https://github.com/ed-donner/llm_engineering?tab=readme-ov-file# Machine- and Deep Learning resources

Machine and deep learning and data analysis resources. Please, contribute and get in touch! See MDmisc notes for other programming and genomics-related notes.

Table of content

Cheatsheets
Awesome Deep Learning
Awesome Machine learning

Cheatsheets

Artificial-intelligence - Awesome AI Learning with +100 AI Cheat-Sheets, Free online Books, Top Courses, Best Videos and Lectures, Papers, Tutorials, +99 Researchers, Premium Websites, +121 Datasets, Conferences, Frameworks, Tools
Over 200 of the Best Machine Learning, NLP, and Python Tutorials — 2018 Edition, Source
101 Machine Learning Algorithms for Data Science with Cheat Sheets - Brief description and R/Python examples of algorithms, categorized into several categories: classification, regression, neural networks, anomaly detection, dimensionality reduction, ensemble learning, clusterint, association rule analysis, regularization
Machine Learning Cheatsheet - Brief visual explanations of machine learning concepts with diagrams, code examples and links to resources for learning more.
Data Science Cheatsheet - Data Science and ML Cheat Sheet, by Maverick Lin. Source
Data Science Cheatsheet - A helpful 4-page data science cheatsheet to assist with exam reviews, interview prep, and anything in-between
cheatsheets-ai - Essential Cheat Sheets for deep learning and machine learning researchers
machine-learning-cheat-sheet - 30-page MachineLearning cheat sheet with classical equations & diagrams, Tweet by Kirk Borne
ml_cheatsheet - A 5-pages only Machine Learning cheatsheet focusing on the most popular algorithms under the hood. Online version
stanford-cs-229-machine-learning - VIP cheatsheets for Stanford's CS 229 Machine Learning. Online version
Machine Learning 101 - Machine and deep learning overview in 100 slides, or 35-min video by Jason Mayers. Tweet
Mathematics-for-ML - A collection of resources to learn mathematics for machine learning. Linka to books, videos.
Here are 450 Ivy League courses you can take online right now for free blog post by Dhawal Shah with links to free courses in Computer Science, Data Science, Programming, Humanities, Business, Art & Design, Science, Social Sciences, Health & Medicine, Engineering, Mathematics, Education & Teaching, and Personal Development
TOP 10 GitHub Repositories for Data Science by Analysics Vidhya (Ayushi Gupta)
machine-learning-resource - Machine- and deep learning notes by Ming Tang

Awesome Deep Learning

Awesome Deep Learning - A curated list of awesome Deep Learning tutorials, projects and communities
Awesome - Most Cited Deep Learning Papers - the most cited deep learning papers
awesome-computer-vision - A curated list of awesome computer vision resources
awesome-kan - A comprehensive collection of KAN(Kolmogorov-Arnold Network)-related resources, including libraries, projects, tutorials, papers, and more, for researchers and developers in the Kolmogorov-Arnold Network field.
awesome-llm-apps - Collection of awesome LLM apps with AI Agents and RAG using OpenAI, Anthropic, Gemini and opensource models.
awesome-local-ai - An awesome repository of local AI tools
AI and DeepRL - source code, links and other learning materials related to Artificial Intelligence, especially focused on Deep Reinforcement Learning
THE NEURAL NETWORK ZOO - infographics of different neural network architectures, explanation of each, references to the original papers
Over 150 of the Best Machine Learning, NLP, and Python Tutorials, Tweet by Andrew Trask

Keras, Tensorflow

Deep learning with R by François Chollet (the creator of Keras) with J. J. Allaire (the founder of RStudio and the author of the R interfaces to Keras and TensorFlow), R notebooks, Python notebooks
Deep Learning with Keras and TensorFlow in R Workflow by Brad Boehmke. GutHub repo with Rmd files for data download, code examples, lectures.
dlaicourse - Deep learning course, TensorFlow, Jupyter notebooks, by Laurence Moroney, Google
easy-tensorflow - Simple and comprehensive tutorials in TensorFlow, by Jahandar Jahanipour. Online version
handson-ml3 - A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2. Example code and solutions for the Hands-on Machine Learning with Scikit-Learn, Keras and TensorFlow book by Aurélien Géron. Run on Google Colab
Learn TensorFlow for Deep Learning: Zero to Mastery book - All course materials for the Zero to Mastery Deep Learning with TensorFlow course. GitHub, Video 1 10h15m, Video 2 4h.
Introduction to Deep Learning - Deep Learning basics with Python, TensorFlow and Keras. Several posts, each ncludes video, text and code tutorial
image_classification_keras_tf - Workshop material for Image Classification & Natural Language Processing with Python, Keras and TensorFlow, by Shirin Glander
keras-workshop - Keras R workshop, by Doug Ashton. slides, simple examples
Machine Learning with TensorFlow and TensorFlow-Book - GitHub with the source code
Machine Learning Foundations - Machine Learning Foundations is a free training course where you’ll learn the fundamentals of building machine learned models using TensorFlow with Laurence Moroney. Computer vision-focused
Tensorflow-101 - Tensorflow Tutorials using Jupyter Notebook with data
TensorFlow-Course - Simple and ready-to-use tutorials for TensorFlow. Step-by-step instructions with screenshots. By Amirsina Torfi
TensorFlow-Examples - TensorFlow Tutorial and Examples for Beginners with Latest APIs, by Aymeric Damien
TensorFlow-LiveLessons - "Deep Learning with TensorFlow" LiveLessons, Jupyter notebooks, by Jon Krohn
TensorFlow 2.0 Complete Course - Python Neural Networks for Beginners - 7 hours of walk-through programming with Tim Ruscica. Links to Google Colaboratory Notebooks are in the description
Text Classification with TensorFlow - Python TensorFlow for Machine Learning – Neural Network Text Classification Tutorial, by Kylie Ying. 1h 54m
useR! 2020: Deep Learning with Keras and TensorFlow (S. Elsinghorst), tutorial 2h 07m video, and the GitLab repo keras_tutorial_user2020
Workshop-R-Tensorflow-Scientific-Computing - Workshop R for Deep Learning with Tensorflow with Applications in Research & Scientific Computing

PyTorch

Awesome-Pytorch-list - A comprehensive list of pytorch related content on github,such as different models,implementations,helper libraries, tutorials etc. Tweet
DEEP LEARNING with PyTorch by Yann LeCun & Alfredo Canziani. Videos, transcripts, slides, practicals. YouTube playlist
Learn PyTorch for Deep Learning: Zero to Mastery book - Materials for the Learn PyTorch for Deep Learning: Zero to Mastery course. GitHub, Video 25h36m
pytorch-tutorial - PyTorch Tutorial for Deep Learning Researchers. Basic, Intermediate, and Advanced code examples, by Yunjey Choi
PyTorch for Deep Learning & Machine Learning – Full Course - video course, 25 hours. GitHub
the-incredible-pytorch - The Incredible PyTorch: a curated list of tutorials, papers, projects, communities and more relating to PyTorch.
tutorials - official PyTorch tutorials, with videos. Website
udlbook - Understanding Deep Learning - Simon J.D. Prince. Jupyter notebooks with comments, slides, figures. Need to be cloned.
Zero to GANs - PyTorch, video course and Jupyter notebooks

JAX

JAX is a combination of Automatic Differentiation and XLA (Accelerated Linear ALgebra). XLA is a compiler developed by Google to work on TPU units. Jax has Numpy as its higher layer of abstraction, and works the same way on CPU, GPU, and TPU (much faster).

