Artificial Intelligence for Medicine and Science @ Harvard Zitnik Lab

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64 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
•176•1.1k•13•10•Updated Mar 17, 2026Mar 17, 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•2•0•0•Updated Mar 17, 2026Mar 17, 2026
CLEF
Public
Controllable Sequence Editing for Counterfactual Generation
patients sequence-models ehr-data
patients sequence-models ehr-data counterfactuals conditional-generation cellular-reprogramming generative-ai
Python
•5•9•1•1•Updated Mar 15, 2026Mar 15, 2026
gates-buildathon
Public
Gates Foundation Build-a-thon on agentic memory.
TypeScript
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MIT License
•4•0•0•0•Updated Mar 12, 2026Mar 12, 2026
ark-agent-cli
Public
Repository to host example code for the ARK Agent.
agents contextual-ai knowledge-retrieval
agents contextual-ai knowledge-retrieval agentic-ai
TypeScript
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MIT License
•4•6•0•1•Updated Mar 12, 2026Mar 12, 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
Jupyter Notebook
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MIT License
•29•204•0•0•Updated Mar 5, 2026Mar 5, 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•6•0•0•Updated Mar 2, 2026Mar 2, 2026
Medea
Public
Medea: An omics AI agent for therapeutic discovery
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
•10•62•1•0•Updated Feb 28, 2026Feb 28, 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
•10•71•2•0•Updated Feb 26, 2026Feb 26, 2026
medical-ai-workshop
Public
TypeScript
•2•0•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
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MIT License
•11•1•0•0•Updated Feb 6, 2026Feb 6, 2026
ark
Public
Autonomous Knowledge Graph Exploration with Adaptive Breadth-Depth Retrieval
retrieval knowledge-graph agentic-ai
retrieval knowledge-graph agentic-ai
Jupyter Notebook
•0•2•0•0•Updated Feb 2, 2026Feb 2, 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
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MIT License
•13•86•2•1•Updated Jan 22, 2026Jan 22, 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
•11•20•0•0•Updated Dec 27, 2025Dec 27, 2025
CUREBench
Public
CUREBench @ NeurIPS 2025: Benchmarking AI reasoning for therapeutic decision-making at scale
agents therapeutics large-language-models
agents therapeutics large-language-models agentic-ai reasoning-language-models neurips-2025
Python
•32•129•11•1•Updated Dec 6, 2025Dec 6, 2025
ProCyon
Public
ProCyon: A multimodal foundation model for protein phenotypes
biology proteins phenotypes
biology proteins phenotypes foundation-models generative-ai generalist-model biomedical-ai
Python
•
MIT License
•13•56•0•0•Updated Nov 25, 2025Nov 25, 2025
Phyla
Public
Phyla: Towards a Foundation Model for Phylogenetic Inference
phylogenetics state-space-model ai-for-science
phylogenetics state-space-model ai-for-science ai-for-biology
Python
•4•28•1•0•Updated Nov 20, 2025Nov 20, 2025
CONCERT
Public
CONCERT predicts niche-aware perturbation responses in spatial transcriptomics
omics spatial-models perturbations
omics spatial-models perturbations spatial-transcriptomics virtual-cell generative-ai
Jupyter Notebook
•
MIT License
•3•15•2•0•Updated Nov 13, 2025Nov 13, 2025
COMPASS-web
Public
Web Companion for 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
•2•5•0•0•Updated Oct 5, 2025Oct 5, 2025
PDGrapher
Public
Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks
drug-discovery causal-inference geometric-deep-learning
drug-discovery causal-inference geometric-deep-learning perturbations graph-neural-networks therapeutics
Jupyter Notebook
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MIT License
•28•114•7•1•Updated Oct 3, 2025Oct 3, 2025
medlog
Public
A protocol for event-level logging of clinical AI.
MIT License
•1•14•0•0•Updated Aug 8, 2025Aug 8, 2025
Madrigal
Public
Madrigal: Multimodal AI predicts clinical outcomes of drug combinations from preclinical data
deep-learning pharmacology precision-medicine
deep-learning pharmacology precision-medicine multimodal-learning drug-combination therapeutics llm
Jupyter Notebook
•
MIT License
•9•40•1•0•Updated Jul 31, 2025Jul 31, 2025
TxAgent
Public
TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools
agents precision-medicine tool-use
agents precision-medicine tool-use therapeutics reasoning-agent reasoning-language-models
Python
•
MIT License
•95•607•11•0•Updated Jul 30, 2025Jul 30, 2025
MedTok
Public
[ICML'25] MedTok: Multimodal Medical Code Tokenizer
tokenizer multimodal ehr-data
tokenizer multimodal ehr-data medical-coding llms medical-llm medical-foundation-model
Python
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MIT License
•3•40•3•0•Updated Jul 20, 2025Jul 20, 2025
TDC
Public
Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science
machine-learning bioinformatics medicine
machine-learning bioinformatics medicine deep-learning chemistry cheminformatics biology artificial-intelligence benchmarks drug-discovery
Jupyter Notebook
•
MIT License
•209•1.2k•61•1•Updated Jul 13, 2025Jul 13, 2025
SHEPHERD
Public
SHEPHERD: Few shot learning for phenotype-driven diagnosis of patients with rare genetic diseases
deep-learning embeddings knowledge-graph
deep-learning embeddings knowledge-graph patients graph-neural-networks graph-representation-learning rare-disease medical-diagnosis
HTML
•
MIT License
•30•79•13•0•Updated Jul 1, 2025Jul 1, 2025
PhylaNeurips
Public
Python
•0•4•0•0•Updated Jun 24, 2025Jun 24, 2025
KUL-KT
Public
MIT License
•0•0•0•0•Updated May 9, 2025May 9, 2025
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•42•1•2•Updated Mar 7, 2025Mar 7, 2025
KGARevion
Public
KGARevion: AI Agent for Knowledge-Intensive Biomedical QA
knowledge-graph ai-agents medical-qa-datasets
knowledge-graph ai-agents medical-qa-datasets medical-qa
Python
•18•44•3•0•Updated Mar 4, 2025Mar 4, 2025