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Preparing the quinoa ML model

Tags: mlbioseries

In two months I'm going to be talking about LLMs and quinoa DNA. Here's a collection of intermediate updates. My plan for the talk is 5 minutes each on bio background, existing LLM research, my own new stuff, and Q&A.

Code updates

Bio updates

OK this is a tangent, but... I am becoming polyploid-pilled. It's very cool. You are getting plants with extra copies of genes and more options for hybridization. This makes good plants better.

Rice is diploid but there are decades of experiments with tetraploid rice and hybridization:

Polyploid plants are characterized by large size, high nutrient and secondary metabolite content. They also show strong vitality and adaptability, drought and cold resistance, and other advantages. [...] Compared with diploid rice, polyploid rice has advantageous agronomic traits which have attracted the widespread attention of rice researchers, such as large grain size, high 1000-grain weight, strong stem, strong stress tolerance, and high adaptability. Polyploid rice was first discovered and reported by Nakamori in 1933

Wild asparagus can be polyploid, which inspired researchers to induce polyploidy in the cultivated species, for resilience.

Chili peppers are generally diploid, but dalle khursani is a polyploid chili grown in West Bengal, Sikkim, and Nepal.

Maize/corn is diploid, but there are papers online about it diverging from a tetraploid genome 10–12 million years ago.

Special 2001 monolith shout-out to a recent hexaploid genome:

Bread wheat […] is a young hexaploid species formed only 8,500–9,000 years ago