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Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) #2

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Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5)#2

Description

@cinmon
cinmon
opened on Jul 15, 2026

Problem

Running the interaction example fails at model loading:

python Interaction_inference.py --device cpu
RuntimeError: Error(s) in loading state_dict for MultiOutputModel:
Missing key(s) in state_dict: "fc.weight", "fc.bias".
Unexpected key(s) in state_dict: "fc1.weight", "fc1.bias", "fc2.weight", "fc2.bias".
size mismatch for base_model.1.conv.3.weight: copying a param with shape
torch.Size([8, 32, 1, 1]) from checkpoint, the shape in current model is
torch.Size([16, 32, 1, 1]).
[...252 size mismatches total]

(my environment is Python 3.7.4, PyTorch from requirements.txt, Linux, CPU)

Cause

The current Interaction_model/model/checkpoint-000100.pth was trained with a different architecture than the one modelv2.py / Mobilev2.py build:

  • Classifier head: checkpoint has fc1 (100→128) + fc2 (128→1); code builds a single fc (100→1)
  • Backbone: checkpoint is MobileNetV2 at width_mult=0.5 (channels 8/48/480, last_channel=128); code builds width_mult=1.0 (16/96/960, last_channel=1280)
  • GCN layers: checkpoint gc1 is (100, 256) and gc2 is (256, 128); code builds (100, 512) and (512, 1280)

Total: 4 unexpected keys, 2 missing keys, 252 size mismatches.

git log shows the checkpoint was replaced after the model code was uploaded, and the code was never updated to match, so I think that's the likely origin.

checkpoint-000100.pth : ca280e5, 4fed02f
modelv2.py : 4fed02f
Mobilev2.py : 4fed02f

Fix (Verified)

The original checkpoint from 4fed02f loads into the current code with zero missing keys, extra keys, or size mismatches, and the pipeline then
runs to completion, producing a valid output/CCI_out.csv:

git show 4fed02f:Interaction_model/model/checkpoint-000100.pth > Interaction_model/model/checkpoint-000100.pth

It looks like ca280e5 overwrote the working checkpoint by mistake. Reverting that file resolves the issue.

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Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) · Issue #2 · JiangBioLab/DeepCCI · GitHub
      Skip to content
      Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) #2
      Open
      Open
      Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5)#2
      Description
      @cinmon
      cinmon
      opened on Jul 15, 2026
      Problem
      Running the interaction example fails at model loading:
      python Interaction_inference.py --device cpu
RuntimeError: Error(s) in loading state_dict for MultiOutputModel:
Missing key(s) in state_dict: "fc.weight", "fc.bias".
Unexpected key(s) in state_dict: "fc1.weight", "fc1.bias", "fc2.weight", "fc2.bias".
size mismatch for base_model.1.conv.3.weight: copying a param with shape
torch.Size([8, 32, 1, 1]) from checkpoint, the shape in current model is
torch.Size([16, 32, 1, 1]).
[...252 size mismatches total]

      (my environment is Python 3.7.4, PyTorch from requirements.txt, Linux, CPU)
      Cause
      The current Interaction_model/model/checkpoint-000100.pth was trained with a different architecture than the one modelv2.py / Mobilev2.py build:
      • Classifier head: checkpoint has fc1 (100→128) + fc2 (128→1); code builds a single fc (100→1)
      • Backbone: checkpoint is MobileNetV2 at width_mult=0.5 (channels 8/48/480, last_channel=128); code builds width_mult=1.0 (16/96/960, last_channel=1280)
      • GCN layers: checkpoint gc1 is (100, 256) and gc2 is (256, 128); code builds (100, 512) and (512, 1280)
      Total: 4 unexpected keys, 2 missing keys, 252 size mismatches.
      git log shows the checkpoint was replaced after the model code was uploaded, and the code was never updated to match, so I think that's the likely origin.
      checkpoint-000100.pth : ca280e5, 4fed02f
modelv2.py : 4fed02f
Mobilev2.py : 4fed02f

      Fix (Verified)
      The original checkpoint from 4fed02f loads into the current code with zero missing keys, extra keys, or size mismatches, and the pipeline then
      
runs to completion, producing a valid output/CCI_out.csv:
      git show 4fed02f:Interaction_model/model/checkpoint-000100.pth > Interaction_model/model/checkpoint-000100.pth
      It looks like ca280e5 overwrote the working checkpoint by mistake. Reverting that file resolves the issue.
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Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) · Issue #2 · JiangBioLab/DeepCCI · GitHub
          Skip to content
          Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) #2
          Open
          Open
          Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5)#2
          Description
          @cinmon
          cinmon
          opened on Jul 15, 2026
          Problem
          Running the interaction example fails at model loading:
          python Interaction_inference.py --device cpu
RuntimeError: Error(s) in loading state_dict for MultiOutputModel:
Missing key(s) in state_dict: "fc.weight", "fc.bias".
Unexpected key(s) in state_dict: "fc1.weight", "fc1.bias", "fc2.weight", "fc2.bias".
size mismatch for base_model.1.conv.3.weight: copying a param with shape
torch.Size([8, 32, 1, 1]) from checkpoint, the shape in current model is
torch.Size([16, 32, 1, 1]).
[...252 size mismatches total]

