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76 repositories

ToolUniverse
Public
Democratizing AI scientists with ToolUniverse
agents autonomous-agents ai-agents
agents autonomous-agents ai-agents tool-use lrm ai-scientists llms reasoning-agent ai-for-science automated-science
Python
•
Apache License 2.0
•244•1.6k•4•12•Updated Aug 10, 2026Aug 10, 2026
mims-harvard.github.io
Public
Lab website
medical-ai therapeutics generative-ai
medical-ai therapeutics generative-ai ai-for-science biomedical-ai agentic-ai multimodal-ai
HTML
•1•3•0•0•Updated Aug 9, 2026Aug 9, 2026
KUL-Rec
Public
Python
•
MIT License
•0•0•0•0•Updated Aug 6, 2026Aug 6, 2026
OptimusKG
Public
A modern multimodal knowledge graph with type-specific metadata across biomedical domains.
python neo4j ontology
python neo4j ontology knowledge-graph biomedical multimodal-data heterogeneous-graphs multimodal-ai graph-ai
Python
•
MIT License
•11•111•2•4•Updated Aug 3, 2026Aug 3, 2026
ATHENA
Public
ATHENA-R1: AI agent for treatment reasoning over a biomedical tool universe
ai-agents ai-for-medicine ai-for-science
ai-agents ai-for-medicine ai-for-science reasoning-models
Python
•
MIT License
•15•64•0•0•Updated Jul 17, 2026Jul 17, 2026
Medea
Public
Medea: An AI agent for therapeutic reasoning across biological contexts
omics immunotherapy ai-agents
omics immunotherapy ai-agents target-discovery tool-use therapeutics synthetic-lethality foundation-models agentic-ai ai-scientist
Python
•
Apache License 2.0
•21•123•2•5•Updated Jul 17, 2026Jul 17, 2026
CASCADE
Public
Python
•
MIT License
•0•1•0•0•Updated Jul 13, 2026Jul 13, 2026
SPATIA
Public
[ICML'26] SPATIA: Multimodal Generation and Prediction of Spatial Cell Phenotypes
spatial-transcriptomics virtual-cell generative-ai
spatial-transcriptomics virtual-cell generative-ai
Python
•
MIT License
•1•3•0•0•Updated Jul 7, 2026Jul 7, 2026
PrimeKG
Public
Precision Medicine Knowledge Graph (PrimeKG)
bioinformatics dataset knowledge-graph
bioinformatics dataset knowledge-graph nlp-machine-learning graph-machine-learning precision-medicine therapeutics network-medicine
Jupyter Notebook
•
MIT License
•156•808•7•0•Updated Jun 30, 2026Jun 30, 2026
ClinVec
Public
ClinVec: Unified Embeddings of Clinical Codes Enable Knowledge-Grounded AI in Medicine
embeddings representation-learning multimodality
embeddings representation-learning multimodality precision-medicine medical-ai graph-transformer clinical-ai
Jupyter Notebook
•
MIT License
•15•96•0•1•Updated Jun 25, 2026Jun 25, 2026
bio-posttrain
Public
How Post-Training Shapes Biological Reasoning Models
post-training reasoning-models mid-training
post-training reasoning-models mid-training multimodal-foundation-models biological-foundation-models
Jupyter Notebook
•
Other
•7•16•1•0•Updated Jun 16, 2026Jun 16, 2026
MedLog
Public
A protocol for event-level logging of clinical AI.
Python
•
MIT License
•2•26•0•0•Updated Jun 11, 2026Jun 11, 2026
ARTIST
Public
[ICML 2026] ARTIST: Adaptive Time Series Reasoning via Segment Selection
reinforcement-learning longitudinal-data multi-step-reasoning
reinforcement-learning longitudinal-data multi-step-reasoning reasoning-models
Python
•0•2•0•0•Updated May 30, 2026May 30, 2026
SPECTRA
Public
SPECTRA: Spectral framework for evaluation of biomedical AI models
benchmarking protein-structure protein-sequences
benchmarking protein-structure protein-sequences benchmark-framework geometric-deep-learning protein-language-model foundation-models large-language-models
Jupyter Notebook
•
MIT License
•6•45•1•2•Updated May 28, 2026May 28, 2026
AutoScientists
Public
AutoScientists: Self-Organizing Agent Teams for Long-Running Scientific Experimentation
agents self-organizing ai-scientists
agents self-organizing ai-scientists ai-for-science automated-science long-running-agents self-evolving-agents ai-for-scientific-discovery
Python
•115•717•1•4•Updated May 28, 2026May 28, 2026
git-graph
Public
TypeScript
