Mahmood Lab @ Harvard/MGB

All

32 repositories

TRIDENT
Public
Toolkit for large-scale whole-slide image processing.
Python
•
Other
•4•60•2•2•Updated Feb 15, 2025Feb 15, 2025
TITAN
Public
Multimodal Whole Slide Foundation Model for Pathology
Jupyter Notebook
•17•159•0•1•Updated Feb 14, 2025Feb 14, 2025
Patho-Bench
Public
Standardized benchmark for computational pathology foundation models.
Python
•
Other
•2•30•0•0•Updated Feb 13, 2025Feb 13, 2025
MADELEINE
Public
MADELEINE: multi-stain slide representation learning (ECCV'24)
ssl cancer pathology multimodal-foundation-model slide-representation-learning molecular-status-prediction
Python
•
Other
•4•42•2•1•Updated Feb 13, 2025Feb 13, 2025
HEST
Public
HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024 (Spotlight)
histology computational-pathology spatial-transcriptomics
Python
•
Other
•19•223•10•0•Updated Feb 8, 2025Feb 8, 2025
TriPath
Public
Analysis of 3D pathology samples using weakly supervised AI - Cell
cell weakly-supervised-learning volumetric-data 3d-path 3d-medical-images 3d-pathology 3d-mil 3d-multiple-instance-learning volumetric-multiple-instance-learning 3d-tissue-imaging
Python
•
Other
•8•97•0•0•Updated Jan 24, 2025Jan 24, 2025
PANTHER
Public
Morphological Prototyping for Unsupervised Slide Representation Learning in Computational Pathology - CVPR 2024
mixture-model optimal-transport histology pathology panther protoype
Jupyter Notebook
•
Other
•12•113•0•0•Updated Jan 20, 2025Jan 20, 2025
CONCH
Public
A vision-language foundation model for computational pathology - Nature Medicine
medical-imaging nlp-machine-learning bioimage-informatics digital-pathology pathology health-informatics computational-pathology bioimage-analysis histopathology conch
Python
•
Other
•23•310•4•1•Updated Jan 15, 2025Jan 15, 2025
UNI
Public
Towards a general-purpose foundation model for computational pathology - Nature Medicine
foundation uni digital-pathology pathology computational-pathology histopathology mahmoodlab foundation-model nature-medicine pathology-foundation-model
Jupyter Notebook
•
Other
•56•389•17•2•Updated Jan 15, 2025Jan 15, 2025
CLAM
Public
Open source tools for computational pathology - Nature BME
deep-learning tcga-data weakly-supervised-learning bioimage-informatics digital-pathology clam pathology whole-slide-imaging computational-pathology camelyon16
Python
•
GNU General Public License v3.0
•391•1.2k•20•7•Updated Dec 6, 2024Dec 6, 2024
SurvPath
Public
Modeling Dense Multimodal Interactions Between Biological Pathways and Histology for Survival Prediction - CVPR 2024
pathways interpretability pathology mahmoodlab histology-transcriptomics pathology-genomics pathology-representation survpath
Python
•6•125•7•0•Updated Nov 19, 2024Nov 19, 2024
TANGLE
Public
Transcriptomics-guided Slide Representation Learning in Computational Pathology - CVPR 2024
tangle pathology contrastive-learning mahmoodlab histology-transcriptomics pathology-genomics slide-representation-learning pathology-representation pathology-transcriptomics
Python
•
Other
•3•92•5•0•Updated Oct 15, 2024Oct 15, 2024
MMP
Public
Multimodal prototyping for cancer survival prediction - ICML 2024
prototype survival optimal-transport pathology multimodal
Jupyter Notebook
•
Other
•7•67•3•0•Updated Sep 16, 2024Sep 16, 2024
hest-website
Public
Jekyll website for HEST-1k
CSS
•
Creative Commons Zero v1.0 Universal
•0•2•0•0•Updated May 31, 2024May 31, 2024
Patch-GCN
Public
Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks - MICCAI 2021
gcn pathology wsi survival-prediction histopathology wsi-images mahmoodlab
