Tutorials

Tutorials on machine learning, artificial intelligence in general, and biomedical research

Photo by National Cancer Institute on Unsplash

 

I collected here a set of tutorials and articles (with complementary codes) about artificial intelligence, machine learning, and data science. I have divided this repository into different sections (each one covers a different macro area of data science). You will find tutorials, code, scripts, datasets, and a list of resources related to the different topics (links to articles, free books, free courses, libraries, and so on).

Here, you will find also the Jupiter Notebook for the tutorial I published on Medium. I suggest reading the tutorial and the companion tutorial code in the order provided in the table below. For practical reasons, I have divided some of the tutorials into more than one part (allowing me to concentrate on one of the tutorials on the theoretical part and the others about the programming). Tutorials dedicated only to the theory have not a linked Jupiter notebook.

Most of the code is written in Python, but you can find also some Excel files that I have created to make it easier to understand some of the concepts. I have also added R scripts (since it is widely used by statisticians, biologists, and so on).

Moreover, you may find here some Colab notebooks without a theoretical tutorial (yet). I decided to upload the code before I finished writing the theoretical part (this would be indicated). I am convinced that the code alone is already beneficial. I would successively publish on Medium the written article (with details and comments on the code).

You may write me with any requests, suggestions, and comments. If you find it useful please follow and/or share (a star is always really appreciated).

Medium account  

Index

This is the general index of this repository:

• About me
• How to use this repository
• Cite this repository
• What is new :fire:
• Index of tutorials
  • Tutorials on machine learning
  • Tutorials and Articles on artificial intelligence
• Datasets - More than 40 available datasets and a list of resources to where find the datasets you need for your project
• Machine Learning
  • Tutorials and code
  • Utility
  • Scripts
• Artificial Intelligence
• Data visualization
• Genomic series

About me

I am Salvatore Raieli, a Senior Data Scientist in a pharmaceutical company. My work consists of applying machine learning and artificial intelligence in the drug discovery process. I have a PhD in immunology and I have years of experience in coding, machine learning, and bioinformatics. I have worked on different projects related to machine learning and biology (for work or for passion). I attended an MSc in Artificial Intelligence to dive inside the theory. I have always been passionate about artificial intelligence, and biology and understand how complex systems work.

I think that artificial intelligence will drive the new wave of innovation and it will revolutionize biology, medicine, and the pharma industry. I always thought that science should be more democratic and that sharing knowledge is fundamental for the improvement of science. For this reason, I have planned to write tutorials where I am trying to explain machine learning and artificial intelligence in the easiest way possible.

Medium account

 

Stay Updated with the most important news and research on machine learning and artificial intelligence, you can find them every week here:

ML news of the week

 

Back to General index -- Index of tutorials

How to use this repository

This repository is intended for those who want to learn artificial intelligence and machine learning in general. I have collected different scripts, additional functions, tutorials, and articles I have written that can be freely used on different topics. Moreover, you can find more than 30 datasets you can use for your projects

Back to General index -- Index of tutorials

Cite this repository

If this repository has been useful for your work, consider citing this repository:

@software{Raieli_Tutorial_and_articles_2024,
author = {Raieli, Salvatore},
license = {Apache-2.0},
month = mar,
title = {{Tutorial and articles on machine learning and artificial intelligence}},
url = {https://github.com/SalvatoreRa/tutorial},
version = {1.0},
year = {2024}
}

Back to General index -- Index of tutorials

What is new

• Oct 25 - updated with all the latest articles
• May 25 - 50 datasets available
• Sep 24 - tutorial reorganization.

Back to General index -- Index of tutorials

Index of tutorials

Here is an index of the different sections and subsections:

• Tutorials on machine learning
  • Introduction to medical image analysis - An introduction to how to use machine learning for image medical analysis. Articles and tutorials in Python.
  • Graph machine learning - A series dedicated to graphs: what they are, how you can work with them, and which algorithms and tasks you can do. Articles and tutorials in Python.
• Tutorials and Articles on artificial intelligence
  • Artificial intelligence's bases - detailed reviews of topics related to the bases of artificial intelligence
  • Tabular learning - A series dedicated to tabular learning and the related open questions with a particular focus on tabular deep learning
  • AI and science - Artificial intelligence is changing all disciplines, but what is AI's impact on science itself?
  • AI and art - AI is impacting art, how? Which are the models that are driving this revolution? how do they work?
  • AI and Climate Change - Climate change is the most pressing issue of mankind. Can AI help us to solve it? Or it is a foe?
  • Natural Language Processing and LLMs - LLMs are revolutionary but it is a fast-paced field, here I am discussing its development, the basis and the challenges
  • RAG and agents - A focus on retrieval-augmented generation (RAG) and agents
  • LLM models - A focus on specific LLM models.
  • Computer vision - all you need and want to know about convolutional neural networks and vision transformers.
  • Artificial intelligence and music - music is a sequence, and AI knows well how to deal with sequences
  • AI and ethics - Artificial intelligence opens important ethical questions that need to be discussed.
  • Articles and tutorials of Bioinformatics/AI/ML applied to Biology - Practical tutorials about applying AI and ML to biological questions.
  • Others - Articles and tutorials that do not fall inside the previous categories

Tutorials on machine learning

This series of tutorials is focused on classical machine learning (regression, classification, dimensional reduction, and so on). I will discuss the basics, the math behind models, and how to implement them.

Introduction to medical image analysis

| Articles | notebook | description | | ------- | ----------- | ------ | | Introduction to medical image analysis | -- | Brief introduction to medical image analysis | | Introduction to point processing | Jupiter Notebook |Whether you are doing medical image analysis or you use Photoshop, you are using point preprocessing| | Introduction to Thresholding | Jupiter Notebook | A simple but powerful system for segmenting images | | A practical guide to neighborhood image processing | Jupiter Notebook | Love thy neighbors: How the neighbors are influencing a pixel| | [A practical guide to morpho