diff --git a/auto_leaderboard.ipynb b/auto_leaderboard.ipynb index 8e41fb9c..188a667a 100644 --- a/auto_leaderboard.ipynb +++ b/auto_leaderboard.ipynb @@ -2,19 +2,19 @@ "cells": [ { "cell_type": "code", - "execution_count": 120, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "from ast import literal_eval\n", "import pandas as pd\n", "import numpy as np\n", - "df = pd.read_csv('/Users/kexinhuang/Downloads/TDC Leaderboard Submission Form 13.csv')" + "df = pd.read_csv('/Users/kexinhuang/Downloads/TDC Leaderboard Submission Form 14.csv')" ] }, { "cell_type": "code", - "execution_count": 121, + "execution_count": 2, "metadata": { "scrolled": true }, @@ -34,7 +34,7 @@ " dtype='object')" ] }, - "execution_count": 121, + "execution_count": 2, "metadata": {}, "output_type": "execute_result" } @@ -45,7 +45,7 @@ }, { "cell_type": "code", - "execution_count": 122, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -67,7 +67,7 @@ }, { "cell_type": "code", - "execution_count": 130, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -83,7 +83,7 @@ }, { "cell_type": "code", - "execution_count": 156, + "execution_count": 5, "metadata": {}, "outputs": [ { @@ -92,7 +92,7 @@ "{'cyp2c9_veith': [0.767, 0.003]}" ] }, - "execution_count": 156, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } @@ -103,7 +103,7 @@ }, { "cell_type": "code", - "execution_count": 131, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -117,7 +117,7 @@ }, { "cell_type": "code", - "execution_count": 132, + "execution_count": 7, "metadata": {}, "outputs": [], "source": [ @@ -137,7 +137,7 @@ }, { "cell_type": "code", - "execution_count": 133, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -146,7 +146,7 @@ }, { "cell_type": "code", - "execution_count": 134, + "execution_count": 9, "metadata": {}, "outputs": [ { @@ -173,7 +173,7 @@ }, { "cell_type": "code", - "execution_count": 136, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -183,7 +183,7 @@ }, { "cell_type": "code", - "execution_count": 137, + "execution_count": 11, "metadata": {}, "outputs": [], "source": [ @@ -217,7 +217,7 @@ }, { "cell_type": "code", - "execution_count": 138, + "execution_count": 12, "metadata": {}, "outputs": [], "source": [ @@ -248,7 +248,7 @@ }, { "cell_type": "code", - "execution_count": 139, + "execution_count": 13, "metadata": {}, "outputs": [], "source": [ @@ -263,7 +263,7 @@ }, { "cell_type": "code", - "execution_count": 140, + "execution_count": 14, "metadata": {}, "outputs": [], "source": [ @@ -274,7 +274,7 @@ }, { "cell_type": "code", - "execution_count": 154, + "execution_count": 15, "metadata": {}, "outputs": [ { @@ -284,7 +284,7 @@ "Name: Result, dtype: object" ] }, - "execution_count": 154, + "execution_count": 15, "metadata": {}, "output_type": "execute_result" } @@ -295,16 +295,16 @@ }, { "cell_type": "code", - "execution_count": 155, + "execution_count": 16, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "\"{'caco2_wang': [0.446, 0.036],\\n 'hia_hou': [0.869, 0.026],\\n 'pgp_broccatelli': [0.908, 0.012],\\n 'bioavailability_ma': [0.613, 0.013],\\n 'lipophilicity_astrazeneca': [0.743, 0.02],\\n 'solubility_aqsoldb': [1.023, 0.023],\\n 'bbb_martins': [0.781, 0.03],\\n 'ppbr_az': [11.106, 0.358],\\n 'vdss_lombardo': [0.226, 0.114],\\n 'cyp2d6_veith': [0.544, 0.053],\\n 'cyp3a4_veith': [0.821, 0.003],\\n 'cyp2c9_veith': [0.713, 0.006],\\n 'cyp2d6_substrate_carbonmangels': [0.485, 0.037],\\n 'cyp3a4_substrate_carbonmangels': [0.662, 0.031],\\n 'cyp2c9_substrate_carbonmangels': [0.367, 0.059],\\n 'half_life_obach': [0.038, 0.138],\\n 'clearance_microsome_az': [0.252, 0.116],\\n 'clearance_hepatocyte_az': [0.235, 0.021],\\n 'herg': [0.754, 0.037],\\n 'ames': [0.776, 0.015],\\n 'dili': [0.792, 0.016],\\n 'ld50_zhu': [0.675, 0.011]}\"" + "\"{'caco2_wang': [0.927, 0.036],\\n 'hia_hou': [0.812, 0.067],\\n 'pgp_broccatelli': [0.886, 0.012],\\n 'bioavailability_ma': [0.61, 0.038],\\n 'lipophilicity_astrazeneca': [0.704, 0.008],\\n 'solubility_aqsoldb': [1.207, 0.02],\\n 'bbb_martins': [0.827, 0.03],\\n 'ppbr_az': [12.83, 0.487],\\n 'vdss_lombardo': [0.307, 0.046],\\n 'cyp2d6_veith': [0.584, 0.019],\\n 'cyp3a4_veith': [0.829, 0.006],\\n 'cyp2c9_veith': [0.71, 0.006],\\n 'cyp2d6_substrate_carbonmangels': [0.677, 0.05],\\n 'cyp3a4_substrate_carbonmangels': [0.633, 0.017],\\n 'cyp2c9_substrate_carbonmangels': [0.368, 0.014],\\n 'half_life_obach': [0.293, 0.139],\\n 'clearance_microsome_az': [0.473, 0.007],\\n 'clearance_hepatocyte_az': [0.239, 0.047],\\n 'herg': [0.741, 0.024],\\n 'ames': [0.802, 0.009],\\n 'dili': [0.837, 0.028],\\n 'ld50_zhu': [0.659, 0.019]}\"" ] }, - "execution_count": 155, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -315,7 +315,7 @@ }, { "cell_type": "code", - "execution_count": 142, + "execution_count": 17, "metadata": {}, "outputs": [], "source": [ @@ -324,7 +324,7 @@ }, { "cell_type": "code", - "execution_count": 143, + "execution_count": 18, "metadata": {}, "outputs": [ { @@ -335,7 +335,7 @@ " 'lipophilicity_astrazeneca': [0.479, 0.007]}" ] }, - "execution_count": 143, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } @@ -346,7 +346,7 @@ }, { "cell_type": "code", - "execution_count": 144, + "execution_count": 19, "metadata": {}, "outputs": [ { @@ -357,7 +357,7 @@ " 'lipophilicity_astrazeneca': [0.479, 0.007]}" ] }, - "execution_count": 144, + "execution_count": 19, "metadata": {}, "output_type": "execute_result" } @@ -368,7 +368,7 @@ }, { "cell_type": "code", - "execution_count": 145, + "execution_count": 20, "metadata": {}, "outputs": [], "source": [ @@ -438,7 +438,7 @@ }, { "cell_type": "code", - "execution_count": 146, + "execution_count": 21, "metadata": {}, "outputs": [], "source": [ @@ -447,7 +447,7 @@ }, { "cell_type": "code", - "execution_count": 147, + "execution_count": 22, "metadata": {}, "outputs": [], "source": [ @@ -456,7 +456,7 @@ }, { "cell_type": "code", - "execution_count": 148, + "execution_count": 23, "metadata": {}, "outputs": [], "source": [ @@ -465,9 +465,831 @@ }, { "cell_type": "code", - "execution_count": 165, + "execution_count": 49, + "metadata": {}, + "outputs": [], + "source": [ + "new_res = {'clearance_microsome_az': [0.555, 0.022], 'bbb_martins': [0.821, 0.112], 'cyp2d6_veith': [0.649, 0.016], 'herg': [0.721, 0.045], 'hia_hou': [0.965, 0.005], 'cyp3a4_veith': [0.862, 0.003], 'caco2_wang': [0.344, 0.015], 'pgp_broccatelli': [0.86, 0.036], 'ames': [0.842, 0.014], 'half_life_obach': [0.265, 0.032], 'cyp2c9_veith': [0.754, 0.002], 'dili': [0.899, 0.008], 'ld50_zhu': [0.606, 0.024], 'clearance_hepatocyte_az': [0.431, 0.006], 'solubility_aqsoldb': [0.829, 0.022], 'cyp2c9_substrate_carbonmangels': [0.382, 0.019], 'bioavailability_ma': [0.581, 0.024], 'vdss_lombardo': [0.491, 0.046], 'cyp3a4_substrate_carbonmangels': [0.596, 0.018], 'ppbr_az': [7.788, 0.21], 'lipophilicity_astrazeneca': [0.47, 0.009], 'cyp2d6_substrate_carbonmangels': [0.632, 0.037]}\n", + "row_index = df_admet[(df_admet.Name == 'Kyle Swanson') & (df_admet.Model == 'Chemprop')].index\n", + "df_admet.at[row_index[0], 'Result'] = new_res" + ] + }, + { + "cell_type": "code", + "execution_count": 52, + "metadata": {}, + "outputs": [], + "source": [ + "new_res = {'clearance_microsome_az': [0.599, 0.025], 'bbb_martins': [0.869, 0.027], 'cyp2d6_veith': [0.673, 0.007], 'herg': [0.84, 0.007], 'hia_hou': [0.981, 0.002], 'cyp3a4_veith': [0.876, 0.003], 'caco2_wang': [0.33, 0.024], 'pgp_broccatelli': [0.886, 0.016], 'ames': [0.85, 0.004], 'half_life_obach': [0.239, 0.019], 'cyp2c9_veith': [0.777, 0.003], 'dili': [0.887, 0.011], 'ld50_zhu': [0.625, 0.022], 'clearance_hepatocyte_az': [0.43, 0.021], 'solubility_aqsoldb': [0.761, 0.025], 'cyp2c9_substrate_carbonmangels': [0.4, 0.008], 'bioavailability_ma': [0.667, 0.068], 'vdss_lombardo': [0.389, 0.075], 'cyp3a4_substrate_carbonmangels': [0.619, 0.03], 'ppbr_az': [8.288, 0.173], 'lipophilicity_astrazeneca': [0.467, 0.006], 'cyp2d6_substrate_carbonmangels': [0.686, 0.031]}\n", + "row_index = df_admet[(df_admet.Name == 'Kyle Swanson') & (df_admet.Model == 'Chemprop-RDKit')].index\n", + "df_admet.at[row_index[0], 'Result'] = new_res" + ] + }, + { + "cell_type": "code", + "execution_count": 55, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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TimeNameEmailGroupModelPaper_URLCode_URLText_ResultHardware#ParamsHonor CodePKL_ResultResult
612/23/2020 14:46:51Kexin Huangkexinhuang@hsph.harvard.eduADMET GroupCNN (DeepPurpose)https://doi.org/10.1093/bioinformatics/btaa1005https://github.com/mims-harvard/TDC/tree/maste...{'caco2_wang': [0.446, 0.036],\\n 'hia_hou': [0...NVIDIA Tesla K80 GPU226625I acknowledge that the reported model performa...NaN{'caco2_wang': [0.446, 0.036], 'hia_hou': [0.8...
712/23/2020 14:47:41Kexin Huangkexinhuang@hsph.harvard.eduADMET GroupRDKit2D + MLP (DeepPurpose)https://doi.org/10.1093/bioinformatics/btaa1005https://github.com/mims-harvard/TDC/tree/maste...{'caco2_wang': [0.393, 0.024],\\n 'hia_hou': [0...NVIDIA Tesla K80 GPU633409I acknowledge that the reported model performa...NaN{'caco2_wang': [0.393, 0.024], 'hia_hou': [0.9...
812/23/2020 14:48:31Kexin Huangkexinhuang@hsph.harvard.eduADMET GroupMorgan + MLP (DeepPurpose)https://doi.org/10.1093/bioinformatics/btaa1005https://github.com/mims-harvard/TDC/tree/maste...{'caco2_wang': [0.908, 0.06],\\n 'hia_hou': [0....NVIDIA Tesla K80 GPU1477185I acknowledge that the reported model performa...NaN{'caco2_wang': [0.908, 0.06], 'hia_hou': [0.80...
2210/15/2021 10:40:27Parker Burchettparkerburchett@gmail.comADMET GroupColorRefinement + Weighted Ensemble LGBMNo paperhttps://github.com/parkerburchett/TDC-DeepLear...{'cyp2c9_veith': [0.767, 0.003]}https://github.com/parkerburchett/TDC-DeepLear...68I acknowledge that the reported model performa...NaN{'cyp2c9_veith': [0.767, 0.003]}
231/10/2022 19:07:47Kexin Huangkexinh@stanford.eduADMET GroupNeuralFPhttps://ieeexplore.ieee.org/document/9412489https://github.com/mims-harvard/TDC/tree/main/...{'caco2_wang': [0.530, 0.102],\\n'hia_hou': [0....NVIDIA GPU480193I acknowledge that the reported model performa...NaN{'caco2_wang': [0.53, 0.102], 'hia_hou': [0.94...
251/10/2022 19:17:01Kexin Huangkexinh@stanford.eduADMET GroupAttentiveFPhttps://pubmed.ncbi.nlm.nih.gov/31408336/https://github.com/mims-harvard/TDC/tree/main/...{'caco2_wang': [0.401, 0.032],\\n'hia_hou': [0....NVIDIA300806I acknowledge that the reported model performa...NaN{'caco2_wang': [0.401, 0.032], 'hia_hou': [0.9...
261/10/2022 19:22:17Kexin Huangkexinh@stanford.eduADMET GroupContextPredhttps://arxiv.org/abs/1905.12265https://github.com/mims-harvard/TDC/tree/main/...{'caco2_wang': [0.502, 0.036],\\n'hia_hou': [0....Titan2067053I acknowledge that the reported model performa...NaN{'caco2_wang': [0.502, 0.036], 'hia_hou': [0.9...
271/10/2022 19:23:20Kexin Huangkexinh@stanford.eduADMET GroupAttrMaskinghttps://arxiv.org/abs/1905.12265https://github.com/mims-harvard/TDC/tree/main/...{'caco2_wang': [0.546, 0.052],\\n'hia_hou': [0....Titan2067053I acknowledge that the reported model performa...NaN{'caco2_wang': [0.546, 0.052], 'hia_hou': [0.9...
281/10/2022 19:24:58Kexin Huangkexinh@stanford.eduADMET GroupGCNhttps://arxiv.org/abs/1609.02907https://github.com/mims-harvard/TDC/tree/main/...{'caco2_wang': [0.599, 0.104],\\n'hia_hou': [0....NVIDIA191810I acknowledge that the reported model performa...NaN{'caco2_wang': [0.599, 0.104], 'hia_hou': [0.9...