Graph Neural Networks

PyG - a PyTorch library for Graph Neural Networks. Documentation.
CS224W: Machine Learning with Graphs - Youtube playlist with course videos, by Jure Leskovec. Main concepts and deep neural networks training on graphs. Course website
Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering - CNN framework for graph learning.
Deep Learning on Graphs book by Yao Ma and Jiliang Tang. Basics, methods, applications, and more. English and Chinese versions. Tweet
GNNPapers - Must-read papers on graph neural networks (GNN). Tweet
GNNs-Recipe - A recipe to study Graph Neural Networks (GNNs), by omarsar
Graph-Neural-Networks-in-Life-Sciences - five-section tutorial (Jupyter notebooks) on Graph Neural Networks in Life Sciences
GraphGym - Design Space for Graph Neural Networks, Platform for designing and evaluating Graph Neural Networks (GNN). GitHub, Paper
GraphSAGE - Representation learning on large graphs using stochastic graph convolutions. Learning on node attributes. Tensorflow implementation, PyTorch available. Project website, Paper

Transformers

DL Books

influential-cs-books - Most influential books on Computer Science/programming
Deep Learning Interviews book by Shlomo Kashani. Hundreds of fully solved job interview questions from a wide range of key topics in AI. GitHub repo has link to free PDF.
Deep Learning for Molecules and Materials, Tweet
The Deep Learning textbook by Ian Goodfellow, Yoshua Bengio and Aaron Courville. Includes lectures in .key and .pdf formats, videos discussing different chapters. https://www.deeplearningbook.org/
Fundamentals-of-Deep-Learning-Book - Python code companion to the O'Reilly "Fundamentals of Deep Learning" book
Dive into Deep Learning - An interactive deep learning book with code, math, and discussions, based on MXNet, useful as general learning material. https://d2l.ai/
Grokking-Deep-Learning - Python code for the "Grokking Deep Learning" book by Andrew Trask
neural-networks-and-deep-learning - Code samples for "Neural Networks and Deep Learning" book. Python/Theano examples, theory, and practice of deep learning by Michael Nielsen
python-machine-learning-book - "Python Machine Learning (3rd Ed.) Code Repository" book by Sebastian Raschka, iPython notebooks
reinforcement-learning-an-introduction - Python code for Sutton & Barto's book "Reinforcement Learning: An Introduction (2nd Edition)"
The Matrix Calculus You Need For Deep Learning paper by Terence Parr and Jeremy Howard
Algorithms for Convex Optimization, by Nisheeth K. Vishnoi. PDF, Tweet
what_are_embeddings - A deep dive into embeddings starting from fundamentals, online and PDF.

DL Courses & Tutorials

courses - a curated collection of links to various courses and resources about Artificial Intelligence (AI).
NYU-DLFL22 - NYU Deep Learning Fall 2022, by Alfredo Canziani & Yann LeCun. Videos, slides, Jupyter notebooks. Links to previous material. GitHub, Youtube.
AI-For-Beginners - 12 Weeks, 24 Lessons, AI for All! PyTorch, Keras/Tensorflow, notebooks. Computer vision, natural language processing, extras. GitHub
The Ultimate FREE Machine Learning Study Plan - A complete study plan to become a Machine Learning Engineer with links to all FREE resources.
dive-into-machine-learning - Dive into Machine Learning with Python Jupyter notebook and scikit-learn! Links to many resources
ml-road-map - The most streamlined road map to learn ML for free. Links to free resources covering topics from general programming to language models.
The Matrix Calculus You Need For Deep Learning by Terence Parr and Jeremy Howard.
CS231n - Convolutional Neural Networks for Visual Recognition course, by Fei-Fei Li, Ranjay Krishna, Danfei Xu, at Stanford. Lecture slides, additional material, Colab notebooks. GitHub
t81_558_deep_learning - Washington University (in St. Louis) Course T81-558: Applications of Deep Neural Networks, by Jeff Heaton. Youtube
CS685: Advanced Natural Language Processing, Tweet
2020 - 2021: Machine-Learning / Deep-Learning / AI -Tutorials - A comprehensive list of Deep Learning / Artificial Intelligence and Machine Learning tutorials - rapidly expanding into areas of AI/Deep Learning / Machine Vision / NLP and industry specific areas such as Climate / Energy, Automotives, Retail, Pharma, Medicine, Healthcare, Policy, Ethics and more
MIT 6.874 Computational Systems Biology: Deep Learning in the Life Sciences - machine/deep learning, genomics, systems biology MIT course, Spring 2020. Taught by David Gifford, Manolis Kellis, Sachit Dinesh Saksena, Corban Swain, Timothy Fei Truong Jr. Lecture videos, slides, reading references. GitHub repo
Colah's blog, articles on neural networks, visualization - Illustrated and highly informative posts on types of neural networks and their applications by Christopher Olah
Introduction to Deep Learning course, D2L, Berkeley STAT 157, Jupyter notebooks, GitHub repository with slides and notebooks, Video course
- d2l.ai - Dive into Deep Learning: An interactive deep learning book with code, math, and discussions, based on the NumPy interface, Jupyter notebooks
- Mathematics for Deep Learning, d2l.ai - systematic deep learning math, linear algebra and matrix operations, eigendecomposition, single- and multivariable calculus, integral calculus, maximum likelihood and optimization, statistics (random variables, distributions, naive Bayes), information theory
OxML-GenAI - material from Oxford ML Generative AI course
Practical Deep Learning for Coders, v3 - FAST.AI main course. Introduction to Machine Learning for Coders - another course by Jeremy Howard, with videos
Step-by-step guides to learn Applied Machine Learning - Machine Learning Mastery web site aggregating structured posts for beginner and intermediate machine learning users, deep learning
Stanford Computer Science courses CS221/229/230 ― Several GitBook-formatted courses on Artificial Intelligence, machine learnint, deep learning
Machine Learning courses by Thorsten Joachims - Thorsten Joachims' home page with links to courses and more. CS4780/CS5780 Machine Learning for Intelligent Systems, CS6780 Advanced Machine Learning, and more. Videos and slides
Machine and deep learning courses by Google - a collection of Google Developers courses
Azure Machine Learning Python SDK notebooks - Python notebooks with ML and deep learning examples with Azure Machine Learning Python SDK, Microsoft
generative-ai-for-beginners - 18 Lessons, Get Started Building with Generative AI. Azure platform, Python-based, with videos
Deep Learning in Computer Vision with Prof. Kosta Derpanis (Ryerson University)
DeepLearningProject - An in-depth machine learning tutorial introducing readers to a whole machine learning pipeline from scratch, by Spandan Madan,Visual Computing Group, Harvard University. Python
homemade-machine-learning - Python examples of popular machine learning algorithms with interactive Jupyter demos and math being explained, by Oleksii Trekhleb. Medium blog post
nn-from-scratch - Implementing a Neural Network from Scratch – An Introduction, by Denny Britz. Notes
Practical_DL - Deep learning course, Python notebooks, PDF lectures, videos. DL course co-developed by YSDA, HSE and Skoltech
stat453-deep-learning-ss20 - Intro to Deep Learning, UW-Madison (Spring 2020) by Sebastian Raschka, videos
stat479-machine-learning-fs19 - Course material for STAT 479: Machine Learning (FS 2019) taught by Sebastian Raschka at University Wisconsin-Madison, pdf slides
stat479-deep-learning-ss19 - Course material for STAT 479: Deep Learning (SS 2019) taught by Sebastian Raschka at University Wisconsin-Madison, pdf slides
UvA deep learning tutorials - upyter notebook tutorials for teaching the Deep Learning Course at the University of Amsterdam (MSc AI), Fall 2022/Spring 2022. PyTorch, JAX. GitHub, YouTube

