update table

app.py

@@ -43,16 +43,16 @@ in-depth evaluation framework for protein foundation models, driving their devel
 ## [Paper](https://www.arxiv.org/pdf/2409.06744) | [Website](https://proteinbench.github.io/) 
 """
 
-def convert_to_float(df):
+def convert_to_float(df, start_col_idx=2):
     columns = df.columns
-    for col in columns[2:]:
+    for col in columns[start_col_idx:]:
         df[col] = df[col].astype('float')
     return df
 
 
 def assign_rank_and_get_sorted_csv(src_csv_path, tag_csv_path, ignore_num=0):
     src_csv = pd.read_csv(src_csv_path)
-    float_csv = convert_to_float(copy.deepcopy(src_csv))
+    float_csv = convert_to_float(copy.deepcopy(src_csv), start_col_idx=1)
     tag_csv = pd.read_csv(tag_csv_path)
     rank_csv = pd.DataFrame()
     
@@ -170,15 +170,25 @@ with demo:
                     headers=multi_state_prediction_csv.columns.to_list(),
                     datatype=['number', 'markdown'] + (len(multi_state_prediction_csv.columns)-1) * ['number'],
                 )
-        with gr.TabItem("🏅 Conformation Prediction Leaderboard", elem_id='conformation-prediction-table', id=8,):
+        # with gr.TabItem("🏅 Conformation Prediction Leaderboard", elem_id='conformation-prediction-table', id=8,):
+        #     with gr.Row():
+        #         conformation_prediction_csv = assign_rank_and_get_sorted_csv('data_link/conformation_prediction.csv', 'data_rank/conformation_prediction.csv')
+        #         conformation_prediction_table = gr.components.DataFrame(
+        #             value=convert_to_float(conformation_prediction_csv).values,
+        #             height=99999,
+        #             interactive=False,
+        #             headers=conformation_prediction_csv.columns.to_list(),
+        #             datatype=['number', 'markdown'] + (len(conformation_prediction_csv.columns)-1) * ['number'],
+        #         )
+        with gr.TabItem("🏅 Distribution Prediction Leaderboard", elem_id='distribution-prediction-table', id=8,):
             with gr.Row():
-                conformation_prediction_csv = assign_rank_and_get_sorted_csv('data_link/conformation_prediction.csv', 'data_rank/conformation_prediction.csv')
-                conformation_prediction_table = gr.components.DataFrame(
-                    value=convert_to_float(conformation_prediction_csv).values,
+                distribution_prediction_csv = assign_rank_and_get_sorted_csv('data_link/distribution_prediction.csv', 'data_rank/distribution_prediction.csv')
+                distribution_prediction_table = gr.components.DataFrame(
+                    value=convert_to_float(distribution_prediction_csv).values,
                     height=99999,
                     interactive=False,
-                    headers=conformation_prediction_csv.columns.to_list(),
-                    datatype=['number', 'markdown'] + (len(conformation_prediction_csv.columns)-1) * ['number'],
+                    headers=distribution_prediction_csv.columns.to_list(),
+                    datatype=['number', 'markdown'] + (len(distribution_prediction_csv.columns)-1) * ['number'],
                 )
 
 

