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TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. #5

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Open
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.#5

Description

@chuangzhao0601
chuangzhao0601
opened on Oct 25, 2024

Hello author, when I reproduce the DeepTalk-singleST.ipynb file, I encountered such error:
dt.File_Train(st_data, pathways, lrpairs_train, meta_data, species, LR_train = 'Sst_Sstr2',
outdir = Test_dir)

dt.data_for_train(st_data,data_dir='/mnt/workspace/test/single-cell/data/',LR_train="Sst_Sstr2")

dt.Train(data_name='Sst_Sstr2',
data_path='/mnt/workspace/test/single-cell/data/',
outdir='/mnt/workspace/test/single-cell/data/Sst_Sstr2/output',
pretrained_embeddings='/mnt/workspace/test/single-cell/data/Sst_Sstr2/data_pca.emd',
n_epochs=30, ft_n_epochs=10)

Loading graph...
DataSet Stats :
Number of Nodes 2399
Number of Edges 119477
Number of Node types 1
Number of relations 1
Graph with 2399 nodes and 119477 edges
2399 2
check torch.Size([2399, 128]) 2399
node2vec tensor torch.Size([2399, 128])
No. of nodes with pretrained embedding: 2399
No. edges in test data: 48252
PRETRAINING

generate walks ...
no. of walks 19192
train /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_train.txt
validate /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_validate.txt
test /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_test.txt

Run model for pre-training ...

Begin Training

Epoch: 0
MinLoss: 1000000.0, CurLoss: 7.9438
epoch time: (s) 138.76754474639893

Epoch: 10
MinLoss: 1000000.0, CurLoss: 7.8022
epoch time: (s) 138.13774728775024

Epoch: 20
MinLoss: 1000000.0, CurLoss: 7.7198
epoch time: (s) 140.38009071350098

Best Epoch: 29
In GenericGraph link Prediction Generation
168882
Generating false edges by random false target
train
valid
test

!!!!
4 4 Linear(in_features=512, out_features=512, bias=True)
Evaluating valid batch 0
Evaluating valid batch 100
Evaluating test batch 0
Evaluating test batch 100
Evaluating test batch 200

Begin evaluation for link prediction...
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.

the important package versions:
deeptalk-st 0.0.4
as for other packages,I followed the Installation guidance

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TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. · Issue #5 · JiangBioLab/DeepTalk · GitHub
    Skip to content
    TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. #5
    Open
    Open
    TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.#5
    Description
    @chuangzhao0601
    chuangzhao0601
    opened on Oct 25, 2024
    Hello author, when I reproduce the DeepTalk-singleST.ipynb file, I encountered such error:
    
dt.File_Train(st_data, pathways, lrpairs_train, meta_data, species, LR_train = 'Sst_Sstr2',
    
outdir = Test_dir)
    dt.data_for_train(st_data,data_dir='/mnt/workspace/test/single-cell/data/',LR_train="Sst_Sstr2")
    dt.Train(data_name='Sst_Sstr2',
    
data_path='/mnt/workspace/test/single-cell/data/',
    
outdir='/mnt/workspace/test/single-cell/data/Sst_Sstr2/output',
    
pretrained_embeddings='/mnt/workspace/test/single-cell/data/Sst_Sstr2/data_pca.emd',
    
n_epochs=30, ft_n_epochs=10)
    Loading graph...
    
DataSet Stats :
    
Number of Nodes 2399
    
Number of Edges 119477
    
Number of Node types 1
    
Number of relations 1
    
Graph with 2399 nodes and 119477 edges
    
2399 2
    
check torch.Size([2399, 128]) 2399
    
node2vec tensor torch.Size([2399, 128])
    
No. of nodes with pretrained embedding: 2399
    
No. edges in test data: 48252
    PRETRAINING
    generate walks ...
    
no. of walks 19192
    
train /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_train.txt
    
validate /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_validate.txt
    
test /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_test.txt
    Run model for pre-training ...
    Begin Training
    Epoch: 0
    
MinLoss: 1000000.0, CurLoss: 7.9438
    
epoch time: (s) 138.76754474639893
    Epoch: 10
    
MinLoss: 1000000.0, CurLoss: 7.8022
    
epoch time: (s) 138.13774728775024
    Epoch: 20
    
MinLoss: 1000000.0, CurLoss: 7.7198
    
epoch time: (s) 140.38009071350098
    Best Epoch: 29
    
In GenericGraph link Prediction Generation
    
168882
    
Generating false edges by random false target
    
train
    
valid
    
test
    !!!!
    
4 4 Linear(in_features=512, out_features=512, bias=True)
    
Evaluating valid batch 0
    
Evaluating valid batch 100
    
Evaluating test batch 0
    
Evaluating test batch 100
    
Evaluating test batch 200
    Begin evaluation for link prediction...
    