DL Videos

ML-YouTube-Courses - A repository to index and organize the latest machine learning courses found on YouTube. Tweet
Applied Deep Learning playlist, short course lectures by Maziar Raissi. GitHub.
3blue1brown Neural Networks playlist, and other 3blue1brown playlists
MIT Introduction to Deep Learning | 6.S191 - MIT video course by Alexander Amini, Ava Soleimani, and guests. Dense and informative ~45min lectures covering various topics of deep learning. introtodeeplearning.com - course web site with slides, video, and other material. GitHub
Deep Learning Crash Course for Beginner - a 1h 25m overview of deep learning techniques, highly informative narrative by Jason Dsouza
Series of eight video lectures on the math of machine learning by Tinnam Ganesh. "Elements of Neural Networks & Deep Learning", Part1,2,3, Parts 4,5, Parts 6,7,8
Coursera Neural Networks for Machine Learning — Geoffrey Hinton - Video course of short lectures introducing theoretical foundations of machine learning
Introduction to Deep Learning course, D2L, Berkeley STAT 157, video lectures by Alex Smola. Accompanies the https://d2l.ai/ book
Machine Learning & Deep Learning Fundamentals, by DeepLizard - information-dense short videos about fundamentals and math behind neural networks. Blog posts
Brandon Rohrer's YouTube channel - short videos about basics of deep learning and neural networks
Undergraduate machine learning at UBC 2012 by Nando de Freitas. Slides
Deep learning at Oxford 2015 by Nando de Freitas. Slides
Undergraduate machine learning at UBC 2012 by Nando de Freitas. Slides
Deep learning at Oxford 2015 by Nando de Freitas. Slides
Heroes of Deep Learning, Interviews by Andrew Ng.
Advanced Deep Learning & Reinforcement Learning - a video-course on deep RL taught at @UCL by DeepMind researchers
Weights & Biases video and code tutorials - Short videos and text with Python code for individual topics, by Lukas Biewald. GitHub repo with code. Weights & Biases Youtube channel
UCL Course on Reinforcement Learning by David Silver. Slides and video lectures
Deep Reinforcement Learning: CS 285 Fall 2020 - Lectures for UC Berkeley CS 285: Deep Reinforcement Learning.

DL Papers

annotated_deep_learning_paper_implementations - a collection of simple PyTorch implementations of neural networks and related algorithms, with explanations. Jupyter notebooks. Website rendering
best_AI_papers_2022 - A curated list of the latest breakthroughs in AI (in 2022) by release date with a clear video explanation, link to a more in-depth article, and code.
DeepMind Research - implementations and illustrative code to accompany DeepMind publications. Jupyter notebooks and data, list of projects
Lee, Benjamin D, Anthony Gitter, Casey S Greene, Sebastian Raschka, Finlay Maguire, Alexander J Titus, Michael D Kessler, et al. “Ten Quick Tips for Deep Learning in Biology.” ArXiv 29 May 2021 - 1. Use appropriate method; 2. Establish baseline; 3. Train reproducibly; 4. Know your data; 5. Select sensible architecture; 6. Optimize hyperparameters; 7. Mitigate overfitting; 8. Maximize interpretability; 9. Avoid over-interpretation; 10. Prioritize research ethics. Summary in Figure 1. References. Latest version
Sebastian Ruder, “An Overview of Gradient Descent Optimization Algorithms.” June 15, 2017 - Gradient descent optimization algorithm review, by . Definitions, intuitive progression of algorithm improvements. Gradient descent variants: Batch, Stochastic, Mini-batch. Gradient descent algorithme: Momentum, Nesterov accelerated gradient, Adagrad, Adadelta, RMSprop, Adam, AdaMax, Nadam. Visualizattion. Parallel implementations.
eugeneyan/applied-ml - Papers & tech blogs by companies sharing their work on data science & machine learning in production.
2020: A Year Full of Amazing AI papers- A Review - A curated list of the latest breakthroughs in AI by release date with a clear video explanation, link to a more in-depth article, and code
awesome-deepbio - A curated list of awesome deep learning publications in the field of computational biology
Deep Learning Papers Reading Roadmap - Deep Learning papers reading roadmap for anyone who are eager to learn this amazing tech!
Papers with code - Systematic collection of machine- and deep learning papers with code, State-of-the-art, Methods, Datasets
Deep_learning_examples - Examples of using deep learning in Bioinformatics. Deep Learning in Bioinformatics
deep_learning_papers - A place to collect papers that are related to deep learning and computational biology, by Harold Pimentel
Deep-Learning-Papers-Reading-Roadmap - Deep Learning papers reading roadmap for anyone who are eager to learn this amazing tech!
deeplearning-biology - A list of papers on deep learning implementations in biology
Machine-learning-for-proteins - List of papers about machine learning for proteins
Key Papers in Deep Reinforcement Learning, Twitter
LeCun, Bengio, and Hinton, “Deep Learning.” - Classical deep learning review. Areas of application, historical development, principles of supervised learning, stochastic gradient descent (Figure 1 - illustration of forward and backpropagation, with equations), convolutional neural networks for image recognition and in other areas, language processing, recurrent neural networks, LSTMs
Vincent et al., “Extracting and Composing Robust Features with Denoising Autoencoders.” - Denoising autoencoder paper, statistical formulations
Schmidhuber, “Deep Learning in Neural Networks.” - Deep overview of deep learning history. Year-by-year description of types of DL, approaches, algorithmic (backpropagation) improvements, problems, and solutions
Scientific-LLM-Survey - Scientific Large Language Models: A Survey on Biological & Chemical Domains
TextGrad - text (prompt) optimization by backpropagating LLM-generated feedback. Each AI system is transformed into a computational graph where components exchange text, code, and images through complex (not necessarily differentiable) functions. TextGrad generates feedback in the form of text to guide the modifications of unstructured variables in a system - textual gradient descent analogy. Tested on LeetCode Hard, Google-proof Question Answering (GPQA), Massive Multitask Language Understanding (MMLU), MathVista, ScienceQA, GSM8k datasets. Outperforms Reflexion, OPRO, DSPy.

Paper
Yuksekgonul, Mert, Federico Bianchi, Joseph Boen, Sheng Liu, Pan Lu, Zhi Huang, Carlos Guestrin, and James Zou. “Optimizing Generative AI by Backpropagating Language Model Feedback.” Nature 639, no. 8055 (March 20, 2025): 609–16. https://doi.org/10.1038/s41586-025-08661-4.