data/conformation_prediction.csv

@@ -1,21 +1,18 @@
-Model,Pairwise RMSD,*RMSF,Pearson r on Pairwise RMSD ↑,Pearson r on *Global RMSF ↑,Pearson r on *Per target RMSF ↑,*RMWD ↓,MD PCA W2 ↓,Joint PCA W2 ↓,PC sim > 0.5% ↑,Weak contacts J ↑,Transient contacts J ↑,*Exposed residue J ↑,*Exposed MI matrix ρ ↑,CA break % ↓,CA clash % ↓,PepBond break % ↓
-MD iid,2.76,1.63,0.96,0.97,0.99,0.71,0.76,0.70,93.9,0.90,0.80,0.93,0.56,0.0,0.1,3.4
-MD 2.5 ns,1.54,0.98,0.89,0.85,0.85,2.21,1.57,1.93,36.6,0.62,0.45,0.64,0.24,0.0,0.1,3.4
-EigenFold,5.96,NaN,-0.04,NaN,NaN,NaN,2.35,7.96,12.2,0.36,0.18,NaN,NaN,0.7,9.6,NaN
-MSA-depth256,0.84,0.53,0.25,0.34,0.59,3.63,1.83,2.90,29.3,0.30,0.28,0.33,0.06,0.0,0.2,5.9
-MSA-depth64,2.03,1.51,0.24,0.30,0.57,4.00,1.87,3.32,18.3,0.38,0.27,0.38,0.12,0.0,0.2,8.4
-MSA-depth32,5.71,7.96,0.07,0.17,0.53,6.12,2.50,5.67,17.1,0.39,0.24,0.36,0.15,0.0,0.5,13.0
-Str2Str-ODE (t=0.1),1.66,NaN,0.13,NaN,NaN,NaN,2.12,4.42,6.1,0.42,0.17,NaN,NaN,0.0,0.1,13.7
-Str2Str-ODE (t=0.3),3.15,NaN,0.12,NaN,NaN,NaN,2.23,4.75,9.8,0.41,0.17,NaN,NaN,0.0,0.1,14.8
-Str2Str-SDE (t=0.1),4.74,NaN,0.10,NaN,NaN,NaN,2.54,8.84,9.8,0.40,0.13,NaN,NaN,1.6,0.2,23.0
-Str2Str-SDE (t=0.3),7.54,NaN,0.00,NaN,NaN,NaN,3.29,12.28,7.3,0.35,0.13,NaN,NaN,1.5,0.2,21.4
-AlphaFlow-PDB,2.58,1.20,0.27,0.46,0.81,2.96,1.66,2.60,37.8,0.44,0.33,0.42,0.18,0.0,0.2,6.6
-AlphaFlow-MD,2.88,1.63,0.53,0.66,0.85,2.68,1.53,2.28,39.0,0.57,0.38,0.50,0.24,0.0,0.2,21.7
-ESMFlow-PDB,3.00,1.68,0.14,0.27,0.71,4.20,1.77,3.54,28.0,0.42,0.29,0.41,0.16,0.0,0.6,5.4
-ESMFlow-MD,3.34,2.13,0.19,0.30,0.76,3.63,1.54,3.15,25.6,0.51,0.33,0.47,0.21,0.0,0.3,10.9
-ConfDiff-Open-ClsFree,3.68,2.12,0.40,0.54,0.83,2.92,1.50,2.54,46.3,0.54,0.33,0.47,0.21,0.0,1.2,5.7
-ConfDiff-Open-PDB,2.90,1.43,0.38,0.51,0.82,2.97,1.57,2.51,34.1,0.47,0.34,0.43,0.18,0.0,0.9,5.7
-ConfDiff-Open-MD,3.43,2.21,0.59,0.67,0.85,2.76,1.44,2.25,35.4,0.59,0.36,0.50,0.24,0.0,0.8,6.3
-ConfDiff-ESM-ClsFree,4.04,2.84,0.31,0.43,0.82,3.82,1.72,3.06,37.8,0.54,0.31,0.47,0.18,0.0,1.8,4.3
-ConfDiff-ESM-PDB,3.42,2.06,0.29,0.40,0.80,3.67,1.70,3.17,34.1,0.48,0.31,0.42,0.18,0.0,1.6,3.9
-ConfDiff-ESM-MD,3.91,2.79,0.35,0.48,0.82,3.67,1.66,2.89,39.0,0.56,0.34,0.48,0.23,0.0,1.5,4.0
+Model,apo-TM ↑,holo-TM ↑,TMens ↑,Pairwise TM,CA clash (%) ↓,CA break (%) ↓,PepBond break (%) ↓
+apo model,1.000,0.790,0.895,N/A,N/A,N/A,N/A
+EigenFold,0.831,0.864,0.847,0.907,3.6,0.3,N/A
+MSA-depth256,0.845,0.889,0.867,0.978,0.2,0.0,4.6
+MSA-depth64,0.844,0.883,0.863,0.950,0.2,0.0,5.7
+MSA-depth32,0.824,0.857,0.841,0.864,0.2,0.0,8.9
+Str2Str-ODE (Tmax=0.1),0.762,0.778,0.770,0.954,0.2,0.0,14.0
+Str2Str-ODE (Tmax=0.3),0.766,0.781,0.774,0.872,0.2,0.0,14.7
+Str2Str-SDE (Tmax=0.1),0.682,0.693,0.688,0.760,0.2,1.5,22.6
+Str2Str-SDE (Tmax=0.3),0.680,0.689,0.684,0.639,0.2,1.4,21.1
+AlphaFlow-PDB,0.855,0.891,0.873,0.924,0.3,0.0,6.6
+AlphaFlow-MD,0.857,0.863,0.860,0.894,0.2,0.0,20.8
+ESMFlow-PDB,0.849,0.882,0.866,0.935,0.3,0.0,4.8
+ESMFlow-MD,0.851,0.864,0.858,0.897,0.1,0.0,10.9
+ConfDiff-Open-ClsFree,0.838,0.879,0.859,0.870,0.8,0.0,5.8
+ConfDiff-Open-MD,0.839,0.874,0.857,0.863,0.4,0.0,6.8
+ConfDiff-ESM-ClsFree,0.837,0.864,0.850,0.846,0.7,0.0,4.6
+ConfDiff-ESM-MD,0.836,0.862,0.849,0.846,0.3,0.0,4.1

