Find open-source science resources

Free-text promptable universal 3D medical image segmentation foundation model enabling zero-shot segmentation of diverse anatomical structures and pathologies via natural language prompts across CT, MRI, and other volumetric imaging modalities (DKFZ, 195+ stars, Apache 2.0)

Self-evolving AI scientist with 6 specialized sub-agents (plan/research/code/debug/analyze/write) and persistent memory, #1 on DeepResearch Bench II and AstaBench, supporting multi-provider LLMs and multi-channel deployment (Apache 2.0, 2026)

High-accuracy RAG for scientific PDFs with citation support, agentic RAG, and contradiction detection

World's first fully open, accelerated weather AI software stack with Medium Range forecasting and Nowcasting models using generative AI (January 2026)

Apache 2.0 single-cell foundation model family scaling to 3B parameters, pretrained on 266M cell profiles including perturbation data and released with training, embedding, and downstream benchmarking workflows for disease-relevant single-cell tasks (2025)

General-purpose biomedical AI agent integrating LLM reasoning with retrieval-augmented planning and code-based execution to autonomously execute diverse biomedical research tasks and generate testable hypotheses (Stanford SNAP, bioRxiv 2025)

Open-source AI workbench for scientific research that automates the full research loop — literature review, hypothesis generation, code writing, experiment execution, database querying, and report writing — with 290+ skills, specialized research agents, and a browser-based workspace (1453+ stars, Apache 2.0, 2026)

Universal components for differentiable scientific computing, packaging heterogeneous scientific tools into self-contained, portable, gradient-propagating components with auto-generated schemas, CLI/REST API/Python SDK interfaces, and reproducible deployment across local, cloud, and HPC environments (105+ stars, Apache 2.0)

Python package for simulation-based inference enabling likelihood-free Bayesian parameter estimation from scientific simulators, with flexible interfaces for neural posterior estimation, sequential methods, and MCMC/variational backends (Mackelab, 825+ stars)

AlphaFold 3 inference pipeline for unified biomolecular structure prediction of proteins, nucleic acids, small molecules, ions, and post-translational modifications (Google DeepMind, Nature 2024)

Scikit-learn compatible tabular foundation model for zero-shot classification and regression on mixed-type tabular datasets via in-context learning; applicable to diverse scientific datasets (1.8K+ stars, Apache 2.0)

Modern LLM-native agent simulation platform for social science research and experimental design, providing a flexible framework for creating and managing intelligent agents in simulated environments (Tsinghua FIB Lab, 984+ stars, 2025)

Molecular dynamics in JAX

Knowledge graph-guided synthetic data generation for LLM fine-tuning, achieving strong performance on scientific QA (GPQA-Diamond) and math reasoning (AIME)

Open-source, all-atom biomolecular foundation model that turns co-folding into a scalable engine for structure prediction, design, and optimization across proteins, nucleic acids, and small molecules in drug discovery; ranked first on PXMeter-AB, FoldBench-AB, and 2026ARK-AB antibody-antigen benchmarks (263+ stars, Apache 2.0)

Pretrained time series foundation model for zero-shot forecasting across diverse scientific and real-world domains; tokenizes continuous time series into discrete bins to train transformer language models on large-scale corpora, achieving strong zero-shot generalization and competitive performance with task-specific supervised models on climate, energy, and health benchmarks (5.3K+ stars, Apache 2.0, 2024-2026)

Google DeepMind's diffusion-based ensemble weather forecasting model at 0.25° resolution, outperforming ECMWF ENS on 97.2% of targets up to 15 days ahead, with open-source code and weights (Nature 2024)

Multimodal AI system generating virtual populations for tumor microenvironment modeling from H&E and multiplex immunofluorescence pathology images, enabling large-scale spatial analysis of cancer biology and therapeutic response prediction (Microsoft Research & Providence, 370+ stars)

Whole-slide pathology foundation model trained on 1.3 billion image tiles from 171K slides using a LongNet-based architecture to encode gigapixel-scale WSIs for cancer subtyping and biomarker prediction (Microsoft Research & Providence, 601+ stars)

ECMWF's unified framework and command-line tool to run AI-based weather forecasting models (GraphCast, Aurora, Pangu, NeuralGCM, FourCastNet) with operational ECMWF data infrastructure, enabling standardized inference and benchmarking across state-of-the-art meteorological AI systems (ECMWF, 576+ stars)

Lean 4 formalizations of ten major advances in mathematics and theoretical computer science, including improved sphere-packing bounds, non-sofic groups, a counterexample to Connes's rigidity conjecture, and quantum parallel repetition; released with the OpenAI paper and reasoning walkthroughs (57+ stars, Apache 2.0)

Fast, differentiable, JIT-free finite element library for PyTorch enabling GPU-native PDE solving with native autograd, tensorized assembly, and sparse linear algebra; part of the TensorGalerkin framework (218+ stars, Apache 2.0)

The Zebrafish Activity Prediction Benchmark for forecasting cellular-resolution neural activity throughout an entire vertebrate brain, combining light-sheet microscopy calcium-imaging data, forecasting tasks, and evaluation tools to advance whole-brain neural dynamics modeling (77+ stars, Apache 2.0)

Next-generation benchmark for data-driven global weather models with standardized evaluation framework and curated datasets for ML forecasting (Google Research, 2024)

