hantaoshu/deepsem

deepsem's Issues

Query on Embedding_tutorial.ipynb

NVIDIA GPU must need?

Hi, great software!
Is the NVIDIA GPU necessary? Or how to deal with the following error. Thanks!

python /home/data/ssy022/DeepSEM/main.py --task celltype_GRN --data_file /home/data/ssy022/cellbender/allday_harmony_process.h5ad --net_file demo_data/GRN_inference/input/500_ChIP-seq_hESC/label.csv --setting new --alpha 0.1 --beta 0.01 --n_epochs 150  --save_name out
Traceback (most recent call last):
  File "/home/data/ssy022/DeepSEM/main.py", line 77, in <module>
    model.train_model()
  File "/home/data/ssy022/DeepSEM/src/DeepSEM_cell_type_specific_GRN_model.py", line 82, in train_model
    vae = VAE_EAD(adj_A_init, 1, self.opt.n_hidden, self.opt.K).float().cuda()
  File "/home/data/ssy022/miniconda3/envs/deepsem/lib/python3.7/site-packages/torch/nn/modules/module.py", line 311, in cuda
    return self._apply(lambda t: t.cuda(device))
  File "/home/data/ssy022/miniconda3/envs/deepsem/lib/python3.7/site-packages/torch/nn/modules/module.py", line 208, in _apply
    module._apply(fn)
  File "/home/data/ssy022/miniconda3/envs/deepsem/lib/python3.7/site-packages/torch/nn/modules/module.py", line 208, in _apply
    module._apply(fn)
  File "/home/data/ssy022/miniconda3/envs/deepsem/lib/python3.7/site-packages/torch/nn/modules/module.py", line 208, in _apply
    module._apply(fn)
  File "/home/data/ssy022/miniconda3/envs/deepsem/lib/python3.7/site-packages/torch/nn/modules/module.py", line 230, in _apply
    param_applied = fn(param)
  File "/home/data/ssy022/miniconda3/envs/deepsem/lib/python3.7/site-packages/torch/nn/modules/module.py", line 311, in <lambda>
    return self._apply(lambda t: t.cuda(device))
  File "/home/data/ssy022/miniconda3/envs/deepsem/lib/python3.7/site-packages/torch/cuda/__init__.py", line 178, in _lazy_init
    _check_driver()
  File "/home/data/ssy022/miniconda3/envs/deepsem/lib/python3.7/site-packages/torch/cuda/__init__.py", line 99, in _check_driver
    http://www.nvidia.com/Download/index.aspx""")
AssertionError:
Found no NVIDIA driver on your system. Please check that you
have an NVIDIA GPU and installed a driver from
http://www.nvidia.com/Download/index.aspx

Issue with pandas DataFrame constructor

Hello! I get the following issue when trying to run the embedding tutorial, any idea what the problem is ?
Thanks!

how to install

hello， I follow the instruction but I met some errors：

scanpy 1.6.0 requires pandas>=0.21, which is not installed.

ERROR: Could not find a version that satisfies the requirement pandas==0.17.1 (from versions: 0.1, 0.2, 0.3.0, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.5.0, 0.6.0, 0.6.1, 0.7.0, 0.7.1, 0.7.2, 0.7.3, 0.8.0, 0.8.1, 0.9.0, 0.9.1, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.15.2, 0.16.0, 0.16.1, 0.16.2, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 0.19.2, 0.20.0, 0.20.1, 0.20.2, 0.20.3, 0.21.0, 0.21.1, 0.22.0, 0.23.0, 0.23.1, 0.23.2, 0.23.3, 0.23.4, 0.24.0, 0.24.1, 0.24.2, 0.25.0, 0.25.1, 0.25.2, 0.25.3, 1.0.0, 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.1.0, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.2.4, 1.2.5, 1.3.0, 1.3.1, 1.3.2, 1.3.3)
ERROR: No matching distribution found for pandas==0.17.1

Thanks

BEELINE integration question

Greetings!

Thank you for using BEELINE in your study. I was wondering if the DeepSEM team integrated the algorithm into BEELINE's pipeline or just used the datasets to benchmark. If the former, do you all still have the scripts for your benchmarking? I'd like to implement DeepSEM as a benchmarkable algorithm in BEELINE.

Thanks,
Tim

some question about code

in paper formula 5 and 6 ,each gene is processed individual, but in code https://github.com/HantaoShu/DeepSEM/blob/master/src/Model.py#L94 , Fusion of genes from different groups.
@HantaoShu

Why transpose the adjacency matrix

X = XWT +Z ，T is a transpose symbol, what does transpose mean here

Some questions about the code

In Model.py，line 131 ：logits, prob, y = self.qyx(x.squeeze(2), temperature) ，I can't understand the specific meaning of logits, prob,y, I hope you can explain it，Thank you.

adj_A_t_inv = torch.inverse(adj_A_t) RuntimeError: inverse_cuda: U(1,1) is zero, singular U.