          (my environment is Python 3.7.4, PyTorch from requirements.txt, Linux, CPU)
          Cause
          The current Interaction_model/model/checkpoint-000100.pth was trained with a different architecture than the one modelv2.py / Mobilev2.py build:
          • Classifier head: checkpoint has fc1 (100→128) + fc2 (128→1); code builds a single fc (100→1)
          • Backbone: checkpoint is MobileNetV2 at width_mult=0.5 (channels 8/48/480, last_channel=128); code builds width_mult=1.0 (16/96/960, last_channel=1280)
          • GCN layers: checkpoint gc1 is (100, 256) and gc2 is (256, 128); code builds (100, 512) and (512, 1280)
          Total: 4 unexpected keys, 2 missing keys, 252 size mismatches.
          git log shows the checkpoint was replaced after the model code was uploaded, and the code was never updated to match, so I think that's the likely origin.
          checkpoint-000100.pth : ca280e5, 4fed02f
modelv2.py : 4fed02f
Mobilev2.py : 4fed02f

          Fix (Verified)
          The original checkpoint from 4fed02f loads into the current code with zero missing keys, extra keys, or size mismatches, and the pipeline then
          
runs to completion, producing a valid output/CCI_out.csv:
          git show 4fed02f:Interaction_model/model/checkpoint-000100.pth > Interaction_model/model/checkpoint-000100.pth
          It looks like ca280e5 overwrote the working checkpoint by mistake. Reverting that file resolves the issue.
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Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) · Issue #2 · JiangBioLab/DeepCCI · GitHub
              Skip to content
              Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) #2
              Open
              Open
              Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5)#2
              Description
              @cinmon
              cinmon
              opened on Jul 15, 2026
              Problem
              Running the interaction example fails at model loading:
              python Interaction_inference.py --device cpu
RuntimeError: Error(s) in loading state_dict for MultiOutputModel:
Missing key(s) in state_dict: "fc.weight", "fc.bias".
Unexpected key(s) in state_dict: "fc1.weight", "fc1.bias", "fc2.weight", "fc2.bias".
size mismatch for base_model.1.conv.3.weight: copying a param with shape
torch.Size([8, 32, 1, 1]) from checkpoint, the shape in current model is
torch.Size([16, 32, 1, 1]).
[...252 size mismatches total]

              (my environment is Python 3.7.4, PyTorch from requirements.txt, Linux, CPU)
              Cause
              The current Interaction_model/model/checkpoint-000100.pth was trained with a different architecture than the one modelv2.py / Mobilev2.py build:
              • Classifier head: checkpoint has fc1 (100→128) + fc2 (128→1); code builds a single fc (100→1)
              • Backbone: checkpoint is MobileNetV2 at width_mult=0.5 (channels 8/48/480, last_channel=128); code builds width_mult=1.0 (16/96/960, last_channel=1280)
              • GCN layers: checkpoint gc1 is (100, 256) and gc2 is (256, 128); code builds (100, 512) and (512, 1280)
              Total: 4 unexpected keys, 2 missing keys, 252 size mismatches.
              git log shows the checkpoint was replaced after the model code was uploaded, and the code was never updated to match, so I think that's the likely origin.
              checkpoint-000100.pth : ca280e5, 4fed02f
modelv2.py : 4fed02f
Mobilev2.py : 4fed02f

              Fix (Verified)
              The original checkpoint from 4fed02f loads into the current code with zero missing keys, extra keys, or size mismatches, and the pipeline then
              
runs to completion, producing a valid output/CCI_out.csv:
              git show 4fed02f:Interaction_model/model/checkpoint-000100.pth > Interaction_model/model/checkpoint-000100.pth
              It looks like ca280e5 overwrote the working checkpoint by mistake. Reverting that file resolves the issue.
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Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) · Issue #2 · JiangBioLab/DeepCCI · GitHub
                  Skip to content
                  Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) #2
                  Open
                  Open
                  Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5)#2
                  Description
                  @cinmon
                  cinmon
                  opened on Jul 15, 2026
                  Problem
                  Running the interaction example fails at model loading:
                  python Interaction_inference.py --device cpu
RuntimeError: Error(s) in loading state_dict for MultiOutputModel:
Missing key(s) in state_dict: "fc.weight", "fc.bias".
Unexpected key(s) in state_dict: "fc1.weight", "fc1.bias", "fc2.weight", "fc2.bias".
size mismatch for base_model.1.conv.3.weight: copying a param with shape
torch.Size([8, 32, 1, 1]) from checkpoint, the shape in current model is
torch.Size([16, 32, 1, 1]).
[...252 size mismatches total]