Trainable PyTorch reproduction of AlphaFold 3

Medical large vision-language model unifying comprehension and generation via heterogeneous knowledge adaptation, enabling holistic medical image understanding, visual question answering, and clinical report generation across diverse modalities (ZJU4HealthCare, 1.6K+ stars)

Transformer that translates fragment ion peaks into peptide sequences for database-free de novo sequencing in large-scale proteomics, with InstaNovo+ extending it as a multinomial diffusion model that iteratively refines predicted sequences, plus InstaNovo-P for phosphoproteomics and Winnow for calibrated confidence with FDR control (130+ stars, Apache 2.0, actively maintained)

PyTorch-based embedding instance segmentation algorithm optimized for accurate, efficient, and portable cell and nucleus segmentation across fluorescence and brightfield microscopy images, achieving state-of-the-art speed and accuracy with lightweight model sizes suitable for edge deployment (224+ stars, Apache 2.0)

Local-first, conversational AI research partner for multi-omics analysis with CLI, desktop app, and 95+ reproducible skills; keeps raw data local while routing natural-language requests to Python/R/CLI tools with persistent memory, autonomous analysis paths, and multi-method consensus workflows (TianGzlab, 155+ stars, Apache 2.0, 2026)

Scientific taste learning framework showing AI can judge and propose research ideas with long-term impact; trains Scientific Judge as a generative reward model and Scientific Thinker as an ideation policy using Reinforcement Learning from Community Feedback (RLCF) on large-scale citation signals, with SciJudgeBench and released HuggingFace model weights (425+ stars, Apache 2.0, 2026)

Advanced OCR with PP-StructureV3 document parsing, 13% accuracy improvement, supports 80+ languages

SDK & library for AI-driven scientific computing applications

200+ AI for Science papers with Chinese interpretations

LLM-driven formal proof search system that pairs large language models with Lean verification to solve open mathematics problems; autonomously resolved 9 of 353 Erdős problems and 44 of 492 OEIS conjectures, with proofs and natural-language prose released for combinatorics, optimization, graph theory, algebraic geometry, and quantum optics collaborations (282+ stars, Apache 2.0)

Open-source implementation of AlphaEvolve's evolutionary coding agent paradigm, enabling LLMs to autonomously discover and optimize algorithms through iterative evolution, matching the approach behind DeepMind's breakthrough matrix multiplication discovery (6.2K+ stars, 2025)

Generalized Attribute Based Ratings Information Extraction Library; official OpenAI toolkit that turns messy qualitative corpora into analysis-ready datasets for social scientists and data scientists, measuring quantitative attributes in text, images, or audio using the GPT API. See the [official blog post](https://openai.com/index/scaling-social-science-research/) and [NBER working paper](http://www.nber.org/papers/w34834) (413+ stars, Apache 2.0)

AI-powered field boundary delineation toolkit combining satellite foundation models, embeddings, and global training data for accurate agricultural parcel/field boundary mapping, with Google Earth Engine integration and PyPI distribution (84+ stars, Apache 2.0, 2026)

Autonomous AI agent for end-to-end spatial proteomics analysis, featuring SP-Bench for agentic multiplexed-imaging workflows (tomtommyyuan, 140+ stars, 2026)

Computational fluid dynamics in JAX, enabling differentiable Navier-Stokes simulations with automatic differentiation for ML-accelerated CFD research, supporting turbulence modeling, convection-diffusion, and complex boundary conditions on CPUs and GPUs (Google Research, 947+ stars)

Democratizing AlphaFold3: PyTorch reimplementation to accelerate protein structure prediction research

Multi-modal foundation model for biomolecular structure prediction (proteins, small molecules, DNA, RNA, glycans) achieving SOTA across benchmarks, with optional MSA/template support (Chai Discovery, 2024)

Deep learning framework for molecular docking extending AutoDock Vina with convolutional neural network scoring functions, achieving superior virtual screening enrichment and pose prediction across diverse target classes; widely adopted in pharmaceutical structure-based drug design (J. Cheminformatics, 915+ stars, actively maintained)

First system progressively surpassing human SOTA on frontier AI tasks (183.7%, 1.9%, 7.9% improvements), month-long autonomous discovery with 20,000+ GPU hours

Automated academic illustration generation for AI scientists, converting research papers into publication-ready figures using VLMs and diffusion models with iterative refinement (PKU & Google Research, 6.2K+ stars, 2026)

First multi-domain generative foundation model for the natural sciences built on a unified scientific grammar, encoding proteins, antibodies, small molecules, chemical reactions, materials, and their spatial interactions into a shared token vocabulary; enables unified generation, prediction, and design across domains under a purely autoregressive paradigm (134+ stars, Apache 2.0, 2026)

DeepMind's graph neural network for materials exploration, discovering 2.2M new crystal structures (380K most stable) equivalent to 800 years of traditional research, with 520K+ materials dataset open-sourced (Nature 2023)

Numerical differential equation solving in JAX

Google's open multimodal medical LLM family built on Gemma 3, including a 4B multimodal model handling medical images (radiology, pathology, dermatology) alongside text and a 27B text model for clinical reasoning; trained on de-identified medical data with checkpoints and inference code released under Apache 2.0 (1.6K+ stars)

Arc Institute's 40B-parameter genome foundation model trained on 9 trillion nucleotides from all domains of life, supporting 1M base pair context for generalist DNA/RNA/protein prediction and design (Nature 2026)

Gene expression prediction