Binning data

Now I am trying to build new SAR expansion method. And to do that, I want to convert a dataset from continues to binned one. I searched google and found some method to achieve that. One is using Numpy and the other one is using Pandas. I thought using pandas is more efficient way. BasicContinue reading “Binning data”

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Graph convolution classification with deepchem

I posted about graph convolution regression using deepchem. And today, I tried graph convolution classification using deepchem. Code is almost same as regression model. The only a difference point is use dc.models.MultitaskGraphClassifier instead of dc.models.MultitaskGraphRegressor. I got sample ( JAK3 inhibitor ) data from chembl and tried to make model. At first I used pandasContinue reading “Graph convolution classification with deepchem”

Graph convolution regression with deepchem

Somedays ago, I posted blog about deepchem. I am still playing with deepchem. Today I tried to use graph convolution regression model. Deepchem provided Graph convolution Regressor. Cool. I used solubility data provided from AstraZeneca. https://www.ebi.ac.uk/chembl/assay/inspect/CHEMBL3301364 My test code is following. Almost same as deepchem”s example code. CSVLoader method is very useful because it canContinue reading “Graph convolution regression with deepchem”

integration of spotfire and pdb viewer

Some years ago, I heard a presentation about implementation of pdb viewer in spotfire in JCUP. It was really impressive for me because spotfire can not handle PDB files. You know, spotfire is one of the popular tool for data visualization. I like the tool. Recently I found unique library for spotfire named ‘JSViz’. TheContinue reading “integration of spotfire and pdb viewer”

how to get molecular graph features

Belated I am interested in deepchem that is an open-source deep learning toolkit for drug discovery. Deep-chem supported many features for chemoinformatics. And one of interested feature is calculation of molecular graphs. It is more primitive than hashed finger print. I tried to caluclate it. Currently the toolkit supports only linux, so I installed deepchemContinue reading “how to get molecular graph features”