DL Genomics

Evo - foundational model for sequence prediction (mutational effect, activity of regulatory DNA, gene essentiality) and generation (CRISPR-Cas complexes, transposons). Striped Hyena-based architecture using 29 Hyena layers, 3 rotary position embedding, over 131K single-nucleotide token window. Pretrained on the OpenGenome dataset with more than 80K bacterial and archaeal genomes, millions of phage and plasmid sequences, viruses excluded. Compared Transformer, Mamba, Hyena, StripedHyena architectures.

Paper
Nguyen, Eric, Michael Poli, Matthew G Durrant, Brian Kang, Dhruva Katrekar, David B Li, Liam J Bartie, et al. “Sequence Modeling and Design from Molecular to Genome Scale with Evo,” 2024. https://www.science.org/doi/10.1126/science.ado9336

Review or genome Language Models (gLMs) using the transformer architecture. Intro about deep learning in genomics, references. DNA tokenization approaches (one-hot, k-mer (overlapping and not), byte-pair encoding). Masked Language Modeling (MLM), Autoregressive Language Modeling (ALM), State Space Models (SSM). The Hyena layer and the Mamba layer. Description of individual models: SATORI (self-attention-based model to detect regulatory element interactions), Enformer, Borzoi, C.Origami, DNABERT (-XL, -2), the Nucleotide transformer, GENA-LM, GPN, HyenaDNA, Evo (Striped Hyena), summarized in Table 1. Benchmarking datasets, the BEND benchmarking paper shows gLMs do not consistently outperform supervised baselines. Limitations - not accounting for long-range interactions, cell type specificity, high computing cost. Interpretability approaches - attention scores, attention flow, rollout, SHAP. Excellent supplementary texts describing the attention mechanisms, each model (SSM, Hyena), add-and-norm layers, skip connections, fully connected layers, encoder-decoder interplay. Supplementary Table S1 - an in-depth summary of all models. Supplementary figures - schematic representation.

Paper
Consens, Micaela E., Cameron Dufault, Michael Wainberg, Duncan Forster, Mehran Karimzadeh, Hani Goodarzi, Fabian J. Theis, Alan Moses, and Bo Wang. “Transformers and Genome Language Models.” Nature Machine Intelligence 7, no. 3 (March 13, 2025): 346–62. https://doi.org/10.1038/s42256-025-01007-9.

genomicsnotebook - Genomics Data Analysis with Jupyter Notebooks on Azure.
LLM-for-genomics-training - Tutorial on large language models for genomics
Machine Learning for Genomics - ML4GLand is a community for that develops and maintains tools (primarily in Python) for genomics sequence based machine learning.
SEQUOIA - a linearized transformer model for gene expression prediction from pathology slides. Uses UNI (foundational model for slides), compared with ResNet50. Compared with tRNAsformer, HE2RNA. Trained on 7584 tumor samples across 16 cancer types (TCGA), validated on independent cohorts (CPTAC, Tempus). BRCA shows best performance, the model predicts the risk of breast cancer recurrence. About 15K out of 20K genes can be predicted, well-known signature genes are predicted best. Detected 272 genes significantly associated with recurrence. Predicts spatially-specific gene expression. Python, GitHub.

Paper
Pizurica, Marija. “Digital Profiling of Gene Expression from Histology Images with Linearized Attention.” Nature Communications, 2024.

HyenaDNA - a genomic foundation model with context lengths of up to 1M tokens at the single nucleotide-level. A Hyena operator (long convolutions and element-wise gate layers). Pretrained on the human reference genome to predict next token, masked tokens. Scales sub-quadratically. Tested on GenomicBenchmarks dataset (classification, prediction), compared with DNABERT, Nucleotide Transformer.

Paper
Nguyen, Eric, Michael Poli, Marjan Faizi, Armin W Thomas, Callum Birch Sykes, Michael Wornow, Aman Patel, et al. “HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution,” https://arxiv.org/abs/2306.15794

Avsec, Žiga, Vikram Agarwal, Daniel Visentin, Joseph R. Ledsam, Agnieszka Grabska-Barwinska, Kyle R. Taylor, Yannis Assael, John Jumper, Pushmeet Kohli, and David R. Kelley. “Effective Gene Expression Prediction from Sequence by Integrating Long-Range Interactions.” Nature Methods, (October 2021) - Enformer - a deep learning model (transformers) to predict epigenetic and gene expression profiles (128bp resolution) from human and mouse cell types using only the DNA sequence as input, incorporating information from up to 100 kb on either side of the target locus (200kb of input DNA sequence). Transformers, allow to increase the receptive field up to 100kb, in contrast to 20kb for Basenji2 or ExPecto. Significant increase in performance. Predictions using CAGE data. Improves variant effect prediction on eQTL data. Excellent transformer description.
Greener, Joe G., Shaun M. Kandathil, Lewis Moffat, and David T. Jones. “A Guide to Machine Learning for Biologists.” Nature Reviews Molecular Cell Biology, September 13, 2021. - Introduction to machine/deep learning, focusing on biology applications. General terms, supervised/unsupervised learning, loss function, parameters and hyperparameters, training/validation/testing, overfitting, bias-variance tradeoff, Classification, regression, clustering, dimensionality reduction, neural networks (CNN, LSTM/RNN/transformers, autoencoders), network training, data leakage. Evaluation of machine learning reports. References on each topic.
Deep Review: Opportunities and obstacles for deep learning in biology and medicine - A collaboratively written review paper on deep learning, genomics, and precision medicine led by Casey Greene and many others
Deep Learning Genomics Primer - This tutorial is a supplement to the manuscript, A Primer on Deep Learning in Genomics (Nature Genetics, 2018) by James Zou, Mikael Huss, Abubakar Abid, Pejman Mohammadi, Ali Torkamani & Amalio Telentil. Box 1 and 2 - concepts and definitions. Box 3 - online resources (cloud platforms, GPU services, software libraries, educational resources, more). Python tutorial on detecting DNA motifs.
Eraslan et al., “Deep Learning.” - Deep learning in genomics review. Big data description, evolution of machine learning into deep learning with the help of GPUs. Supervised learning - Four major classes of neural networks (fully connected, convolutional, recurrent and graph convolutional). Two unsupervised learning techniques, autoencoders and generative adversarial networks (GANs). From basic logistic regression to each network architecture illustrated on figures, theory descriptions, examples of applications in genomics. Transfer learning, model zoos, interpretation/feature importance.
Angermueller et al., “Deep Learning for Computational Biology.” - Review on machine learning, (epi)genomics examples. Supervised vs. unsupervised learning. Deep neural networks. Box 1 - network basics. Box 2 - convolutional NN. TOOLS: Caffe, Theano, Torch7, TensorFlow. Data preparation, model training and optimization
Min, Lee, and Yoon, “Deep Learning in Bioinformatics.” - Deep neural networks in bioinformatics. Overview of deep learning development, programming libraries, basic structure of neural networks, convolutional NNs, recurrent NNs. Table 4 - Omics applications, biomedical imaging, biomedical signal processing. References. Code examples (Jupyter notebooks) of eight bioinformatics deep learning applications
Zou et al., “A Primer on Deep Learning in Genomics.” - Deep learning in genomics overview (feed-forward, convolutional, recurrent) and a Python tutorial on detecting DNA motifs. Box 1 and 2 - concepts and definitions. Box 3 - online resources (cloud platforms, GPU services, software libraries, educational resources, more). GitHub repo and Colab notebook with Interactive tutorial to build a convolutional neural network to discover DNA-binding motifs
Pérez-Enciso, and Zingaretti. “A Guide for Using Deep Learning for Complex Trait Genomic Prediction.” Genes, 2019 - Deep learning for predicting phenotypes from genomics data. Deep learning basics, definitions
Sakellaropoulos, Theodore, Konstantinos Vougas, Sonali Narang, Filippos Koinis, Athanassios Kotsinas, Alexander Polyzos, Tyler J. Moss, et al. “A Deep Learning Framework for Predicting Response to Therapy in Cancer.” Cell Reports, December 2019 - Drug response prediction from gene expression data. Deep Neural Network (DNN, H2O.ai framework) compared with Elastic Net, Random Forest. Trained on highly variable (by MAD) gene expression in 1001 cell lines and 251 drugs pharmacogenomic dataset (GDSC. CCLP) to predict IC50. Hyper-parameter optimization using 5-fold cross-validation and minimizing Mean Square Error. Batch correction between the datasets Tested on unseen patient cohorts (OCCAMS, MD Anderson, TCGA, Multiple Myeloma Consortium) to predict IC50 and test low, medium, high IC50 groups for survival differences. RDS files data, R code
M. Jannesari, M. Habibzadeh, H. Aboulkheyr, P. Khosravi, O. Elemento, M. Totonchi, and I. Hajirasouliha. “Breast Cancer Histopathological Image Classification: A Deep Learning Approach.” In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018 - Breast cancer image classification. Data from Stanford Tissue Microarray Database (TMAD) and Breast Cancer Histopathological Database (BreakHis), >6K images. Different variants of ResNet and Inception architectures. Data augmentation (resizing, rotation, cropping, flipping). Training details. Classification into malignant and benign, or into subtypes. Can handle images at different magnifications. ResNet performs better. GitHub repository includes crawler to get images

