Tutorial

Molecular Docking in Google Colab

Molecular docking is an essential process in scientific drug discovery. By using the recent advances in generative deep learning the runtime required for such docking studies can be reduced significantly without comprimising accuracy compared to traditional methods. In this article, let us get familiarize ourselves with one open-source molecular docking codebase. The codebase named DiffDock …

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svm hyperplane

Essential Concepts and Implementation of Support Vector Machines

What are Support Vector Machines? Support Vector Machines (SVM) is one of the most elegant methods used for classification and regression in machine learning (ML). We can use SVM when we have a bunch of objects/features which we want to classify. SVM performs the classification by drawing a hyperplane (Figure.1) to separate each category of …

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Visualizing 3D Protein Structures and Exporting Into images Using Jupyter Notebook.

The Jupyter Notebook is best suited for doing as well as documenting empirical research. It can contain text, code images, videos, interactive content, and also nicely typesetting equations. This makes anyone doing simulations or empirical research prototype their work and share it with their colleagues. In this blog post, I am going to show how …

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matpotlib

Python Matplotlib Tip: Overlapping Curves and Multiple Axes

In STEM fields it is often required to communicate ideas using graphs or infographics. Many times the dimensionality of data will be higher and require clever hacks to represent so that the reader gets the idea quickly. There have been systematic studies on how to do data visualization effectively. For data scientists or machine learning …

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Bivariate Gaussian Distribution

Hacking the Bivariate Gaussian Distribution

In one of our earlier posts, we have seen how we can visually relate the parts of the one-dimensional Gaussian distribution equation. In this post, we will follow the same strategy to understand the terms that comes up with a Multivariable Gaussian distribution. We will focus on the Bivariate Gaussian distribution as distributions of higher-order …

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Normal distribution visual explanation

Gaussian Distribution Explained Visually

Gaussian distribution appears in various parts of science and engineering. Apart from a distribution often appear in nature, it has got important properties such as its relation to Central Limit Theorem (CLT). The figure above shows one-dimensional Gaussian distributions of various mean and variance values. Libraries like NumPy provide functions that can return Gaussian distribution …

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TwoStateMDP

Coding a Simple Markov Decision Process

This is a quick tutorial on how to implement a two-state Markov Decision Process (MDP). It has only two states: state 1 and state 2. Applications MDPs often appear in machine learning and reinforcement learning. At any stage, the agent can take any of the two actions. The actions are to stay or switch. The …

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