve
Epoch 00012: val_loss did not improve
Epoch 00013: val_loss did not improve
Epoch 00014: val_loss did not improve
Epoch 00015: val_loss did not improve
Epoch 00016: val_loss did not improve
2 Train on SEED 31
Epoch 00001: val_loss improved from inf to 0.00106, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_2-weights.h5
Epoch 00002: val_loss did not improve
Epoch 00003: val_loss did not improve
Epoch 00004: val_loss did not improve
Epoch 00005: val_loss did not improve
Epoch 00006: val_loss did not improve
Epoch 00007: val_loss did not improve
Epoch 00008: val_loss did not improve
Epoch 00009: val_loss did not improve
Epoch 00010: val_loss did not improve
Epoch 00011: val_loss did not improve
Testing weigths ['org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_0-weights.h5', 'org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_2-weights.h5', 'org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_1-weights.h5']
MCC = 0.721370498851
Selected BEST
=================================================================
tp fp tn fn
36 18 83 1
_________________________________________________________________
Prec Sn Sp Acc F1 Mcc
0.667 0.973 0.822 0.862 0.791 0.721
=================================================================
MCC = 0.781528412286
Selected BEST
=================================================================
tp fp tn fn
36 13 88 1
_________________________________________________________________
Prec Sn Sp Acc F1 Mcc
0.735 0.973 0.871 0.899 0.837 0.782
=================================================================
MCC = 0.80315483975
Selected BEST
=================================================================
tp fp tn fn
33 7 94 4
_________________________________________________________________
Prec Sn Sp Acc F1 Mcc
0.825 0.892 0.931 0.92 0.857 0.803
=================================================================
Deleting weight: org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_0-weights.h5
Deleting weight: org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_2-weights.h5
Deleting weight: org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_1-weights.h5
Selected BEST: org_Bacillus-batch_8-emb_9-rout_3-partition_1-seed_1-weights.h5 (0.80315483975)
>>> Testing PARTITION 2
(1235, 51)
(1235,)
__________________________________________________________________________________________________
Layer (type) Output Shape Param # Connected to
==================================================================================================
input_1 (InputLayer) (None, 51) 0
__________________________________________________________________________________________________
embedding_1 (Embedding) (None, 51, 9) 36 input_1[0][0]
__________________________________________________________________________________________________
conv1 (Conv1D) (None, 43, 256) 20992 embedding_1[0][0]
__________________________________________________________________________________________________
dropout_1 (Dropout) (None, 43, 256) 0 conv1[0][0]
__________________________________________________________________________________________________
conv1d_1 (Conv1D) (None, 18, 256) 590080 dropout_1[0][0]
__________________________________________________________________________________________________
reshape_1 (Reshape) (None, 576, 8) 0 conv1d_1[0][0]
__________________________________________________________________________________________________
lambda_1 (Lambda) (None, 576, 8) 0 reshape_1[0][0]
__________________________________________________________________________________________________
digitcaps (CapsuleLayer) (None, 1, 16) 74304 lambda_1[0][0]
__________________________________________________________________________________________________
input_2 (InputLayer) (None, 1) 0
__________________________________________________________________________________________________
mask_1 (Mask) (None, 16) 0 digitcaps[0][0]
input_2[0][0]
__________________________________________________________________________________________________
dense_1 (Dense) (None, 512) 8704 mask_1[0][0]
__________________________________________________________________________________________________
dense_2 (Dense) (None, 1024) 525312 dense_1[0][0]
__________________________________________________________________________________________________
out_caps (Length) (None, 1) 0 digitcaps[0][0]
__________________________________________________________________________________________________
dense_3 (Dense) (None, 51) 52275 dense_2[0][0]
==================================================================================================
Total params: 1,271,703
Trainable params: 1,271,127
Non-trainable params: 576
__________________________________________________________________________________________________
0 Train on SEED 23
Epoch 00001: val_loss improved from inf to 0.05601, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_2-seed_0-weights.h5
Epoch 00002: val_loss improved from 0.05601 to 0.01544, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_2-seed_0-weights.h5
Epoch 00003: val_loss improved from 0.01544 to 0.01034, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_2-seed_0-weights.h5
Epoch 00004: val_loss did not improve
Epoch 00005: val_loss did not improve
Epoch 00006: val_loss improved from 0.01034 to 0.00509, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_2-seed_0-weights.h5
Epoch 00007: val_loss improved from 0.00509 to 0.00361, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_2-seed_0-weights.h5
Epoch 00008: val_loss did not improve
Epoch 00009: val_loss did not improve
Epoch 00010: val_loss did not improve
Epoch 00011: val_loss did not improve
Epoch 00012: val_loss did not improve
Epoch 00013: val_loss did not improve
Epoch 00014: val_loss did not improve
Epoch 00015: val_loss did not improve
Epoch 00016: val_loss did not improve
Epoch 00017: val_loss did not improve
1 Train on SEED 29
Epoch 00001: val_loss improved from inf to 0.00558, saving model to ./result/org_Bacillus-batch_8-emb_9-rout_3-partition_2-seed_1-weights.h5
Epoch 00002: val_loss did not improve