Open manolik opened 4 years ago
@manolik this is great, thanks for the suggestions. I see many benefits to a major reorganization:
The only real downside is that it will take more effort to write and especially to edit. I'm okay with that. If we put out a call for help with specific pieces, we can attract domain experts to contribute.
If others generally think this is a good idea, we can create add a new outline to the repository starting from the spreadsheet above.
I support the idea of a re-org as well
I also strongly support the idea of reorganization. I wonder if it would make sense to have a Imaging, Text, and EHR (perhaps in that order?) in a module. EHRs are hot as an area, but it might help to lead off with how folks are handling many of the components of them before jumping into them.
I made @manolik's into a markdown version of the table.
Introduction | -1 | DL's role outside of biology | |
---|---|---|---|
How this document was composed (online, open, living) & context for those who read prior version | |||
Module0 | 0 | Foundations | ML and Deep Learning |
CNNs, RNNs, Model Architectures | |||
Training, Regularization | |||
Dimensionality reduction | |||
Autoencoders, Generative Models, GANs | |||
Module1 | 1 | Pre-Tx | DNA accessibility |
Promoters and enhancers | |||
Transcription factors | |||
DNA methylation | |||
2 | Expression | Gene expression | |
Single-cell data | |||
3 | Post-Tx | Splicing | |
Micro-RNA binding | |||
Module2 | 4 | Variation | Sequencing and variant calling |
Comparative genomics | |||
Alignment, Evolution | |||
5 | Genetics | Population genetics, phasing | |
eQTLs | |||
Genetics, GWAS, Rare variants | |||
6 | EHRs | Patient categorization | |
Electronic health records | |||
7 | Specialized | Neuroscience | |
Metagenomics | |||
Cancer | |||
Module3 | 8 | PPIs | Protein-protein interactions |
PPI networks and graph analysis | |||
9 | Protein Structure | Protein secondary and tertiary structure | |
Structure determination and cryoEM | |||
10 | 3D structure | MHC-peptide binding | |
11 | Therapeutics | Drug development | |
Drug repositioning | |||
Module4 | 12 | Imaging | Morphological phenotypes |
Imaging applications in healthcare | |||
Video processing and analysis | |||
13 | Text | Text applications in healthcare | |
Clinical decision making | |||
Interactive question/answer systems | |||
Module5 | 14 | Models | Customizing: bias-vs-variance |
Uncertainty quantification | |||
Multimodal, multi-task, and transfer learning | |||
Interpretation | |||
15 | Practical issues | Optimization | |
Data limitations | |||
Hardware limitations and scaling | |||
Data, code, and model sharing | |||
Module6 | 16 | Conclusions | Summarize how field has changed since prior review (mid 2017) |
17 | Methods | Summarize number of contributors, number of commits, use of manubot, etc. Primarily for others undertaking similar efforts. |
I added a brief intro / conclusions section. While I could see the adjustments I proposed, I think they are small when compared to the scale of the reorganization. I like where this is going and strongly support this concept! 👏
Yes, greatly agree.
about intro on "DL beyond bio". To avoid distracting from the main message, I would perhaps put this as a section at the end of the "Module0.Foundations" module, after introducing the core methods, which i think are more relevant.
About how the article was written, i would add that to the beginning of Module6-section 17, as folks reading this article/book will care more about the content than the (very awesomely cool) way it was written
I agree. Reorganizing things in this manner looks like a good idea.
This structure looks good. I am just wondering if sections 6 and 7 would be fit better later on. The progression could be:
I do think imaging, text, and EHRs make a lot of sense together. Perhaps what's currently "specialized" could have it's own module just before Module 5. These sections would likely be shorter, but that's ok. Sleep, if I understand correctly, might go into neuroscience there for instance.
Hi all, This is such an awesome review, and i'd love to use it as a basis for teaching, but i've had to jump back-and-forth through sections, as the current structure doesn't flow as naturally for a class. I had some thoughts about potentially restructuring and wanted to get folks' feedback on this. What do you think? https://www.dropbox.com/s/guv6eovze8e1s6g/Deep%20Learning%20Review%20Reorganization.xlsx?dl=0 Thanks! Manolis![image](https://user-images.githubusercontent.com/4958253/76797476-f7074380-67a3-11ea-8132-f9390eb426fc.png)