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> It also proved that deep learning models are a valid approach to bioinformatics A lot of bioinformatics tools using deep learning appeared around 2017-2018.
by jltsiren 2y ago
> It also proved that deep learning models are a valid approach to bioinformatics
A lot of bioinformatics tools using deep learning appeared around 2017-2018. But rather than being big breakthroughs like AlphaFold, most of them were just incremental improvements to various technical tasks in the middle of a pipeline.
- a_bonobo 2y agoand since a lot of those tools are incremental improvements they disappeared again, imho - what's the point for 2% higher accuracy when you need a GPU you don't have? Not many DL based tools I see these days regularly applied in genomics. Maybe: Tiara for 'high level' taxonomic classification, DeepVariant in some papers for SNP calling, that's about it? Some interesting gene prediction tools coming up like Tiberius. AlphaFold, of course. Lots of papers but not much day-to-day usage from my POV.
- jltsiren 2y agoMost Oxford Nanopore basecallers use DL these days. And if you want a high quality de novo assembly, DL based methods are often used for error correction and final polishing. There are a lot of differences between the cutting-edge methods that produce the best results, the established tools the average researcher is comfortable using, and whatever you are allowed to use in a clinical setting.