Hosein Fooladi

tiny-diffusion. A character-level language diffusion model trained on Tiny Shakespeare

blender-mcp. Open-source MCP to use Blender with any LLM

Benchmark_VS. Integrating Machine Learning-Based Pose Sampling with Established Scoring Functions for Virtual Screening

ALineMol. Exploring performance of machine learning model on out-of-distribution data in chemical domain

llama3-from-scratch. llama3 implementation one matrix multiplication at a time

llm.c. LLM training in simple, raw C/CUDA

build-your-own-x. Master programming by recreating your favorite technologies from scratch.

HFooladi.github.io. A personal blog where I write my ideas and thoughts.

DrugOOD. OOD Dataset Curator and Benchmark for AI-aided Drug Discovery

Prompt-Engineering-Guide. 🐙 Guides, papers, lessons, notebooks and resources for prompt engineering, context engineering, RAG, and AI Agents.

DIG. A library for graph deep learning research

Ax. Adaptive Experimentation Platform

rdkit. The official sources for the RDKit library

torch-dftd. pytorch implementation of dftd2 & dftd3 (not actively maintained)

lightdock. Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

nequip. NequIP is a code for building E(3)-equivariant interatomic potentials

cgdms. Differentiable molecular simulation of proteins with a coarse-grained potential

ColabFold. Making Protein folding accessible to all!

jaxopt. Hardware accelerated, batchable and differentiable optimizers in JAX.

jax-md. Differentiable, Hardware Accelerated, Molecular Dynamics

hydra. Hydra is a framework for elegantly configuring complex applications

equivariant-MLP. A library for programmatically generating equivariant layers through constraint solving

pytorch-lightning. Pretrain, finetune ANY AI model of ANY size on 1 or 10,000+ GPUs with zero code changes.

pytorch_geometric. Graph Neural Network Library for PyTorch

rich. Rich is a Python library for rich text and beautiful formatting in the terminal.

esm. Evolutionary Scale Modeling (esm): Pretrained language models for proteins

checklist. Beyond Accuracy: Behavioral Testing of NLP models with CheckList

awesome-mlops. A curated list of references for MLOps

system-design-primer. Learn how to design large-scale systems. Prep for the system design interview. Includes Anki flashcards.

DeepPurpose. A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

reinforcement-learning-an-introduction. Python Implementation of Reinforcement Learning: An Introduction

uncertainty-toolbox. Uncertainty Toolbox: a Python toolbox for predictive uncertainty quantification, calibration, metrics, and visualization

neural-processes. This repository contains notebook implementations of the following Neural Process variants: Conditional Neural Processes (CNPs), Neural Processes (NPs), Attentive Neural Processes (ANPs).

deepchem. Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

jraph. A Graph Neural Network Library in Jax

modAL. A modular active learning framework for Python

awesome. 😎 Awesome lists about all kinds of interesting topics

the-incredible-pytorch. The Incredible PyTorch: a curated list of tutorials, papers, projects, communities and more relating to PyTorch.

retro_star. Retro*: Learning Retrosynthetic Planning with Neural Guided A* Search

penrose. Create beautiful diagrams just by typing notation in plain text.

numpyro. Probabilistic programming with NumPy powered by JAX for autograd and JIT compilation to GPU/TPU/CPU.

fourier-feature-networks. Fourier Features Let Networks Learn High Frequency Functions in Low Dimensional Domains

manim. Animation engine for explanatory math videos

jax-unirep. Reimplementation of the UniRep protein featurization model.

lagrangian_nns. Lagrangian Neural Networks

neural-tangents. Fast and Easy Infinite Neural Networks in Python

jax. Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

autograd. Efficiently computes derivatives of NumPy code.

PRML. PRML algorithms implemented in Python

tldr. Collaborative cheatsheets for console commands 📚.

qTox. qTox is a chat, voice, video, and file transfer IM client using the encrypted peer-to-peer Tox protocol.

awful-ai. 😈Awful AI is a curated list to track current scary usages of AI - hoping to raise awareness

causality. In which I play with the ideas surrounding causality

tdl. Course "Theories of Deep Learning"

MathsDL-spring19. Mathematics of Deep Learning, Courant Insititute, Spring 19

SciMLBook. Parallel Computing and Scientific Machine Learning (SciML): Methods and Applications (MIT 18.337J/6.338J)

open_spiel. OpenSpiel is a collection of environments and algorithms for research in general reinforcement learning and search/planning in games.

pychemlp. Easy-to-use python module for training multi-layer perceptrons (neural networks) from molecular SMILES and known associated properties

notes-on-writing. Notes on writing

rust. Empowering everyone to build reliable and efficient software.

interactive-coding-challenges. 120+ interactive Python coding interview challenges (algorithms and data structures). Includes Anki flashcards.

YouTokenToMe. Unsupervised text tokenizer focused on computational efficiency

py-spy. Sampling profiler for Python programs

numpy. The fundamental package for scientific computing with Python.

Genomic-ULMFiT. ULMFiT for Genomic Sequence Data

spacy-course. 👩‍🏫 Advanced NLP with spaCy: A free online course

PyTorch-BigGraph. Generate embeddings from large-scale graph-structured data.

keras. Deep Learning for humans

bert. TensorFlow code and pre-trained models for BERT

transformers. 🤗 Transformers: the model-definition framework for state-of-the-art machine learning models in text, vision, audio, and multimodal models, for both inference and training.

nmt. TensorFlow Neural Machine Translation Tutorial

spinningup. An educational resource to help anyone learn deep reinforcement learning.

transformer-xl. Python

probability. Probabilistic reasoning and statistical analysis in TensorFlow

tensor2tensor. Library of deep learning models and datasets designed to make deep learning more accessible and accelerate ML research.

TensorFlow-Examples. TensorFlow Tutorial and Examples for Beginners (support TF v1 & v2)

models. Models and examples built with TensorFlow

Probabilistic-Programming-and-Bayesian-Methods-for-Hackers. aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

dgl. Python package built to ease deep learning on graph, on top of existing DL frameworks.

trfl. TensorFlow Reinforcement Learning

graph_nets. Build Graph Nets in Tensorflow

reinforcement-learning. Implementation of Reinforcement Learning Algorithms. Python, OpenAI Gym, Tensorflow. Exercises and Solutions to accompany Sutton's Book and David Silver's course.

dopamine. Dopamine is a research framework for fast prototyping of reinforcement learning algorithms.

ParlAI. A framework for training and evaluating AI models on a variety of openly available dialogue datasets.

fastText. Library for fast text representation and classification.

d3. Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

pymc. Bayesian Modeling and Probabilistic Programming in Python

bokeh. Interactive Data Visualization in the browser, from Python

freeCodeCamp. freeCodeCamp.org's open-source codebase and curriculum. Learn math, programming, and computer science for free.