DeepChem — A framework for using ML and DL for Life Science and Chemoinformatics

DeepChem — A framework for using ML and DL for Life Science and Chemoinformatics

Application of Machine Learning and Deep Learning for Drug Discovery, Genomics, Microsocopy and Quantum Chemistry can create radical impact and holds the potential to significantly accelerate the process of medical research and vaccine development, which is a necessity for any pandemic like Covid19.

Application of Machine Learning and Deep Learning for Drug Discovery, Genomics, Microsocopy and Quantum Chemistry can create radical impact and holds the potential to significantly accelerate the process of medical research and vaccine development, which is a necessity for any pandemic like Covid19.

Before we even begin, this article is a very high level one and specifically targeted for Data Scientists and ML Researchers interested in Drug Discovery, especially during the time of an existing pandemic like Covid19_. _If you are some one with a strong background in Bio-informatics or Chem-informatics and wants to venture into the world of data science for these use-cases, please reach out to me through any of the options mentioned here, and we can discuss few interesting opportunities for the greater good of mankind.

DeepChem, an open source framework, which internally uses TensorFlow, that has been specifically designed to simplify the creation of deep learning models for various life science applications.

In this tutorial, we will see how to setup DeepChem and we will see how to use DeepChem for :

1. training a model that can predict toxicity of molecules

2. training a model to predict solubility of molecules

3. using SMART strings to query molecular structures.

Setting Up DeepChem

Although, in multiple sources, I have seen users have expressed their concern in setting up DeepChem in Windows, Linux and Mac environments, but I found it quite easy to do that using pip installer.

The DeepChem development team, is very active and they do provide daily builds, so I would like everyone to take a look at their pypi page: https://pypi.org/project/deepchem/#history and install a suitable version in case if the latest version has any issue. A simple _pip install deepchem _would install the very latest version.

Next, along with DeepChem, you would require TensorFlow to be installed. I had installed the latest version of TensorFlow using pip install tensorflow _and RDkit which is an open source Cheminformatics software package. For RDkit and for installing in Windows, I did not find any reliable pip installer, so that installed it from https://anaconda.org/rdkit/rdkit using the conda installer : _conda install -c rdkit rdkit

Once these three modules are installed, we are ready to start with our experiments.

drug-discovery deepchem bioinformatics cheminformatics aditya-bhattacharya data science

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