Benjamin-Lee/deep-rules

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Ten Quick Tips for Deep Learning in Biology

Stars: 226
Forks: 44
Open beginner issues: 0
Indexed issues: 65

Dominant language: HTML
License: No license data
Last GitHub push: Nov 30, 2021
Latest indexed: Sep 14, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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65 open issues indexed

mlf-core: a framework for deterministic machine learning Open

paper

Difficulty 1/5 1-3 hours Newbie friendliness 35/100

Benjamin-Lee/deep-rules#361 · 1 comment · Opened May 14, 2021
Give specific example of relevant metrics for overfitting Open

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

Benjamin-Lee/deep-rules#267 · Opened Oct 13, 2020
Outstanding issues not specific to any tips Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/deep-rules#252 · 10 comments · Opened Oct 7, 2020
Overall discussion for Tip 10 Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#251 · 1 comment · Opened Oct 7, 2020
Overall discussion for Tip 9 Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/deep-rules#250 · Opened Oct 7, 2020
Overall discussion for Tip 8 Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#249 · 1 comment · Opened Oct 7, 2020
Overall discussion for Tip 7 Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#248 · 2 comments · Opened Oct 7, 2020
Overall discussion for Tip 6 Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/deep-rules#247 · Opened Oct 7, 2020
Overall discussion for Tip 5 Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/deep-rules#246 · Opened Oct 7, 2020
Overall discussion for Tip 4 Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Benjamin-Lee/deep-rules#245 · 7 comments · Opened Oct 7, 2020
Overall discussion for Tip 3 Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#244 · Opened Oct 7, 2020
Overall discussion for Tip 2 Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#243 · 2 comments · Opened Oct 7, 2020
Overall discussion for Tip 1 Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

Benjamin-Lee/deep-rules#242 · 2 comments · Opened Oct 7, 2020
supervised vs unsupervised models Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#231 · Opened Sep 29, 2020
Reviewer suggestions Open

meta

Difficulty 5/5 Over a week Newbie friendliness 10/100

Benjamin-Lee/deep-rules#227 · 8 comments · Opened Sep 29, 2020
Review all tips for relevance to deep learning and biology Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Benjamin-Lee/deep-rules#215 · 1 comment · 4 reactions · Opened Jun 8, 2020
Can someone review relevant papers published in the last year? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Benjamin-Lee/deep-rules#211 · 2 comments · Opened Jun 4, 2020
The Secrets of Machine Learning: Ten Things You Wish You Had Known Earlier to be More Effective at Data Analysis Open

paper

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/deep-rules#206 · 1 comment · Opened Jan 12, 2020
Setting the standards for machine learning in biology Open

paper

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/deep-rules#203 · Opened Sep 28, 2019
Add requested merge style to `CONTRIBUTING.md` Open

meta

Benjamin-Lee/deep-rules#198 · 2 comments · 1 assignee · Opened Aug 2, 2019
Dealing with class imbalance in Deep Learning Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Benjamin-Lee/deep-rules#193 · 4 comments · 1 reaction · Opened Jul 21, 2019
Unsupervised learning for protein sequences Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#190 · Opened May 7, 2019
add a tip about appropriate documentation, publication, and sharing to ensure reproducibility and enable reuse Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#186 · Opened May 1, 2019
Excellent recent review on DL in bioimage analysis Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

Benjamin-Lee/deep-rules#185 · Opened May 1, 2019
Review: Machine learning and complex biological data Open

paper

Difficulty 4/5 3-5 days Newbie friendliness 20/100

Benjamin-Lee/deep-rules#178 · Opened Apr 17, 2019
Review: Recent Advances of Deep Learning in Bioinformatics and Computational Biology Open

paper

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/deep-rules#176 · Opened Apr 16, 2019
Review: Deep learning: new computational modelling techniques for genomics Open

paper

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/deep-rules#175 · 2 reactions · Opened Apr 14, 2019
AlphaFold: Using AI for scientific discovery Open

paper

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

Benjamin-Lee/deep-rules#166 · 5 comments · Opened Mar 12, 2019
Privacy in Pharmacogenetics: An End-to-End Case Study of Personalized Warfarin Dosing Open

paper

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

Benjamin-Lee/deep-rules#161 · Opened Mar 10, 2019
Deep learning in bioinformatics: introduction, application, and perspective in big data era Open

paper

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

Benjamin-Lee/deep-rules#154 · 7 comments · Opened Mar 1, 2019
Abstract as much as possible Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#138 · 7 comments · 1 reaction · Opened Feb 13, 2019
Fun example that highlights over fitting (not DL specific) Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

Benjamin-Lee/deep-rules#128 · 2 comments · Opened Feb 3, 2019
New paper on DA for scRNA-seq Open

paper

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

Benjamin-Lee/deep-rules#127 · 5 comments · Opened Jan 31, 2019
Close issues that have been addressed Open

help wanted meta

Benjamin-Lee/deep-rules#116 · 16 comments · 3 assignees · Opened Jan 11, 2019
PLOS Medicine special issue on ML in health and medicine Open

paper

Difficulty 3/5 1-2 days Newbie friendliness 25/100

Benjamin-Lee/deep-rules#110 · 1 reaction · Opened Jan 2, 2019
JAMA viewpoint on deep learning in medicine Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

Benjamin-Lee/deep-rules#101 · 1 comment · 1 reaction · Opened Dec 18, 2018
Have access to adequate infrastructure Open

Tip

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#82 · 4 comments · 2 reactions · Opened Dec 9, 2018
Use training/tuning/testing dataset terminology Open

meta

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Benjamin-Lee/deep-rules#74 · 11 comments · 3 reactions · Opened Dec 6, 2018
Future-proof: Plan how you will support and share your model Open

Tip

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#63 · 6 comments · Opened Nov 29, 2018
Feature engineering is still (or is no longer) important Open

Tip

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#60 · 8 comments · Opened Nov 27, 2018
A primer on deep learning in genomics Open

paper

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Benjamin-Lee/deep-rules#59 · 4 comments · 1 reaction · Opened Nov 27, 2018
Be suspicious: high prediction accuracy may backfire Open

Tip

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#55 · 1 comment · Opened Nov 21, 2018
Perform sanity checks and follow good coding practices Open

Tip

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Benjamin-Lee/deep-rules#52 · 8 comments · Opened Nov 21, 2018
Use a simple linear and non-linear model as a baseline for measuring progress. Open

Tip

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#41 · 8 comments · Opened Nov 14, 2018
Make sure you are optimizing the right objective function! Open

Tip

Difficulty 5/5 Over a week Newbie friendliness 15/100

Benjamin-Lee/deep-rules#38 · 3 comments · Opened Nov 14, 2018
Don't forget your ML fundamentals/Rules that apply to ML also apply to DL Open

Tip

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#37 · 2 comments · 3 reactions · Opened Nov 14, 2018
Your deep learning model does not need to be a black box. Open

Tip

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#36 · 1 reaction · Opened Nov 13, 2018
Treat it as a statistical model Open

Tip

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#33 · 1 comment · Opened Nov 12, 2018
Know your resources Open

Tip

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#31 · Opened Nov 11, 2018
So you have a model/classifier....now what Open

Tip

Difficulty 5/5 Over a week Newbie friendliness 25/100

Benjamin-Lee/deep-rules#30 · Opened Nov 11, 2018

Benjamin-Lee/deep-rules

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