gandlf
A generalizable application framework for segmentation, regression, and classification using PyTorch
Science Score: 77.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com -
✓Committers with academic emails
6 of 60 committers (10.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.9%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
A generalizable application framework for segmentation, regression, and classification using PyTorch
Basic Info
- Host: GitHub
- Owner: mlcommons
- License: apache-2.0
- Language: Python
- Default Branch: master
- Homepage: https://gandlf.org
- Size: 69.9 MB
Statistics
- Stars: 183
- Watchers: 8
- Forks: 89
- Open Issues: 9
- Releases: 18
Topics
Metadata Files
README.md
The Generally Nuanced Deep Learning Framework for segmentation, regression and classification.
Why use this?
- Supports multiple
- Deep Learning model architectures
- Data dimensions (2D/3D)
- Channels/images/sequences
- Prediction classes
- Domain modalities (i.e., Radiology Scans and Digitized Histopathology Tissue Sections)
- Problem types (segmentation, regression, classification)
- Multi-GPU (on same machine) training
- Built-in
- Nested cross-validation (and related combined statistics)
- Support for parallel HPC-based computing
- Support for training check-pointing
- Support for Automatic mixed precision
- Robust data augmentation, courtesy of TorchIO
- Handles imbalanced classes (e.g., very small tumor in large organ)
- Leverages robust open source software
- No need to write any code to generate robust models
Citation
Please cite the following article for GaNDLF (full paper):
bib
@article{pati2023gandlf,
author={Pati, Sarthak and Thakur, Siddhesh P. and Hamamc{\i}, {\.{I}}brahim Ethem and Baid, Ujjwal and Baheti, Bhakti and Bhalerao, Megh and G{\"u}ley, Orhun and Mouchtaris, Sofia and Lang, David and Thermos, Spyridon and Gotkowski, Karol and Gonz{\'a}lez, Camila and Grenko, Caleb and Getka, Alexander and Edwards, Brandon and Sheller, Micah and Wu, Junwen and Karkada, Deepthi and Panchumarthy, Ravi and Ahluwalia, Vinayak and Zou, Chunrui and Bashyam, Vishnu and Li, Yuemeng and Haghighi, Babak and Chitalia, Rhea and Abousamra, Shahira and Kurc, Tahsin M. and Gastounioti, Aimilia and Er, Sezgin and Bergman, Mark and Saltz, Joel H. and Fan, Yong and Shah, Prashant and Mukhopadhyay, Anirban and Tsaftaris, Sotirios A. and Menze, Bjoern and Davatzikos, Christos and Kontos, Despina and Karargyris, Alexandros and Umeton, Renato and Mattson, Peter and Bakas, Spyridon},
title={GaNDLF: the generally nuanced deep learning framework for scalable end-to-end clinical workflows},
journal={Communications Engineering},
year={2023},
month={May},
day={16},
volume={2},
number={1},
pages={23},
abstract={Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.},
issn={2731-3395},
doi={10.1038/s44172-023-00066-3},
url={https://doi.org/10.1038/s44172-023-00066-3}
}
Documentation
GaNDLF has extensive documentation and it is arranged in the following manner:
Contributing
Please see the contributing guide for more information.
Weekly Meeting
The GaNDLF development team hosts a weekly meeting to discuss feature additions, issues, and general future directions. If you are interested to join, please send us an email!
Disclaimer
- The software has been designed for research purposes only and has neither been reviewed nor approved for clinical use by the Food and Drug Administration (FDA) or by any other federal/state agency.
- This code (excluding dependent libraries) is governed by the Apache License, Version 2.0 provided in the LICENSE file unless otherwise specified.
Contact
For more information or any support, please post on the Discussions section.
Owner
- Name: MLCommons
- Login: mlcommons
- Kind: organization
- Repositories: 79
- Profile: https://github.com/mlcommons
Citation (CITATION.cff)
cff-version: "1.2.0"
date-released: 2023-05-16
message: "If you use this software, please cite it using this manuscript."
title: "GaNDLF: the generally nuanced deep learning framework for scalable end-to-end clinical workflows"
url: "https://gandlf.org/"
authors:
- family-names: Pati
given-names: Sarthak
- family-names: Thakur
given-names: "Siddhesh P."
- family-names: Hamamci
given-names: "Ibrahim E."