                  (my environment is Python 3.7.4, PyTorch from requirements.txt, Linux, CPU)
                  Cause
                  The current Interaction_model/model/checkpoint-000100.pth was trained with a different architecture than the one modelv2.py / Mobilev2.py build:
                  • Classifier head: checkpoint has fc1 (100→128) + fc2 (128→1); code builds a single fc (100→1)
                  • Backbone: checkpoint is MobileNetV2 at width_mult=0.5 (channels 8/48/480, last_channel=128); code builds width_mult=1.0 (16/96/960, last_channel=1280)
                  • GCN layers: checkpoint gc1 is (100, 256) and gc2 is (256, 128); code builds (100, 512) and (512, 1280)
                  Total: 4 unexpected keys, 2 missing keys, 252 size mismatches.
                  git log shows the checkpoint was replaced after the model code was uploaded, and the code was never updated to match, so I think that's the likely origin.
                  checkpoint-000100.pth : ca280e5, 4fed02f
modelv2.py : 4fed02f
Mobilev2.py : 4fed02f

                  Fix (Verified)
                  The original checkpoint from 4fed02f loads into the current code with zero missing keys, extra keys, or size mismatches, and the pipeline then
                  
runs to completion, producing a valid output/CCI_out.csv:
                  git show 4fed02f:Interaction_model/model/checkpoint-000100.pth > Interaction_model/model/checkpoint-000100.pth
                  It looks like ca280e5 overwrote the working checkpoint by mistake. Reverting that file resolves the issue.
                  Metadata
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Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) · Issue #2 · JiangBioLab/DeepCCI · GitHub
                      Skip to content
                      Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) #2
                      Open
                      Open
                      Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5)#2
                      Description
                      @cinmon
                      cinmon
                      opened on Jul 15, 2026
                      Problem
                      Running the interaction example fails at model loading:
                      python Interaction_inference.py --device cpu
RuntimeError: Error(s) in loading state_dict for MultiOutputModel:
Missing key(s) in state_dict: "fc.weight", "fc.bias".
Unexpected key(s) in state_dict: "fc1.weight", "fc1.bias", "fc2.weight", "fc2.bias".
size mismatch for base_model.1.conv.3.weight: copying a param with shape
torch.Size([8, 32, 1, 1]) from checkpoint, the shape in current model is
torch.Size([16, 32, 1, 1]).
[...252 size mismatches total]

                      (my environment is Python 3.7.4, PyTorch from requirements.txt, Linux, CPU)
                      Cause
                      The current Interaction_model/model/checkpoint-000100.pth was trained with a different architecture than the one modelv2.py / Mobilev2.py build:
                      • Classifier head: checkpoint has fc1 (100→128) + fc2 (128→1); code builds a single fc (100→1)
                      • Backbone: checkpoint is MobileNetV2 at width_mult=0.5 (channels 8/48/480, last_channel=128); code builds width_mult=1.0 (16/96/960, last_channel=1280)
                      • GCN layers: checkpoint gc1 is (100, 256) and gc2 is (256, 128); code builds (100, 512) and (512, 1280)
                      Total: 4 unexpected keys, 2 missing keys, 252 size mismatches.
                      git log shows the checkpoint was replaced after the model code was uploaded, and the code was never updated to match, so I think that's the likely origin.
                      checkpoint-000100.pth : ca280e5, 4fed02f
modelv2.py : 4fed02f
Mobilev2.py : 4fed02f

                      Fix (Verified)
                      The original checkpoint from 4fed02f loads into the current code with zero missing keys, extra keys, or size mismatches, and the pipeline then
                      
runs to completion, producing a valid output/CCI_out.csv:
                      git show 4fed02f:Interaction_model/model/checkpoint-000100.pth > Interaction_model/model/checkpoint-000100.pth
                      It looks like ca280e5 overwrote the working checkpoint by mistake. Reverting that file resolves the issue.
                      Metadata
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                          No branches or pull requests
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Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) · Issue #2 · JiangBioLab/DeepCCI · GitHub
                          Skip to content
                          Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) #2
                          Open
                          Open
                          Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5)#2
                          Description
                          @cinmon
                          cinmon
                          opened on Jul 15, 2026
                          Problem
                          Running the interaction example fails at model loading:
                          python Interaction_inference.py --device cpu
RuntimeError: Error(s) in loading state_dict for MultiOutputModel:
Missing key(s) in state_dict: "fc.weight", "fc.bias".
Unexpected key(s) in state_dict: "fc1.weight", "fc1.bias", "fc2.weight", "fc2.bias".
size mismatch for base_model.1.conv.3.weight: copying a param with shape
torch.Size([8, 32, 1, 1]) from checkpoint, the shape in current model is
torch.Size([16, 32, 1, 1]).
[...252 size mismatches total]

