Skip to content

Commit

Permalink
update
Browse files Browse the repository at this point in the history
  • Loading branch information
@kexinhuang12345
kexinhuang12345 committed Jul 9, 2023
1 parent c9cd710 commit b4e9958
Show file tree
Hide file tree
Showing 24 changed files with 1,475 additions and 3,887 deletions.
4,640 changes: 922 additions & 3,718 deletions auto_leaderboard.ipynb
View file

Large diffs are not rendered by default.

32 changes: 24 additions & 8 deletions benchmark/admet_group/01caco2/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -363,70 +363,86 @@ <h3 id="leaderboard">Leaderboard</h3>
</tr>
<tr>
<td> 5 </td>
<td> Chemprop-RDKit </td>
<td><a href="mailto:[email protected]">Kyle Swanson</a></td>
<td><a href="https://github.com/chemprop/chemprop"> GitHub</a>, <a href="https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00237">Paper </a></td>
<td> N/A </td>
<td>0.328 <span>&#177;</span> 0.024 </td>
</tr>
<tr>
<td> 6 </td>
<td> Chemprop </td>
<td><a href="mailto:[email protected]">Kyle Swanson</a></td>
<td><a href="https://github.com/chemprop/chemprop"> GitHub</a>, <a href="https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00237">Paper </a></td>
<td> N/A </td>
<td>0.340 <span>&#177;</span> 0.016 </td>
</tr>
<tr>
<td> 7 </td>
<td> Euclia ML model </td>
<td><a href="mailto:[email protected]">Euclia</a></td>
<td><a href="https://github.com/euclia/public-models"> GitHub</a>, <a href="https://github.com/euclia/public-models">Paper </a></td>
<td> 50 </td>
<td>0.341 <span>&#177;</span> 0.004 </td>
</tr>
<tr>
<td> 6 </td>
<td> 8 </td>
<td> RDKit2D + MLP (DeepPurpose) </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/master/examples/single_pred/admet"> GitHub</a>, <a href="https://doi.org/10.1093/bioinformatics/btaa1005">Paper </a></td>
<td> 633,409 </td>
<td>0.393 <span>&#177;</span> 0.024 </td>
</tr>
<tr>
<td> 7 </td>
<td> 9 </td>
<td> AttentiveFP </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/31408336/">Paper </a></td>
<td> 300,806 </td>
<td>0.401 <span>&#177;</span> 0.032 </td>
</tr>
<tr>
<td> 8 </td>
<td> 10 </td>
<td> CNN (DeepPurpose) </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/master/examples/single_pred/admet"> GitHub</a>, <a href="https://doi.org/10.1093/bioinformatics/btaa1005">Paper </a></td>
<td> 226,625 </td>
<td>0.446 <span>&#177;</span> 0.036 </td>
</tr>
<tr>
<td> 9 </td>
<td> 11 </td>
<td> ContextPred </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://arxiv.org/abs/1905.12265">Paper </a></td>
<td> 2,067,053 </td>
<td>0.502 <span>&#177;</span> 0.036 </td>
</tr>
<tr>
<td> 10 </td>
<td> 12 </td>
<td> NeuralFP </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://ieeexplore.ieee.org/document/9412489">Paper </a></td>
<td> 480,193 </td>
<td>0.530 <span>&#177;</span> 0.102 </td>
</tr>
<tr>
<td> 11 </td>
<td> 13 </td>
<td> AttrMasking </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://arxiv.org/abs/1905.12265">Paper </a></td>
<td> 2,067,053 </td>
<td>0.546 <span>&#177;</span> 0.052 </td>
</tr>
<tr>
<td> 12 </td>
<td> 14 </td>
<td> GCN </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://arxiv.org/abs/1609.02907">Paper </a></td>
<td> 191,810 </td>
<td>0.599 <span>&#177;</span> 0.104 </td>
</tr>
<tr>
<td> 13 </td>
<td> 15 </td>
<td> Morgan + MLP (DeepPurpose) </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/master/examples/single_pred/admet"> GitHub</a>, <a href="https://doi.org/10.1093/bioinformatics/btaa1005">Paper </a></td>
Expand Down
36 changes: 26 additions & 10 deletions benchmark/admet_group/02hia/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -339,86 +339,102 @@ <h3 id="leaderboard">Leaderboard</h3>
</tr>
<tr>
<td> 2 </td>
<td> Chemprop-RDKit </td>
<td><a href="mailto:[email protected]">Kyle Swanson</a></td>
<td><a href="https://github.com/chemprop/chemprop"> GitHub</a>, <a href="https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00237">Paper </a></td>
<td> N/A </td>
<td>0.981 <span>&#177;</span> 0.002 </td>
</tr>
<tr>
