add eval to readme
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README.md
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@@ -14,6 +14,10 @@ configs:
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data_files:
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- split: finetuning
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path: "proteins_finetuning.csv"
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- config_name: research
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data_files:
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- split: research
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@@ -75,6 +79,21 @@ Removed PubMed reference numbers to avoid training models to hallucinate PubMed
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In the current state of plant genomics research, about half of the finetuning split are from rice and related
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species, a fifth are from Papilionoideae/Faboideae, and seven taxa have less than 1% each.
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## Research split
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Proteins from quinoa (~99%), cañihua, and the three species of amaranth which are currently grown for grain.
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@@ -93,5 +112,5 @@ Understanding reviewed/unreviewed proteins: https://www.uniprot.org/help/uniprot
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The reviewed sequences are often similar to unreviewed sequences from related species and accessions, and are not suitable to test predicting/infilling/completion.
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Species include inedible wild relatives.<br/>
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Some people have allergic reactions to wheat/gluten, nightshades, maize, and other crops.<br/>
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Chili peppers can be painfully spicy.
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data_files:
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- split: finetuning
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path: "proteins_finetuning.csv"
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- config_name: evaluation
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data_files:
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- split: evaluation
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path: "proteins_evaluation.csv"
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- config_name: research
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data_files:
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- split: research
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In the current state of plant genomics research, about half of the finetuning split are from rice and related
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species, a fifth are from Papilionoideae/Faboideae, and seven taxa have less than 1% each.
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## Evaluation split
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**Reviewed proteins (Swiss-Prot)** from other genera (avocado, carrot, cassava, lychee, prunus (i.e. peaches, cherries, plums)).
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Each row contains a gene name, species or subspecies, an amino acid sequence, and comments / annotations available in UniProt.
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A gene name may match multiple entries on UniProt from different accessions.
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Annotations may be empty, or may include information such as:
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- likely function, written in English
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- location inside of cell (e.g. "Subcellular locations: Vacuole")
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- locations in the plant (e.g. "Expressed in roots, stems")
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Removed PubMed reference numbers to avoid training models to hallucinate PubMed references.
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## Research split
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Proteins from quinoa (~99%), cañihua, and the three species of amaranth which are currently grown for grain.
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The reviewed sequences are often similar to unreviewed sequences from related species and accessions, and are not suitable to test predicting/infilling/completion.
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Species include inedible wild relatives.<br/>
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Some people have allergic reactions to wheat/gluten, nightshades, maize, lychee, and other crops.<br/>
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Chili peppers can be painfully spicy.
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