Rafael

Hi Carla, if I understood your problem correctly, you want to obtain the following summary_plot: ``` explanation_val = explainer.shap_values(X) shap.summary_plot(explanation_val) ``` From an Explanation object. explanation_val is a list which,...

I have encountered the same problem, but only when I installed tmap using pip. Installing using conda solves this issue. In case you are using Google Colab: ``` !pip install...

I also noticed that this function will not standardize tautomeric forms. I guess it just doesn't do what I thought it would. The function shown [here](https://bitsilla.com/blog/2021/06/standardizing-a-molecule-using-rdkit/) seems to do the...

Thank you for the prompt reply! I must inform you that the "runpy" command is still showing the same error to me (I even created a new env to check),...

The shap value produced for classification problems is a continuous value that ranges from - infinity to + infinity and is called log-odds. It is related to the probability by...

> the sum of the shap values of all the variables is equal to ln(P/1-P) where P is the final prediction? Yes, but P is not the prediction, it is...

Beautiful! I really enjoy this topic of interpretability of models. Could you comment on the problem (if there is one) of using a 1024-bit fingerprint to train a ML model...

Hi, not sure if this will help you, but I was able to use tmap on Google Colab (Python 3.7.12) Here is a Gist with a very simple working example:...

Update: I commented out the `os.unlink(tmp_file.name)` line and it appeared to work, with the warning: ``` C:\Users\rafae\miniconda3\envs\molfeat-env\lib\site-packages\dgl\core.py:82: DGLWarning: The input graph for the user-defined edge function does not contain valid...

There seems to be a compatibility problem with JTVAE. From https://github.com/awslabs/dgl-lifesci: If you need to work on the example of JTVAE, then you need RDKit 2018.09.3. And this is not...