292/14/2022 10:02:00Suman Kalyan Berasuman@katanagraph.comADMET GroupSimGCNhttps://github.com/KatanaGraph/SimGCN-TDC/blob...https://github.com/KatanaGraph/SimGCN-TDC{ 'pgp_broccatelli': [0.929, 0.01], \\n'bioavai...CPU (AWS c5.12xlarge)1103000I acknowledge that the reported model performa...NaN{'pgp_broccatelli': [0.929, 0.01], 'bioavailab...
303/24/2022 20:58:47Shuai Shi310284598@qq.comADMET GroupQuGINhttps://arxiv.org/pdf/1810.00826.pdfhttps://github.com/NumnumM/QuGIN.git{'ld50_zhu': [0.622, 0.015]}RTX 30601797506I acknowledge that the reported model performa...NaN{'ld50_zhu': [0.622, 0.015]}
324/26/2022 13:51:38Alexander Scarlatascarlat@mitre.orgADMET GroupMACCS keys + autoMLNaNhttps://github.com/scarlat1/AcuteToxicityLD50{'ld50_zhu': [0.588, 0.005]}Default Kaggle config: 15Gb RAM, No GPUEnsemble of 25 modelsI acknowledge that the reported model performa...NaN{'ld50_zhu': [0.588, 0.005]}
357/2/2022 23:17:04Nilavo Boralnilavoboral@gmail.comADMET GroupBasic MLhttps://www.biorxiv.org/content/10.1101/2022.0...https://github.com/NilavoBoral/Therapeutics-Da...{'ames': [0.716, 0.0],\\n 'bbb_martins': [0.811...Google Colab (without any Hardware accelerator...Median value: 3. Models with parameters given ...I acknowledge that the reported model performa...NaN{'ames': [0.716, 0.0], 'bbb_martins': [0.811, ...
409/27/2022 20:57:09Andrew Liandrew@oloren.aiADMET GroupXGBoosthttps://github.com/Oloren-AI/OCE-TDC/blob/main...https://github.com/Oloren-AI/OCE-TDC/blob/main...{'caco2_wang': [0.289, 0.011]}AMD Epyc CPU, A100 GPU with CUDA12I acknowledge that the reported model performa...NaN{'caco2_wang': [0.289, 0.011]}
419/27/2022 20:59:21Andrew Liandrew@oloren.aiADMET GroupRFStackerhttps://github.com/Oloren-AI/OCE-TDC/blob/main...https://github.com/Oloren-AI/OCE-TDC/blob/main...{'hia_hou': [0.988, 0.002], 'clearance_microso...AMD Epyc CPU, A100 GPU with CUDA1858225I acknowledge that the reported model performa...NaN{'hia_hou': [0.988, 0.002], 'clearance_microso...
4610/10/2022 11:04:12Andrew Liandrew@oloren.aiADMET GroupBaseBoostinghttps://github.com/Oloren-AI/OCE-TDC/blob/main...https://github.com/Oloren-AI/OCE-TDC{'caco2_wang': [0.285, 0.005]}AMD Epyc CPU, A100 GPU with CUDA365713I acknowledge that the reported model performa...NaN{'caco2_wang': [0.285, 0.005]}
4810/10/2022 11:07:00Andrew Liandrew@oloren.aiADMET GroupRandom Foresthttps://github.com/Oloren-AI/OCE-TDC/blob/main...https://github.com/Oloren-AI/OCE-TDC{'cyp2c9_substrate_carbonmangels': [0.437, 0.0...AMD Epyc CPU, A100 GPU with CUDA9I acknowledge that the reported model performa...NaN{'cyp2c9_substrate_carbonmangels': [0.437, 0.0...
5012/21/2022 12:18:33Gemma Turongemma@ersilia.ioADMET GroupZairaChemhttps://www.biorxiv.org/content/10.1101/2022.1...https://github.com/ersilia-os/zaira-chem-tdc-b...{'bioavailability_ma': [0.706, 0.031],\\n 'hia_...System: Ubuntu LTS 20.04 / Trained on CPU>1 Million. ZairaChem is an autoML tool that t...I acknowledge that the reported model performa...NaN{'bioavailability_ma': [0.706, 0.031], 'hia_ho...
511/12/2023 2:15:19Eucliaeuclia@euclia.ioADMET GroupVoting Regressor (KNN, SVM){'half_life_obach': [0.544, 0.034]}4 CPUs5I acknowledge that the reported model performa...NaN{'half_life_obach': [0.544, 0.034]}
522/2/2023 21:14:42Shen Wan Xiangwanxiang.shen@u.nus.eduADMET GroupMolMapNet-Dhttps://www.nature.com/articles/s42256-021-003...https://github.com/shenwanxiang/bidd-molmap/tr...{'caco2_wang': [0.287, 0.005]}NVIDIA GeForce RTX 3080 Ti, 12GiB407617I acknowledge that the reported model performa...NaN{'caco2_wang': [0.287, 0.005]}
543/13/2023 3:12:06Eucliaeuclia@euclia.ioADMET GroupEuclia ML modelhttps://github.com/euclia/public-modelshttps://github.com/euclia/public-models{\"half_life_obach\": [0.547, 0.032], \"vdss_lomb...8-core CPU50I acknowledge that the reported model performa...NaN{'half_life_obach': [0.547, 0.032], 'vdss_lomb...
595/19/2023 14:03:58David Huangdavid@oloren.aiADMET GroupBaseBoosting KyQVZ6b2https://chemrxiv.org/engage/chemrxiv/article-d...https://github.com/Oloren-AI/OCE-TDC/tree/main{'LD50_Zhu': [0.552, 0.009], 'PPBR_AZ': [7.914...CPU (AMD EPYC 7542) + GPU (A100 80GB)NaNI acknowledge that the reported model performa...NaN{'ld50_zhu': [0.552, 0.009], 'ppbr_az': [7.914...
617/6/2023 11:09:07Kyle Swansonswansonk@stanford.eduADMET GroupChemprophttps://pubs.acs.org/doi/full/10.1021/acs.jcim...https://github.com/chemprop/chemprop{'clearance_microsome_az': [0.555, 0.021], 'bb...8 CPUs, 1 GPU (< 8 GB GPU memory required)355,201I acknowledge that the reported model performa...NaN{'clearance_microsome_az': [0.555, 0.022], 'bb...
627/6/2023 11:09:49Kyle Swansonswansonk@stanford.eduADMET GroupChemprop-RDKithttps://pubs.acs.org/doi/full/10.1021/acs.jcim...https://github.com/chemprop/chemprop{'clearance_microsome_az': [0.599, 0.026], 'bb...8 CPUs, 1 GPU (< 8 GB GPU memory required)415,201I acknowledge that the reported model performa...NaN{'clearance_microsome_az': [0.599, 0.025], 'bb...
