Data Science for Computational Drug Discovery using Python (Part 2 with PyCaret)

This video is Part 2, where I will show you how to apply the same dataset (molecular solubility dataset) on the PyCaret Python library to generate several machine learning models in a few simple steps.

⭕ Code:

📚Delaney's ORIGINAL ARTICLE entitled
"ESOL:  Estimating Aqueous Solubility Directly from Molecular Structure"

📚Read my EDITORIAL ARTICLE entitled
"Maximizing computational tools for successful drug discovery"

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[Mario-oxdm]

This is awesome that you're sharing your knowledge in PyCaret! Thank you!

[gabrielparra]

Thanks Chanin for this powerful demo of PyCaret!

[bikashpradhan]

Love this drug discovery series using python curious to know more about this in future vdo

[KenJee_ds]

Great stuff Chanin! I think I should use pycaret in the future. Automl is the future! Have you used h20.ai?

[michaeloladunjoye]

Thanks Data Professor. This will help me further in learning.

[zeinabezz]

Thank you, Can you recommend a good book for learning computatioanl drug disovery using machine learning?

[royalslifezone]

why aren't we using (tuned_et ) in the hold out testing?
would the result vary in both?


*prediction_holdout = predict_model(et)* given

[muhammadtanveerkhalil]

how will i use this for my undergrade thesis

[sagarhm]

Sir how to create conda environment in herok u

[larigiba]

Thank you for this tutorial! I think projects that combine topics (such as with chemistry in this case) are really interesting and original. Do you always prefer Colab Notebooks over Jupyter Notebooks?

[catherinemangare]

I'm beginner in the field of Bioinformatics and required to use Network based algorithms for drug re-purposing. I don't know where to start. Please guide me

[sagarhm]

Sir how can herok can be installed conda pakage by setup py. Plzzzz help me

[sagarhm]

Can Gromacs can be run in heroku Plzz help me to solve these problem

[shwetaredkar]

As usual, the best video and explanation and the best professor !! Just for curiosity, When RF was performing better than why ET was selected as the best model?

[khanhnguyentan]

Anyone can help me ?
I have a list of receptors (chemical compounds). Are there any ways to do docking process by autodock vina with python code on Jupyter ?
Thank you !

[pcliang]

Dear professor, can you help me solve this code problem?

code：

tuned_et = tune_model('et', n_iter = 50, optimize = 'mae')

Error message：

## An exception has occurred, use %tb to see the full traceback.

## SystemExit: (Type Error): The behavior of tune_model in version 1.0.1 is changed. Please pass trained model object.

[pcliang]

code：

tuned_et = tune_model('et', n_iter = 50, optimize = 'mae')

Error message：

## An exception has occurred, use %tb to see the full traceback.

## SystemExit: (Type Error): The behavior of tune_model in version 1.0.1 is changed. Please pass trained model object.

[ernestbonat]

Excellent videos by the Data Professor. Feel free to read the following blog paper on Medium website “Apply Machine Learning
Algorithms for Genomics Data Classification”. This will help you to understand how to apply Machine Learning algorithms for
genomic data classification. This blog paper contains the latest ML/AI technologies applied to human genomic data classification today.

[AyeshaFatima-urbk]

I ran the pycaret tutorial. It gives me the error for shap at the 'Model Interpretation" step. I have already installed shap, imported shap and also installed the pycaret [analysis] module. the error still persists. what could be the problem? The error is as follows

'''ModuleNotFoundError Traceback (most recent call last)
in <cell line: 1>()
----> 1 interpret_model(et)

4 frames
in _check_soft_dependencies(package, severity, extra, install_name)
150 if severity == "error":
151 logger.exception(f"{msg}")
--> 152 raise ModuleNotFoundError(msg)
153 elif severity == "warning":
154 logger.warning(f"{msg}")

ModuleNotFoundError:
'shap' is a soft dependency and not included in the pycaret installation. Please run: `pip install shap` to install.
Alternately, you can install this by running `pip install pycaret[analysis]`''''