README.md

---
language: en
license: cc0-1.0
source_datasets: curated
task_categories: 
- tabular-classification
- tabular-regression
tags:
- chemistry
- biology
- medical
pretty_name: Blood-Brain Barrier Database (B3DB)
dataset_summary: >-
  Curation of 50 published resources of categorical and numeric measurements of
  Blood-Brain Barrier penetration.
citation: >-
  @article{
    Meng_A_curated_diverse_2021,
    author = {Meng, Fanwang and Xi, Yang and Huang, Jinfeng and Ayers, Paul W.},
    doi = {10.1038/s41597-021-01069-5},
    journal = {Scientific Data},
    number = {289},
    title = {A curated diverse molecular database of blood-brain barrier permeability with chemical descriptors},
    volume = {8},
    year = {2021},
    url = {https://www.nature.com/articles/s41597-021-01069-5},
    publisher = {Springer Nature}
  }
size_categories:
- 1K<n<10K
config_names:
- B3DB_classification
- B3DB_classification_extended
- B3DB_regression
- B3DB_regression_extended
configs:
- config_name: B3DB_classification
  data_files:
  - split: test
    path: B3DB_classification/test.csv
  - split: train
    path: B3DB_classification/train.csv    
- config_name: B3DB_classification_extended
  data_files:
  - split: test
    path: B3DB_classification_extended/test.csv
  - split: train
    path: B3DB_classification_extended/train.csv
- config_name: B3DB_regression
  data_files:
  - split: test
    path: B3DB_regression/test.csv
  - split: train
    path: B3DB_regression/train.csv       
- config_name: B3DB_regression_extended
  data_files:
  - split: test
    path: B3DB_regression_extended/test.csv
  - split: train
    path: B3DB_regression_extended/train.csv      
dataset_info:
- config_name: B3DB_classification
  features:
    - name: "B3DB_classification_index"
      dtype: string             
    - name: "compound_name"   
      dtype: string  
    - name: "IUPAC_name"       
      dtype: string 
    - name: "SMILES"          
      dtype: string            
    - name: "CID"   
      dtype: float64  
    - name: "logBB"       
      dtype: float64 
    - name: "Y"            
      dtype:
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          names:
            0: "BBB-"
            1: "BBB+"
    - name: "Inchi"   
      dtype: string 
    - name: "threshold"       
      dtype: float64
    - name: "reference"       
      dtype: string
    - name: "group"            
      dtype: string            
    - name: "comments" 
      dtype: string 
    - name: "ClusterNo"       
      dtype: int64
    - name: "MolCount"       
      dtype: int64
  splits:
    - name: train
      num_bytes: 656000
      num_examples: 5856
    - name: test
      num_bytes: 218640
      num_examples: 1951
- config_name: B3DB_classification_extended
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    - name: "group"
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    - name: "comments"
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    - name: "SpMax_Dzp"
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    - name: "SpDiam_Dzp"
      dtype: float64
    - name: "SpAD_Dzp"
      dtype: float64
    - name: "SpMAD_Dzp"
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    - name: "LogEE_Dzp"
      dtype: float64
    - name: "SM1_Dzp"
      dtype: float64
    - name: "VE1_Dzp"
      dtype: float64
    - name: "VE2_Dzp"
      dtype: float64
    - name: "VE3_Dzp"
      dtype: float64
    - name: "VR1_Dzp"
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    - name: "VR2_Dzp"
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    - name: "VR3_Dzp"
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    - name: "SpAbs_Dzi"
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    - name: "SpMax_Dzi"
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    - name: "SpDiam_Dzi"
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    - name: "SpAD_Dzi"
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    - name: "SpMAD_Dzi"
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    - name: "LogEE_Dzi"
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    - name: "SM1_Dzi"
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    - name: "VE1_Dzi"
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    - name: "VE2_Dzi"
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    - name: "VE3_Dzi"
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    - name: "VR1_Dzi"
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    - name: "VR2_Dzi"
      dtype: float64
    - name: "VR3_Dzi"
      dtype: float64
    - name: "BertzCT"
      dtype: float64
    - name: "nBonds"
      dtype: int64
    - name: "nBondsO"
      dtype: int64
    - name: "nBondsS"
      dtype: int64
    - name: "nBondsD"
      dtype: int64
    - name: "nBondsT"
      dtype: int64
    - name: "nBondsA"
      dtype: int64
    - name: "nBondsM"
      dtype: int64
    - name: "nBondsKS"
      dtype: int64
    - name: "nBondsKD"
      dtype: int64
    - name: "RNCG"
      dtype: float64
    - name: "RPCG"
      dtype: float64
    - name: "C1SP1"
