Owner

Benjamin-Lee

5 indexed repositories · View on GitHub

deep-rules
Ten Quick Tips for Deep Learning in Biology

HTML · 226 stars
CodonAdaptationIndex
Python Implementation of Codon Adaption Index

Jupyter Notebook · 38 stars
vdsearch
Viroid-like circRNA discovery and analysis suite

Python · 20 stars
DNAvisualization.org
🧬📈 Turn DNA sequences into interactive visualizations

Vue · 13 stars
viroiddb
A curated database of all available viroid-like RNA sequences

Vue · 5 stars

Open All

115 open issues indexed

Don't use deep learning if you don't have to. Open

Tip

Benjamin-Lee/deep-rules#3 · 5 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
When it comes to data, size matters. Open

Tip

Benjamin-Lee/deep-rules#5 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Use existing model architectures whenever possible. Open

Tip

Benjamin-Lee/deep-rules#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Normalize, normalize, normalize. Open

Tip

Benjamin-Lee/deep-rules#7 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
If you don't have enough data, consider whether there is other data that can help pre-train a model. Open

Tip

Benjamin-Lee/deep-rules#8 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Understand the data Open

Tip

Benjamin-Lee/deep-rules#12 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Discuss computational issues Open

Benjamin-Lee/deep-rules#15 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Strive for balance between training, tuning, and testing datasets Open

Tip

Benjamin-Lee/deep-rules#19 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
For full reproducibility, always report all details of your analyses, including sharing of data, methods, and models Open

Tip

Benjamin-Lee/deep-rules#21 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Make sure your problem is a good fit for deep learning. Open

Tip

Benjamin-Lee/deep-rules#22 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Understand the trade-off between interpretability and performance Open

Tip

Benjamin-Lee/deep-rules#25 · 2 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
If a human can't perform the task with ease, be surprised if a machine can. Open

Tip

Benjamin-Lee/deep-rules#26 · 11 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Fairly validate your model with proper test/train data Open

Tip

Benjamin-Lee/deep-rules#27 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Understand, protect against, and benchmark possible overfitting Open

Tip

Benjamin-Lee/deep-rules#28 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
There's more than one way to do it: find the learning that's right for you (and your data) Open

Tip

Benjamin-Lee/deep-rules#29 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
So you have a model/classifier....now what Open

Tip

Benjamin-Lee/deep-rules#30 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Know your resources Open

Tip

Benjamin-Lee/deep-rules#31 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Treat it as a statistical model Open

Tip

Benjamin-Lee/deep-rules#33 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Your deep learning model does not need to be a black box. Open

Tip

Benjamin-Lee/deep-rules#36 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Don't forget your ML fundamentals/Rules that apply to ML also apply to DL Open

Tip

Benjamin-Lee/deep-rules#37 · 2 comments · 3 reactions · 0 assignees · Indexed Sep 14, 2026
Make sure you are optimizing the right objective function! Open

Tip

Benjamin-Lee/deep-rules#38 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Use a simple linear and non-linear model as a baseline for measuring progress. Open

Tip

Benjamin-Lee/deep-rules#41 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Perform sanity checks and follow good coding practices Open

Tip

Benjamin-Lee/deep-rules#52 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Be suspicious: high prediction accuracy may backfire Open

Tip

Benjamin-Lee/deep-rules#55 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
A primer on deep learning in genomics Open

paper

Benjamin-Lee/deep-rules#59 · 4 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Feature engineering is still (or is no longer) important Open

Tip

Benjamin-Lee/deep-rules#60 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Future-proof: Plan how you will support and share your model Open

Tip

Benjamin-Lee/deep-rules#63 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Use training/tuning/testing dataset terminology Open

meta

Benjamin-Lee/deep-rules#74 · 11 comments · 3 reactions · 0 assignees · Indexed Sep 14, 2026
Have access to adequate infrastructure Open

Tip

Benjamin-Lee/deep-rules#82 · 4 comments · 2 reactions · 0 assignees · Indexed Sep 14, 2026
JAMA viewpoint on deep learning in medicine Open

Benjamin-Lee/deep-rules#101 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 14, 2026
PLOS Medicine special issue on ML in health and medicine Open

paper

Benjamin-Lee/deep-rules#110 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Close issues that have been addressed Open

help wanted meta

Benjamin-Lee/deep-rules#116 · 16 comments · 0 reactions · 3 assignees · Indexed Sep 14, 2026
New paper on DA for scRNA-seq Open

paper

Benjamin-Lee/deep-rules#127 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Fun example that highlights over fitting (not DL specific) Open

Benjamin-Lee/deep-rules#128 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Abstract as much as possible Open

Benjamin-Lee/deep-rules#138 · 7 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Deep learning in bioinformatics: introduction, application, and perspective in big data era Open

paper

Benjamin-Lee/deep-rules#154 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Privacy in Pharmacogenetics: An End-to-End Case Study of Personalized Warfarin Dosing Open

paper

Benjamin-Lee/deep-rules#161 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
AlphaFold: Using AI for scientific discovery Open

paper

Benjamin-Lee/deep-rules#166 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Review: Deep learning: new computational modelling techniques for genomics Open

paper

Benjamin-Lee/deep-rules#175 · 0 comments · 2 reactions · 0 assignees · Indexed Sep 14, 2026
Review: Recent Advances of Deep Learning in Bioinformatics and Computational Biology Open

paper

Benjamin-Lee/deep-rules#176 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Review: Machine learning and complex biological data Open

paper

Benjamin-Lee/deep-rules#178 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Excellent recent review on DL in bioimage analysis Open

Benjamin-Lee/deep-rules#185 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
add a tip about appropriate documentation, publication, and sharing to ensure reproducibility and enable reuse Open

Benjamin-Lee/deep-rules#186 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Unsupervised learning for protein sequences Open

Benjamin-Lee/deep-rules#190 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Dealing with class imbalance in Deep Learning Open

Benjamin-Lee/deep-rules#193 · 4 comments · 1 reaction · 0 assignees · Indexed Sep 14, 2026
Add requested merge style to `CONTRIBUTING.md` Open

meta

Benjamin-Lee/deep-rules#198 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Setting the standards for machine learning in biology Open

paper

Benjamin-Lee/deep-rules#203 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
The Secrets of Machine Learning: Ten Things You Wish You Had Known Earlier to be More Effective at Data Analysis Open

paper

Benjamin-Lee/deep-rules#206 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Can someone review relevant papers published in the last year? Open

Benjamin-Lee/deep-rules#211 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Review all tips for relevance to deep learning and biology Open

Benjamin-Lee/deep-rules#215 · 1 comment · 4 reactions · 0 assignees · Indexed Sep 14, 2026

Benjamin-Lee

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