638/30/2023 7:38:38Rick Fontenotrick@lanternpharma.comADMET GroupLantern RADR Ensemblehttps://github.com/lanternpharma/tdc-bbb-marti...https://github.com/lanternpharma/tdc-bbb-martins{'bbb_martins': [0.915, 0.002]}CPU, 16 cores / 128 GB RAM267,439I acknowledge that the reported model performa...NaN{'bbb_martins': [0.915, 0.002]}
648/30/2023 7:40:31Rick Fontenotrick@lanternpharma.comADMET GroupLantern RADR Logistic Regressionhttps://github.com/lanternpharma/tdc-bbb-marti...https://github.com/lanternpharma/tdc-bbb-martins{'bbb_martins': [0.903, 0.002]}CPU, 16 cores / 128 GB RAM456I acknowledge that the reported model performa...NaN{'bbb_martins': [0.903, 0.002]}
658/30/2023 7:41:57Rick Fontenotrick@lanternpharma.comADMET GroupLantern RADR Deep Neural Networkhttps://github.com/lanternpharma/tdc-bbb-marti...https://github.com/lanternpharma/tdc-bbb-martins{'bbb_martins': [0.912, 0.003]}CPU, 16 cores / 128 GB RAM266,881I acknowledge that the reported model performa...NaN{'bbb_martins': [0.912, 0.003]}
668/30/2023 7:43:18Rick Fontenotrick@lanternpharma.comADMET GroupLantern RADR Random Foresthttps://github.com/lanternpharma/tdc-bbb-marti...https://github.com/lanternpharma/tdc-bbb-martins{'bbb_martins': [0.908, 0.002]}CPU, 16 cores / 128 GB RAM319I acknowledge that the reported model performa...NaN{'bbb_martins': [0.908, 0.002]}
678/30/2023 7:45:11Rick Fontenotrick@lanternpharma.comADMET GroupLantern RADR SVMhttps://github.com/lanternpharma/tdc-bbb-marti...https://github.com/lanternpharma/tdc-bbb-martins{'bbb_martins': [0.905, 0.007]}CPU, 16 cores / 128 GB RAM241I acknowledge that the reported model performa...NaN{'bbb_martins': [0.905, 0.007]}
\n", + "
" + ], + "text/plain": [ + " Time Name Email \\\n", + "6 12/23/2020 14:46:51 Kexin Huang kexinhuang@hsph.harvard.edu \n", + "7 12/23/2020 14:47:41 Kexin Huang kexinhuang@hsph.harvard.edu \n", + "8 12/23/2020 14:48:31 Kexin Huang kexinhuang@hsph.harvard.edu \n", + "22 10/15/2021 10:40:27 Parker Burchett parkerburchett@gmail.com \n", + "23 1/10/2022 19:07:47 Kexin Huang kexinh@stanford.edu \n", + "25 1/10/2022 19:17:01 Kexin Huang kexinh@stanford.edu \n", + "26 1/10/2022 19:22:17 Kexin Huang kexinh@stanford.edu \n", + "27 1/10/2022 19:23:20 Kexin Huang kexinh@stanford.edu \n", + "28 1/10/2022 19:24:58 Kexin Huang kexinh@stanford.edu \n", + "29 2/14/2022 10:02:00 Suman Kalyan Bera suman@katanagraph.com \n", + "30 3/24/2022 20:58:47 Shuai Shi 310284598@qq.com \n", + "32 4/26/2022 13:51:38 Alexander Scarlat ascarlat@mitre.org \n", + "35 7/2/2022 23:17:04 Nilavo Boral nilavoboral@gmail.com \n", + "40 9/27/2022 20:57:09 Andrew Li andrew@oloren.ai \n", + "41 9/27/2022 20:59:21 Andrew Li andrew@oloren.ai \n", + "46 10/10/2022 11:04:12 Andrew Li andrew@oloren.ai \n", + "48 10/10/2022 11:07:00 Andrew Li andrew@oloren.ai \n", + "50 12/21/2022 12:18:33 Gemma Turon gemma@ersilia.io \n", + "51 1/12/2023 2:15:19 Euclia euclia@euclia.io \n", + "52 2/2/2023 21:14:42 Shen Wan Xiang wanxiang.shen@u.nus.edu \n", + "54 3/13/2023 3:12:06 Euclia euclia@euclia.io \n", + "59 5/19/2023 14:03:58 David Huang david@oloren.ai \n", + "61 7/6/2023 11:09:07 Kyle Swanson swansonk@stanford.edu \n", + "62 7/6/2023 11:09:49 Kyle Swanson swansonk@stanford.edu \n", + "63 8/30/2023 7:38:38 Rick Fontenot rick@lanternpharma.com \n", + "64 8/30/2023 7:40:31 Rick Fontenot rick@lanternpharma.com \n", + "65 8/30/2023 7:41:57 Rick Fontenot rick@lanternpharma.com \n", + "66 8/30/2023 7:43:18 Rick Fontenot rick@lanternpharma.com \n", + "67 8/30/2023 7:45:11 Rick Fontenot rick@lanternpharma.com \n", + "\n", + " Group Model \\\n", + "6 ADMET Group CNN (DeepPurpose) \n", + "7 ADMET Group RDKit2D + MLP (DeepPurpose) \n", + "8 ADMET Group Morgan + MLP (DeepPurpose) \n", + "22 ADMET Group ColorRefinement + Weighted Ensemble LGBM \n", + "23 ADMET Group NeuralFP \n", + "25 ADMET Group AttentiveFP \n", + "26 ADMET Group ContextPred \n", + "27 ADMET Group AttrMasking \n", + "28 ADMET Group GCN \n", + "29 ADMET Group SimGCN \n", + "30 ADMET Group QuGIN \n", + "32 ADMET Group MACCS keys + autoML \n", + "35 ADMET Group Basic ML \n", + "40 ADMET Group XGBoost \n", + "41 ADMET Group RFStacker \n", + "46 ADMET Group BaseBoosting \n", + "48 ADMET Group Random Forest \n", + "50 ADMET Group ZairaChem \n", + "51 ADMET Group Voting Regressor (KNN, SVM) \n", + "52 ADMET Group MolMapNet-D \n", + "54 ADMET Group Euclia ML model \n", + "59 ADMET Group BaseBoosting KyQVZ6b2 \n", + "61 ADMET Group Chemprop \n", + "62 ADMET Group Chemprop-RDKit \n", + "63 ADMET Group Lantern RADR Ensemble \n", + "64 ADMET Group Lantern RADR Logistic Regression \n", + "65 ADMET Group Lantern RADR Deep Neural Network \n", + "66 ADMET Group Lantern RADR Random Forest \n", + "67 ADMET Group Lantern RADR SVM \n", + "\n", + " Paper_URL \\\n", + "6 https://doi.org/10.1093/bioinformatics/btaa1005 \n", + "7 https://doi.org/10.1093/bioinformatics/btaa1005 \n", + "8 https://doi.org/10.1093/bioinformatics/btaa1005 \n", + "22 No paper \n", + "23 https://ieeexplore.ieee.org/document/9412489 \n", + "25 https://pubmed.ncbi.nlm.nih.gov/31408336/ \n", + "26 https://arxiv.org/abs/1905.12265 \n", + "27 https://arxiv.org/abs/1905.12265 \n", + "28 https://arxiv.org/abs/1609.02907 \n", + "29 https://github.com/KatanaGraph/SimGCN-TDC/blob... \n", + "30 https://arxiv.org/pdf/1810.00826.pdf \n", + "32 NaN \n", + "35 https://www.biorxiv.org/content/10.1101/2022.0... \n", + "40 