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    - name: "C2SP1"
      dtype: int64
    - name: "C1SP2"
      dtype: int64
    - name: "C2SP2"
      dtype: int64
    - name: "C3SP2"
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    - name: "C1SP3"
      dtype: int64
    - name: "C2SP3"
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    - name: "C3SP3"
      dtype: int64
    - name: "C4SP3"
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    - name: "HybRatio"
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    - name: "FCSP3"
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    - name: "Xch-3d"
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    - name: "Xch-4d"
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    - name: "Xch-5d"
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    - name: "Xch-6d"
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    - name: "Xch-7d"
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    - name: "Xch-3dv"
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    - name: "Xch-4dv"
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    - name: "Xch-5dv"
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    - name: "Xch-6dv"
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    - name: "Xch-7dv"
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    - name: "Xc-3d"
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    - name: "Xc-4d"
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    - name: "Xc-5d"
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    - name: "Xc-6d"
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    - name: "Xc-3dv"
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    - name: "Xc-4dv"
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    - name: "Xc-5dv"
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    - name: "Xc-6dv"
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    - name: "Xpc-4d"
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    - name: "Xpc-5d"
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    - name: "Xpc-6d"
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    - name: "Xpc-4dv"
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    - name: "Xpc-5dv"
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    - name: "Xpc-6dv"
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    - name: "Xp-0d"
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    - name: "Xp-1d"
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    - name: "Xp-2d"
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    - name: "Xp-3d"
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    - name: "Xp-4d"
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    - name: "Xp-5d"
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    - name: "Xp-6d"
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    - name: "Xp-7d"
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    - name: "AXp-0d"
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    - name: "AXp-1d"
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    - name: "AXp-2d"
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    - name: "AXp-3d"
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    - name: "AXp-4d"
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    - name: "AXp-5d"
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    - name: "AXp-6d"
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    - name: "AXp-7d"
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    - name: "Xp-0dv"
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    - name: "Xp-1dv"
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    - name: "Xp-2dv"
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    - name: "Xp-3dv"
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    - name: "Xp-4dv"
      dtype: float64
    - name: "Xp-5dv"
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    - name: "Xp-6dv"
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    - name: "Xp-7dv"
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    - name: "AXp-0dv"
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    - name: "AXp-1dv"
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    - name: "AXp-2dv"
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    - name: "AXp-3dv"
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    - name: "AXp-4dv"
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    - name: "AXp-5dv"
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    - name: "AXp-6dv"
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    - name: "AXp-7dv"
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    - name: "SZ"
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    - name: "Sm"
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    - name: "Sv"
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    - name: "Sse"
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    - name: "Spe"
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    - name: "Sare"
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    - name: "Sp"