DL Tools

Interactive_Tools - Interactive Tools for Machine Learning, Deep Learning and Math. Play with deep neural network in browser
ivy - The Unified Machine Learning Framework supporting JAX, TensorFlow, PyTorch, MXNet, and Numpy. Python module. Documentation
keras - Deep Learning for humans http://keras.io/
MXNet-Gluon-Style-Transfer - neural artistic style transfer using MXNet. PyTorch and Torch implementations available
openai.com - GPT-3 Access Without the Wait (API access to GPT-3)
OpenCV - Open Source Computer Vision library. GitHub, opencv-python - CPU-only OpenCV packages for Python. Documentation. Video - 3h OpenCV crash course
pathology_learning - Using traditional machine learning and deep learning methods to predict stuff from TCGA pathology slides
ruta - Unsupervised Deep Architechtures in R, autoencoders. Requires Keras and TensorFlow. Book
tensor2tensor - Library of deep learning models and datasets designed to make deep learning more accessible and accelerate ML research
Janggu - deep learning interface to genomic data (FASTA, BAM, BigWig, BED, GFF). Numpy-like Bioseq and Cover objects accessable by Keras. Includes model evaluation and interpretation features. Pypi, Docs, Janggu - Deep learning for genomics
maui - Multi-omics Autoencoder Integration. Latent factors from different data types (stacked variational autoencoders), and their clustering, testing for association with survival. Tested vs. latent factors extracted using Multifactor Analysis (MFA) and iCluster+, on TCGA colorectal cancer RNA-seq, SNPs, CNVs. Evaluation of Colorectal Cancer Subtypes and Cell Lines Using Deep Learning
Ludwig is a toolbox built on top of TensorFlow that allows to train and test deep learning models without the need to write code. GitHub
Mask_RCNN - Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow
PennAI - AI-Driven Data Science, entry-level machine learning interface for non-experts. A System for Accessible Artificial Intelligence

Auto ML

autokeras - Keras-based AutoML library for deep learning. Tutorials for image/text/data classification/regression
ClearML - Auto-Magical Suite of tools (Python) to streamline your ML workflow Experiment Manager, MLOps and Data-Management. Documentation, Youtube channel
nni - An open source AutoML toolkit for automate machine learning lifecycle, including feature engineering, neural architecture search, model compression and hyper-parameter tuning. Documentation
TPOT - A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming. Simplified interface to many machine learning algorithms. Scaling Tree-Based Automated Machine Learning to Biomedical Big Data with a Feature Set Selector

DL models

PyTorch model zoos
Keras model zoos
Tensorflow model zoos
Kipoi - a model zoo for genomics. Examples of transfer learning, predicting pathogenic variants, TFBSs. Avsec et al., “The Kipoi Repository Accelerates Community Exchange and Reuse of Predictive Models for Genomics.”, GitHub repo
Caffe Model Zoo
BERT, Bidirectional Encoder Representations from Transformers, for natural language processing tasks. Model architecture, implemented using TensorFlow. Applications - Masked Language Model, next sentence prediction. Excels in several benchmarks. Pretrained models and code. See also BioBert
- Devlin, Jacob, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova. “BERT: Pre-Training of Deep Bidirectional Transformers for Language Understanding”
DNABERT - pre-trained Bidirectional Encoder Representation from Transformers (BERT) model for DNA sequence, captures contextual information, 512bp window. Input - overlapping k-mer tokens (6-mer perform best). Architecture details (12 transformer encoder layers, learning rate increased then decreased, 120 epochs sufficient), comparison with RNN, CNN, Transformers. Outperforms DeePromoter, PromID, FPROM, FirstEF promoter prediction methods, DeepBind, DeepSEA, Basset, DeepSite, DanQ, DESSO on on TFBS prediction. Pretrained on 10-510-long sequences, to predict missing nucleotides. Fine-tuned for promoter region prediction, transcription factor binding sites, splicing sites, genetic variants. visualization of learned attention patterns. [CLS] classification token at the beginning of sequence, [SEP] at the end. Visualization of attention scores. Supplementary material contains detailed description of the model's architecture, input data, training, evaluation, various case scenarios, visualization. Bringing BERT to the field blog post contains more details and links to transformer resources.

Paper
Ji, Yanrong, Zhihan Zhou, Han Liu, and Ramana V Davuluri. “[DNABERT: Pre-Trained Bidirectional Encoder Representations from Transformers Model for DNA-Language in Genome](https://doi.org/10.1093/bioinformatics/btab083).” Bioinformatics, (August 9, 2021)

TabPFN - the Tabular Prior-data Fitted Network, a tabular foundational model (generative transformer-based), outperforms other models, excels on small datasets but scalable, fast. Classification or regression problems Leverages in-context learning (ICL), generates a large corpus of synthetic tabular datasets (prior in Bayesian terms, approach based on structural causal models, SCMs) and then train a self-attention-based transformer neural network. Pre-training - predict masked targets of all synthetic datasets. Z-normalization of inputs. Sample-specific learning, feature-specific attention attending to features across samples, invariant to the order of samples and features. Tested on two benchmark datasets, AutoML benchmark and OpenML-CTR23, outperforms XGBoost, CatBoost, random forest. Approaches for interpretation. Python implementation.

