Statistics and machine learning — Editorial Board Home

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Editorial Board

orcid logoFabio Cumbo avatar Fabio CumboMarzia A Cremona avatar Marzia A CremonaAnup Kumar avatar Anup Kumar

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Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
Foundational Aspects of Machine Learning using Python ✅ ✅ ✅ ✅
Pretraining a Large Language Model (LLM) from Scratch on DNA Sequences ✅ ✅ ✅ ✅
Fine-tuning a LLM for DNA Sequence Classification ✅ ✅ ✅ ✅
Predicting Mutation Impact with Zero-shot Learning using a pretrained DNA LLM ✅ ✅ ✅ ✅
Generating Artificial Yeast DNA Sequences using a DNA LLM ✅ ✅ ✅ ✅
Optimizing DNA Sequences for Biological Functions using a DNA LLM ✅ ✅ ✅ ✅
Identifing Survival Markers of Brain tumor with Flexynesis ❌ ✅
Modeling Breast Cancer Subtypes with Flexynesis ❌ ✅
Prepare Data from CbioPortal for Flexynesis Integration ❌ ✅
Unsupervised Analysis of Bone Marrow Cells with Flexynesis ❌ ✅
A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy ✅ ✅ ✅
Age prediction using machine learning ✅ ✅
Basics of machine learning ✅ ✅
Building the LORIS LLR6 PanCancer Model Using 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 ✅ ✅ ✅
Image classification in Galaxy with fruit 360 dataset ❌ ✅ ✅
Interval-Wise Testing for omics data ❌ ✅
Introduction to Machine Learning using R ✅ ✅ ✅ ❌
Introduction to deep learning ✅ ✅
Machine learning: classification and regression ✅ ✅
PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis ❌ ✅
Regression in Machine Learning ✅ ✅
Supervised Learning with Hyperdimensional Computing ❌ ✅
Text-mining with the SimText toolset ❌ ✅
Train and Test a Deep learning image classifier with Galaxy-Ludwig ❌ ✅
Neural networks using Python ✅ ✅ ✅ ✅
Deep Learning (without Generative Artificial Intelligence) using Python ✅ ✅ ✅ ✅
Regulations/standards for AI using DOME ✅ ✅

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
Identifing Survival Markers of Brain tumor with Flexynesis Final - Survival Markers of Lower Grade Aug 25, 2025 1 ✅ ✅ ❌
Modeling Breast Cancer Subtypes with Flexynesis Final - Modeling Breast Cancer Subtypes + TABPFN Aug 25, 2025 1 ✅ ✅ ✅
Prepare Data from CbioPortal for Flexynesis Integration Flexynesis - get data from Cbioportal Aug 25, 2025 1 ✅ ✅ ❌
Unsupervised Analysis of Bone Marrow Cells with Flexynesis Final - Unsupervised Analysis of Bone Marrow Cells Aug 25, 2025 1 ✅ ✅ ❌
A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy gpu_jupytool Aug 25, 2025 1 ❌ ❌ ❌
Age prediction using machine learning Age Prediction DNA Methylation Aug 25, 2025 6 ❌ ❌ ❌
Age prediction using machine learning Age Prediction RNA-Seq Aug 25, 2025 6 ❌ ❌ ❌
Basics of machine learning Machine Learning Aug 25, 2025 5 ✅ ❌ ❌
Building the LORIS LLR6 PanCancer Model Using PyCaret Ludwig - Image recognition model - MNIST Aug 25, 2025 1 ✅ ❌ ❌
Classification in Machine Learning ml_classification Aug 25, 2025 3 ✅ ✅ ❌
Clustering in Machine Learning Clustering in Machine Learning Aug 25, 2025 2 ✅ ❌ ❌
Deep Learning (Part 1) - Feedforward neural networks (FNN) Intro_To_FNN_v1_0_10_0 Aug 25, 2025 1 ✅ ❌ ❌
Deep Learning (Part 2) - Recurrent neural networks (RNN) Intro_To_RNN_v1_0_10_0 Aug 25, 2025 2 ✅ ❌ ❌
Deep Learning (Part 3) - Convolutional neural networks (CNN) Intro_To_CNN_v1.0.11.0 Aug 25, 2025 1 ✅ ❌ ❌
Image classification in Galaxy with fruit 360 dataset fruit_360 Aug 25, 2025 2 ❌ ❌ ❌
Interval-Wise Testing for omics data Workflow Constructed From History 'IWTomics Workflow' Aug 25, 2025 5 ❌ ❌ ❌
Introduction to deep learning Intro_To_Deep_Learning Aug 25, 2025 1 ❌ ❌ ❌
Machine learning: classification and regression Classification LSVC Aug 25, 2025 6 ✅ ❌ ❌
Machine learning: classification and regression Regression GradientBoosting Aug 25, 2025 6 ✅ ❌ ❌
PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis papaa@0.1.9_PI3K_OG_model_tutorial Aug 25, 2025 1 ❌ ❌ ❌
Regression in Machine Learning ml_regression Aug 25, 2025 1 ✅ ❌ ❌
Text-mining with the SimText toolset Simtext training workflow Aug 25, 2025 1 ❌ ❌ ❌
Train and Test a Deep learning image classifier with Galaxy-Ludwig Ludwig - Image recognition model - MNIST Aug 25, 2025 2 ✅ ❌ ❌

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TODO once this is merged: https://github.com/galaxyproject/training-material/pull/4963

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