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    - name: "Si"
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    - name: "MZ"
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    - name: "Mm"
      dtype: float64
    - name: "Mv"
      dtype: float64
    - name: "Mse"
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    - name: "Mpe"
      dtype: float64
    - name: "Mare"
      dtype: float64
    - name: "Mp"
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    - name: "Mi"
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    - name: "SpAbs_Dt"
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    - name: "SpMax_Dt"
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    - name: "SpDiam_Dt"
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    - name: "SpAD_Dt"
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    - name: "SpMAD_Dt"
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    - name: "LogEE_Dt"
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    - name: "SM1_Dt"
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    - name: "VE1_Dt"
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    - name: "VE2_Dt"
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    - name: "VE3_Dt"
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    - name: "VR1_Dt"
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    - name: "VR2_Dt"
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    - name: "VR3_Dt"
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    - name: "DetourIndex"
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    - name: "SpAbs_D"
      dtype: float64
    - name: "SpMax_D"
      dtype: float64
    - name: "SpDiam_D"
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    - name: "SpAD_D"
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    - name: "SpMAD_D"
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    - name: "LogEE_D"
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    - name: "VE1_D"
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    - name: "VE2_D"
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    - name: "VE3_D"
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    - name: "VR1_D"
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    - name: "VR2_D"
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    - name: "VR3_D"
      dtype: float64
    - name: "NsLi"
      dtype: int64
    - name: "NssBe"
      dtype: int64
    - name: "NssssBe"
      dtype: int64
    - name: "NssBH"
      dtype: int64
    - name: "NsssB"
      dtype: int64
    - name: "NssssB"
      dtype: int64
    - name: "NsCH3"
      dtype: int64
    - name: "NdCH2"
      dtype: int64
    - name: "NssCH2"
      dtype: int64
    - name: "NtCH"
      dtype: int64
    - name: "NdsCH"
      dtype: int64
    - name: "NaaCH"
      dtype: int64
    - name: "NsssCH"
      dtype: int64
    - name: "NddC"
      dtype: int64
    - name: "NtsC"
      dtype: int64
    - name: "NdssC"
      dtype: int64
    - name: "NaasC"
      dtype: int64
    - name: "NaaaC"
      dtype: int64
    - name: "NssssC"
      dtype: int64
    - name: "NsNH3"
      dtype: int64
    - name: "NsNH2"
      dtype: int64
    - name: "NssNH2"
      dtype: int64
    - name: "NdNH"
      dtype: int64
    - name: "NssNH"
      dtype: int64
    - name: "NaaNH"
      dtype: int64
    - name: "NtN"
      dtype: int64
    - name: "NsssNH"
      dtype: int64
    - name: "NdsN"
      dtype: int64
    - name: "NaaN"
      dtype: int64
    - name: "NsssN"
      dtype: int64
    - name: "NddsN"
      dtype: int64
    - name: "NaasN"
      dtype: int64
    - name: "NssssN"
      dtype: int64
    - name: "NsOH"
      dtype: int64
    - name: "NdO"
      dtype: int64
    - name: "NssO"
      dtype: int64
    - name: "NaaO"
      dtype: int64
    - name: "NsF"
      dtype: int64
    - name: "NsSiH3"
      dtype: int64
    - name: "NssSiH2"
      dtype: int64
    - name: "NsssSiH"
      dtype: int64
    - name: "NssssSi"
      dtype: int64
    - name: "NsPH2"
      dtype: int64
    - name: "NssPH"
      dtype: int64
    - name: "NsssP"
      dtype: int64
    - name: "NdsssP"
      dtype: int64
    - name: "NsssssP"
      dtype: int64
    - name: "NsSH"
      dtype: int64
    - name: "NdS"
      dtype: int64
    - name: "NssS"
      dtype: int64
    - name: "NaaS"
      dtype: int64
    - name: "NdssS"
      dtype: int64
    - name: "NddssS"
      dtype: int64
    - name: "NsCl"
      dtype: int64
    - name: "NsGeH3"
      dtype: int64
    - name: "NssGeH2"
      dtype: int64
    - name: "NsssGeH"
      dtype: int64
    - name: "NssssGe"
      dtype: int64
    - name: "NsAsH2"
      dtype: int64
    - name: "NssAsH"
      dtype: int64
    - name: "NsssAs"
      dtype: int64
    - name: "NsssdAs"
      dtype: int64
    - name: "NsssssAs"
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    - name: "NsSeH"
      dtype: int64
    - name: "NdSe"
      dtype: int64
    - name: "NssSe"
      dtype: int64
    - name: "NaaSe"
      dtype: int64
    - name: "NdssSe"
      dtype: int64
    - name: "NddssSe"