Paper
Hollmann, N., Müller, S., Purucker, L. et al. Accurate predictions on small data with a tabular foundation model. Nature 637, 319–326 (2025). https://doi.org/10.1038/s41586-024-08328-6

folding_tools - a collection of protein folding tools
progressive_growing_of_gans - Progressive Growing of GANs for Improved Quality, Stability, and Variation — Official TensorFlow implementation of the ICLR 2018 paper

DL projects

ai-collection - A collection of generative AI applications, for text, code, image, video, audio, etc.
awesome-colab-notebooks - Collection of google colaboratory notebooks for fast and easy experiments
awesome-generative-ai - A curated list of modern Generative Artificial Intelligence projects and services.
DeepSearch - extracts and structures data from PDF documents in four steps: Parse, Interpret, Index, and Integrate. Parses tables, images, paragraphs, output in json. deepsearch-toolkit - Python interface to the DeepSearch platform for new knowledge explorations and discoveries, Documentation.
bert-finetuning-catalyst - Code for BERT classifier finetuning for multiclass text classification, code and video, by Yury Kashnitsky
Deeplearning-digital-pathology - Python code demonstrating image classification using Keras with Caffe or TensorFlow backend, image manipulation utilities
Weights & Biases Gallery of Curated machine learning reports - selected examples with code
Machine learning lessons and teaching projects designed for engineers - GitHub repo by Lukas Biewald, the founder of Weights and Biases. Code and video tutorials
Weights & Biases GitHub examples of deep learning projects
neuralart_tensorflow - Implementation of "A Neural Algorithm of Artistic Style" by Tensorflow
MyGirlGPT - a personal AI girlfriend running on a local server. Telegram chatbot integration. Voice messages, photos.
openai-cookbook - Examples and guides for using the OpenAI API. GPT-3, DALL-E2, other models.
practical-ml - Learn by experimenting on state-of-the-art machine learning models and algorithms with Jupyter Notebooks. Computer vision, NLP, speech, notebooks open in Colab.
NVIDIA Deep Learning Examples for Tensor Cores - This repository provides State-of-the-Art Deep Learning examples that are easy to train and deploy, achieving the best reproducible accuracy and performance with NVIDIA CUDA-X software stack running on NVIDIA Volta, Turing and Ampere GPUs.

Language models

ChatGPT, Gemini, NotebookLM, Claude, OpenRouter, Groq, Storm, Qwen, DeepSeek, Perplexity.ai, Together.ai

awesome-chatgpt - Curated list of awesome tools, demos, docs for ChatGPT and GPT-3
awesome-llm-courses - A curated list of awesome online courses about Large Langage Models (LLMs)
agenticSeek - A 100% local alternative to Manus AI, this voice-enabled AI assistant autonomously browses the web, writes code, and plans tasks while keeping all data on your device. Tailored for local reasoning models, it runs entirely on your hardware, ensuring complete privacy and zero cloud dependency.
chatbox - User-friendly Desktop Client App for AI Models/LLMs (GPT, Claude, Gemini, Ollama...)
chatgpt-clone - Build Yo'own ChatGPT with OpenAI API & Gradio. A Python app for web browser intercage to ChatGPT.
DeepSeek-V3 - a strong Mixture-of-Experts (MoE) language model with 671B total parameters with 37B activated for each token. Excellent performance at a fraction of the cost. Web chatbot.
h2ogpt - open-source GPT with document and image Q&A, 100% private chat, no data leaks, Apache 2.0 https://arxiv.org/pdf/2306.08161.pdf Live Demo: https://gpt.h2o.ai/
Hands-On-Large-Language-Models - Official code repo for the O'Reilly Book - "Hands-On Large Language Models" by Jay Alammar and Maarten Grootendorst. PyTorch, Jupyter notebooks, can be opened in Google colab.
litellm - Python SDK, Proxy Server (LLM Gateway) to call 100+ LLM APIs in OpenAI format - [Bedrock, Azure, OpenAI, VertexAI, Cohere, Anthropic, Sagemaker, HuggingFace, Replicate, Groq]. Docs
llm-course - Course to get into Large Language Models (LLMs) with roadmaps and Colab notebooks.
llm_engineering - repo for the Mastering AI and LLM Engineering course. Python, includes videos.
LLMs-from-scratch - Implementing a ChatGPT-like LLM from scratch, step by step, the Python code for coding, pretraining, and finetuning a GPT-like LLM. By Sebastian Raschka. For the book Build a Large Language Model (From Scratch).
LLMsPracticalGuide - A curated list of practical guide resources of LLMs (LLMs Tree, Examples, Papers)
lobe-chat - an open-source, modern-design AI chat framework. Supports Multi AI Providers( OpenAI / Claude 3 / Gemini / Ollama / Azure / DeepSeek), Knowledge Base (file upload / knowledge management / RAG ), Multi-Modals (Vision/TTS/Plugins/Artifacts). One-click FREE deployment of your private ChatGPT/ Claude application.
mlc-llm - Enable everyone to develop, optimize and deploy AI models natively on everyone's devices. Documentation
nanoGPT - The simplest, fastest repository for training/finetuning medium-sized GPTs.
ollama - Get up and running with Llama 2 and other large language models locally.
openai-cookbook - Examples and guides for using the OpenAI API. Rendered version
privateGPT - Interact privately with your documents using the power of GPT, 100% privately, no data leaks.
Qwen - LLM created by Alibaba Cloud. Transformer-based, lightweight but among top performers. Website
Storm - An LLM-powered knowledge curation system that researches a topic and generates a full-length report with citations. GitHub

Music, voice, audio

buzz - Buzz transcribes and translates audio offline on your personal computer. Powered by OpenAI's Whisper.
ebook2audiobook - Convert ebooks to audiobooks with chapters and metadata using dynamic AI models and voice cloning. Supports 1,107+ languages!
ElevenReader - text to speech converter, for ebooks (EPUB), PDFs, text files. iOS and Android mobile apps.
Jukebox - music generation neural network. Hierarchical Vector Quantised-Variational AutoEncoder (VQ-VAE) architecture, three separate temporal resolutions. Able to generate singing from lyrics, extend music examples. Dhariwal et al., “Jukebox: A Generative Model for Music.”, Blog post with examples of generated music
june - Local voice chatbot for engaging conversations, powered by Ollama, Hugging Face Transformers, and Coqui TTS Toolkit
Magenta - Music and Art Generation with Machine Intelligence
OpenVoice - voice cloning tool, transfer voice tones to pronounce different words, even in different language.
Real-Time-Voice-Cloning - Clone a voice in 5 seconds to generate arbitrary speech in real-time. Learn voice characteristics from a short audio clip and perform text-to-speech conversion using this voice.
Project DeepSpeech - A TensorFlow implementation of Baidu's DeepSpeech architecture. Transcribe audio data, English model available. Documentation
SpeechBrain - A PyTorch-based Speech Toolkit for speech/speaker recognition, speech enhancement, processing, and more. GitHub repo
vampnet - music generation with masked transformers. arXiv paper, supplementary page