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.
    the important package versions:
    
deeptalk-st 0.0.4
    
as for other packages,I followed the Installation guidance
    Metadata
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, 'i');
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var __re = new RegExp('^' + ".*" + '
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. · Issue #5 · JiangBioLab/DeepTalk · GitHub
      Skip to content
      TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. #5
      Open
      Open
      TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.#5
      Description
      @chuangzhao0601
      chuangzhao0601
      opened on Oct 25, 2024
      Hello author, when I reproduce the DeepTalk-singleST.ipynb file, I encountered such error:
      
dt.File_Train(st_data, pathways, lrpairs_train, meta_data, species, LR_train = 'Sst_Sstr2',
      
outdir = Test_dir)
      dt.data_for_train(st_data,data_dir='/mnt/workspace/test/single-cell/data/',LR_train="Sst_Sstr2")
      dt.Train(data_name='Sst_Sstr2',
      
data_path='/mnt/workspace/test/single-cell/data/',
      
outdir='/mnt/workspace/test/single-cell/data/Sst_Sstr2/output',
      
pretrained_embeddings='/mnt/workspace/test/single-cell/data/Sst_Sstr2/data_pca.emd',
      
n_epochs=30, ft_n_epochs=10)
      Loading graph...
      
DataSet Stats :
      
Number of Nodes 2399
      
Number of Edges 119477
      
Number of Node types 1
      
Number of relations 1
      
Graph with 2399 nodes and 119477 edges
      
2399 2
      
check torch.Size([2399, 128]) 2399
      
node2vec tensor torch.Size([2399, 128])
      
No. of nodes with pretrained embedding: 2399
      
No. edges in test data: 48252
      PRETRAINING
      generate walks ...
      
no. of walks 19192
      
train /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_train.txt
      
validate /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_validate.txt
      
test /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_test.txt
      Run model for pre-training ...
      Begin Training
      Epoch: 0
      
MinLoss: 1000000.0, CurLoss: 7.9438
      
epoch time: (s) 138.76754474639893
      Epoch: 10
      
MinLoss: 1000000.0, CurLoss: 7.8022
      
epoch time: (s) 138.13774728775024
      Epoch: 20
      
MinLoss: 1000000.0, CurLoss: 7.7198
      
epoch time: (s) 140.38009071350098
      Best Epoch: 29
      
In GenericGraph link Prediction Generation
      
168882
      
Generating false edges by random false target
      
train
      
valid
      
test
      !!!!
      
4 4 Linear(in_features=512, out_features=512, bias=True)
      
Evaluating valid batch 0
      
Evaluating valid batch 100
      
Evaluating test batch 0
      
Evaluating test batch 100
      
Evaluating test batch 200
      Begin evaluation for link prediction...
      
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.
      the important package versions:
      
deeptalk-st 0.0.4
      
as for other packages,I followed the Installation guidance
      Metadata
      Metadata
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        Labels
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        No branches or pull requests
        Issue actions
        
, 'i');
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var __m = "*";
var __re = new RegExp('^' + ".*" + '
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. · Issue #5 · JiangBioLab/DeepTalk · GitHub
        Skip to content
        TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. #5
        Open
        Open
        TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.#5
        Description
        @chuangzhao0601
        chuangzhao0601
        opened on Oct 25, 2024
        Hello author, when I reproduce the DeepTalk-singleST.ipynb file, I encountered such error:
        
dt.File_Train(st_data, pathways, lrpairs_train, meta_data, species, LR_train = 'Sst_Sstr2',
        
outdir = Test_dir)
        dt.data_for_train(st_data,data_dir='/mnt/workspace/test/single-cell/data/',LR_train="Sst_Sstr2")
        dt.Train(data_name='Sst_Sstr2',
        
data_path='/mnt/workspace/test/single-cell/data/',
        
outdir='/mnt/workspace/test/single-cell/data/Sst_Sstr2/output',
        
pretrained_embeddings='/mnt/workspace/test/single-cell/data/Sst_Sstr2/data_pca.emd',
        
n_epochs=30, ft_n_epochs=10)
        Loading graph...
        
DataSet Stats :
        
Number of Nodes 2399
        
Number of Edges 119477
        
Number of Node types 1
        
Number of relations 1
        
Graph with 2399 nodes and 119477 edges
        
2399 2
        
check torch.Size([2399, 128]) 2399
        
node2vec tensor torch.Size([2399, 128])
        
No. of nodes with pretrained embedding: 2399
        
No. edges in test data: 48252
        PRETRAINING
        generate walks ...
        
no. of walks 19192
        
train /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_train.txt
        
validate /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_validate.txt
        
test /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_test.txt
        Run model for pre-training ...
        Begin Training
        Epoch: 0
        
MinLoss: 1000000.0, CurLoss: 7.9438
        
epoch time: (s) 138.76754474639893
        Epoch: 10
        
MinLoss: 1000000.0, CurLoss: 7.8022
        
epoch time: (s) 138.13774728775024
        Epoch: 20
        
MinLoss: 1000000.0, CurLoss: 7.7198
        
epoch time: (s) 140.38009071350098
        Best Epoch: 29
        
In GenericGraph link Prediction Generation
        
168882
        
Generating false edges by random false target
        
train
        
valid
        
test
        !!!!
        
