Artificial Intelligence for Medicine and Science @ Harvard

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49 repositories

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
•44•347•3•0•Updated Mar 26, 2025Mar 26, 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
•6•20•0•0•Updated Mar 25, 2025Mar 25, 2025
mims-harvard.github.io
Public
Lab website
therapeutics generative-ai biomedical-ai agentic-ai multimodal-ai
HTML
•0•1•0•0•Updated Mar 24, 2025Mar 24, 2025
TDC
Public
Therapeutics Commons (TDC-2): 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
•187•1.1k•47•0•Updated Mar 22, 2025Mar 22, 2025
AIM2
Public
Artificial Intelligence in Medicine II
medicine artificial-intelligence representation-learning precision-medicine multimodal-learning medical-ai foundation-models llms generative-ai
HTML
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Other
•0•3•0•0•Updated Mar 22, 2025Mar 22, 2025
Phyla
Public
Phyla: Towards a Foundation Model for Phylogenetic Inference
phylogenetics state-space-model ai-for-science ai-for-biology
Python
•1•7•0•0•Updated Mar 21, 2025Mar 21, 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
•13•78•1•0•Updated Mar 20, 2025Mar 20, 2025
tdc2website-flask
Public
flask+nextjs implementation for tdc-2 website
HTML
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MIT License
•7•0•3•2•Updated Mar 14, 2025Mar 14, 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•38•1•1•Updated Mar 7, 2025Mar 7, 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
•7•31•0•1•Updated Mar 5, 2025Mar 5, 2025
KGARevion
Public
KGARevion: AI Agent for Knowledge-Intensive Biomedical QA
knowledge-graph ai-agents medical-qa-datasets medical-qa
Python
•2•7•0•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•5•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
•21•82•0•1•Updated Feb 14, 2025Feb 14, 2025
Clinical-knowledge-embeddings
Public
Unified Clinical Vocabulary Embeddings for Advancing Precision Medicine
embeddings representation-learning multimodality precision-medicine medical-ai graph-transformer clinical-ai
Jupyter Notebook
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MIT License
•5•51•1•0•Updated Dec 20, 2024Dec 20, 2024
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
•5•23•2•0•Updated Dec 17, 2024Dec 17, 2024
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
•72•516•24•0•Updated Sep 26, 2024Sep 26, 2024
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
•18•52•6•0•Updated Aug 27, 2024Aug 27, 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
•28•121•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
•107•513•4•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
•30•184•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
•85•466•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
•39•185•12•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•4•0•0•Updated May 3, 2024May 3, 2024
scCIPHER
Public
scCIPHER: Contextual deep learning on single-cell-enriched knowledge graphs in neurological disorders
knowledge-graph precision-medicine single-cell-analysis neurological-disease
Jupyter Notebook
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MIT License
•1•9•0•0•Updated Dec 13, 2023Dec 13, 2023
TimeX
Public
Time series explainability via self-supervised model behavior consistency
deep-learning time-series transformers time-series-analysis interpretability interpretable-deep-learning explainable-ai explainability
Python
•2•45•3•0•Updated Oct 22, 2023Oct 22, 2023
fastGNMF
Public
Fast graph-regularized matrix factorization
graphs embeddings matrix-factorization nearest-neighbors graph-priors
Python
•5•20•0•2•Updated Oct 3, 2023Oct 3, 2023
scikit-fusion
Public
scikit-fusion: Data fusion via collective latent factor models
embeddings data-integration latent-features knowledge-graphs matrix-factorization data-fusion
Python
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Other
•43•147•2•3•Updated Aug 10, 2023Aug 10, 2023
GNNGuard
Public
Defending graph neural networks against adversarial attacks (NeurIPS 2020)
robust-learning deep-learning graph-convolutional-networks adversarial-attacks graph-neural-networks
Python
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Other
•16•63•4•2•Updated Jul 6, 2023Jul 6, 2023
Raincoat
Public
Domain Adaptation for Time Series Under Feature and Label Shifts
deep-learning time-series domain-adaptation time-series-classification data-shift distribution-shift
Jupyter Notebook
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MIT License
•11•118•8•0•Updated Jun 21, 2023Jun 21, 2023
metapaths
Public
Similarity search in heterogeneous knowledge graphs using meta paths.
r network graphs knowledge-graph hetnets hetnet-connectivity-search metapaths
R
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Mozilla Public License 2.0
•3•1•0•0•Updated Jun 14, 2023Jun 14, 2023