Image, video, vision

Krea - image and video generation from text prompt, enhancing image quality, image editing from text prompt.
Sora - OpenAI's text-to-video generation tool that allows users to create, animate, and remix videos from text prompts, images, and existing videos.
18 All-Time Classic Open Source Computer Vision Projects for Beginners by Analytics Vidhya
500-AI-Machine-learning-Deep-learning-Computer-vision-NLP-Projects-with-code - links to many ML/DL projects and resources
Top 10 Computer Vision Papers 2020 - A list of the top 10 computer vision papers in 2020 with video demos, articles, code and paper reference.
awesome-ai-art-image-synthesis - A list of awesome tools, ideas, prompt engineering tools, colabs, models, and helpers for the prompt designer playing with aiArt and image synthesis. Covers Dalle2, MidJourney, StableDiffusion, and open source tools.
Bringing-Old-Photos-Back-to-Life - Old Photo Restoration (Official PyTorch Implementation)
CLIP - CLIP (Contrastive Language-Image Pretraining), Predict the most relevant text snippet given an image
CogView2 - official code repo for paper "CogView2: Faster and Better Text-to-Image Generation via Hierarchical Transformers" (ArXiv), Example
Cosmos - Cosmos is a world model development platform that consists of world foundation models, tokenizers and video processing pipeline to accelerate the development of Physical AI at Robotics & AV labs. Cosmos is purpose built for physical AI. The Cosmos repository will enable end users to run the Cosmos models, run inference scripts and generate videos. Docker options.
HunyuanVideo - A Systematic Framework For Large Video Generation Model
DALL-E-2 - a new AI system that can create realistic images and art from a description in natural language. Tweet. How This A.I. Draws Anything You Describe 16m video by ColdFusion. HOW DALL-E COULD POWER A CREATIVE REVOLUTION, The Verge. DALLE2-pytorch - Implementation of DALL-E 2, OpenAI's updated text-to-image synthesis neural network, in Pytorch. min-dalle - min(DALL·E) is a fast, minimal port of DALL·E Mini to PyTorch
Deep-Live-Cam - real time face swap and one-click video deepfake with only a single image.
JoJoGAN - Official PyTorch repo for JoJoGAN: One Shot Face Stylization. Arxiv
Photo restoration with GFP-GAN - GFPGAN aims at developing Practical Algorithms for Real-world Face Restoration. Online version
Selfie2Anime online tool and a GitHub repo
stablediffusion - High-Resolution Image Synthesis with Latent Diffusion Models
VGG - Visual Geometry Group. Large source of image datasets. Also, practicals, demos, software, publications, more.

DL Misc

100_days_of_CUDA - notes about learning CUDA
geospy.ai - location identification from photos
app.wombo.art - deep generative model dreaming awesome images from text, Android and iOS apps available. Tweet describing the VQGAN+CLIP technology behind it
CSrankings - A web app for ranking computer science departments according to their research output in selective venues, and for finding active faculty across a wide range of areas. Website
ColossalAI - A Unified Deep Learning System for Big Model Era. Scaling deep learning models using data, pipeline, tensor, and sequence parallelism. 1D, 2D, 2.5D, 3D distributed operators. Examples of each. Written in PyTorch, needs a configuration file defining parallelism. Benchmarked against DeepSpeed, Megatron-LM.

Paper
Li, Shenggui, Jiarui Fang, Zhengda Bian, Hongxin Liu, Yuliang Liu, Haichen Huang, Boxiang Wang, and Yang You. “Colossal-AI: A Uniﬁed Deep Learning System For Large-Scale Parallel Training,” n.d.

Elvis Saravia - machine learning researcher at Facebook AI, Twitter account to follow. His starred repos are gold.
traingenerator.jrieke.com - A web app to generate template code for machine learning. GitHub, Tweet
Deep-learning-in-cloud - List of deep learning cloud providers
Deep learning resources - (cloud) platforms, software, educational resources. From Zou et al., “A Primer on Deep Learning in Genomics.”
Collections of GitHub repositories of deep learning projects, Analytics Vidhya
Google Colab Free GPU Tutorial
tpu-starter - Everything you want to know about Google Cloud TPU
How to use R with Google Colaboratory?, direct link to a new R-notebook
Deep-Reinforcement-Learning-Algorithms-with-PyTorch - PyTorch implementations of deep reinforcement learning algorithms and environments
ML Visuals - Visuals contains figures and templates which you can reuse and customize to improve your scientific writing. Google Slides
Machine-Learning-Figures - images of most representative concepts and diagrams for machine- and deep learning.

Awesome Machine learning

awesome-machine-learning - A curated list of awesome Machine Learning frameworks, libraries and software
awesome-machine-learning-interpretability - A curated list of awesome machine learning interpretability resources
awesome-machine-learning-operations - A curated list of awesome open source libraries to deploy, monitor, version and scale your machine learning
awesome-courses - List of awesome university courses for learning Computer Science
Best-of Machine Learning with Python - A ranked list of awesome machine learning Python libraries. Updated weekly.
data-science - "Path to a free self-taught education in Data Science!" - Open Source Society University, a collection of free online courses in logical order of learning data science. Massive list of courses, from linear algebra and calculus to R/Python programming/machine learning
Data-science-best-resources - Carefully curated resource links for data science in one place
free-data-science - Thematic list of high-quality data science resources. R, Python, Shell, Regular Expressions, Git, Docker, Markdown/Latex, Statistics, Machine/Deep learning, Visualization, Time Series, Spatial Analysis, more.
machine_learning - Machine learning in R notes by Dave Tang
machine-learning-interview - Machine Learning Interviews from FAANG, Snapchat, LinkedIn. More info at mlengineer.io
machine-learning-notes - Collection of useful machine learning codes and snippets, Jupyter notebooks, by Sebastian Raschka.

ML Books

Probabilistic Machine Learning: An Introduction by Kevin Patrick Murphy, 2022 edition. Intro (probability, statistics, decision theory, information theory, linear algebra), linear models, nonparametric modeling, deep neural networks, dimensionality reduction, clustering, more. GitHub, Tweet1, Tweet2
Mathematics for Machine Learning, 2020 by Marc Peter Deisenroth, A. Aldo Faisal, and Cheng Soon Ong.
Linear_Algebra_With_Python - Lecture Notes for Linear Algebra Featuring Python. These lecture notes are intended for introductory linear algebra courses, suitable for university students, programmers, data analysts, algorithmic traders and etc.
Mathematics for Machine Learning by Garrett Thomas. Tweet
A Machine Learning Primer by Mihail Eric @mihail_eric. Tweet
100+ Free Data Science Books
ciml - book "A Course in Machine Learning". Online version
Interpretable Machine Learning book by Christoph Molnar, A Guide for Making Black Box Models Explainable. LearnPub
Introduction to Machine Learning book by Nils Nilsson, free PDF
hands-on-machine-learning-with-r - Hands-on Machine Learning with R: An applied book covering the fundamentals of machine learning with R. Supplementary material, Online version
mit-deep-learning-book-pdf - MIT Deep Learning Book, PDF of the original http://www.deeplearningbook.org/ book.
ML_for_Hackers - Code accompanying the book "Machine Learning for Hackers"
rtemis - Advanced Machine Learning and Visualization in R. Book
Feature Engineering and Selection: A Practical Approach for Predictive Models by Kuhn and Johnson, GitHub