•0•0•0•0•Updated May 27, 2026May 27, 2026
rel-reasoning
Public
Evaluating Relational Reasoning in LLMs with REL
benchmarking reasoning relational-reasoning
benchmarking reasoning relational-reasoning llm
Python
•
MIT License
•0•2•0•0•Updated May 25, 2026May 25, 2026
COMPASS
Public
Generalizable AI predicts immunotherapy outcomes across cancers and treatments
immunology immunotherapy generalization
immunology immunotherapy generalization multimodal-learning therapeutics concept-bottleneck-models
Jupyter Notebook
•
MIT License
•13•108•2•0•Updated May 19, 2026May 19, 2026
PINNACLE
Public
Contextual AI models for single-cell protein biology
proteins context-aware contextual
proteins context-aware contextual geometric-deep-learning graph-neural-networks therapeutics
Python
•
MIT License
•27•110•3•3•Updated May 7, 2026May 7, 2026
ark
Public
Autonomous Knowledge Graph Exploration with Adaptive Breadth-Depth Retrieval
retrieval knowledge-graph agentic-ai
retrieval knowledge-graph agentic-ai
Jupyter Notebook
•1•15•0•0•Updated Apr 18, 2026Apr 18, 2026
ATOMICA
Public
Learning Universal Representations of Intermolecular Interactions with ATOMICA
proteins molecular-structures ions
proteins molecular-structures ions peptides nucleic-acids geometric-deep-learning atomistic-modelling small-molecules molecular-interactions
Python
•
MIT License
•30•226•0•0•Updated Apr 13, 2026Apr 13, 2026
Qworld
Public
Qworld: Question-Specific Evaluation Criteria for LLMs
benchmarking llm llm-evaluation
benchmarking llm llm-evaluation llm-evaluation-framework llm-as-a-judge agentic-ai agent-as-a-judge reasoning-language-models
Python
•
MIT License
•4•33•1•9•Updated Mar 26, 2026Mar 26, 2026
CLEF
Public
CLEF: Controllable Sequence Editing for Biological and Clinical Trajectories
patients sequence-models ehr-data
patients sequence-models ehr-data counterfactuals conditional-generation cellular-reprogramming generative-ai
Python
•5•13•1•1•Updated Mar 15, 2026Mar 15, 2026
gates-buildathon
Public
Gates Foundation Build-a-thon on agentic memory.
TypeScript
•
MIT License
•6•0•0•0•Updated Mar 12, 2026Mar 12, 2026
ark-agent-cli
Public
Terminal based chat implementation of ARK agent
agents contextual-ai knowledge-retrieval
agents contextual-ai knowledge-retrieval agentic-ai
TypeScript
•
MIT License
•6•14•0•1•Updated Mar 12, 2026Mar 12, 2026
StratCP
Public
Act or Defer: Error-Controlled Decision Policies for Medical Foundation Models
calibration ai-safety oncology
calibration ai-safety oncology conformal-prediction medical-ai ophtalmology foundation-models vision-language-model ai-implementation
Python
•
MIT License
•3•10•0•0•Updated Mar 2, 2026Mar 2, 2026
medical-ai-workshop
Public
TypeScript
•2•1•0•0•Updated Feb 21, 2026Feb 21, 2026
PROTON-GEM
Public
Graph AI generates neurological hypotheses validated in molecular, organoid, and clinical systems
Jupyter Notebook
•
MIT License
•15•3•0•0•Updated Feb 6, 2026Feb 6, 2026
PROTON
Public
Graph AI generates neurological hypotheses validated in molecular, organoid, and clinical systems
drug-repurposing alzheimers-disease parkinsons-disease
drug-repurposing alzheimers-disease parkinsons-disease neurology organoids bipolar-disorder ai-for-science graph-ai
Jupyter Notebook
•
MIT License
•15•33•0•0•Updated Dec 27, 2025Dec 27, 2025
proton-website
Public
TypeScript
•0•1•0•0•Updated Dec 17, 2025Dec 17, 2025

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Artificial Intelligence for Medicine and Science @ Harvard Zitnik Lab

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All

76 repositories

ToolUniverse

mims-harvard.github.io

KUL-Rec

OptimusKG

ATHENA

Medea

CASCADE

SPATIA

PrimeKG

ClinVec

bio-posttrain

MedLog

ARTIST

SPECTRA

AutoScientists

git-graph

rel-reasoning

COMPASS

PINNACLE

ark

ATOMICA

Qworld

CLEF

gates-buildathon

ark-agent-cli

StratCP

medical-ai-workshop

PROTON-GEM

PROTON

proton-website

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76 repositories