Update README.md

README.md

@@ -1,81 +1,133 @@
+  - split: dev           
+    path: dataset/ncRNAFam/gene/multi_class/dev/dev.csv           
+  - split: test           
+    path: dataset/ncRNAFam/gene/multi_class/test/test.csv           
+  - split: label           
+    path: dataset/ncRNAFam/gene/multi_class/label.txt           
 
----
-configs:
-
-- config_name: CentralDogma    
-  data_files:          
-  - split: train                
-    path: dataset/CentralDogma/gene_protein/binary_class/train/train.csv           
-  - split: dev                       
-    path: dataset/CentralDogma/gene_protein/binary_class/dev/dev.csv           
-  - split: test                   
-    path: dataset/CentralDogma/gene_protein/binary_class/test/test.csv           
-
-- config_name: CentralDogmaCDSProtein                 
-  data_files:                      
-  - split: train                      
-    path: dataset/CentralDogmaCDSProtein/gene_protein/binary_class/train/train.csv                      
-  - split: dev                     
-    path: dataset/CentralDogmaCDSProtein/gene_protein/binary_class/dev/dev.csv           
-  - split: test                     
-    path: dataset/CentralDogmaCDSProtein/gene_protein/binary_class/test/test.csv                        
-
-- config_name: CentralDogmaV2                 
-  data_files:                     
-  - split: train                     
-    path: dataset/CentralDogmaV2/gene_protein/binary_class/train/train.csv           
-  - split: dev                     
-    path: dataset/CentralDogmaV2/gene_protein/binary_class/dev/dev.csv           
-  - split: test                     
-    path: dataset/CentralDogmaV2/gene_protein/binary_class/test/test.csv     
-
-- config_name: CrossSpeciesHomologousGenePairsV1                
-  data_files:                     
-  - split: train                     
-    path: dataset/CrossSpeciesHomologousGenePairsV1/gene_protein/binary_class/train/train.csv                     
-  - split: dev                               
-    path: dataset/CrossSpeciesHomologousGenePairsV1/gene_protein/binary_class/dev/dev.csv                     
-  - split: test                     
-    path: dataset/CrossSpeciesHomologousGenePairsV1/gene_protein/binary_class/test/test.csv
-    
-- config_name: CrossSpeciesHomologousGenePairsV2                   
+
+- config_name: ncRPI                   
+  data_files:           
+  - split: train           
+    path: dataset/ncRPI/gene_protein/binary_class/train/train.csv           
+  - split: dev           
+    path: dataset/ncRPI/gene_protein/binary_class/dev/dev.csv           
+  - split: test           
+    path: dataset/ncRPI/gene_protein/binary_class/test/test.csv
+
+- config_name: PPI     
+  data_files:           
+  - split: train           
+    path: dataset/PPI/protein/binary_class/train/train.csv           
+  - split: dev           
+    path: dataset/PPI/protein/binary_class/dev/dev.csv           
+  - split: test           
+    path: dataset/PPI/protein/binary_class/test/test.csv       
+
+
+- config_name: ProtLoc           
+  data_files:           
+  - split: train           
+    path: dataset/ProtLoc/protein/multi_class/train/train.csv           
+  - split: dev           
+    path: dataset/ProtLoc/protein/multi_class/dev/dev.csv           
+  - split: test           
+    path: dataset/ProtLoc/protein/multi_class/test/test.csv  
+
+
+- config_name: ProtLocCDSGene                   
   data_files:           
   - split: train           
-    path: dataset/CrossSpeciesHomologousGenePairsV2/gene_protein/binary_class/train/train.csv           
+    path: dataset/ProtLocCDSGene/gene/multi_class/train/train.csv           
   - split: dev           
-    path: dataset/CrossSpeciesHomologousGenePairsV2/gene_protein/binary_class/dev/dev.csv           
+    path: dataset/ProtLocCDSGene/gene/multi_class/dev/dev.csv           
   - split: test           
-    path: dataset/CrossSpeciesHomologousGenePairsV2/gene_protein/binary_class/test/test.csv           
+    path: dataset/ProtLocCDSGene/gene/multi_class/test/test.csv               
 
-- config_name: GenusTax                   
+- config_name: ProtLocCDSProt                      
   data_files:           
   - split: train           
-    path: dataset/GenusTax/gene/multi_class/train/train.csv           
+    path: dataset/ProtLocCDSProt/protein/multi_class/train/train.csv           
   - split: dev           
-    path: dataset/GenusTax/gene/multi_class/dev/dev.csv           
+    path: dataset/ProtLocCDSProt/protein/multi_class/dev/dev.csv           
   - split: test           
-    path: dataset/GenusTax/gene/multi_class/test/test.csv                   
+    path: dataset/ProtLocCDSProt/protein/multi_class/test/test.csv           
+  - split: label           
+    path: dataset/ProtLocCDSProt/protein/multi_class/label.txt                      
 