- family-names: Baid
given-names: Ujjwal
- family-names: Baheti
given-names: Bhakti
- family-names: Bhalerao
given-names: Megh
- family-names: Orhun
given-names: Guley
- family-names: Mouchtaris
given-names: Sofia
- family-names: Lang
given-names: David
- family-names: Thermos
given-names: Spyridon
- family-names: Gotkowski
given-names: Karol
- family-names: Gonzalez
given-names: Camila
- family-names: Grenko
given-names: Caleb
- family-names: Getka
given-names: Alexander
- family-names: Edwards
given-names: Brandon
- family-names: Sheller
given-names: Micah
- family-names: Wu
given-names: Junwen
- family-names: Karkada
given-names: Deepthi
- family-names: Panchumarthy
given-names: Ravi
- family-names: Ahluwalia
given-names: Vinayak
- family-names: Zou
given-names: Chunrui
- family-names: Bashyam
given-names: Vishnu
- family-names: Li
given-names: Yuemeng
- family-names: Haghighi
given-names: Babak
- family-names: Chitalia
given-names: Rhea
- family-names: Abousamra
given-names: Shahira
- family-names: Kurc
given-names: "Tahsin M."
- family-names: Gastounioti
given-names: Aimilia
- family-names: Er
given-names: Sezgin
- family-names: Bergman
given-names: Mark
- family-names: Saltz
given-names: "Joel H."
- family-names: Fan
given-names: Yong
- family-names: Shah
given-names: Prashant
- family-names: Mukhopadhyay
given-names: Anirban
- family-names: Tsaftaris
given-names: "Sotirios A."
- family-names: Menze
given-names: Bjoern
- family-names: Davatzikos
given-names: Christos
- family-names: Kontos
given-names: Despina
- family-names: Karargyris
given-names: Alexandros
- family-names: Umeton
given-names: Renato
- family-names: Mattson
given-names: Peter
- family-names: Bakas
given-names: Spyridon
preferred-citation:
type: article
authors:
- family-names: Pati
given-names: Sarthak
- family-names: Thakur
given-names: "Siddhesh P."
- family-names: Hamamci
given-names: "Ibrahim E."
- family-names: Baid
given-names: Ujjwal
- family-names: Baheti
given-names: Bhakti
- family-names: Bhalerao
given-names: Megh
- family-names: Orhun
given-names: Guley
- family-names: Mouchtaris
given-names: Sofia
- family-names: Lang
given-names: David
- family-names: Thermos
given-names: Spyridon
- family-names: Gotkowski
given-names: Karol
- family-names: Gonzalez
given-names: Camila
- family-names: Grenko
given-names: Caleb
- family-names: Getka
given-names: Alexander
- family-names: Edwards
given-names: Brandon
- family-names: Sheller
given-names: Micah
- family-names: Wu
given-names: Junwen
- family-names: Karkada
given-names: Deepthi
- family-names: Panchumarthy
given-names: Ravi
- family-names: Ahluwalia
given-names: Vinayak
- family-names: Zou
given-names: Chunrui
- family-names: Bashyam
given-names: Vishnu
- family-names: Li
given-names: Yuemeng
- family-names: Haghighi
given-names: Babak
- family-names: Chitalia
given-names: Rhea
- family-names: Abousamra
given-names: Shahira
- family-names: Kurc
given-names: "Tahsin M."
- family-names: Gastounioti
given-names: Aimilia
- family-names: Er
given-names: Sezgin
- family-names: Bergman
given-names: Mark
- family-names: Saltz
given-names: "Joel H."
- family-names: Fan
given-names: Yong
- family-names: Shah
given-names: Prashant
- family-names: Mukhopadhyay
given-names: Anirban
- family-names: Tsaftaris
given-names: "Sotirios A."