      dtype: int64
    - name: "NsBr"
      dtype: int64
    - name: "NsSnH3"
      dtype: int64
    - name: "NssSnH2"
      dtype: int64
    - name: "NsssSnH"
      dtype: int64
    - name: "NssssSn"
      dtype: int64
    - name: "NsI"
      dtype: int64
    - name: "NsPbH3"
      dtype: int64
    - name: "NssPbH2"
      dtype: int64
    - name: "NsssPbH"
      dtype: int64
    - name: "NssssPb"
      dtype: int64
    - name: "SsLi"
      dtype: int64
    - name: "SssBe"
      dtype: int64
    - name: "SssssBe"
      dtype: int64
    - name: "SssBH"
      dtype: int64
    - name: "SsssB"
      dtype: float64
    - name: "SssssB"
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    - name: "SsCH3"
      dtype: float64
    - name: "SdCH2"
      dtype: float64
    - name: "SssCH2"
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    - name: "StCH"
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    - name: "SdsCH"
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    - name: "SaaCH"
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    - name: "SsssCH"
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    - name: "SddC"
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    - name: "StsC"
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    - name: "SdssC"
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    - name: "SaasC"
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    - name: "SaaaC"
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    - name: "SssssC"
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    - name: "SsNH3"
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    - name: "SsNH2"
      dtype: float64
    - name: "SssNH2"
      dtype: int64
    - name: "SdNH"
      dtype: float64
    - name: "SssNH"
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    - name: "SaaNH"
      dtype: float64
    - name: "StN"
      dtype: float64
    - name: "SsssNH"
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    - name: "SdsN"
      dtype: float64
    - name: "SaaN"
      dtype: float64
    - name: "SsssN"
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    - name: "SddsN"
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    - name: "SaasN"
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    - name: "SssssN"
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    - name: "SsOH"
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    - name: "SdO"
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    - name: "SssO"
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    - name: "SaaO"
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    - name: "SsF"
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    - name: "SsSiH3"
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    - name: "SssSiH2"
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    - name: "SsssSiH"
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    - name: "SssssSi"
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    - name: "SsPH2"
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    - name: "SssPH"
      dtype: int64
    - name: "SsssP"
      dtype: int64
    - name: "SdsssP"
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    - name: "SsssssP"
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    - name: "SsSH"
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    - name: "SdS"
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    - name: "SssS"
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    - name: "SaaS"
      dtype: float64
    - name: "SdssS"
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    - name: "SddssS"
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    - name: "SsCl"
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    - name: "SsGeH3"
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    - name: "SssGeH2"
      dtype: int64
    - name: "SsssGeH"
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    - name: "SssssGe"
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    - name: "SsAsH2"
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    - name: "SssAsH"
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    - name: "SsssAs"
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    - name: "SsssdAs"
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    - name: "SsssssAs"
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    - name: "SsSeH"
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    - name: "SdSe"
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    - name: "SssSe"
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    - name: "SaaSe"
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    - name: "SdssSe"
      dtype: int64
    - name: "SddssSe"
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    - name: "SsBr"
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    - name: "SsSnH3"
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    - name: "SssSnH2"
      dtype: int64
    - name: "SsssSnH"
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    - name: "SsI"
