I can't reproduce vignette results

[grokkaine]

maui_vignette.zip

I like maui and explore the possibility of VAEs in a cancer subtyping project, but I am having a hard time to reproduce your vignette results. The issue arises at plotting the losses, I pretty much have no recorded loss, and from then on everything goes south, ROC curves are deflated etc. I wonder if it has anything to do with me using Keras 2.3? I got this user warning:

miniconda3/envs/iomics/lib/python3.7/site-packages/keras/engine/training_utils.py:819: UserWarning: Output reconstruction missing from loss dictionary. We assume this was done on purpose. The fit and evaluate APIs will not be expecting any data to be passed to reconstruction.
  'be expecting any data to be passed to {0}.'.format(name))

It almost looks as the fit function doesn't update weights from one epoch to another. Have you encountered such error? I attach my vignette, went a bit past the loss plot and then I stopped testing, but at teh end you can see my pip freeze.

[messersc]

Hi,

not sure if that's useful for you after this much time. You are right, your loss curves look very suspicious. I can run your notebook fine, looks like some newer version broke something, not sure what though. Might be that python 3.7 needs to be downgraded.

Find below the conda env that I used for maui:

# packages in environment at /vol/home-vol3/wbi/messersc/miniconda3/envs/maui:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
absl-py                   0.8.1                    pypi_0    pypi
astor                     0.8.1                    pypi_0    pypi
attrs                     19.3.0                   pypi_0    pypi
backcall                  0.1.0                    pypi_0    pypi
bleach                    3.1.0                    pypi_0    pypi
ca-certificates           2019.11.27                    0  
cachetools                3.1.1                    pypi_0    pypi
certifi                   2019.11.28               py36_0  
chardet                   3.0.4                    pypi_0    pypi
cycler                    0.10.0                   pypi_0    pypi
decorator                 4.4.1                    pypi_0    pypi
defusedxml                0.6.0                    pypi_0    pypi
entrypoints               0.3                      pypi_0    pypi
gast                      0.2.2                    pypi_0    pypi
google-auth               1.8.1                    pypi_0    pypi
google-auth-oauthlib      0.4.1                    pypi_0    pypi
google-pasta              0.1.8                    pypi_0    pypi
grpcio                    1.25.0                   pypi_0    pypi
h5py                      2.10.0                   pypi_0    pypi
idna                      2.8                      pypi_0    pypi
importlib-metadata        1.3.0                    pypi_0    pypi
ipykernel                 5.1.3                    pypi_0    pypi
ipyparallel               6.2.4                    pypi_0    pypi
ipython                   7.10.1                   pypi_0    pypi
ipython-genutils          0.2.0                    pypi_0    pypi
ipywidgets                7.5.1                    pypi_0    pypi
jedi                      0.15.1                   pypi_0    pypi
jinja2                    2.10.3                   pypi_0    pypi
joblib                    0.14.1                   pypi_0    pypi
jsonschema                3.2.0                    pypi_0    pypi
jupyter                   1.0.0                    pypi_0    pypi
jupyter-client            5.3.4                    pypi_0    pypi
jupyter-console           6.0.0                    pypi_0    pypi
jupyter-core              4.6.1                    pypi_0    pypi
keras                     2.2.5                    pypi_0    pypi
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.0                    pypi_0    pypi
kiwisolver                1.1.0                    pypi_0    pypi
libedit                   3.1.20181209         hc058e9b_0  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 9.1.0                hdf63c60_0  
libstdcxx-ng              9.1.0                hdf63c60_0  
markdown                  3.1.1                    pypi_0    pypi
markupsafe                1.1.1                    pypi_0    pypi
matplotlib                3.1.2                    pypi_0    pypi
maui-tools                0.1.7                     dev_0    <develop>
mistune                   0.8.4                    pypi_0    pypi
more-itertools            8.0.2                    pypi_0    pypi
nbconvert                 5.6.1                    pypi_0    pypi
nbformat                  4.4.0                    pypi_0    pypi
ncurses                   6.1                  he6710b0_1  
notebook                  6.0.2                    pypi_0    pypi
numpy                     1.17.4                   pypi_0    pypi
oauthlib                  3.1.0                    pypi_0    pypi
openssl                   1.1.1d               h7b6447c_3  
opt-einsum                3.1.0                    pypi_0    pypi
packaging                 19.2                     pypi_0    pypi
pandas                    0.25.3                   pypi_0    pypi
pandocfilters             1.4.2                    pypi_0    pypi
parso                     0.5.1                    pypi_0    pypi
pexpect                   4.7.0                    pypi_0    pypi
pickleshare               0.7.5                    pypi_0    pypi
pip                       19.3.1                   py36_0  
pluggy                    0.13.1                   pypi_0    pypi
prometheus-client         0.7.1                    pypi_0    pypi
prompt-toolkit            3.0.2                    pypi_0    pypi
protobuf                  3.11.1                   pypi_0    pypi
ptyprocess                0.6.0                    pypi_0    pypi
py                        1.8.0                    pypi_0    pypi
pyasn1                    0.4.8                    pypi_0    pypi
pyasn1-modules            0.2.7                    pypi_0    pypi
pygments                  2.5.2                    pypi_0    pypi
pyparsing                 2.4.5                    pypi_0    pypi
pyrsistent                0.15.6                   pypi_0    pypi
pytest                    5.3.1                    pypi_0    pypi
python                    3.6.9                h265db76_0  
python-dateutil           2.8.1                    pypi_0    pypi
pytz                      2019.3                   pypi_0    pypi
pyyaml                    5.2                      pypi_0    pypi
pyzmq                     18.1.1                   pypi_0    pypi
qtconsole                 4.6.0                    pypi_0    pypi
readline                  7.0                  h7b6447c_5  
requests                  2.22.0                   pypi_0    pypi
requests-oauthlib         1.3.0                    pypi_0    pypi
rsa                       4.0                      pypi_0    pypi
scikit-learn              0.22                     pypi_0    pypi
scipy                     1.2.1                    pypi_0    pypi
seaborn                   0.9.0                    pypi_0    pypi
send2trash                1.5.0                    pypi_0    pypi
setuptools                42.0.2                   py36_0  
six                       1.13.0                   pypi_0    pypi
sqlite                    3.30.1               h7b6447c_0  
tensorboard               1.14.0                   pypi_0    pypi
tensorflow                1.14.0                   pypi_0    pypi
tensorflow-estimator      1.14.0                   pypi_0    pypi
termcolor                 1.1.0                    pypi_0    pypi
terminado                 0.8.3                    pypi_0    pypi
testpath                  0.4.4                    pypi_0    pypi
tk                        8.6.8                hbc83047_0  
tornado                   6.0.3                    pypi_0    pypi
traitlets                 4.3.3                    pypi_0    pypi
urllib3                   1.25.7                   pypi_0    pypi
wcwidth                   0.1.7                     dev_0    <develop>
webencodings              0.5.1                    pypi_0    pypi
werkzeug                  0.16.0                   pypi_0    pypi
wheel                     0.33.6                   py36_0  
widgetsnbextension        3.5.1                    pypi_0    pypi
wrapt                     1.11.2                   pypi_0    pypi
xz                        5.2.4                h14c3975_4  
zipp                      0.6.0                    pypi_0    pypi
zlib                      1.2.11               h7b6447c_3