Statistics and machine learning

Statistical Analyses for omics data and machine learning using Galaxy tools

Material

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

Machine Learning

Tutorials introducing fundamental concepts and techniques, guiding learners through data preprocessing, model training, evaluation, and application.

Lesson Slides Hands-on Recordings Input dataset Workflows
Foundational Aspects of Machine Learning using Python
elixir ai-ml jupyter-notebook

Generative Artificial Intelligence and Large Langage Model

Tutorials covering the creation, pretraining, and applications of Generative Artificial Intelligence and Large Language Models.

Lesson Slides Hands-on Recordings Input dataset Workflows
Pretraining a Large Language Model (LLM) from Scratch on DNA Sequences
elixir ai-ml Large Language Model jupyter-notebook
Fine-tuning a LLM for DNA Sequence Classification
elixir ai-ml Large Language Model jupyter-notebook
Predicting Mutation Impact with Zero-shot Learning using a pretrained DNA LLM
elixir ai-ml Large Language Model jupyter-notebook
Generating Artificial Yeast DNA Sequences using a DNA LLM
elixir ai-ml Large Language Model jupyter-notebook

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy
interactive-tools machine-learning deep-learning jupyter-lab image-segmentation protein-3D-structure
Age prediction using machine learning
Basics of machine learning
Building the LORIS LLR6 PanCancer Model Using PyCaret
LORIS Score Model Machine Learning PyCaret
Classification in Machine Learning
Clustering in Machine Learning
Deep Learning (Part 1) - Feedforward neural networks (FNN)
Deep Learning (Part 2) - Recurrent neural networks (RNN)
Deep Learning (Part 3) - Convolutional neural networks (CNN)
Fine tune large protein model (ProtTrans) using HuggingFace
interactive-tools machine-learning deep-learning jupyter-lab fine-tuning dephosphorylation-site-prediction
Image classification in Galaxy with fruit 360 dataset
Interval-Wise Testing for omics data
Introduction to Machine Learning using R
interactive-tools
Introduction to deep learning
Machine learning: classification and regression
PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis
Machine learning Pan-cancer cancer biomarkers oncogenes and tumor suppressor genes
Regression in Machine Learning
Supervised Learning with Hyperdimensional Computing
Text-mining with the SimText toolset
interactive-tools
Train and Test a Deep learning image classifier with Galaxy-Ludwig
MNIST Deep learning Ludwig
Regulations/standards for AI using DOME
elixir ai-ml

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Editorial Board

This material is reviewed by our Editorial Board:

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Contributors

This material was contributed to by:

Kaivan Kamali avatar Kaivan Kamaliorcid logoArmin Dadras avatar Armin Dadrasorcid logoAlireza Khanteymoori avatar Alireza Khanteymooriorcid logoMarie Gramm avatar Marie Grammorcid logoPaulo Cilas Morais Lyra Junior avatar Paulo Cilas Morais Lyra Juniororcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoJeremy Goecks avatar Jeremy Goecksorcid logoHelena Rasche avatar Helena Rascheorcid logoBérénice Batut avatar Bérénice BatutMarzia A Cremona avatar Marzia A Cremonaorcid logoMichelle Terese Savage avatar Michelle Terese Savageorcid logoStella Fragkouli avatar Stella FragkouliRalf Gabriels avatar Ralf GabrielsVijay avatar VijayMélanie Petera avatar Mélanie Peteraorcid logoJunhao Qiu avatar Junhao QiuWandrille Duchemin avatar Wandrille DucheminAnup Kumar avatar Anup KumarDennis Lal group avatar Dennis Lal grouporcid logoTeresa Müller avatar Teresa MüllerRaphael Mourad avatar Raphael MouradGildas Le Corguillé avatar Gildas Le Corguilléorcid logoMartin Čech avatar Martin Čechorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoFabio Cumbo avatar Fabio Cumboorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosEkaterina Polkh avatar Ekaterina Polkhorcid logoNate Coraor avatar Nate CoraorSimon Bray avatar Simon Brayorcid logoBjörn Grüning avatar Björn Grüning

Funding

These individuals or organisations provided funding support for the development of this resource

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EuroScienceGateway
EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.
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de.NBI
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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
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UFR
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ELIXIR Europe