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    - name: "SsPbH3"
      dtype: int64
    - name: "SssPbH2"
      dtype: int64
    - name: "SsssPbH"
      dtype: int64
    - name: "SssssPb"
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    - name: "MAXsLi"
      dtype: float64
    - name: "MAXssBe"
      dtype: float64
    - name: "MAXssssBe"
      dtype: float64
    - name: "MAXssBH"
      dtype: float64
    - name: "MAXsssB"
      dtype: float64
    - name: "MAXssssB"
      dtype: float64
    - name: "MAXsCH3"
      dtype: float64
    - name: "MAXdCH2"
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    - name: "MAXssCH2"
      dtype: float64
    - name: "MAXtCH"
      dtype: float64
    - name: "MAXdsCH"
      dtype: float64
    - name: "MAXaaCH"
      dtype: float64
    - name: "MAXsssCH"
      dtype: float64
    - name: "MAXddC"
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    - name: "MAXtsC"
      dtype: float64
    - name: "MAXdssC"
      dtype: float64
    - name: "MAXaasC"
      dtype: float64
    - name: "MAXaaaC"
      dtype: float64
    - name: "MAXssssC"
      dtype: float64
    - name: "MAXsNH3"
      dtype: float64
    - name: "MAXsNH2"
      dtype: float64
    - name: "MAXssNH2"
      dtype: float64
    - name: "MAXdNH"
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    - name: "MAXssNH"
      dtype: float64
    - name: "MAXaaNH"
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    - name: "MAXtN"
      dtype: float64
    - name: "MAXsssNH"
      dtype: float64
    - name: "MAXdsN"
      dtype: float64
    - name: "MAXaaN"
      dtype: float64
    - name: "MAXsssN"
      dtype: float64
    - name: "MAXddsN"
      dtype: float64
    - name: "MAXaasN"
      dtype: float64
    - name: "MAXssssN"
      dtype: float64
    - name: "MAXsOH"
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    - name: "MAXdO"
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    - name: "MAXssO"
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    - name: "MAXaaO"
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    - name: "MAXsF"
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    - name: "MAXsSiH3"
      dtype: float64
    - name: "MAXssSiH2"
      dtype: float64
    - name: "MAXsssSiH"
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    - name: "MAXssssSi"
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    - name: "MAXsPH2"
      dtype: float64
    - name: "MAXssPH"
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    - name: "MAXsssP"
      dtype: float64
    - name: "MAXdsssP"
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    - name: "MAXsssssP"
      dtype: float64
    - name: "MAXsSH"
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    - name: "MAXdS"
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    - name: "MAXssS"
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    - name: "MAXaaS"
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    - name: "MAXdssS"
      dtype: float64
    - name: "MAXddssS"
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    - name: "MAXsCl"
      dtype: float64
    - name: "MAXsGeH3"
      dtype: float64
    - name: "MAXssGeH2"
      dtype: float64
    - name: "MAXsssGeH"
      dtype: float64
    - name: "MAXssssGe"
      dtype: float64
    - name: "MAXsAsH2"
      dtype: float64
    - name: "MAXssAsH"
      dtype: float64
    - name: "MAXsssAs"
      dtype: float64
    - name: "MAXsssdAs"
      dtype: float64
    - name: "MAXsssssAs"
      dtype: float64
    - name: "MAXsSeH"
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    - name: "MAXdSe"
      dtype: float64
    - name: "MAXssSe"
      dtype: float64
    - name: "MAXaaSe"
      dtype: float64
    - name: "MAXdssSe"
      dtype: float64
    - name: "MAXddssSe"
      dtype: float64
    - name: "MAXsBr"
      dtype: float64
    - name: "MAXsSnH3"
      dtype: float64
    - name: "MAXssSnH2"
      dtype: float64
    - name: "MAXsssSnH"
      dtype: float64
    - name: "MAXssssSn"
      dtype: float64
    - name: "MAXsI"
      dtype: float64
    - name: "MAXsPbH3"
      dtype: float64
    - name: "MAXssPbH2"
      dtype: float64
    - name: "MAXsssPbH"
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    - name: "MAXssssPb"
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    - name: "MINsLi"
      dtype: float64
    - name: "MINssBe"
      dtype: float64
    - name: "MINssssBe"
      dtype: float64
    - name: "MINssBH"
      dtype: float64
    - name: "MINsssB"
      dtype: float64
    - name: "MINssssB"
      dtype: float64
    - name: "MINsCH3"
      dtype: float64
    - name: "MINdCH2"
      dtype: float64
    - name: "MINssCH2"
      dtype: float64
    - name: "MINtCH"
      dtype: float64
    - name: "MINdsCH"
      dtype: float64
    - name: "MINaaCH"
      dtype: float64
    - name: "MINsssCH"
      dtype: float64
    - name: "MINddC"
      dtype: float64
    - name: "MINtsC"
      dtype: float64
    - name: "MINdssC"
      dtype: float64
    - name: "MINaasC"
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    - name: "MINaaaC"