<td> 3 </td>
<td> AttrMasking </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://arxiv.org/abs/1905.12265">Paper </a></td>
<td> 2,067,053 </td>
<td>0.978 <span>&#177;</span> 0.006 </td>
</tr>
<tr>
<td> 3 </td>
<td> 4 </td>
<td> ContextPred </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://arxiv.org/abs/1905.12265">Paper </a></td>
<td> 2,067,053 </td>
<td>0.975 <span>&#177;</span> 0.004 </td>
</tr>
<tr>
<td> 4 </td>
<td> 5 </td>
<td> AttentiveFP </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/31408336/">Paper </a></td>
<td> 300,806 </td>
<td>0.974 <span>&#177;</span> 0.007 </td>
</tr>
<tr>
<td> 5 </td>
<td> 6 </td>
<td> RDKit2D + MLP (DeepPurpose) </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/master/examples/single_pred/admet"> GitHub</a>, <a href="https://doi.org/10.1093/bioinformatics/btaa1005">Paper </a></td>
<td> 633,409 </td>
<td>0.972 <span>&#177;</span> 0.008 </td>
</tr>
<tr>
<td> 6 </td>
<td> 7 </td>
<td> Chemprop </td>
<td><a href="mailto:[email protected]">Kyle Swanson</a></td>
<td><a href="https://github.com/chemprop/chemprop"> GitHub</a>, <a href="https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00237">Paper </a></td>
<td> N/A </td>
<td>0.965 <span>&#177;</span> 0.005 </td>
</tr>
<tr>
<td> 8 </td>
<td> ZairaChem </td>
<td><a href="mailto:[email protected]">Gemma Turon </a></td>
<td><a href="https://github.com/ersilia-os/zaira-chem-tdc-benchmark"> GitHub</a>, <a href="https://www.biorxiv.org/content/10.1101/2022.12.13.520154v1">Paper </a></td>
<td> N/A </td>
<td>0.948 <span>&#177;</span> 0.018 </td>
</tr>
<tr>
<td> 7 </td>
<td> 9 </td>
<td> NeuralFP </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://ieeexplore.ieee.org/document/9412489">Paper </a></td>
<td> 480,193 </td>
<td>0.943 <span>&#177;</span> 0.014 </td>
</tr>
<tr>
<td> 8 </td>
<td> 10 </td>
<td> GCN </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://arxiv.org/abs/1609.02907">Paper </a></td>
<td> 191,810 </td>
<td>0.936 <span>&#177;</span> 0.024 </td>
</tr>
<tr>
<td> 9 </td>
<td> 11 </td>
<td> Euclia ML model </td>
<td><a href="mailto:[email protected]">Euclia</a></td>
<td><a href="https://github.com/euclia/public-models"> GitHub</a>, <a href="https://github.com/euclia/public-models">Paper </a></td>
<td> 50 </td>
<td>0.926 <span>&#177;</span> 0.017 </td>
</tr>
<tr>
<td> 10 </td>
<td> 12 </td>
<td> CNN (DeepPurpose) </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/master/examples/single_pred/admet"> GitHub</a>, <a href="https://doi.org/10.1093/bioinformatics/btaa1005">Paper </a></td>
<td> 226,625 </td>
<td>0.869 <span>&#177;</span> 0.026 </td>
</tr>
<tr>
<td> 11 </td>
<td> 13 </td>
<td> Basic ML </td>
<td><a href="mailto:[email protected]">Nilavo Boral</a></td>
<td><a href="https://github.com/NilavoBoral/Therapeutics-Data-Commons"> GitHub</a>, <a href="https://www.biorxiv.org/content/10.1101/2022.06.29.115436v1">Paper </a></td>
<td> N/A </td>
<td>0.818 <span>&#177;</span> 0.010 </td>
</tr>
<tr>
<td> 12 </td>
<td> 14 </td>
<td> Morgan + MLP (DeepPurpose) </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/master/examples/single_pred/admet"> GitHub</a>, <a href="https://doi.org/10.1093/bioinformatics/btaa1005">Paper </a></td>
Expand Down
20 changes: 18 additions & 2 deletions benchmark/admet_group/03pgp/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -403,22 +403,38 @@ <h3 id="leaderboard">Leaderboard</h3>
</tr>
<tr>
<td> 10 </td>
<td> Chemprop-RDKit </td>
<td><a href="mailto:[email protected]">Kyle Swanson</a></td>
<td><a href="https://github.com/chemprop/chemprop"> GitHub</a>, <a href="https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00237">Paper </a></td>
<td> N/A </td>
<td>0.883 <span>&#177;</span> 0.016 </td>
</tr>
<tr>
<td> 11 </td>
<td> Morgan + MLP (DeepPurpose) </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/master/examples/single_pred/admet"> GitHub</a>, <a href="https://doi.org/10.1093/bioinformatics/btaa1005">Paper </a></td>
<td> 1,477,185 </td>
<td>0.880 <span>&#177;</span> 0.006 </td>
