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gvar's Introduction

👋 Hi! My name is Ričards Marcinkevičs. 🎓 Currently, I am a PhD student at the Institute for Machine Learning, Department of Computer Science, ETH Zurich. I am a Medical Data Science group member supervised by Prof. Dr. Julia E. Vogt and co-advised by Prof. Dr. Fanny Yang.

🤖 At the moment, I am broadly interested in interpretable and explainable machine learning. In particular, I would like to understand what are the inductive biases for neural networks that may render the model interpretable in specific use-cases and how such inductive biases may be incorporated into the model? Moreover, how can we leverage interpretations and explanations to obtain actionable insights about the data or the model itself, for instance, to perform scientific discovery or make our models fairer and more robust? From the application perspective, I work on time series and survival analysis and enjoy participating in interdisciplinary projects and leveraging ML methods to analyse biomedical data.

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gvar's Issues

IndexError: index 0 is out of bounds for dimension 0 with size 0

Hi! When I try running the training_procedure method on my own dataset (numpy array of size (3999,25)), the model runs for 3 epochs and then gives the following error: IndexError: index 0 is out of bounds for dimension 0 with size 0. How do I fix this?

This is the specific call: training_procedure(series, 10, 3, 3, 2, 0.1, 0.1)

Tuning the regularization parameters

Hi,

In practical settings, when the true GC connections are unknown, how would you recommend the regularization parameters (both lambda and gamma) be tuned? In particular, using test (R)MSEs would probably not work well due to the issue raised in Appendix M.

Thank you for your time!
Suryadi

can't install

(base) ..\Network\GVAR> conda env create -f environment.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:

  • libpng==1.6.37=hbc83047_0
  • zstd==1.4.5=h9ceee32_0
  • libxcb==1.14=h7b6447c_0
  • sip==4.19.8=py37hf484d3e_0
  • lcms2==2.11=h396b838_0
  • glib==2.65.0=h3eb4bd4_0
  • intel-openmp==2019.4=243
  • numpy==1.18.5=py37ha1c710e_0
  • qt==5.9.7=h5867ecd_1
  • gst-plugins-base==1.14.0=hbbd80ab_1
  • sqlite==3.32.3=h62c20be_0
  • libuuid==1.0.3=h1bed415_2
  • statsmodels==0.11.1=py37h7b6447c_0
  • tk==8.6.10=hbc83047_0
  • mkl_fft==1.1.0=py37h23d657b_0
  • dbus==1.13.16=hb2f20db_0
  • libtiff==4.1.0=h2733197_1
  • ld_impl_linux-64==2.33.1=h53a641e_7
  • expat==2.2.9=he6710b0_2
  • pillow==7.2.0=py37hb39fc2d_0
  • mkl-service==2.3.0=py37he904b0f_0
  • zlib==1.2.11=h7b6447c_3
  • ninja==1.9.0=py37hfd86e86_0
  • readline==8.0=h7b6447c_0
  • lz4-c==1.9.2=he6710b0_1
  • pcre==8.44=he6710b0_0
  • freetype==2.10.2=h5ab3b9f_0
  • numpy-base==1.18.5=py37hde5b4d6_0
  • matplotlib-base==3.2.1=py37hef1b27d_0
  • libffi==3.3=he6710b0_1
  • jpeg==9b=h024ee3a_2
  • libstdcxx-ng==9.1.0=hdf63c60_0
  • python==3.7.7=hcff3b4d_5
  • openssl==1.1.1g=h7b6447c_0
  • tornado==6.0.4=py37h7b6447c_1
  • libgcc-ng==9.1.0=hdf63c60_0
  • scikit-learn==0.22.1=py37hd81dba3_0
  • mkl==2019.4=243
  • pandas==1.0.5=py37h0573a6f_0
  • kiwisolver==1.2.0=py37hfd86e86_0
  • cudatoolkit==10.1.243=h6bb024c_0
  • libxml2==2.9.10=he19cac6_1
  • xz==5.2.5=h7b6447c_0
  • libedit==3.1.20191231=h7b6447c_0
  • pyqt==5.9.2=py37h05f1152_2
  • gstreamer==1.14.0=hb31296c_0
  • libgfortran-ng==7.3.0=hdf63c60_0
  • pytorch==1.6.0=py3.7_cuda10.1.243_cudnn7.6.3_0
  • fontconfig==2.13.0=h9420a91_0
  • cffi==1.14.0=py37he30daa8_1
  • scipy==1.5.0=py37h0b6359f_0
  • mkl_random==1.0.4=py37hd81dba3_0
  • ncurses==6.2=he6710b0_1
  • icu==58.2=he6710b0_3

Direction of causal matrix

Your logged causal matrix in CSV file seems to have different direction from Figure 2 in published paper.

Entreis (i, j) in logged causal matrix (result of run_grid_search function) means i causes j or j causes i?

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