- family-names: Menze
given-names: Bjoern
- family-names: Davatzikos
given-names: Christos
- family-names: Kontos
given-names: Despina
- family-names: Karargyris
given-names: Alexandros
- family-names: Umeton
given-names: Renato
- family-names: Mattson
given-names: Peter
- family-names: Bakas
given-names: Spyridon
journal: "Communications Engineering"
year: 2023
month: 05
volume: 2
number: 1
pages: 23
title: "GaNDLF: the generally nuanced deep learning framework for scalable end-to-end clinical workflows"
url: "https://www.nature.com/articles/s44172-023-00066-3"
doi: 10.1038/s44172-023-00066-3
GitHub Events
Total
- Fork event: 8
- Create event: 23
- Commit comment event: 6
- Release event: 3
- Issues event: 43
- Watch event: 23
- Delete event: 21
- Issue comment event: 313
- Push event: 130
- Pull request review comment event: 72
- Gollum event: 7
- Pull request event: 93
- Pull request review event: 144
Last Year
- Fork event: 8
- Create event: 23
- Commit comment event: 6
- Release event: 3
- Issues event: 43
- Watch event: 23
- Delete event: 21
- Issue comment event: 313
- Push event: 130
- Pull request review comment event: 72
- Gollum event: 7
- Pull request event: 93
- Pull request review event: 144
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| sarthakpati | s****i@h****m | 5,145 |
| scap3yvt | 1****t | 493 |
| Siddhesh Thakur | s****r@g****m | 416 |
| Megh Bhalerao Megh.Bhalerao@Pennmedicine.upenn.edu | m****o@g****m | 302 |
| alexandergetka | a****a@g****m | 209 |
| vmalefioudakis | b****f@h****m | 189 |
| szmazurek | s****7@g****m | 167 |
| Viacheslav Kukushkin | v****n@g****m | 154 |
| Junwen Wu | j****u@i****m | 103 |
| Sofia-Mouchtaris | 5****s | 54 |
| Alexander Getka | 5****a | 54 |
| Orhun | o****y@g****m | 53 |
| Shubham Innani | 2****5@s****n | 44 |
| Ainesh Nanda | a****a@g****m | 40 |
| Megh Bhalerao Megh.Bhalerao@Pennmedicine.upenn.edu | m****o@p****u | 34 |
| hasan7n | h****7@h****m | 30 |
| FelixSteinbauer | 4****r | 29 |
| Edwards | e****b@s****m | 20 |
| pranayasinghcsmpl | r****a@c****m | 18 |
| ujjwalbaid0408 | u****8@g****m | 17 |
| Cory Gwin | g****1@g****m | 16 |
| vavali08 | 1****8 | 15 |
| Edwards | e****b@s****m | 12 |
| Akis Linardos | m****z@g****m | 12 |
| grenkoca | g****a@g****m | 10 |
| Patrick Foley | p****y@i****m | 8 |
| sylwiamm | S****c@P****u | 8 |
| pranaya.singh | p****h@c****h | 6 |
| Pradeep, Sakhamoori | p****i@g****m | 6 |
| karkadad | d****a@i****m | 5 |
| and 30 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 169
- Total pull requests: 315
- Average time to close issues: 2 months
- Average time to close pull requests: 12 days
- Total issue authors: 30
- Total pull request authors: 40
- Average comments per issue: 2.54
- Average comments per pull request: 3.71
- Merged pull requests: 253
- Bot issues: 0
- Bot pull requests: 3
Past Year
- Issues: 31
- Pull requests: 85
- Average time to close issues: about 1 month
- Average time to close pull requests: 14 days
- Issue authors: 10
- Pull request authors: 14
- Average comments per issue: 2.65
- Average comments per pull request: 3.93
- Merged pull requests: 65
- Bot issues: 0
- Bot pull requests: 2
Top Authors
Issue Authors
- sarthakpati (93)
- szmazurek (13)
- Geeks-Sid (11)
- benmalef (5)
- VukW (5)
- sylwiamm (4)
- scap3yvt (4)
- Linardos (4)
- aristizabal95 (3)
- MarkBergman-cbica (2)
- vahluw (2)
- sanashah007 (1)
- Aayush2003Gupta (1)
- hasan7n (1)
- skoudoro (1)
Pull Request Authors
- scap3yvt (129)
- sarthakpati (90)
- benmalef (33)
- szmazurek (29)
- VukW (24)
- pranayasinghcsmpl (23)
- Geeks-Sid (15)
- hasan7n (6)
- Linardos (6)
- AlexanderGetka-cbica (6)
- sylwiamm (5)
- Dana-Farber (4)
- rachitsaluja (4)
- dependabot[bot] (4)
- FelixSteinbauer (4)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 8
conda-forge.org: gandlf
- Homepage: https://mlcommons.github.io/GaNDLF/
- License: Apache-2.0
-
Latest release: 0.0.15
published over 3 years ago
Rankings
Dependencies
- github-pages >= 0 development
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- actions/checkout v2 composite
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