      dtype: float64
    - name: "MINssssC"
      dtype: float64
    - name: "MINsNH3"
      dtype: float64
    - name: "MINsNH2"
      dtype: float64
    - name: "MINssNH2"
      dtype: float64
    - name: "MINdNH"
      dtype: float64
    - name: "MINssNH"
      dtype: float64
    - name: "MINaaNH"
      dtype: float64
    - name: "MINtN"
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    - name: test
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- config_name: B3DB_regression
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    - name: "VE3_Dzpe"
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    - name: "VR1_Dzpe"
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    - name: "VR2_Dzpe"
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    - name: "VR3_Dzpe"
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    - name: "SpAbs_Dzare"
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    - name: "SpMax_Dzare"
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    - name: "SpDiam_Dzare"
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    - name: "SpAD_Dzare"
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    - name: "SpMAD_Dzare"
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    - name: "LogEE_Dzare"
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    - name: "SM1_Dzare"
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    - name: "VE2_Dzare"
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    - name: "VR2_Dzare"
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    - name: "VR3_Dzare"
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    - name: "SpMAD_Dzp"
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    - name: "LogEE_Dzp"
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    - name: "SpMAD_Dzi"
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    - name: "LogEE_Dzi"
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    - name: "SM1_Dzi"
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    - name: "BertzCT"
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    - name: "nBonds"
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    - name: "nBondsO"
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    - name: "nBondsS"
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    - name: "nBondsD"
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    - name: "nBondsT"
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    - name: "nBondsA"
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    - name: "nBondsM"
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    - name: "nBondsKS"
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    - name: "nBondsKD"
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    - name: "Xpc-5dv"
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    - name: "Spe"
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    - name: "Mpe"
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    - name: "Mi"
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    - name: "SpMax_Dt"
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    - name: "NaaCH"
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    - name: "NddC"
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    - name: "NtsC"
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    - name: "NdssC"
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    - name: "NaasC"
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    - name: "NaaaC"
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    - name: "NsNH2"
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    - name: "NssNH2"
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    - name: "NdNH"
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    - name: "NssNH"
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    - name: "NaaNH"
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    - name: "NtN"
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    - name: "NsssNH"
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    - name: "NdsN"
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    - name: "NaaN"
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    - name: "NsssN"
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    - name: "NddsN"
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    - name: "NaasN"
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    - name: "NssssN"
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    - name: "NsOH"
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    - name: "NdO"
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    - name: "NssO"
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    - name: "NaaO"
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    - name: "NsF"
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    - name: "NsSiH3"
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    - name: "NssSiH2"
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    - name: "NsssSiH"
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    - name: "NssssSi"