https://github.com/Oloren-AI/OCE-TDC/blob/main... \n", + "41 https://github.com/Oloren-AI/OCE-TDC/blob/main... \n", + "46 https://github.com/Oloren-AI/OCE-TDC/blob/main... \n", + "48 https://github.com/Oloren-AI/OCE-TDC/blob/main... \n", + "50 https://www.biorxiv.org/content/10.1101/2022.1... \n", + "51 \n", + "52 https://www.nature.com/articles/s42256-021-003... \n", + "54 https://github.com/euclia/public-models \n", + "59 https://chemrxiv.org/engage/chemrxiv/article-d... \n", + "61 https://pubs.acs.org/doi/full/10.1021/acs.jcim... \n", + "62 https://pubs.acs.org/doi/full/10.1021/acs.jcim... \n", + "63 https://github.com/lanternpharma/tdc-bbb-marti... \n", + "64 https://github.com/lanternpharma/tdc-bbb-marti... \n", + "65 https://github.com/lanternpharma/tdc-bbb-marti... \n", + "66 https://github.com/lanternpharma/tdc-bbb-marti... \n", + "67 https://github.com/lanternpharma/tdc-bbb-marti... \n", + "\n", + " Code_URL \\\n", + "6 https://github.com/mims-harvard/TDC/tree/maste... \n", + "7 https://github.com/mims-harvard/TDC/tree/maste... \n", + "8 https://github.com/mims-harvard/TDC/tree/maste... \n", + "22 https://github.com/parkerburchett/TDC-DeepLear... \n", + "23 https://github.com/mims-harvard/TDC/tree/main/... \n", + "25 https://github.com/mims-harvard/TDC/tree/main/... \n", + "26 https://github.com/mims-harvard/TDC/tree/main/... \n", + "27 https://github.com/mims-harvard/TDC/tree/main/... \n", + "28 https://github.com/mims-harvard/TDC/tree/main/... \n", + "29 https://github.com/KatanaGraph/SimGCN-TDC \n", + "30 https://github.com/NumnumM/QuGIN.git \n", + "32 https://github.com/scarlat1/AcuteToxicityLD50 \n", + "35 https://github.com/NilavoBoral/Therapeutics-Da... \n", + "40 https://github.com/Oloren-AI/OCE-TDC/blob/main... \n", + "41 https://github.com/Oloren-AI/OCE-TDC/blob/main... \n", + "46 https://github.com/Oloren-AI/OCE-TDC \n", + "48 https://github.com/Oloren-AI/OCE-TDC \n", + "50 https://github.com/ersilia-os/zaira-chem-tdc-b... \n", + "51 \n", + "52 https://github.com/shenwanxiang/bidd-molmap/tr... \n", + "54 https://github.com/euclia/public-models \n", + "59 https://github.com/Oloren-AI/OCE-TDC/tree/main \n", + "61 https://github.com/chemprop/chemprop \n", + "62 https://github.com/chemprop/chemprop \n", + "63 https://github.com/lanternpharma/tdc-bbb-martins \n", + "64 https://github.com/lanternpharma/tdc-bbb-martins \n", + "65 https://github.com/lanternpharma/tdc-bbb-martins \n", + "66 https://github.com/lanternpharma/tdc-bbb-martins \n", + "67 https://github.com/lanternpharma/tdc-bbb-martins \n", + "\n", + " Text_Result \\\n", + "6 {'caco2_wang': [0.446, 0.036],\\n 'hia_hou': [0... \n", + "7 {'caco2_wang': [0.393, 0.024],\\n 'hia_hou': [0... \n", + "8 {'caco2_wang': [0.908, 0.06],\\n 'hia_hou': [0.... \n", + "22 {'cyp2c9_veith': [0.767, 0.003]} \n", + "23 {'caco2_wang': [0.530, 0.102],\\n'hia_hou': [0.... \n", + "25 {'caco2_wang': [0.401, 0.032],\\n'hia_hou': [0.... \n", + "26 {'caco2_wang': [0.502, 0.036],\\n'hia_hou': [0.... \n", + "27 {'caco2_wang': [0.546, 0.052],\\n'hia_hou': [0.... \n", + "28 {'caco2_wang': [0.599, 0.104],\\n'hia_hou': [0.... \n", + "29 { 'pgp_broccatelli': [0.929, 0.01], \\n'bioavai... \n", + "30 {'ld50_zhu': [0.622, 0.015]} \n", + "32 {'ld50_zhu': [0.588, 0.005]} \n", + "35 {'ames': [0.716, 0.0],\\n 'bbb_martins': [0.811... \n", + "40 {'caco2_wang': [0.289, 0.011]} \n", + "41 {'hia_hou': [0.988, 0.002], 'clearance_microso... \n", + "46 {'caco2_wang': [0.285, 0.005]} \n", + "48 {'cyp2c9_substrate_carbonmangels': [0.437, 0.0... \n", + "50 {'bioavailability_ma': [0.706, 0.031],\\n 'hia_... \n", + "51 {'half_life_obach': [0.544, 0.034]} \n", + "52 {'caco2_wang': [0.287, 0.005]} \n", + "54 {\"half_life_obach\": [0.547, 0.032], \"vdss_lomb... \n", + "59 {'LD50_Zhu': [0.552, 0.009], 'PPBR_AZ': [7.914... \n", + "61 {'clearance_microsome_az': [0.555, 0.021], 'bb... \n", + "62 {'clearance_microsome_az': [0.599, 0.026], 'bb... \n", + "63 {'bbb_martins': [0.915, 0.002]} \n", + "64 {'bbb_martins': [0.903, 0.002]} \n", + "65 {'bbb_martins': [0.912, 0.003]} \n", + "66 {'bbb_martins': [0.908, 0.002]} \n", + "67 {'bbb_martins': [0.905, 0.007]} \n", + "\n", + " Hardware \\\n", + "6 NVIDIA Tesla K80 GPU \n", + "7 NVIDIA Tesla K80 GPU \n", + "8 NVIDIA Tesla K80 GPU \n", + "22 https://github.com/parkerburchett/TDC-DeepLear... \n", + "23 NVIDIA GPU \n", + "25 NVIDIA \n", + "26 Titan \n", + "27 Titan \n", + "28 NVIDIA \n", + "29 CPU (AWS c5.12xlarge) \n", + "30 RTX 3060 \n", + "32 Default Kaggle config: 15Gb RAM, No GPU \n", + "35 Google Colab (without any Hardware accelerator... \n", + "40 AMD Epyc CPU, A100 GPU with CUDA \n", + "41 AMD Epyc CPU, A100 GPU with CUDA \n", + "46 AMD Epyc CPU, A100 GPU with CUDA \n", + "48 AMD Epyc CPU, A100 GPU with CUDA \n", + "50 System: Ubuntu LTS 20.04 / Trained on CPU \n", + "51 4 CPUs \n", + "52 NVIDIA GeForce RTX 3080 Ti, 12GiB \n", + "54 8-core CPU \n", + "59 CPU (AMD EPYC 7542) + GPU (A100 80GB) \n", + "61 8 CPUs, 1 GPU (< 8 GB GPU memory required) \n", + "62 8 CPUs, 1 GPU (< 8 GB GPU memory required) \n", + "63 CPU, 16 cores / 128 GB RAM \n", + "64 CPU, 16 cores / 128 GB RAM \n", + "65 CPU, 16 cores / 128 GB RAM \n", + "66 CPU, 16 cores / 128 GB RAM \n", + "67 CPU, 16 cores / 128 GB RAM \n", + "\n", + " #Params \\\n", + "6 226625 \n", + "7 633409 \n", + "8 1477185 \n", + "22 68 \n", + "23 480193 \n", + "25 300806 \n", + "26 