4 4 Linear(in_features=512, out_features=512, bias=True)
        
Evaluating valid batch 0
        
Evaluating valid batch 100
        
Evaluating test batch 0
        
Evaluating test batch 100
        
Evaluating test batch 200
        Begin evaluation for link prediction...
        
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.
        the important package versions:
        
deeptalk-st 0.0.4
        
as for other packages,I followed the Installation guidance
        Metadata
        Metadata
        Assignees
        No one assigned
          Labels
          No labels
          No labels
          Projects
          No projects
          Milestone
          No milestone
          Relationships
          None yet
          Development
          No branches or pull requests
          Issue actions
          
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
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var __re = new RegExp('^' + "youtube\\.com" + '
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. · Issue #5 · JiangBioLab/DeepTalk · GitHub
          Skip to content
          TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. #5
          Open
          Open
          TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.#5
          Description
          @chuangzhao0601
          chuangzhao0601
          opened on Oct 25, 2024
          Hello author, when I reproduce the DeepTalk-singleST.ipynb file, I encountered such error:
          
dt.File_Train(st_data, pathways, lrpairs_train, meta_data, species, LR_train = 'Sst_Sstr2',
          
outdir = Test_dir)
          dt.data_for_train(st_data,data_dir='/mnt/workspace/test/single-cell/data/',LR_train="Sst_Sstr2")
          dt.Train(data_name='Sst_Sstr2',
          
data_path='/mnt/workspace/test/single-cell/data/',
          
outdir='/mnt/workspace/test/single-cell/data/Sst_Sstr2/output',
          
pretrained_embeddings='/mnt/workspace/test/single-cell/data/Sst_Sstr2/data_pca.emd',
          
n_epochs=30, ft_n_epochs=10)
          Loading graph...
          
DataSet Stats :
          
Number of Nodes 2399
          
Number of Edges 119477
          
Number of Node types 1
          
Number of relations 1
          
Graph with 2399 nodes and 119477 edges
          
2399 2
          
check torch.Size([2399, 128]) 2399
          
node2vec tensor torch.Size([2399, 128])
          
No. of nodes with pretrained embedding: 2399
          
No. edges in test data: 48252
          PRETRAINING
          generate walks ...
          
no. of walks 19192
          
train /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_train.txt
          
validate /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_validate.txt
          
test /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_test.txt
          Run model for pre-training ...
          Begin Training
          Epoch: 0
          
MinLoss: 1000000.0, CurLoss: 7.9438
          
epoch time: (s) 138.76754474639893
          Epoch: 10
          
MinLoss: 1000000.0, CurLoss: 7.8022
          
epoch time: (s) 138.13774728775024
          Epoch: 20
          
MinLoss: 1000000.0, CurLoss: 7.7198
          
epoch time: (s) 140.38009071350098
          Best Epoch: 29
          
In GenericGraph link Prediction Generation
          
168882
          
Generating false edges by random false target
          
train
          
valid
          
test
          !!!!
          
4 4 Linear(in_features=512, out_features=512, bias=True)
          
Evaluating valid batch 0
          
Evaluating valid batch 100
          
Evaluating test batch 0
          
Evaluating test batch 100
          
Evaluating test batch 200
          Begin evaluation for link prediction...
          
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.
          the important package versions:
          
deeptalk-st 0.0.4
          
as for other packages,I followed the Installation guidance
          Metadata
          Metadata
          Assignees
          No one assigned
            Labels
            No labels
            No labels
            Projects
            No projects
            Milestone
            No milestone
            Relationships
            None yet
            Development
            No branches or pull requests
            Issue actions
            
, 'i');
if (__m === '*' || __re.test(location.href)) {
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function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
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}
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var lastUrl = location.href;
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if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
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observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. · Issue #5 · JiangBioLab/DeepTalk · GitHub
            Skip to content
            TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. #5
            Open
            Open
            TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.#5
            Description
            @chuangzhao0601
            chuangzhao0601
            opened on Oct 25, 2024
            Hello author, when I reproduce the DeepTalk-singleST.ipynb file, I encountered such error:
            
dt.File_Train(st_data, pathways, lrpairs_train, meta_data, species, LR_train = 'Sst_Sstr2',
            
outdir = Test_dir)
            dt.data_for_train(st_data,data_dir='/mnt/workspace/test/single-cell/data/',LR_train="Sst_Sstr2")
            dt.Train(data_name='Sst_Sstr2',
            
data_path='/mnt/workspace/test/single-cell/data/',
            
outdir='/mnt/workspace/test/single-cell/data/Sst_Sstr2/output',
            
pretrained_embeddings='/mnt/workspace/test/single-cell/data/Sst_Sstr2/data_pca.emd',
            
n_epochs=30, ft_n_epochs=10)
            Loading graph...
            