-- config_name: InfA                  
+
+- config_name: ProtStab                  
   data_files:           
   - split: train           
-    path: dataset/InfA/gene_gene/binary_class/train/train.csv           
+    path: dataset/ProtStab/protein/regression/train/train.csv           
   - split: dev           
-    path: dataset/InfA/gene_gene/binary_class/dev/dev.csv
+    path: dataset/ProtStab/protein/regression/dev/dev.csv           
   - split: test           
-    path: dataset/InfA/gene_gene/binary_class/test/test.csv                  
+    path: dataset/ProtStab/protein/regression/test/test.csv              
+
 
-- config_name: ncRNAFam                     
-  data_files:            
+- config_name: SpeciesTax       
+  data_files:
   - split: train           
-    path: dataset/ncRNAFam/gene/multi_class/train/train.csv           
+    path: dataset/SpeciesTax/gene/multi_class/train/train.csv           
   - split: dev           
+    path: dataset/SpeciesTax/gene/multi_class/dev/dev.csv           
+  - split: test           
+    path: dataset/SpeciesTax/gene/multi_class/test/test.csv                   
+
+
+- config_name: SupKTax                     
+  data_files:           
+  - split: train           
+    path: dataset/SupKTax/gene/multi_class/train/train.csv           
+  - split: dev           
+    path: dataset/SupKTax/gene/multi_class/dev/dev.csv           
+  - split: test           
+    path: dataset/SupKTax/gene/multi_class/test/test.csv                             
+
+
+---
+
+
+# LucaOne-Downstream-Task-Datasets   
+This directory includes all the downstream task datasets of the LucaOne paper (https://www.nature.com/articles/s42256-025-01044-4).
+
+
+## Dataset Structure
+
+
+This dataset includes three splits and a label info file:
+
+
+- `train`(training dataset)
+- `dev` (validation dataset)
+- `test` (testing dataset)
+- `label.txt` (label name to label index in `*.csv`, label_idx=${the line number of label_name - 1})
+
+
+
+
+## Usage:
+
+
+```python
+from datasets import load_dataset
+
+
+# load ncRPI dataset
+ds = load_dataset("LucaGroup/LucaOne-Downstream-Task-Datasets", name="ncRPI")
+```
+
+
+## Github
+https://github.com/LucaOne/  - split: dev           
     path: dataset/ncRNAFam/gene/multi_class/dev/dev.csv           
   - split: test           
     path: dataset/ncRNAFam/gene/multi_class/test/test.csv           
   - split: label           
     path: dataset/ncRNAFam/gene/multi_class/label.txt           
 
+
 - config_name: ncRPI                   
   data_files:           
   - split: train           
@@ -84,7 +136,7 @@ configs:
     path: dataset/ncRPI/gene_protein/binary_class/dev/dev.csv           
   - split: test           
     path: dataset/ncRPI/gene_protein/binary_class/test/test.csv
-    
+
 - config_name: PPI     
   data_files:           
   - split: train           
@@ -94,6 +146,7 @@ configs:
   - split: test           
     path: dataset/PPI/protein/binary_class/test/test.csv       
 
+
 - config_name: ProtLoc           
   data_files:           
   - split: train           
@@ -103,6 +156,7 @@ configs:
   - split: test           
     path: dataset/ProtLoc/protein/multi_class/test/test.csv  
 
+
 - config_name: ProtLocCDSGene                   
   data_files:           
   - split: train           
@@ -111,7 +165,7 @@ configs:
     path: dataset/ProtLocCDSGene/gene/multi_class/dev/dev.csv           
   - split: test           
     path: dataset/ProtLocCDSGene/gene/multi_class/test/test.csv               
- 
+
 - config_name: ProtLocCDSProt                      
   data_files:           
   - split: train           
@@ -123,6 +177,7 @@ configs:
   - split: label           
     path: dataset/ProtLocCDSProt/protein/multi_class/label.txt                      
 
+
 - config_name: ProtStab                  
   data_files:           
   - split: train           
@@ -132,6 +187,7 @@ configs:
   - split: test           
     path: dataset/ProtStab/protein/regression/test/test.csv              
 
+
 - config_name: SpeciesTax       
   data_files:
   - split: train           
@@ -141,6 +197,7 @@ configs:
   - split: test           
     path: dataset/SpeciesTax/gene/multi_class/test/test.csv                   
 
+
 - config_name: SupKTax                     
   data_files:           
   - split: train           
@@ -150,26 +207,39 @@ configs:
   - split: test           
     path: dataset/SupKTax/gene/multi_class/test/test.csv                             
 
+
 ---
 
+
 # LucaOne-Downstream-Task-Datasets   
 This directory includes all the downstream task datasets of the LucaOne paper (https://www.nature.com/articles/s42256-025-01044-4).
 
+
 ## Dataset Structure
 
+
 This dataset includes three splits and a label info file:
 
+
 - `train`(training dataset)
 - `dev` (validation dataset)
 - `test` (testing dataset)
 - `label.txt` (label name to label index in `*.csv`, label_idx=${the line number of label_name - 1})
 
 
+
+
 ## Usage:
 
+
 ```python
 from datasets import load_dataset
 
+
 # load ncRPI dataset
 ds = load_dataset("LucaGroup/LucaOne-Downstream-Task-Datasets", name="ncRPI")
 ```
+
+
+## Github
+https://github.com/LucaOne/