deepchem / deepchem/deepanimal
Virus-Host Identification
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- Stars
- 3
- Forks
- 2
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Description
This is a [nice paper](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027631) from my old adviser that attempts to identify what host a virus can infect based on its genome using multiclass Adaboost. It'd be cool to reproduce this with work with a DNN. Also the author is currently a postdoc at Stanford.
Furthermore, we could expand on this to find more subtle patterns. For example, this was a [really cool paper](http://mbio.asm.org/content/5/5/e01484-14.full) from UCSF that found ball pythons being infected with a virus of possible mouse-origin. If we could make a model that can predict the potential of these sorts of cross-species events (a.k.a zoonoses), it would be a game-changer for viral epidemiology, especially for diseases like influenza.
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by reading the linked virus-host and zoonosis papers to identify the datasets, labels, and baseline methods needed for a bounded reproduction. No repository files, tests, or entry points are mentioned. Done would require a defined DNN experiment that reproduces the baseline and reports whether cross-species prediction is feasible.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, machine-learning
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100