ML Courses & Tutorials

Harvard CS50 (2023) – Full Computer Science University Course. An introduction to the intellectual enterprises of computer science and the art of programming. 26h video.
Machine Learning 2021 - a seven-module course covering basics of machine learning, by Bioinformatics.ca. Youtube playlist, Course material on Google Drive
Full Stack Deep Learning - from development to deployment of machine learning methods
40+ Modern Tutorials Covering All Aspects of Machine Learning, Tweet
100-Days-Of-ML-Code - 100 Days of Machine Learning Coding as proposed by Siraj Raval. Illustrated step-by-step guides with code and data. Links to videos.
Code for Workshop: Introduction to Machine Learning with R by Shirin Glander. More in her blog posts, twitter etc.
aml-london-2019 - Course materials for Applied Machine Learning course in 2019 in London, by Max Kuhn
aml-training - The most recent version of the Applied Machine Learning notes, related to the parsnip R package by Max Kuhn
cs-video-courses - List of 800+ Computer Science courses with video lectures, Tweet
Data-Analysis-and-Machine-Learning-Projects - Randy Olson's data analysis and machine learning projects
google-interview-university - List of ML/CS courses. A complete daily plan for studying to become a Google software engineer
H2O-3 - The third version of H2OAI - Open Source Fast Scalable Machine Learning Platform For Smarter Applications: Deep Learning, Gradient Boosting & XGBoost, Random Forest, Generalized Linear Modeling (Logistic Regression, Elastic Net), K-Means, PCA, Stacked Ensembles, Automatic Machine Learning (AutoML), etc.
machine-learning-for-software-engineers - A complete daily plan for studying to become a machine learning engineer
Machine-Learning-in-R - Workshop (6 hours): preprocessing, cross-validation, lasso, decision trees, random forest, xgboost, superlearner ensembles
LatinR-2019-h2o-tutorial - H2O Machine Learning Tutorial in R
lecture_i2ml - Introduction to Machine Learning (regression/classification, performance evaluation, parameter tuning, random forests), Python
mlcourse.ai - Open Machine Learning course mlcourse.ai, 2018 English version. Online version, Video
MLfromscratch - Machine Learning algorithm implementations from scratch. Youtube videos
MTH594_MachineLearning - The materials for the course MTH 594 Advanced data mining: theory and applications (Dmitry Efimov, American University of Sharjah)
pattern_classification - A collection of tutorials and examples for solving and understanding machine learning and pattern classification tasks
sklearn-classification - Data Science Notebook on a Classification Task, using sklearn and Tensorflow. Jupyter Notebook, the Census Income Dataset to predict whether an individual's income exceeds $50K/yr based on census data. Docker-wrapped
supervised-ML-case-studies-course - Supervised machine learning case studies in R. Book
useR-machine-learning-tutorial - useR! 2016 Tutorial: Machine Learning Algorithmic Deep Dive. IPython notebooks running R kernel

ML Videos

Probabilistic Machine Learning — Philipp Hennig, 2021, Tweet
10 Powerful YouTube Channels for Data Science Aspirants - Analytics Vidhya's post. Sentdex, 3Blue1Brown, freeCodeCamp.org, StatQuest, Krish Naik, Python Programmer, Corey Schafer, Tech With Tim, Brandon Foltz, 365 Data Science
NC ASA Webinar: Introduction to Machine Learning, by Dr. Funda Gunes, Part 1, Part 2. A one hour overview of the main machine learning concepts
Learning from data - Statistical learning theory course from Caltech, taught by Feynman Prize winner Professor Yaser Abu-Mostafa. Videos, slides
Machine Learning for Everybody – Full Course - 3h 53m video, from intro, kNN, Naive Bayes, regression, SVM to TensorFlow
Statistical Machine Learning: Spring 2017 by Ryan Tibshirani, Larry Wasserman, Carnegie Mellon University.

ML Papers

Whalen, Sean, Jacob Schreiber, William S. Noble, and Katherine S. Pollard. “Navigating the Pitfalls of Applying Machine Learning in Genomics.” Nature Reviews Genetics 23, no. 3 (March 2022): 169–81. https://doi.org/10.1038/s41576-021-00434-9. - Five machine learning problems in genomics, distributional differences, dependency structure, confounding variables, information leakage, unbalanced data. Description, examples, solutions.
Domingos, Pedro. “A Few Useful Things to Know about Machine Learning.” Communications of the ACM 55, no. 10 (October 1, 2012): 78. https://doi.org/10.1145/2347736.2347755. Twelve lessons for machine learning. Overview of machine learning problems and algorithms, problem of overfitting, causes and solutions, curse of dimensionality, issues with high-dimensional data, feature engineering, bagging, boosting, stacking, model sparsity. Video lectures

ML Tools

mlr3 - Machine learning in R R package, the unified interface to classification, regression, survival analysis, and other machine learning tasks. GitHub repo, mlr3gallery - Examples of problems and code solutions, mlr3 Manual - mlr3 bookdown. More on the mlr3 package site, including videos

ML Misc

The Algorithms - R - GitHub repo with code examples of main machine learning algorithms
algorithms_in_ipython_notebooks - A repository with IPython notebooks of algorithms implemented in Python. [https://github.com/rasbt/algorithms_in_ipython_notebooks]
awesome-decision-tree-papers - A collection of research papers on decision, classification and regression trees with implementations
Understanding the Bias-Variance Tradeoff - bias, variance, total error, classic figures and explanation by Scott Fortmann-Roe.
lares - R Library for Analytics and Machine Learning
ml_techniques - R code for performing typical ML tasks and techniques, e.g., naive Bayes, random forest, by Shirin Glander
ML-From-Scratch - Bare bones Python implementations of some of the fundamental Machine Learning models and algorithms
Gradient Boosting Essentials in R Using XGBOOST
MLPB - Machine Learning Problem Bible, problems and solutions in R. XGBoost, SVM, neural networks, and other methods
resources_2025 - Machine Learning in Drug Discovery Resources 2024
Best XGBoost settings: "a second xgboost version (xgboost_best) with the best parameter settings that I obtained in on of my publications. These are: nrounds=500, eta=0.0518715, subsample=0.8734055, booster=”gbtree”, max_depth=11, min_child_weight=1.750185, colsample_bytree=0.7126651, colsample_bylevel=0.6375492." From Is catboost the best gradient boosting R package? post on r-bloggers.com

Material in Chinese

Autopilot-Notes - Autonomous driving notes summarizing the basics, hardware, perception, position, planning, control, product, tools, and manufacturing plan topics.

Material in Russian

Scientific_graphics_in_python - matplotlib for scientific graphics. 3 parts, 13 chapters. By Pavel Shabanov
ml-course-hse - machine learning course at the Computer Sciences Department, High Schoool of Economy. Multiple years, videos
mlcourse_open - OpenDataScience Machine Learning course (Both in English and Russian). Python-based ML course, with video lectures. Video
DL_CSHSE_spring2018 - Deep learning, Anton Osokin, Higher School of Economics, Computer Sciences Department (Russian), course material, and video lectures
Ordinary Differential Equations - Обыкновенные дифференциальные уравнения, Интерактивный учебник, Илья Щуров (НИУ ВШЭ)
Calculus - Математический анализ, Записки лекций, Илья Щуров (НИУ ВШЭ). Tweet
mathprofi.ru - Высшая математика – просто и доступно. Mirror

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