Artificial Intelligence for Medicine and Science @ Harvard

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56 repositories

PDGrapher
Public
Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks
drug-discovery causal-inference geometric-deep-learning perturbations graph-neural-networks therapeutics
Jupyter Notebook
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MIT License
•7•28•1•1•Updated Sep 2, 2025Sep 2, 2025
mims-harvard.github.io
Public
Lab website
therapeutics generative-ai biomedical-ai agentic-ai multimodal-ai
HTML
•0•1•0•0•Updated Sep 2, 2025Sep 2, 2025
COMPASS
Public
Generalizable AI predicts immunotherapy outcomes across cancers and treatments
immunology immunotherapy generalization multimodal-learning therapeutics concept-bottleneck-models
Jupyter Notebook
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MIT License
•8•37•0•0•Updated Aug 27, 2025Aug 27, 2025
ProCyon
Public
ProCyon: A multimodal foundation model for protein phenotypes
biology proteins phenotypes foundation-models generative-ai generalist-model biomedical-ai
Python
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MIT License
•11•39•0•1•Updated Aug 24, 2025Aug 24, 2025
ClinVec
Public
ClinVec: Unified Embeddings of Clinical Codes Enable Knowledge-Grounded AI in Medicine
embeddings representation-learning multimodality precision-medicine medical-ai graph-transformer clinical-ai
Jupyter Notebook
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MIT License
•8•67•1•1•Updated Aug 13, 2025Aug 13, 2025
CUREBench
Public
CUREBench @ NeurIPS 2025: Benchmarking AI reasoning for therapeutic decision-making at scale
agents therapeutics large-language-models agentic-ai reasoning-language-models neurips-2025
Python
•15•88•7•0•Updated Aug 11, 2025Aug 11, 2025
medlog
Public
A protocol for event-level logging of clinical AI.
MIT License
•0•0•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 multimodal-learning drug-combination therapeutics llm
Jupyter Notebook
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MIT License
•8•35•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 therapeutics reasoning-agent reasoning-language-models
Python
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MIT License
•78•523•8•0•Updated Jul 30, 2025Jul 30, 2025
MedTok
Public
[ICML'25] MedTok: Multimodal Medical Code Tokenizer
tokenizer multimodal ehr-data medical-coding llms medical-llm medical-foundation-model
Python
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MIT License
•1•24•0•0•Updated Jul 20, 2025Jul 20, 2025
ATOMICA
Public
Learning Universal Representations of Intermolecular Interactions with ATOMICA
proteins molecular-structures ions peptides nucleic-acids geometric-deep-learning atomistic-modelling small-molecules molecular-interactions
Python
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MIT License
•24•174•0•0•Updated Jul 16, 2025Jul 16, 2025
ToolUniverse
Public
ToolUniverse is a collection of biomedical tools designed for AI agents
agents precision-medicine tool-use therapeutics reasoning-agent reasoning-language-models
Python
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MIT License
•27•206•2•3•Updated Jul 15, 2025Jul 15, 2025
TDC
Public
Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science
machine-learning bioinformatics medicine deep-learning chemistry cheminformatics biology artificial-intelligence benchmarks drug-discovery
Jupyter Notebook
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MIT License
•196•1.1k•53•0•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 patients graph-neural-networks graph-representation-learning rare-disease medical-diagnosis
HTML
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MIT License
•23•70•10•0•Updated Jul 1, 2025Jul 1, 2025
Phyla
Public
Phyla: Towards a Foundation Model for Phylogenetic Inference
phylogenetics state-space-model ai-for-science ai-for-biology
Python
•4•22•2•0•Updated Jun 26, 2025Jun 26, 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
COMPASS-web
Public
Web Companion for Generalizable AI predicts immunotherapy outcomes across cancers and treatments
immunology immunotherapy generalization multimodal-learning therapeutics concept-bottleneck-models
Jupyter Notebook
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MIT License
•1•4•0•0•Updated May 1, 2025May 1, 2025
AIM2
Public
Artificial Intelligence in Medicine II
medicine artificial-intelligence representation-learning agents precision-medicine multimodal-learning medical-ai foundation-models llms generative-ai
HTML
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Other
•0•3•0•0•Updated Apr 28, 2025Apr 28, 2025
SPECTRA
Public
SPECTRA: Spectral framework for evaluation of biomedical AI models
benchmarking protein-structure protein-sequences benchmark-framework geometric-deep-learning protein-language-model foundation-models large-language-models
Jupyter Notebook
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MIT License
•7•40•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 medical-qa
Python
•9•33•3•0•Updated Mar 4, 2025Mar 4, 2025
CLEF
Public
Controllable Sequence Editing for Counterfactual Generation
patients sequence-models ehr-data counterfactuals conditional-generation cellular-reprogramming generative-ai
Python
•1•6•1•0•Updated Feb 17, 2025Feb 17, 2025
PINNACLE
Public
Contextual AI models for single-cell protein biology
proteins context-aware contextual geometric-deep-learning graph-neural-networks therapeutics
Python
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MIT License
•24•88•0•1•Updated Feb 14, 2025Feb 14, 2025
UniTS
Public
A unified multi-task time series model.
time-series eeg ecg forecasting classification imputation multi-task zero-shot anomaly-detection few-shot
Python
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MIT License
•82•565•25•0•Updated Sep 26, 2024Sep 26, 2024
G-Meta
Public
Graph meta learning via local subgraphs (NeurIPS 2020)
massive-interactomics machine-learning deep-learning transfer-learning meta-learning few-shot-learning graph-neural-networks
Python
•29•126•4•1•Updated Jul 25, 2024Jul 25, 2024
PrimeKG
Public
Precision Medicine Knowledge Graph (PrimeKG)
bioinformatics dataset knowledge-graph nlp-machine-learning graph-machine-learning precision-medicine therapeutics network-medicine
Jupyter Notebook
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MIT License
•128•606•5•0•Updated May 27, 2024May 27, 2024
GraphXAI
Public
GraphXAI: Resource to support the development and evaluation of GNN explainers
benchmarking embeddings graph-machine-learning interpretability explainable-ai explainable-ml explainability deep-learning graph-neural-networks
Python
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MIT License
•32•195•4•1•Updated May 22, 2024May 22, 2024
TFC-pretraining
Public
Self-supervised contrastive learning for time series via time-frequency consistency
deep-learning time-series representation-learning self-supervised-learning pre-trained-model consistency-models contrastive-learning
Python
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MIT License
•87•494•16•0•Updated May 7, 2024May 7, 2024
TxGNN
Public
TxGNN: Zero-shot prediction of therapeutic use with geometric deep learning and clinician centered design
knowledge-graph drug-discovery drug-design precision-medicine geometric-deep-learning therapeutics indications-and-warning graph-neural-networks
Jupyter Notebook
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MIT License
•57•220•18•0•Updated May 6, 2024May 6, 2024
BMI702
Public
Biomedical Artificial Intelligence
medicine artificial-intelligence multimodal-learning medical-ai generative-ai biomedical-ai
HTML
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MIT License
•0•6•0•0•Updated May 3, 2024May 3, 2024