Python
•
GNU General Public License v3.0
•29•136•6•1•Updated May 14, 2024May 14, 2024
CPATH_demographics
Public
Demographic bias in misdiagnosis by computational pathology models - Nature Medicine
tcga-data fairness digital-pathology computational-pathology ai-health ai-fairness bias-fairness-metrics ai4health health-disparities ebrains
Python
•
Other
•2•13•0•0•Updated Apr 29, 2024Apr 29, 2024
tox-foundation-ui
Public
JavaScript
•
MIT License
•0•0•0•0•Updated Apr 7, 2024Apr 7, 2024
HIPT
Public
Hierarchical Image Pyramid Transformer - CVPR 2022 (Oral)
deep-learning pytorch transfer-learning high-resolution unsupervised-learning hierarchical-attention-networks cvpr weakly-supervised-learning pretrained-weights computational-pathology
Jupyter Notebook
•
Other
•93•535•20•3•Updated Mar 19, 2024Mar 19, 2024
MAPS
Public
Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
cell-annotation multiplexed-imaging mpif
Jupyter Notebook
•
Other
•9•50•1•0•Updated Mar 14, 2024Mar 14, 2024
MAXIM
Public
MArker imputation model for multiple\underlineX IMages
Jupyter Notebook
•
Other
•0•1•0•0•Updated Oct 23, 2023Oct 23, 2023
MI-Zero
Public
Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images - CVPR 2023
mil digital-pathology zero-shot-learning pathology computational-pathology mahmoodlab vision-language-pathology image-text-pathology zero-shot-pathology quantitative-pathology
Python
•
Other
•5•99•6•0•Updated Jun 19, 2023Jun 19, 2023
SISH
Public
Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
fish deep-learning image-retrieval histology bioimage-informatics pathology bioimage-analysis image-search-engine histopathology vqvae
Python
•
GNU General Public License v3.0
•26•99•0•0•Updated Jun 9, 2023Jun 9, 2023
multimodal-cancer-origin-prediction
Public
Deep learning-based multimodal integration of histology and genomics to improves cancer origin prediction
Python
•2•24•0•0•Updated Mar 28, 2023Mar 28, 2023
MANTA
Public
Multimodal AI for Renal Allograft Biopsy Assessment
Python
•
GNU General Public License v3.0
•1•4•0•0•Updated Mar 21, 2023Mar 21, 2023
PORPOISE
Public
Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell
genomics histology pan-cancer-analysis wsi-images mahmoodlab
Jupyter Notebook
•
GNU General Public License v3.0
•38•197•7•0•Updated Feb 7, 2023Feb 7, 2023
varpool
Public
Variance pooling to incorporate ITH in CPath models - MICCAI 2022
Python
•5•23•0•0•Updated Sep 27, 2022Sep 27, 2022
PathomicFusion
Public
Fusing Histology and Genomics via Deep Learning - IEEE TMI
genomics fusion transcriptomics pathology multimodal histopathology computational-pathogenomics pathomic multimodal-network mahmoodlab
Jupyter Notebook
•
GNU General Public License v3.0
•84•292•8•1•Updated Aug 22, 2022Aug 22, 2022
NucleiSegmentation
Public
cGAN-based Multi Organ Nuclei Segmentation
gan segmentation nuclei pathology histopathology cgan
Python
•62•187•6•1•Updated Jun 10, 2022Jun 10, 2022
CRANE
Public
Deep learning enabled assessment of cardiac allograft rejection from endomyocardial biopsies- Nature Medicine
histology weakly-supervised-learning pathology whole-slide-imaging biopsy-screening endomyocardial
Python
•
GNU General Public License v3.0
•8•30•1•0•Updated May 17, 2022May 17, 2022
MCAT
Public
Multimodal Co-Attention Transformer for Survival Prediction in Gigapixel Whole Slide Images - ICCV 2021
genomics pathology mcat multimodal multimodal-deep-learning multimodal-fusion mahmoodlab early-fusion
Jupyter Notebook
•
GNU General Public License v3.0
•37•184•12•0•Updated Mar 11, 2022Mar 11, 2022