ValueError: Imaginary component #15
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Just browsing here for a different reason... just to make sure... does this also happen with more than 2 molecules? (since it calculates the variance...) |
renzph
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1. Changes to `get_one_hot` Problems are given in: - #14 - #17 - #13 I discarded the changes in the PRs and and added more comprehensive handling of the input data in the `SmilesDataset` class and the `get_one_hot` function. 2. Imaginary components Frechet distance calculation fails to work for some cases because of badly conditioned matrices, as described here #15. Could not reproduce the error locally, but could do so on colab. Fixed it in `calculate_frechet_distance` by checking if the first `covmean` computation is real add a small value to the diagonal. This made it work for me and I got the same result as the original implementation run locally. 3. Added some more tests and changed to pytest 4. As described in #16 I changed the data type of the activations to float32 in the `get_predictions` function, which saves memory for larger datasets.
renzph
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Apr 1, 2024
1. Changes to `get_one_hot` Problems are given in: - #14 - #17 - #13 I discarded the changes in the PRs and and added more comprehensive handling of the input data in the `SmilesDataset` class and the `get_one_hot` function. 2. Imaginary components Frechet distance calculation fails to work for some cases because of badly conditioned matrices, as described here #15. Could not reproduce the error locally, but could do so on colab. Fixed it in `calculate_frechet_distance` by checking if the first `covmean` computation is real add a small value to the diagonal. This made it work for me and I got the same result as the original implementation run locally. 3. Added some more tests and changed to pytest 4. As described in #16 I changed the data type of the activations to float32 in the `get_predictions` function, which saves memory for larger datasets.
renzph
added a commit
that referenced
this issue
Apr 1, 2024
1. Changes to `get_one_hot` Problems are given in: - #14 - #17 - #13 I discarded the changes in the PRs and and added more comprehensive handling of the input data in the `SmilesDataset` class and the `get_one_hot` function. 2. Imaginary components Frechet distance calculation fails to work for some cases because of badly conditioned matrices, as described here #15. Could not reproduce the error locally, but could do so on colab. Fixed it in `calculate_frechet_distance` by checking if the first `covmean` computation is real add a small value to the diagonal. This made it work for me and I got the same result as the original implementation run locally. 3. Added some more tests and changed to pytest 4. As described in #16 I changed the data type of the activations to float32 in the `get_predictions` function, which saves memory for larger datasets.
renzph
added a commit
that referenced
this issue
Apr 1, 2024
1. Changes to `get_one_hot` Problems are given in: - #14 - #17 - #13 I discarded the changes in the PRs and and added more comprehensive handling of the input data in the `SmilesDataset` class and the `get_one_hot` function. 2. Imaginary components Frechet distance calculation fails to work for some cases because of badly conditioned matrices, as described here #15. Could not reproduce the error locally, but could do so on colab. Fixed it in `calculate_frechet_distance` by checking if the first `covmean` computation is real add a small value to the diagonal. This made it work for me and I got the same result as the original implementation run locally. 3. Added some more tests and changed to pytest 4. As described in #16 I changed the data type of the activations to float32 in the `get_predictions` function, which saves memory for larger datasets.
renzph
added a commit
that referenced
this issue
Apr 1, 2024
1. Changes to `get_one_hot` Problems are given in: - #14 - #17 - #13 I discarded the changes in the PRs and and added more comprehensive handling of the input data in the `SmilesDataset` class and the `get_one_hot` function. 2. Imaginary components Frechet distance calculation fails to work for some cases because of badly conditioned matrices, as described here #15. Could not reproduce the error locally, but could do so on colab. Fixed it in `calculate_frechet_distance` by checking if the first `covmean` computation is real add a small value to the diagonal. This made it work for me and I got the same result as the original implementation run locally. 3. Added some more tests and changed to pytest 4. As described in #16 I changed the data type of the activations to float32 in the `get_predictions` function, which saves memory for larger datasets.
renzph
added a commit
that referenced
this issue
Apr 1, 2024
1. Changes to `get_one_hot` Problems are given in: - #14 - #17 - #13 I discarded the changes in the PRs and and added more comprehensive handling of the input data in the `SmilesDataset` class and the `get_one_hot` function. 2. Imaginary components Frechet distance calculation fails to work for some cases because of badly conditioned matrices, as described here #15. Could not reproduce the error locally, but could do so on colab. Fixed it in `calculate_frechet_distance` by checking if the first `covmean` computation is real add a small value to the diagonal. This made it work for me and I got the same result as the original implementation run locally. 3. Added some more tests and changed to pytest 4. As described in #16 I changed the data type of the activations to float32 in the `get_predictions` function, which saves memory for larger datasets. 5. Change to pyproject.toml
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Hey @parkyjmit, It turned out to be a numerical issue. I fixed it in the new release and it should be working on colab now. |
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Hello, I've got an issue for get_fcd function.
I reproduced this error in google colab
and I've got this result.
ValueError Traceback (most recent call last)
in <cell line: 3>()
1 smiles_list1 = ['COc1cccc(NC(=O)Cc2coc3ccc(OC)cc23)c1', 'Cc1noc(C)c1CN(C)C(=O)Nc1cc(F)cc(F)c1']
2 smiles_list2 = ['Oc1ccccc1-c1cccc2cnccc12', 'Cc1noc(C)c1CN(C)C(=O)Nc1cc(F)cc(F)c1']
----> 3 get_fcd(smiles_list1, smiles_list2)
1 frames
/usr/local/lib/python3.10/dist-packages/fcd/utils.py in calculate_frechet_distance(mu1, sigma1, mu2, sigma2, eps)
171 if not np.allclose(np.diagonal(covmean).imag, 0, atol=1e-3):
172 m = np.max(np.abs(covmean.imag))
--> 173 raise ValueError("Imaginary component {}".format(m))
174 covmean = covmean.real
175
ValueError: Imaginary component 1.90603044681631e+39
Do you have any idea to solve this?
I have to get fcd value for my project
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