Macs in Chemistry

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Machine learning

Updated Conda

 

I've been checking a few things since I updated. One thing that was immediately apparent was the similarity maps in RDKit are much nicer! As you can see from the output of the HERG prediction.

hergactiverdkit

Feel like I got something for free.


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Accessing a Jupyter Notebook HERG model from Vortex

 

A recent paper "The Catch-22 of Predicting hERG Blockade Using Publicly Accessible Bioactivity Data" DOI described a classification model for HERG activity. I was delighted to see that all the datasets used in the study, including the training and external datasets, and the models generated using these datasets were provided as individual data files (CSV) and Python Jupyter notebooks, respectively, on GitHub https://github.com/AGPreissner/Publications).

The models were downloaded and the Random Forest Jupyter Notebooks (using RDKit) modified to save the generated model using pickle to store the predictive model, and then another Jupyter notebook was created to access the model without the need to rebuild the model each time. This notebook was exported as a python script to allow command line access, and Vortex scripts created that allow the user to run the model within Vortex and import the results and view the most significant features.

All models and scripts are available for download.

Full details are here…

hergactiveVortex


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Deep Learning Cheat Sheet (using Python Libraries)

 

Just came across this really invaluable resource.

  • Deep Learning Cheat Sheet (using Python Libraries)
  • PySpark Cheat Sheet: Spark in Python
  • Data Science in Python: Pandas Cheat Sheet
  • Cheat Sheet: Python Basics For Data Science
  • A Cheat Sheet on Probability
  • Cheat Sheet: Data Visualization with R
  • New Machine Learning Cheat Sheet by Emily Barry
  • Matplotlib Cheat Sheet
  • One-page R: a survival guide to data science with R
  • Cheat Sheet: Data Visualization in Python
  • Stata Cheat Sheet
  • Common Probability Distributions: The Data Scientist’s Crib Sheet
  • Data Science Cheat Sheet
  • 24 Data Science, R, Python, Excel, and Machine Learning Cheat Sheets
  • 14 Great Machine Learning, Data Science, R , DataViz Cheat Sheets



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A tutorial on KNIME Deeplearning4J Integration

 

An interesting blog post

https://www.knime.com/blog/learning-deep-learning

The aim of this blog post is to highlight some of the key features of the KNIME Deeplearning4J (DL4J) integration, and help newcomers to either Deep Learning or KNIME to be able to take their first steps with Deep Learning in KNIME Analytics Platform.


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Accessing Jupyter Notebook model from Vortex

 

I've become a great fan of Jupyter Notebooks as a way of modelling cheminformatics data, and I've published some of the notebooks here.

The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, machine learning and much more.

In the predicting AMES activity notebook I also looked at the use of pickle to store the predictive model and then access it using a Jupyter notebook without the need to rebuild the model. Whilst a notebook is a nice way to access the predictive model it might also be useful to be able to access it from other applications or from the command line.

In this tutorial we look at providing command line access to the model and then incorporating it into a Vortex script.

Scripting Vortex 38


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Data-driven Advice for Applying Machine Learning to Bioinformatics Problems

 

A very useful paper https://arxiv.org/abs/1708.05070

Here we contribute a thorough analysis of 13 state-of-the-art, commonly used machine learning algorithms on a set of 165 publicly available classification problems in order to provide data-driven algorithm recommendations to current researchers. We present a number of statistical and visual comparisons of algorithm performance and quantify the effect of model selection and algorithm tuning for each algorithm and dataset. The analysis culminates in the recommendation of five algorithms with hyperparameters that maximize classifier performance across the tested problems, as well as general guidelines for applying machine learning to supervised classification problems.

Good to see my preferred method Random Forest close to the top of the ranking based on performance over 165 datasets.

The rankings show the strength of ensemble-based tree algorithms in generating accurate models: The first, second, and fourth-ranked algorithms belong to this class of algorithms.

All 13 ML algorithms were used as implemented in scikit-learn, a popular ML library implemented in Python.


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Weekend Reading

 

A couple of things for your weekend reading ;-)

When not to use deep learning

What makes Python super popular

Googles online Python Class

Machine Learning in Python tutorial


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Free machine learning and data science ebooks

 

An interesting post By Matthew Mayo, KDnuggets.

Here is a quick collection of such books to start your fair weather study off on the right foot. The list begins with a base of statistics, moves on to machine learning foundations, progresses to a few bigger picture titles, has a quick look at an advanced topic or 2, and ends off with something that brings it all together. A mix of classic and contemporary titles, hopefully you find something new (to you) and of interest here.


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Predicting AMES activity Jupyter Notebook

 

I've been experimenting with the use of Jupyter Notebooks (aka iPython Notebooks) as an electronic lab notebook but also a means to share computational models. The aim would be to see how easy it would be to share a model together with the associated training data together with an explanation of how the model was built and how it can be used for novel molecules.

The Ames test is a widely employed method that uses bacteria to test whether a given chemical can cause mutations in the DNA of the test organism. More formally, it is a biological assay to assess the mutagenic potential of chemical compounds. PNAS. 70 (8): 2281–5. doi

In this first notebook a random forest model to predict AMES activity is described….


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