data/distribution_prediction.csv

@@ -0,0 +1,21 @@
+Model,Pairwise RMSD,*RMSF,Pearson r on Pairwise RMSD ↑,Pearson r on *Global RMSF ↑,Pearson r on *Per target RMSF ↑,*RMWD ↓,MD PCA W2 ↓,Joint PCA W2 ↓,PC sim > 0.5% ↑,Weak contacts J ↑,Transient contacts J ↑,*Exposed residue J ↑,*Exposed MI matrix ρ ↑,CA break % ↓,CA clash % ↓,PepBond break % ↓
+MD iid,2.76,1.63,0.96,0.97,0.99,0.71,0.76,0.70,93.9,0.90,0.80,0.93,0.56,0.0,0.1,3.4
+MD 2.5 ns,1.54,0.98,0.89,0.85,0.85,2.21,1.57,1.93,36.6,0.62,0.45,0.64,0.24,0.0,0.1,3.4
+EigenFold,5.96,NaN,-0.04,NaN,NaN,NaN,2.35,7.96,12.2,0.36,0.18,NaN,NaN,0.7,9.6,NaN
+MSA-depth256,0.84,0.53,0.25,0.34,0.59,3.63,1.83,2.90,29.3,0.30,0.28,0.33,0.06,0.0,0.2,5.9
+MSA-depth64,2.03,1.51,0.24,0.30,0.57,4.00,1.87,3.32,18.3,0.38,0.27,0.38,0.12,0.0,0.2,8.4
+MSA-depth32,5.71,7.96,0.07,0.17,0.53,6.12,2.50,5.67,17.1,0.39,0.24,0.36,0.15,0.0,0.5,13.0
+Str2Str-ODE (t=0.1),1.66,NaN,0.13,NaN,NaN,NaN,2.12,4.42,6.1,0.42,0.17,NaN,NaN,0.0,0.1,13.7
+Str2Str-ODE (t=0.3),3.15,NaN,0.12,NaN,NaN,NaN,2.23,4.75,9.8,0.41,0.17,NaN,NaN,0.0,0.1,14.8
+Str2Str-SDE (t=0.1),4.74,NaN,0.10,NaN,NaN,NaN,2.54,8.84,9.8,0.40,0.13,NaN,NaN,1.6,0.2,23.0
+Str2Str-SDE (t=0.3),7.54,NaN,0.00,NaN,NaN,NaN,3.29,12.28,7.3,0.35,0.13,NaN,NaN,1.5,0.2,21.4
+AlphaFlow-PDB,2.58,1.20,0.27,0.46,0.81,2.96,1.66,2.60,37.8,0.44,0.33,0.42,0.18,0.0,0.2,6.6
+AlphaFlow-MD,2.88,1.63,0.53,0.66,0.85,2.68,1.53,2.28,39.0,0.57,0.38,0.50,0.24,0.0,0.2,21.7
+ESMFlow-PDB,3.00,1.68,0.14,0.27,0.71,4.20,1.77,3.54,28.0,0.42,0.29,0.41,0.16,0.0,0.6,5.4
+ESMFlow-MD,3.34,2.13,0.19,0.30,0.76,3.63,1.54,3.15,25.6,0.51,0.33,0.47,0.21,0.0,0.3,10.9
+ConfDiff-Open-ClsFree,3.68,2.12,0.40,0.54,0.83,2.92,1.50,2.54,46.3,0.54,0.33,0.47,0.21,0.0,1.2,5.7
+ConfDiff-Open-PDB,2.90,1.43,0.38,0.51,0.82,2.97,1.57,2.51,34.1,0.47,0.34,0.43,0.18,0.0,0.9,5.7
+ConfDiff-Open-MD,3.43,2.21,0.59,0.67,0.85,2.76,1.44,2.25,35.4,0.59,0.36,0.50,0.24,0.0,0.8,6.3
+ConfDiff-ESM-ClsFree,4.04,2.84,0.31,0.43,0.82,3.82,1.72,3.06,37.8,0.54,0.31,0.47,0.18,0.0,1.8,4.3
+ConfDiff-ESM-PDB,3.42,2.06,0.29,0.40,0.80,3.67,1.70,3.17,34.1,0.48,0.31,0.42,0.18,0.0,1.6,3.9
+ConfDiff-ESM-MD,3.91,2.79,0.35,0.48,0.82,3.67,1.66,2.89,39.0,0.56,0.34,0.48,0.23,0.0,1.5,4.0