</tr>
<tr>
<td> 11 </td>
<td> 12 </td>
<td> Chemprop </td>
<td><a href="mailto:[email protected]">Kyle Swanson</a></td>
<td><a href="https://github.com/chemprop/chemprop"> GitHub</a>, <a href="https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00237">Paper </a></td>
<td> N/A </td>
<td>0.858 <span>&#177;</span> 0.036 </td>
</tr>
<tr>
<td> 13 </td>
<td> Euclia ML model </td>
<td><a href="mailto:[email protected]">Euclia</a></td>
<td><a href="https://github.com/euclia/public-models"> GitHub</a>, <a href="https://github.com/euclia/public-models">Paper </a></td>
<td> 50 </td>
<td>0.845 <span>&#177;</span> 0.003 </td>
</tr>
<tr>
<td> 12 </td>
<td> 14 </td>
<td> Basic ML </td>
<td><a href="mailto:[email protected]">Nilavo Boral</a></td>
<td><a href="https://github.com/NilavoBoral/Therapeutics-Data-Commons"> GitHub</a>, <a href="https://www.biorxiv.org/content/10.1101/2022.06.29.115436v1">Paper </a></td>
Expand Down
30 changes: 23 additions & 7 deletions benchmark/admet_group/04bioav/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -363,62 +363,78 @@ <h3 id="leaderboard">Leaderboard</h3>
</tr>
<tr>
<td> 5 </td>
<td> Chemprop-RDKit </td>
<td><a href="mailto:[email protected]">Kyle Swanson</a></td>
<td><a href="https://github.com/chemprop/chemprop"> GitHub</a>, <a href="https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00237">Paper </a></td>
<td> N/A </td>
<td>0.668 <span>&#177;</span> 0.069 </td>
</tr>
<tr>
<td> 6 </td>
<td> AttentiveFP </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/31408336/">Paper </a></td>
<td> 300,806 </td>
<td>0.632 <span>&#177;</span> 0.039 </td>
</tr>
<tr>
<td> 6 </td>
<td> 7 </td>
<td> NeuralFP </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://ieeexplore.ieee.org/document/9412489">Paper </a></td>
<td> 480,193 </td>
<td>0.632 <span>&#177;</span> 0.036 </td>
</tr>
<tr>
<td> 7 </td>
<td> 8 </td>
<td> Euclia ML model </td>
<td><a href="mailto:[email protected]">Euclia</a></td>
<td><a href="https://github.com/euclia/public-models"> GitHub</a>, <a href="https://github.com/euclia/public-models">Paper </a></td>
<td> 50 </td>
<td>0.613 <span>&#177;</span> 0.015 </td>
</tr>
<tr>
<td> 8 </td>
<td> 9 </td>
<td> CNN (DeepPurpose) </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/master/examples/single_pred/admet"> GitHub</a>, <a href="https://doi.org/10.1093/bioinformatics/btaa1005">Paper </a></td>
<td> 226,625 </td>
<td>0.613 <span>&#177;</span> 0.013 </td>
</tr>
<tr>
<td> 9 </td>
<td> 10 </td>
<td> Morgan + MLP (DeepPurpose) </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/master/examples/single_pred/admet"> GitHub</a>, <a href="https://doi.org/10.1093/bioinformatics/btaa1005">Paper </a></td>
<td> 1,477,185 </td>
<td>0.581 <span>&#177;</span> 0.086 </td>
</tr>
<tr>
<td> 10 </td>
<td> 11 </td>
<td> Chemprop </td>
<td><a href="mailto:[email protected]">Kyle Swanson</a></td>
<td><a href="https://github.com/chemprop/chemprop"> GitHub</a>, <a href="https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00237">Paper </a></td>
<td> N/A </td>
<td>0.579 <span>&#177;</span> 0.023 </td>
</tr>
<tr>
<td> 12 </td>
<td> AttrMasking </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://arxiv.org/abs/1905.12265">Paper </a></td>
<td> 2,067,053 </td>
<td>0.577 <span>&#177;</span> 0.087 </td>
</tr>
<tr>
<td> 11 </td>
<td> 13 </td>
<td> GCN </td>
<td><a href="mailto:[email protected]">Kexin Huang</a></td>
<td><a href="https://github.com/mims-harvard/TDC/tree/main/examples/single_pred/admet"> GitHub</a>, <a href="https://arxiv.org/abs/1609.02907">Paper </a></td>
<td> 191,810 </td>
<td>0.566 <span>&#177;</span> 0.115 </td>
</tr>
<tr>
<td> 12 </td>
<td> 14 </td>
<td> Basic ML </td>
<td><a href="mailto:[email protected]">Nilavo Boral</a></td>
<td><a href="https://github.com/NilavoBoral/Therapeutics-Data-Commons"> GitHub</a>, <a href="https://www.biorxiv.org/content/10.1101/2022.06.29.115436v1">Paper </a></td>
Expand Down
Loading

0 comments on commit b4e9958

Please sign in to comment.