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    - name: "NsPH2"
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    - name: "NdsssP"
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    - name: "NsSH"
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    - name: "NdS"
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    - name: "NaaS"
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    - name: "NdssS"
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    - name: "NsCl"
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    - name: "NsGeH3"
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    - name: "NssGeH2"
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    - name: "NsssGeH"
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    - name: "NssssGe"
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    - name: "NssSnH2"
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    - name: "NsssSnH"
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    - name: "n5FARing"
      dtype: int64
    - name: "n6FARing"
      dtype: int64
    - name: "n7FARing"
      dtype: int64
    - name: "n8FARing"
      dtype: int64
    - name: "n9FARing"
      dtype: int64
    - name: "n10FARing"
      dtype: int64
    - name: "n11FARing"
      dtype: int64
    - name: "n12FARing"
      dtype: int64
    - name: "nG12FARing"
      dtype: int64
    - name: "nFAHRing"
      dtype: int64
    - name: "n4FAHRing"
      dtype: int64
    - name: "n5FAHRing"
      dtype: int64
    - name: "n6FAHRing"
      dtype: int64
    - name: "n7FAHRing"
      dtype: int64
    - name: "n8FAHRing"
      dtype: int64
    - name: "n9FAHRing"
      dtype: int64
    - name: "n10FAHRing"
      dtype: int64
    - name: "n11FAHRing"
      dtype: int64
    - name: "n12FAHRing"
      dtype: int64
    - name: "nG12FAHRing"
      dtype: int64
    - name: "nRot"
      dtype: int64
    - name: "RotRatio"
      dtype: float64
    - name: "SLogP"
      dtype: float64
    - name: "SMR"
      dtype: float64
    - name: "TopoPSA(NO)"
      dtype: float64
    - name: "TopoPSA"
      dtype: float64
    - name: "GGI1"
      dtype: float64
    - name: "GGI2"
      dtype: float64
    - name: "GGI3"
      dtype: float64
    - name: "GGI4"
      dtype: float64
    - name: "GGI5"
      dtype: float64
    - name: "GGI6"
      dtype: float64
    - name: "GGI7"
      dtype: float64
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      dtype: float64
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      dtype: float64
    - name: "GGI10"
      dtype: float64
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      dtype: float64
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      dtype: float64
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      dtype: float64
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      dtype: float64
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      dtype: float64
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      dtype: float64
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      dtype: float64
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      dtype: float64
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      dtype: float64
    - name: "JGT10"
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    - name: "Diameter"
      dtype: int64
    - name: "Radius"
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    - name: "TopoShapeIndex"
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    - name: "PetitjeanIndex"
      dtype: float64
    - name: "Vabc"
      dtype: float64
    - name: "VAdjMat"
      dtype: float64
    - name: "MWC01"
      dtype: int64
    - name: "MWC02"
      dtype: float64
    - name: "MWC03"
      dtype: float64
    - name: "MWC04"
      dtype: float64
    - name: "MWC05"
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    - name: "MWC06"
      dtype: float64
    - name: "MWC07"
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    - name: "MWC09"
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    - name: "MWC10"
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    - name: "TMWC10"
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    - name: "SRW03"
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    - name: "SRW07"
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    - name: "SRW08"
      dtype: float64
    - name: "SRW09"
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    - name: "SRW10"
      dtype: float64
    - name: "TSRW10"
      dtype: float64
    - name: "MW"
      dtype: float64
    - name: "AMW"
      dtype: float64
    - name: "WPath"
      dtype: int64
    - name: "WPol"
      dtype: int64
    - name: "Zagreb1"
      dtype: int64
    - name: "Zagreb2"
      dtype: int64
    - name: "mZagreb1"
      dtype: float64
    - name: "mZagreb2"
      dtype: float64
    - name: "ClusterNo"
      dtype: int64
    - name: "MolCount"
      dtype: int64
  splits:
    - name: train
      num_bytes: 10347848
      num_examples: 795
    - name: test
      num_bytes: 3423336
      num_examples: 263
---

