Open bfurtwa opened 5 years ago
Hi, I still cannot reproduce this error. I used exactly the same datasets and command:
python capsule_network_emb_cpu.py
and got the result:
[Epoch 1] Testing Loss: 0.0661 (MSE: 7.0000)
>> Corr on 27464 testing samples: 0.94613 | 0.95537
[Epoch 2] Testing Loss: 0.0504 (MSE: 7.0000)
>> Corr on 27464 testing samples: 0.96649 | 0.97090
What's your PyTorch version?
I tried pytorch-cpu 0.4.1 and pytorch 0.4.0 from conda install pytorch-cpu=0.x.0 -c pytorch
With 0.4.0 and a new git clone it looks like that:
D:\Benni\Code\DeepRT\DeepRTplus>python capsule_network_emb_cpu.py
0 -> *
1 -> 1
2 -> 2
3 -> A
4 -> D
5 -> E
6 -> F
7 -> G
8 -> H
9 -> I
10 -> K
11 -> L
12 -> M
13 -> N
14 -> P
15 -> Q
16 -> R
17 -> S
18 -> T
19 -> V
20 -> W
21 -> Y
>> number of aa: 22
>> note: using seq mode.
>> note: using >>>embedding<<< method.
DeepRT: using max length defined by user: 50
Read training data done; source: data/MapAlignerIdentificationuRTdata_train_2.tx
t
Note: didn't load val data.
Read testing data done; source: data/MapAlignerIdentificationuRTdata_test_2.txt
0 -> *
1 -> 1
2 -> 2
3 -> A
4 -> D
5 -> E
6 -> F
7 -> G
8 -> H
9 -> I
10 -> K
11 -> L
12 -> M
13 -> N
14 -> P
15 -> Q
16 -> R
17 -> S
18 -> T
19 -> V
20 -> W
21 -> Y
# parameters: 2869704
0%| | 0/115 [00:00<?, ?it/s]0
-> *
1 -> 1
2 -> 2
3 -> A
4 -> D
5 -> E
6 -> F
7 -> G
8 -> H
9 -> I
10 -> K
11 -> L
12 -> M
13 -> N
14 -> P
15 -> Q
16 -> R
17 -> S
18 -> T
19 -> V
20 -> W
21 -> Y
>> number of aa: 22
>> note: using seq mode.
capsule_network_emb_cpu.py:575: UserWarning: invalid index of a 0-dim tensor. Th
is will be an error in PyTorch 0.5. Use tensor.item() to convert a 0-dim tensor
to a Python number
meter_loss.add(state['loss'].data[0])
100%|████████████████████████████████████████| 115/115 [05:51<00:00, 3.06s/it]
[Epoch 1] Training Loss: 0.1141 (MSE: 7.0000)
0 -> *
1 -> 1
2 -> 2
3 -> A
4 -> D
5 -> E
6 -> F
7 -> G
8 -> H
9 -> I
10 -> K
11 -> L
12 -> M
13 -> N
14 -> P
15 -> Q
16 -> R
17 -> S
18 -> T
19 -> V
20 -> W
21 -> Y
>> number of aa: 22
>> note: using seq mode.
[Epoch 1] Testing Loss: 0.0767 (MSE: 7.0000)
Traceback (most recent call last):
File "capsule_network_emb_cpu.py", line 743, in <module>
engine.train(processor, get_rt_iterator(True), maxepoch=NUM_EPOCHS, optimize
r=optimizer)
File "D:\Programs\anaconda3\lib\site-packages\torchnet\engine\engine.py", line
67, in train
self.hook('on_end_epoch', state)
File "D:\Programs\anaconda3\lib\site-packages\torchnet\engine\engine.py", line
31, in hook
self.hooks[name](state)
File "capsule_network_emb_cpu.py", line 664, in on_end_epoch
test_batch = Variable(corpus.test[bi*PRED_BATCH:(bi+1)*PRED_BATCH,:])
RuntimeError: dimension out of range (expected to be in range of [-1, 0], but go
t 1)
This is my minimal python environment
(DeepRT) D:\Benni\Code\DeepRT\DeepRTplus>conda list
# packages in environment at D:\Programs\anaconda3\envs\DeepRT:
#
# Name Version Build Channel
blas 1.0 mkl
certifi 2018.10.15 py36_0
cffi 1.11.5 py36h74b6da3_1
chardet 3.0.4 <pip>
icc_rt 2017.0.4 h97af966_0
idna 2.7 <pip>
intel-openmp 2019.0 118
mkl 2019.0 118
mkl_fft 1.0.6 py36hdbbee80_0
mkl_random 1.0.1 py36h77b88f5_1
numpy 1.15.3 py36ha559c80_0
numpy-base 1.15.3 py36h8128ebf_0
pandas 0.23.4 py36h830ac7b_0
Pillow 5.3.0 <pip>
pip 10.0.1 py36_0
pycparser 2.19 py36_0
python 3.6.7 h33f27b4_1
python-dateutil 2.7.3 py36_0
pytorch-cpu 0.4.0 py36_cpuhe774522_1 pytorch
pytz 2018.5 py36_0
pyzmq 17.1.2 <pip>
requests 2.20.0 <pip>
scipy 1.1.0 <pip>
setuptools 40.4.3 py36_0
six 1.11.0 py36_1
six 1.11.0 <pip>
torchfile 0.1.0 <pip>
torchnet 0.0.4 <pip>
torchvision 0.2.1 <pip>
tornado 5.1.1 <pip>
tqdm 4.26.0 py36h28b3542_0
urllib3 1.24 <pip>
vc 14.1 h0510ff6_4
visdom 0.1.8.5 <pip>
vs2015_runtime 14.15.26706 h3a45250_0
websocket-client 0.53.0 <pip>
wheel 0.32.2 py36_0
wincertstore 0.2 py36h7fe50ca_0
I used a dataset with modifications encoded as "1" and "2". data.txt
And the same data with all modified peptides removed. data_no_mods.txt
With the modified peptides, I got this error: