Repositories list

• plurel

  Public
  PluRel: Synthetic Data unlocks Scaling Laws for Relational Foundation Models

  synthetic-datarelational-datascaling-laws+ 2foundation-modelsrelational-foundation-models

  Python

  •

  MIT License

  •2•35•0•0•Updated Feb 23, 2026Feb 23, 2026

• Biomni

  Public

  snap-stanford/Biomni’s past year of commit activity
  Biomni: a general-purpose biomedical AI agent

  agentaibiomedicine

  Python

  •

  Apache License 2.0

  •471•2.7k•42•14•Updated Feb 23, 2026Feb 23, 2026

• relbench

  Public
  RelBench: Relational Deep Learning Benchmark

  Python

  •

  MIT License

  •81•345•1•2•Updated Feb 21, 2026Feb 21, 2026

• optimas

  Public
  (ICLR 2026) Optimas: Optimizing Compound AI Systems

  optimizationmultiagent-systemsreward-learning+ 1compound-ai-systems

  Python

  •

  Apache License 2.0

  •8•76•2•1•Updated Feb 6, 2026Feb 6, 2026

• stark

  Public
  (NeurIPS D&B 2024) STaRK: Benchmarking LLM Retrieval on Textual and Relational Knowledge Bases

  nlpinformation-retrievalgraph+ 4knowledge-basesemi-structured-datamultimodalllm

  Python

  •

  MIT License

  •51•328•5•2•Updated Feb 6, 2026Feb 6, 2026

• relational-transformer

  Public
  Relational Transformer: Toward Zero-Shot Foundation Models for Relational Data

  Rust

  •12•49•0•0•Updated Feb 5, 2026Feb 5, 2026

• precice

  Public
  Python

  •2•9•1•0•Updated Jan 26, 2026Jan 26, 2026

• ogb-web

  Public
  OGB website

  SCSS

  •

  MIT License

  •1•0•0•0•Updated Jan 22, 2026Jan 22, 2026

• PULSAR

  Public
  PULSAR: a Foundation Model for Multi-scale and Multicellular Biology

  aigeneticssingle-cell+ 2virtual-cellfoundation-models

  Python

  •

  MIT License

  •3•26•0•1•Updated Nov 26, 2025Nov 26, 2025

• deepsnap

  Public
  Python library assists deep learning on graphs

  deep-learningpytorchgraph-neural-networks

  Python

  •

  MIT License

  •56•568•23•1•Updated Nov 24, 2025Nov 24, 2025

• relgt

  Public
  Relational Graph Transformer

  transformersrelational-databasesgraph-neural-networks+ 2relational-deep-learninggraph-transformer

  Python

  •

  MIT License

  •15•60•1•0•Updated Jul 10, 2025Jul 10, 2025

• BioDiscoveryAgent

  Public
  BioDiscoveryAgent is an LLM-based AI agent for closed-loop design of genetic perturbation experiments

  Python

  •

  MIT License

  •23•97•2•0•Updated Jul 6, 2025Jul 6, 2025

• llm-social-network

  Public
  Jupyter Notebook

  •9•29•0•0•Updated Jun 30, 2025Jun 30, 2025

• RelGNN

  Public
  [ICML 2025] RelGNN: Composite Message Passing for Relational Deep Learning

  Python

  •

  MIT License

  •4•17•2•0•Updated Jun 12, 2025Jun 12, 2025

• stage-gnn

  Public
  Python

  •

  MIT License

  •0•6•0•0•Updated Jun 12, 2025Jun 12, 2025

• POPPER

  Public
  Automated Hypothesis Testing with Agentic Sequential Falsifications

  agenthypothesis-testingllm+ 1ai-for-science

  Python

  •27•246•4•1•Updated May 14, 2025May 14, 2025

• ogb

  Public
  Benchmark datasets, data loaders, and evaluators for graph machine learning

  deep-learningdatasetsgraph-machine-learning+ 1graph-neural-networks

  Python

  •

  MIT License

  •407•2.1k•35•8•Updated May 6, 2025May 6, 2025

• GreaseLM

  Public
  [ICLR 2022 spotlight]GreaseLM: Graph REASoning Enhanced Language Models for Question Answering

  knowledge-graphquestion-answeringlanguage-model+ 3commonsense-reasoninggraph-neural-networksbiomedical-ques

  Python

  •

  MIT License

  •43•240•14•0•Updated Apr 23, 2025Apr 23, 2025

• planet

  Public
  PlaNet: Predicting population response to drugs via clinical knowledge graph

  knowledge-graphlanguage-modelgraph-neural-networks+ 1biomedicine

  Python

  •

  MIT License

  •5•33•0•0•Updated Mar 13, 2025Mar 13, 2025

• KGWAS

  Public
  KGWAS: novel genetics discovery enabled by massive functional genomics knowledge graph

  aigeneticsknowledge-graph+ 1functional-genomics

  Python

  •

  MIT License

  •10•79•5•2•Updated Mar 7, 2025Mar 7, 2025

• UCE

  Public
  UCE is a zero-shot foundation model for single-cell gene expression data

  Python

  •

  MIT License

  •36•244•2•1•Updated Feb 27, 2025Feb 27, 2025

• supply-chains

  Public
  Python

  •3•14•1•1•Updated Feb 25, 2025Feb 25, 2025

• GEARS

  Public
  GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

  Python

  •

  MIT License

  •80•334•17•4•Updated Feb 1, 2025Feb 1, 2025

• ViRel

  Public
  ViRel: Unsupervised Visual Relations Discovery with Graph-level Analogy

  machine-learninggraphrepresentation-learning+ 3unsupervised-learningreasoninggraph-neural-networks

  Python

  •4•10•2•1•Updated Aug 10, 2024Aug 10, 2024

• relbench-user-study

  Public
  Python

  •5•4•2•0•Updated Aug 7, 2024Aug 7, 2024

• SATURN

  Public
  Jupyter Notebook

  •

  MIT License

  •26•157•2•0•Updated Jul 3, 2024Jul 3, 2024

• neural-subgraph-learning-GNN

  Public
  Jupyter Notebook

  •73•366•21•3•Updated Jun 25, 2024Jun 25, 2024

• MLAgentBench

  Public
  Python

  •

  MIT License

  •64•330•4•2•Updated Jun 19, 2024Jun 19, 2024

• ipf-network-inference

  Public
  Jupyter Notebook

  •2•0•0•0•Updated Jun 18, 2024Jun 18, 2024

• plato

  Public
  Python

  •

  MIT License

  •3•70•1•0•Updated Mar 22, 2024Mar 22, 2024