# Blood-Brain Barrier Database (B3DB)

The [Blood-Brain Barrier Database (B3DB)](https://www.nature.com/articles/s41597-021-01069-5)
is a large benchmark dataset compiled from 50 published resources
(as summarized at raw_data/raw_data_summary.tsv) and categorized based on the consistency between
different experimental references/measurements. This dataset was
[published in Scientific Data](https://www.nature.com/articles/s41597-021-01069-5) and
a mirror of the [theochem/B3DB](https://github.com/theochem/B3DB) the official Github repo where it is
occasionally uploaded with new experimental data. Scientists who would like
to contribute data should contact the database's maintainers (e.g., by creating a
[new Issue](https://github.com/theochem/B3DB/issues) in the database).

A subset of the molecules in B3DB has numerical `logBB` values (1058 compounds),
while the whole dataset has categorical (`BBB+` or `BBB-`) BBB permeability labels
(7807 compounds). Some physicochemical properties of the molecules are also provided.


## Quickstart Usage

### Load a dataset in python
Each subset can be loaded into python using the Huggingface [datasets](https://huggingface.co/docs/datasets/index) library.
First, from the command line install the `datasets` library

    $ pip install datasets

then, from within python load the datasets library

    >>> import datasets
   
and load one of the `B3DB` datasets, e.g.,

    >>> B3DB_classification = datasets.load_dataset("maomlab/B3DB", name = "B3DB_classification")
    Downloading readme: 100%|████████████████████████| 4.40k/4.40k [00:00<00:00, 1.35MB/s]
    Downloading data: 100%|██████████████████████████| 680k/680k [00:00<00:00, 946kB/s]
    Downloading data: 100%|██████████████████████████| 2.11M/2.11M [00:01<00:00, 1.28MB/s]
    Generating test split: 100%|█████████████████████| 1951/1951 [00:00<00:00, 20854.95 examples/s]
    Generating train split: 100%|████████████████████| 5856/5856 [00:00<00:00, 144260.80 examples/s]

and inspecting the loaded dataset

    >>> B3DB_classification
    B3DB_classification
    DatasetDict({
      test: Dataset({
         features: ['B3DB_classification_index', 'compound_name', 'IUPAC_name', 'SMILES', 'CID', 'logBB', 'Y', 'Inchi', 'threshold', 'reference', 'group', 'comments', 'ClusterNo', 'MolCount'],
         num_rows: 1951
      })
      train: Dataset({
          features: ['B3DB_classification_index', 'compound_name', 'IUPAC_name', 'SMILES', 'CID', 'logBB', 'Y', 'Inchi', 'threshold', 'reference', 'group', 'comments', 'ClusterNo', 'MolCount'],
          num_rows: 5856
      })
    })

### Use a dataset to train a model
One way to use the dataset is through the [MolFlux](https://exscientia.github.io/molflux/) package developed by Exscientia.
First, from the command line, install `MolFlux` library with `catboost` and `rdkit` support

    pip install 'molflux[catboost,rdkit]'

then load, featurize, split, fit, and evaluate the a catboost model

    import json
    from datasets import load_dataset
    from molflux.datasets import featurise_dataset
    from molflux.features import load_from_dicts as load_representations_from_dicts
    from molflux.splits import load_from_dict as load_split_from_dict
    from molflux.modelzoo import load_from_dict as load_model_from_dict
    from molflux.metrics import load_suite
    
    split_dataset = load_dataset('maomlab/B3DB', name = 'B3DB_classification')
    
    split_featurised_dataset = featurise_dataset(
      split_dataset,
      column = "SMILES",
      representations = load_representations_from_dicts([{"name": "morgan"}, {"name": "maccs_rdkit"}]))

    model = load_model_from_dict({
        "name": "cat_boost_classifier",
        "config": {
            "x_features": ['SMILES::morgan', 'SMILES::maccs_rdkit'],
            "y_features": ['Y']}})
    
    model.train(split_featurised_dataset["train"])
    preds = model.predict(split_featurised_dataset["test"])
    
    classification_suite = load_suite("classification")
    
    scores = classification_suite.compute(
        references=split_featurised_dataset["test"]['Y'],
        predictions=preds["cat_boost_classifier::Y"])


## About the DB3B

### Features of *B3DB*

1. The largest dataset with numerical and categorical values for Blood-Brain Barrier small molecules
    (to the best of our knowledge, as of February 25, 2021).

2. Inclusion of stereochemistry information with isomeric SMILES with chiral specifications if
    available. Otherwise, canonical SMILES are used.

3. Characterization of uncertainty of experimental measurements by grouping the collected molecular
    data records.

4. Extended datasets for numerical and categorical data with precomputed physicochemical properties
    using [mordred](https://github.com/mordred-descriptor/mordred).


### Data splits
The original B3DB dataset does not define splits, so here we have used the `Realistic Split` method described
in [(Martin et al., 2018)](https://doi.org/10.1021/acs.jcim.7b00166).

### Citation
Please use the following citation in any publication using our *B3DB* dataset:

```md
@article{Meng_A_curated_diverse_2021,
author = {Meng, Fanwang and Xi, Yang and Huang, Jinfeng and Ayers, Paul W.},
doi = {10.1038/s41597-021-01069-5},
journal = {Scientific Data},
number = {289},
title = {A curated diverse molecular database of blood-brain barrier permeability with chemical descriptors},
volume = {8},
year = {2021},
url = {https://www.nature.com/articles/s41597-021-01069-5},
publisher = {Springer Nature}
}
```