                          (my environment is Python 3.7.4, PyTorch from requirements.txt, Linux, CPU)
                          Cause
                          The current Interaction_model/model/checkpoint-000100.pth was trained with a different architecture than the one modelv2.py / Mobilev2.py build:
                          • Classifier head: checkpoint has fc1 (100→128) + fc2 (128→1); code builds a single fc (100→1)
                          • Backbone: checkpoint is MobileNetV2 at width_mult=0.5 (channels 8/48/480, last_channel=128); code builds width_mult=1.0 (16/96/960, last_channel=1280)
                          • GCN layers: checkpoint gc1 is (100, 256) and gc2 is (256, 128); code builds (100, 512) and (512, 1280)
                          Total: 4 unexpected keys, 2 missing keys, 252 size mismatches.
                          git log shows the checkpoint was replaced after the model code was uploaded, and the code was never updated to match, so I think that's the likely origin.
                          checkpoint-000100.pth : ca280e5, 4fed02f
modelv2.py : 4fed02f
Mobilev2.py : 4fed02f

                          Fix (Verified)
                          The original checkpoint from 4fed02f loads into the current code with zero missing keys, extra keys, or size mismatches, and the pipeline then
                          
runs to completion, producing a valid output/CCI_out.csv:
                          git show 4fed02f:Interaction_model/model/checkpoint-000100.pth > Interaction_model/model/checkpoint-000100.pth
                          It looks like ca280e5 overwrote the working checkpoint by mistake. Reverting that file resolves the issue.
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Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) · Issue #2 · JiangBioLab/DeepCCI · GitHub
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                              Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5) #2
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                              Open
                              Interaction_inference.py fails: checkpoint-000100.pth does not match modelv2.py (commit ca280e5)#2
                              Description
                              @cinmon
                              cinmon
                              opened on Jul 15, 2026
                              Problem
                              Running the interaction example fails at model loading:
                              python Interaction_inference.py --device cpu
RuntimeError: Error(s) in loading state_dict for MultiOutputModel:
Missing key(s) in state_dict: "fc.weight", "fc.bias".
Unexpected key(s) in state_dict: "fc1.weight", "fc1.bias", "fc2.weight", "fc2.bias".
size mismatch for base_model.1.conv.3.weight: copying a param with shape
torch.Size([8, 32, 1, 1]) from checkpoint, the shape in current model is
torch.Size([16, 32, 1, 1]).
[...252 size mismatches total]

                              (my environment is Python 3.7.4, PyTorch from requirements.txt, Linux, CPU)
                              Cause
                              The current Interaction_model/model/checkpoint-000100.pth was trained with a different architecture than the one modelv2.py / Mobilev2.py build:
                              • Classifier head: checkpoint has fc1 (100→128) + fc2 (128→1); code builds a single fc (100→1)
                              • Backbone: checkpoint is MobileNetV2 at width_mult=0.5 (channels 8/48/480, last_channel=128); code builds width_mult=1.0 (16/96/960, last_channel=1280)
                              • GCN layers: checkpoint gc1 is (100, 256) and gc2 is (256, 128); code builds (100, 512) and (512, 1280)
                              Total: 4 unexpected keys, 2 missing keys, 252 size mismatches.
                              git log shows the checkpoint was replaced after the model code was uploaded, and the code was never updated to match, so I think that's the likely origin.
                              checkpoint-000100.pth : ca280e5, 4fed02f
modelv2.py : 4fed02f
Mobilev2.py : 4fed02f

                              Fix (Verified)
                              The original checkpoint from 4fed02f loads into the current code with zero missing keys, extra keys, or size mismatches, and the pipeline then
                              
runs to completion, producing a valid output/CCI_out.csv:
                              git show 4fed02f:Interaction_model/model/checkpoint-000100.pth > Interaction_model/model/checkpoint-000100.pth
                              It looks like ca280e5 overwrote the working checkpoint by mistake. Reverting that file resolves the issue.
                              Metadata
                              Metadata
                              Assignees
                              No one assigned
                                Labels
                                No labels
                                No labels
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                                No projects
                                  Milestone
                                  No milestone
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                                  None yet
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                                  Issue actions