monsoon-nlp
commited on
Commit
•
99d26f0
1
Parent(s):
af67f30
add eval to readme
Browse files
README.md
CHANGED
@@ -14,6 +14,10 @@ configs:
|
|
14 |
data_files:
|
15 |
- split: finetuning
|
16 |
path: "proteins_finetuning.csv"
|
|
|
|
|
|
|
|
|
17 |
- config_name: research
|
18 |
data_files:
|
19 |
- split: research
|
@@ -75,6 +79,21 @@ Removed PubMed reference numbers to avoid training models to hallucinate PubMed
|
|
75 |
In the current state of plant genomics research, about half of the finetuning split are from rice and related
|
76 |
species, a fifth are from Papilionoideae/Faboideae, and seven taxa have less than 1% each.
|
77 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
78 |
## Research split
|
79 |
|
80 |
Proteins from quinoa (~99%), cañihua, and the three species of amaranth which are currently grown for grain.
|
@@ -93,5 +112,5 @@ Understanding reviewed/unreviewed proteins: https://www.uniprot.org/help/uniprot
|
|
93 |
The reviewed sequences are often similar to unreviewed sequences from related species and accessions, and are not suitable to test predicting/infilling/completion.
|
94 |
|
95 |
Species include inedible wild relatives.<br/>
|
96 |
-
Some people have allergic reactions to wheat/gluten, nightshades, maize, and other crops.<br/>
|
97 |
Chili peppers can be painfully spicy.
|
|
|
14 |
data_files:
|
15 |
- split: finetuning
|
16 |
path: "proteins_finetuning.csv"
|
17 |
+
- config_name: evaluation
|
18 |
+
data_files:
|
19 |
+
- split: evaluation
|
20 |
+
path: "proteins_evaluation.csv"
|
21 |
- config_name: research
|
22 |
data_files:
|
23 |
- split: research
|
|
|
79 |
In the current state of plant genomics research, about half of the finetuning split are from rice and related
|
80 |
species, a fifth are from Papilionoideae/Faboideae, and seven taxa have less than 1% each.
|
81 |
|
82 |
+
## Evaluation split
|
83 |
+
|
84 |
+
**Reviewed proteins (Swiss-Prot)** from other genera (avocado, carrot, cassava, lychee, prunus (i.e. peaches, cherries, plums)).
|
85 |
+
Each row contains a gene name, species or subspecies, an amino acid sequence, and comments / annotations available in UniProt.
|
86 |
+
|
87 |
+
A gene name may match multiple entries on UniProt from different accessions.
|
88 |
+
|
89 |
+
Annotations may be empty, or may include information such as:
|
90 |
+
|
91 |
+
- likely function, written in English
|
92 |
+
- location inside of cell (e.g. "Subcellular locations: Vacuole")
|
93 |
+
- locations in the plant (e.g. "Expressed in roots, stems")
|
94 |
+
|
95 |
+
Removed PubMed reference numbers to avoid training models to hallucinate PubMed references.
|
96 |
+
|
97 |
## Research split
|
98 |
|
99 |
Proteins from quinoa (~99%), cañihua, and the three species of amaranth which are currently grown for grain.
|
|
|
112 |
The reviewed sequences are often similar to unreviewed sequences from related species and accessions, and are not suitable to test predicting/infilling/completion.
|
113 |
|
114 |
Species include inedible wild relatives.<br/>
|
115 |
+
Some people have allergic reactions to wheat/gluten, nightshades, maize, lychee, and other crops.<br/>
|
116 |
Chili peppers can be painfully spicy.
|