About input data format

hello, i find that the demo input data format is gene as column, that is different from the instructions on the home page about input data format. can you tell me what is right, thank you~~~

Query on Embedding_tutorial.ipynb output

Hi DeepSEM team,

I am trying to understand the output from Embedding_tutorial.ipynb

My understanding is that after running the 'embedding' task, I should get a AnnData of the shape:

n_samples x n_hidden
where,
n_samples=no. of samples in my input data, and
n_hidden=opt.n_hidden specified by me in main.py settings

therefore, implying that my input data has been embedded into a lower dimensional (=n_hidden) space.

However, the dimension I am getting in the output is:
n_samples x n_genes
where, n_genes=no. of genes in my input data

This implies that I am not getting a lower-dimensional embedding that I am looking for.

Can you please explain if I am missing something here?

Thanks,
Vivek

AssertionError: Found no NVIDIA driver on your system

hello，I try to run DeepSEM following the toturials on my cluster which has no GPU

python main.py  --task non_celltype_GRN --data_file demo_data/GRN_inference/input/500_STRING_hESC/data.csv \
        --net_file demo_data/GRN_inference/input/500_STRING_hESC/label.csv --setting new --alpha 100 \
        --beta 1 --n_epoch 90 --save_name out_test

and I got the errors:

dir exist
Traceback (most recent call last):
  File "main.py", line 53, in <module>
    model.train_model()
  File "path/DeepSEM/src/DeepSEM_cell_type_non_specific_GRN_model.py", line 71, in train_model
    vae = VAE_EAD(adj_A_init, 1, opt.n_hidden, opt.K).float().cuda()
  File "path/env_DeepSEM/lib/python3.7/site-packages/torch/nn/modules/module.py", line 311, in cuda
    return self._apply(lambda t: t.cuda(device))
  File "path/env_DeepSEM/lib/python3.7/site-packages/torch/nn/modules/module.py", line 208, in _apply
    module._apply(fn)
  File "path/env_DeepSEM/lib/python3.7/site-packages/torch/nn/modules/module.py", line 208, in _apply
    module._apply(fn)
  File "path/env_DeepSEM/lib/python3.7/site-packages/torch/nn/modules/module.py", line 208, in _apply
    module._apply(fn)
  File "path/env_DeepSEM/lib/python3.7/site-packages/torch/nn/modules/module.py", line 230, in _apply
    param_applied = fn(param)
  File "path/env_DeepSEM/lib/python3.7/site-packages/torch/nn/modules/module.py", line 311, in <lambda>
    return self._apply(lambda t: t.cuda(device))
  File "path/env_DeepSEM/lib/python3.7/site-packages/torch/cuda/__init__.py", line 178, in _lazy_init
    _check_driver()
  File "path/env_DeepSEM/lib/python3.7/site-packages/torch/cuda/__init__.py", line 99, in _check_driver
    http://www.nvidia.com/Download/index.aspx""")
AssertionError: 
Found no NVIDIA driver on your system. Please check that you
have an NVIDIA GPU and installed a driver from
http://www.nvidia.com/Download/index.aspx

Is there possible I can run DeepSEM on my cluster wihch has no GPU?

Thanks ！！！

FileNotFoundError but not mentioning the name of file

I am running the GRN inference step but getting the FileNotFoundError: [Errno 2]. it is not clear that which file is not found.
Please help.

I have installed all the required packages using pip

Thanks in advance
Ekta

python main.py --task celltype_GRN --data_file counts_normazile_log_transformed.csv --setting new --alpha 100 --beta 1 --n_epoch 90 --save_name out1
Traceback (most recent call last):
File "main.py", line 77, in
model.train_model()
File "/home/ekta/Documents/1_ekta_research_work/covid_Pancreas/Qc_doublet_removal/res_4_5/analysis/anticipated_revision/DeepSEM-master/src/DeepSEM_cell_type_specific_GRN_model.py", line 80, in train_model
dataloader, Evaluate_Mask, num_nodes, num_genes, data, truth_edges, TFmask2, gene_name = self.init_data()
File "/home/ekta/Documents/1_ekta_research_work/covid_Pancreas/Qc_doublet_removal/res_4_5/analysis/anticipated_revision/DeepSEM-master/src/DeepSEM_cell_type_specific_GRN_model.py", line 32, in init_data
Ground_Truth = pd.read_csv(self.opt.net_file, header=0)
File "/home/ekta/anaconda3/lib/python3.8/site-packages/pandas/io/parsers.py", line 686, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/ekta/anaconda3/lib/python3.8/site-packages/pandas/io/parsers.py", line 452, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/home/ekta/anaconda3/lib/python3.8/site-packages/pandas/io/parsers.py", line 936, in init
self._make_engine(self.engine)
File "/home/ekta/anaconda3/lib/python3.8/site-packages/pandas/io/parsers.py", line 1168, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/ekta/anaconda3/lib/python3.8/site-packages/pandas/io/parsers.py", line 1998, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: ''

Using DeepSEM to build Co-expression network and identify hub gene ?

Hello,

I want to ask if I can use this software to do gene co-network analysis, such as replacing transcription factors (the first column in the file label.csv) with highly expressed genes that I am interested in.

Thanks !!!

Best