DataSet Stats :
            
Number of Nodes 2399
            
Number of Edges 119477
            
Number of Node types 1
            
Number of relations 1
            
Graph with 2399 nodes and 119477 edges
            
2399 2
            
check torch.Size([2399, 128]) 2399
            
node2vec tensor torch.Size([2399, 128])
            
No. of nodes with pretrained embedding: 2399
            
No. edges in test data: 48252
            PRETRAINING
            generate walks ...
            
no. of walks 19192
            
train /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_train.txt
            
validate /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_validate.txt
            
test /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_test.txt
            Run model for pre-training ...
            Begin Training
            Epoch: 0
            
MinLoss: 1000000.0, CurLoss: 7.9438
            
epoch time: (s) 138.76754474639893
            Epoch: 10
            
MinLoss: 1000000.0, CurLoss: 7.8022
            
epoch time: (s) 138.13774728775024
            Epoch: 20
            
MinLoss: 1000000.0, CurLoss: 7.7198
            
epoch time: (s) 140.38009071350098
            Best Epoch: 29
            
In GenericGraph link Prediction Generation
            
168882
            
Generating false edges by random false target
            
train
            
valid
            
test
            !!!!
            
4 4 Linear(in_features=512, out_features=512, bias=True)
            
Evaluating valid batch 0
            
Evaluating valid batch 100
            
Evaluating test batch 0
            
Evaluating test batch 100
            
Evaluating test batch 200
            Begin evaluation for link prediction...
            
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.
            the important package versions:
            
deeptalk-st 0.0.4
            
as for other packages,I followed the Installation guidance
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TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. · Issue #5 · JiangBioLab/DeepTalk · GitHub
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              TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first. #5
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              Open
              TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.#5
              Description
              @chuangzhao0601
              chuangzhao0601
              opened on Oct 25, 2024
              Hello author, when I reproduce the DeepTalk-singleST.ipynb file, I encountered such error:
              
dt.File_Train(st_data, pathways, lrpairs_train, meta_data, species, LR_train = 'Sst_Sstr2',
              
outdir = Test_dir)
              dt.data_for_train(st_data,data_dir='/mnt/workspace/test/single-cell/data/',LR_train="Sst_Sstr2")
              dt.Train(data_name='Sst_Sstr2',
              
data_path='/mnt/workspace/test/single-cell/data/',
              
outdir='/mnt/workspace/test/single-cell/data/Sst_Sstr2/output',
              
pretrained_embeddings='/mnt/workspace/test/single-cell/data/Sst_Sstr2/data_pca.emd',
              
n_epochs=30, ft_n_epochs=10)
              Loading graph...
              
DataSet Stats :
              
Number of Nodes 2399
              
Number of Edges 119477
              
Number of Node types 1
              
Number of relations 1
              
Graph with 2399 nodes and 119477 edges
              
2399 2
              
check torch.Size([2399, 128]) 2399
              
node2vec tensor torch.Size([2399, 128])
              
No. of nodes with pretrained embedding: 2399
              
No. edges in test data: 48252
              PRETRAINING
              generate walks ...
              
no. of walks 19192
              
train /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_train.txt
              
validate /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_validate.txt
              
test /mnt/workspace/test/single-cell/data//Sst_Sstr2/outdir/Sst_Sstr2_walks_test.txt
              Run model for pre-training ...
              Begin Training
              Epoch: 0
              
MinLoss: 1000000.0, CurLoss: 7.9438
              
epoch time: (s) 138.76754474639893
              Epoch: 10
              
MinLoss: 1000000.0, CurLoss: 7.8022
              
epoch time: (s) 138.13774728775024
              Epoch: 20
              
MinLoss: 1000000.0, CurLoss: 7.7198
              
epoch time: (s) 140.38009071350098
              Best Epoch: 29
              
In GenericGraph link Prediction Generation
              
168882
              
Generating false edges by random false target
              
train
              
valid
              
test
              !!!!
              
4 4 Linear(in_features=512, out_features=512, bias=True)
              
Evaluating valid batch 0
              
Evaluating valid batch 100
              
Evaluating test batch 0
              
Evaluating test batch 100
              
Evaluating test batch 200
              Begin evaluation for link prediction...
              
TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first.
              the important package versions:
              
deeptalk-st 0.0.4
              
as for other packages,I followed the Installation guidance
              Metadata
              Metadata
              Assignees
              No one assigned
                Labels
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