2067053 \n", + "27 2067053 \n", + "28 191810 \n", + "29 1103000 \n", + "30 1797506 \n", + "32 Ensemble of 25 models \n", + "35 Median value: 3. Models with parameters given ... \n", + "40 12 \n", + "41 1858225 \n", + "46 365713 \n", + "48 9 \n", + "50 >1 Million. ZairaChem is an autoML tool that t... \n", + "51 5 \n", + "52 407617 \n", + "54 50 \n", + "59 NaN \n", + "61 355,201 \n", + "62 415,201 \n", + "63 267,439 \n", + "64 456 \n", + "65 266,881 \n", + "66 319 \n", + "67 241 \n", + "\n", + " Honor Code PKL_Result \\\n", + "6 I acknowledge that the reported model performa... NaN \n", + "7 I acknowledge that the reported model performa... NaN \n", + "8 I acknowledge that the reported model performa... NaN \n", + "22 I acknowledge that the reported model performa... NaN \n", + "23 I acknowledge that the reported model performa... NaN \n", + "25 I acknowledge that the reported model performa... NaN \n", + "26 I acknowledge that the reported model performa... NaN \n", + "27 I acknowledge that the reported model performa... NaN \n", + "28 I acknowledge that the reported model performa... NaN \n", + "29 I acknowledge that the reported model performa... NaN \n", + "30 I acknowledge that the reported model performa... NaN \n", + "32 I acknowledge that the reported model performa... NaN \n", + "35 I acknowledge that the reported model performa... NaN \n", + "40 I acknowledge that the reported model performa... NaN \n", + "41 I acknowledge that the reported model performa... NaN \n", + "46 I acknowledge that the reported model performa... NaN \n", + "48 I acknowledge that the reported model performa... NaN \n", + "50 I acknowledge that the reported model performa... NaN \n", + "51 I acknowledge that the reported model performa... NaN \n", + "52 I acknowledge that the reported model performa... NaN \n", + "54 I acknowledge that the reported model performa... NaN \n", + "59 I acknowledge that the reported model performa... NaN \n", + "61 I acknowledge that the reported model performa... NaN \n", + "62 I acknowledge that the reported model performa... NaN \n", + "63 I acknowledge that the reported model performa... NaN \n", + "64 I acknowledge that the reported model performa... NaN \n", + "65 I acknowledge that the reported model performa... NaN \n", + "66 I acknowledge that the reported model performa... NaN \n", + "67 I acknowledge that the reported model performa... NaN \n", + "\n", + " Result \n", + "6 {'caco2_wang': [0.446, 0.036], 'hia_hou': [0.8... \n", + "7 {'caco2_wang': [0.393, 0.024], 'hia_hou': [0.9... \n", + "8 {'caco2_wang': [0.908, 0.06], 'hia_hou': [0.80... \n", + "22 {'cyp2c9_veith': [0.767, 0.003]} \n", + "23 {'caco2_wang': [0.53, 0.102], 'hia_hou': [0.94... \n", + "25 {'caco2_wang': [0.401, 0.032], 'hia_hou': [0.9... \n", + "26 {'caco2_wang': [0.502, 0.036], 'hia_hou': [0.9... \n", + "27 {'caco2_wang': [0.546, 0.052], 'hia_hou': [0.9... \n", + "28 {'caco2_wang': [0.599, 0.104], 'hia_hou': [0.9... \n", + "29 {'pgp_broccatelli': [0.929, 0.01], 'bioavailab... \n", + "30 {'ld50_zhu': [0.622, 0.015]} \n", + "32 {'ld50_zhu': [0.588, 0.005]} \n", + "35 {'ames': [0.716, 0.0], 'bbb_martins': [0.811, ... \n", + "40 {'caco2_wang': [0.289, 0.011]} \n", + "41 {'hia_hou': [0.988, 0.002], 'clearance_microso... \n", + "46 {'caco2_wang': [0.285, 0.005]} \n", + "48 {'cyp2c9_substrate_carbonmangels': [0.437, 0.0... \n", + "50 {'bioavailability_ma': [0.706, 0.031], 'hia_ho... \n", + "51 {'half_life_obach': [0.544, 0.034]} \n", + "52 {'caco2_wang': [0.287, 0.005]} \n", + "54 {'half_life_obach': [0.547, 0.032], 'vdss_lomb... \n", + "59 {'ld50_zhu': [0.552, 0.009], 'ppbr_az': [7.914... \n", + "61 {'clearance_microsome_az': [0.555, 0.022], 'bb... \n", + "62 {'clearance_microsome_az': [0.599, 0.025], 'bb... \n", + "63 {'bbb_martins': [0.915, 0.002]} \n", + "64 {'bbb_martins': [0.903, 0.002]} \n", + "65 {'bbb_martins': [0.912, 0.003]} \n", + "66 {'bbb_martins': [0.908, 0.002]} \n", + "67 {'bbb_martins': [0.905, 0.007]} " + ] + }, + "execution_count": 55, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df_admet" + ] + }, + { + "cell_type": "code", + "execution_count": null, "metadata": { - "scrolled": true + "scrolled": false }, "outputs": [ { @@ -475,7 +1297,7 @@ "output_type": "stream", "text": [ "[0.446 0.393 0.908 0.53 0.401 0.502 0.546 0.599 0.321 0.289 0.285 0.287\n", - " 0.341 0.34 0.328]\n", + " 0.341 0.344 0.33 ]\n", "---- caco2_wang ------\n", "---- mae ------\n", " \n", @@ -516,18 +1338,10 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.328 ± 0.024 \n", + " 0.330 ± 0.024 \n", "\n", " \n", " 6 \n", - " Chemprop \n", - " Kyle Swanson \n", - " GitHub, Paper \n", - " N/A \n", - " 0.340 ± 0.016 \n", - "\n", - " \n", - " 7 \n", " Euclia ML model \n", " Euclia \n", " GitHub, Paper \n", @@ -535,6 +1349,14 @@ " 0.341 ± 0.004 \n", "\n", " \n", + " 7 \n", + " Chemprop \n", + " Kyle Swanson \n", + " GitHub, Paper \n", + " N/A \n", + " 0.344 ± 0.015 \n", + "\n", + " \n", " 8 \n", " RDKit2D + MLP (DeepPurpose) \n", " Kexin Huang \n", @@ -723,7 +1545,7 @@ "text": [ "\n", "[0.908 0.918 0.88 0.902 0.892 0.923 0.929 0.895 0.929 0.818 0.935 0.845\n", - " 0.858 0.883]\n", + " 0.86 0.886]\n", "---- pgp_broccatelli ------\n", "---- roc-auc ------\n", " \n", @@ -804,7 +1626,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.883 ± 0.016 \n", + " 0.886 ± 0.016 \n", "\n", " \n", " 11 \n", @@ -820,7 +1642,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.858 ± 0.036 \n", + " 0.860 ± 0.036 \n", "\n", " \n", " 13 \n", @@ -840,7 +1662,7 @@ "\n", "\n", "[0.613 0.672 0.581 0.632 0.632 0.671 0.577 0.566 0.748 0.523 0.706 0.613\n", - " 0.579 0.668]\n", + " 0.581 0.667]\n", "---- bioavailability_ma ------\n", "---- roc-auc ------\n", " \n", @@ -881,7 +1703,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.668 ± 0.069 \n", + " 0.667 ± 0.068 \n", "\n", " \n", " 6 \n", @@ -917,6 +1739,14 @@ "\n", " \n", " 10 \n", + " Chemprop \n", + " Kyle Swanson \n", + " GitHub, Paper \n", + " N/A \n", + " 0.581 ± 0.024 \n", + "\n", + " \n", + " 11 \n", " Morgan + MLP (DeepPurpose) \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -924,14 +1754,6 @@ " 0.581 ± 0.086 \n", "\n", " \n", - " 11 \n", - " Chemprop \n", - " Kyle Swanson \n", - " GitHub, Paper \n", - " N/A \n", - " 0.579 ± 0.023 \n", - "\n", - " \n", " 12 \n", " AttrMasking \n", " Kexin Huang \n", @@ -962,8 +1784,8 @@ "output_type": "stream", "text": [ "\n", - "[0.743 0.574 0.701 0.563 0.572 0.535 0.547 0.541 0.617 0.621 0.479 0.469\n", - " 0.466]\n", + "[0.743 0.574 0.701 0.563 0.572 0.535 0.547 0.541 0.617 0.621 0.479 0.47\n", + " 0.467]\n", "---- lipophilicity_astrazeneca ------\n", "---- mae ------\n", " \n", @@ -972,7 +1794,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.466 ± 0.006 \n", + " 0.467 ± 0.006 \n", "\n", " \n", " 2 \n", @@ -980,7 +1802,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.469 ± 0.005 \n", + " 0.470 ± 0.009 \n", "\n", " \n", " 3 \n", @@ -1071,7 +1893,7 @@ " 0.743 ± 0.020 \n", "\n", "\n", - "[1.023 0.827 1.203 0.947 0.776 1.04 1.026 0.907 0.828 1.076 0.818 0.762]\n", + "[1.023 0.827 1.203 0.947 0.776 1.04 1.026 0.907 0.828 1.076 0.829 0.761]\n", "---- solubility_aqsoldb ------\n", "---- mae ------\n", " \n", @@ -1080,7 +1902,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.762 ± 0.020 \n", + " 0.761 ± 0.025 \n", "\n", " \n", " 2 \n", @@ -1092,14 +1914,6 @@ "\n", " \n", " 3 \n", - " Chemprop \n", - " Kyle Swanson \n", - " GitHub, Paper \n", - " N/A \n", - " 0.818 ± 0.010 \n", - "\n", - " \n", - " 4 \n", " RDKit2D + MLP (DeepPurpose) \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -1107,7 +1921,7 @@ " 0.827 ± 0.047 \n", "\n", " \n", - " 5 \n", + " 4 \n", " Basic ML \n", " Nilavo Boral \n", " GitHub, Paper \n", @@ -1115,6 +1929,14 @@ " 0.828 ± 0.002 \n", "\n", " \n", + " 5 \n", + " Chemprop \n", + " Kyle Swanson \n", + " GitHub, Paper \n", + " N/A \n", + " 0.829 ± 0.022 \n", + "\n", + " \n", " 6 \n", " GCN \n", " Kexin Huang \n", @@ -1178,7 +2000,7 @@ "text": [ "\n", "[0.781 0.889 0.823 0.836 0.855 0.897 0.892 0.842 0.901 0.811 0.91 0.725\n", - " 0.928 0.956 0.949 0.962 0.82 0.868]\n", + " 0.821 0.869 0.915 0.903 0.912 0.908 0.905]\n", "---- bbb_martins ------\n", "---- roc-auc ------\n", " \n", @@ -1186,24 +2008,24 @@ " Lantern RADR Ensemble \n", " Rick Fontenot \n", " GitHub, Paper \n", - " 267,439 \n", - " 0.962 ± 0.003 \n", + " N/A \n", + " 0.915 ± 0.002 \n", "\n", " \n", " 2 \n", - " Lantern RADR Logistic Regression \n", + " Lantern RADR Deep Neural Network \n", " Rick Fontenot \n", " GitHub, Paper \n", - " 456 \n", - " 0.956 ± 0.006 \n", + " N/A \n", + " 0.912 ± 0.003 \n", "\n", " \n", " 3 \n", - " Lantern RADR Deep Neural Network \n", - " Rick Fontenot \n", - " GitHub, Paper \n", - " 266,881 \n", - " 0.949 ± 0.004 \n", + " ZairaChem \n", + " Gemma Turon \n", + " GitHub, Paper \n", + " N/A \n", + " 0.910 ± 0.024 \n", "\n", " \n", " 4 \n", @@ -1211,18 +2033,26 @@ " Rick Fontenot \n", " GitHub, Paper \n", " 319 \n", - " 0.928 ± 0.002 \n", + " 0.908 ± 0.002 \n", "\n", " \n", " 5 \n", - " ZairaChem \n", - " Gemma Turon \n", - " GitHub, Paper \n", - " N/A \n", - " 0.910 ± 0.024 \n", + " Lantern RADR SVM \n", + " Rick Fontenot \n", + " GitHub, Paper \n", + " 241 \n", + " 0.905 ± 0.007 \n", "\n", " \n", " 6 \n", + " Lantern RADR Logistic Regression \n", + " Rick Fontenot \n", + " GitHub, Paper \n", + " 456 \n", + " 0.903 ± 0.002 \n", + "\n", + " \n", + " 7 \n", " SimGCN \n", " Suman Kalyan Bera \n", " GitHub, Paper \n", @@ -1230,7 +2060,7 @@ " 0.901 ± 0.007 \n", "\n", " \n", - " 7 \n", + " 8 \n", " ContextPred \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -1238,7 +2068,7 @@ " 0.897 ± 0.004 \n", "\n", " \n", - " 8 \n", + " 9 \n", " AttrMasking \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -1246,7 +2076,7 @@ " 0.892 ± 0.012 \n", "\n", " \n", - " 9 \n", + " 10 \n", " RDKit2D + MLP (DeepPurpose) \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -1254,15 +2084,15 @@ " 0.889 ± 0.016 \n", "\n", " \n", - " 10 \n", + " 11 \n", " Chemprop-RDKit \n", " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.868 ± 0.027 \n", + " 0.869 ± 0.027 \n", "\n", " \n", - " 11 \n", + " 12 \n", " AttentiveFP \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -1270,7 +2100,7 @@ " 0.855 ± 0.011 \n", "\n", " \n", - " 12 \n", + " 13 \n", " GCN \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -1278,7 +2108,7 @@ " 0.842 ± 0.016 \n", "\n", " \n", - " 13 \n", + " 14 \n", " NeuralFP \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -1286,7 +2116,7 @@ " 0.836 ± 0.009 \n", "\n", " \n", - " 14 \n", + " 15 \n", " Morgan + MLP (DeepPurpose) \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -1294,15 +2124,15 @@ " 0.823 ± 0.015 \n", "\n", " \n", - " 15 \n", + " 16 \n", " Chemprop \n", " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.820 ± 0.112 \n", + " 0.821 ± 0.112 \n", "\n", " \n", - " 16 \n", + " 17 \n", " Basic ML \n", " Nilavo Boral \n", " GitHub, Paper \n", @@ -1310,7 +2140,7 @@ " 0.811 ± 0.013 \n", "\n", " \n", - " 17 \n", + " 18 \n", " CNN (DeepPurpose) \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -1318,7 +2148,7 @@ " 0.781 ± 0.030 \n", "\n", " \n", - " 18 \n", + " 19 \n", " Euclia ML model \n", " Euclia \n", " GitHub, Paper \n", @@ -1327,7 +2157,7 @@ "\n", "\n", "[11.106 9.994 12.848 9.292 9.373 9.445 10.075 10.194 9.185 9.942\n", - " 7.914 7.811 8.312]\n", + " 7.914 7.788 8.288]\n", "---- ppbr_az ------\n", "---- mae ------\n", " \n", @@ -1336,7 +2166,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 7.811 ± 0.163 \n", + " 7.788 ± 0.210 \n", "\n", " \n", " 2 \n", @@ -1352,7 +2182,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 8.312 ± 0.180 \n", + " 8.288 ± 0.173 \n", "\n", " \n", " 4 \n", @@ -1441,8 +2271,8 @@ "output_type": "stream", "text": [ "\n", - "[0.226 0.561 0.493 0.258 0.241 0.485 0.559 0.457 0.582 0.627 0.609 0.474\n", - " 0.394]\n", + "[0.226 0.561 0.493 0.258 0.241 0.485 0.559 0.457 0.582 0.627 0.609 0.491\n", + " 0.389]\n", "---- vdss_lombardo ------\n", "---- pcc ------\n", " \n", @@ -1495,6 +2325,14 @@ "\n", " \n", " 7 \n", + " Chemprop \n", + " Kyle Swanson \n", + " GitHub, Paper \n", + " N/A \n", + " 0.491 ± 0.046 \n", + "\n", + " \n", + " 8 \n", " ContextPred \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -1502,14 +2340,6 @@ " 0.485 ± 0.092 \n", "\n", " \n", - " 8 \n", - " Chemprop \n", - " Kyle Swanson \n", - " GitHub, Paper \n", - " N/A \n", - " 0.474 ± 0.048 \n", - "\n", - " \n", " 9 \n", " GCN \n", " Kexin Huang \n", @@ -1523,7 +2353,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.394 ± 0.076 \n", + " 0.389 ± 0.075 \n", "\n", " \n", " 11 \n", @@ -1551,7 +2381,7 @@ "\n", "\n", "[0.713 0.742 0.715 0.767 0.739 0.749 0.839 0.829 0.735 0.556 0.786 0.536\n", - " 0.75 0.78 ]\n", + " 0.754 0.777]\n", "---- cyp2c9_veith ------\n", "---- pr-auc ------\n", " \n", @@ -1584,7 +2414,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.780 ± 0.001 \n", + " 0.777 ± 0.003 \n", "\n", " \n", " 5 \n", @@ -1600,7 +2430,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.750 ± 0.004 \n", + " 0.754 ± 0.002 \n", "\n", " \n", " 7 \n", @@ -1673,8 +2503,8 @@ "output_type": "stream", "text": [ "\n", - "[0.544 0.616 0.587 0.627 0.646 0.739 0.721 0.616 0.358 0.644 0.348 0.645\n", - " 0.672]\n", + "[0.544 0.616 0.587 0.627 0.646 0.739 0.721 0.616 0.358 0.644 0.348 0.649\n", + " 0.673]\n", "---- cyp2d6_veith ------\n", "---- pr-auc ------\n", " \n", @@ -1699,10 +2529,18 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.672 ± 0.008 \n", + " 0.673 ± 0.007 \n", "\n", " \n", " 4 \n", + " Chemprop \n", + " Kyle Swanson \n", + " GitHub, Paper \n", + " N/A \n", + " 0.649 ± 0.016 \n", + "\n", + " \n", + " 5 \n", " AttentiveFP \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -1710,14 +2548,6 @@ " 0.646 ± 0.014 \n", "\n", " \n", - " 5 \n", - " Chemprop \n", - " Kyle Swanson \n", - " GitHub, Paper \n", - " N/A \n", - " 0.645 ± 0.018 \n", - "\n", - " \n", " 6 \n", " ZairaChem \n", " Gemma Turon \n", @@ -1783,7 +2613,7 @@ "\n", "\n", "[0.821 0.829 0.827 0.849 0.851 0.904 0.902 0.84 0.654 0.875 0.696 0.862\n", - " 0.874]\n", + " 0.876]\n", "---- cyp3a4_veith ------\n", "---- pr-auc ------\n", " \n", @@ -1804,19 +2634,19 @@ "\n", " \n", " 3 \n", - " ZairaChem \n", - " Gemma Turon \n", - " GitHub, Paper \n", + " Chemprop-RDKit \n", + " Kyle Swanson \n", + " GitHub, Paper \n", " N/A \n", - " 0.875 ± 0.002 \n", + " 0.876 ± 0.003 \n", "\n", " \n", " 4 \n", - " Chemprop-RDKit \n", - " Kyle Swanson \n", - " GitHub, Paper \n", + " ZairaChem \n", + " Gemma Turon \n", + " GitHub, Paper \n", " N/A \n", - " 0.874 ± 0.004 \n", + " 0.875 ± 0.002 \n", "\n", " \n", " 5 \n", @@ -1824,7 +2654,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.862 ± 0.004 \n", + " 0.862 ± 0.003 \n", "\n", " \n", " 6 \n", @@ -1898,7 +2728,7 @@ "text": [ "\n", "[0.367 0.36 0.38 0.359 0.375 0.392 0.381 0.344 0.433 0.281 0.437 0.441\n", - " 0.347 0.387 0.407]\n", + " 0.347 0.382 0.4 ]\n", "---- cyp2c9_substrate_carbonmangels ------\n", "---- pr-auc ------\n", " \n", @@ -1931,7 +2761,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.407 ± 0.020 \n", + " 0.400 ± 0.008 \n", "\n", " \n", " 5 \n", @@ -1947,7 +2777,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.387 ± 0.012 \n", + " 0.382 ± 0.019 \n", "\n", " \n", " 7 \n", @@ -2022,8 +2852,8 @@ " 0.281 ± 0.000 \n", "\n", "\n", - "[0.485 0.677 0.671 0.572 0.574 0.736 0.704 0.617 0.478 0.685 0.498 0.624\n", - " 0.684]\n", + "[0.485 0.677 0.671 0.572 0.574 0.736 0.704 0.617 0.478 0.685 0.498 0.632\n", + " 0.686]\n", "---- cyp2d6_substrate_carbonmangels ------\n", "---- pr-auc ------\n", " \n", @@ -2044,19 +2874,19 @@ "\n", " \n", " 3 \n", - " ZairaChem \n", - " Gemma Turon \n", - " GitHub, Paper \n", + " Chemprop-RDKit \n", + " Kyle Swanson \n", + " GitHub, Paper \n", " N/A \n", - " 0.685 ± 0.029 \n", + " 0.686 ± 0.031 \n", "\n", " \n", " 4 \n", - " Chemprop-RDKit \n", - " Kyle Swanson \n", - " GitHub, Paper \n", + " ZairaChem \n", + " Gemma Turon \n", + " GitHub, Paper \n", " N/A \n", - " 0.684 ± 0.029 \n", + " 0.685 ± 0.029 \n", "\n", " \n", " 5 \n", @@ -2080,7 +2910,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.624 ± 0.046 \n", + " 0.632 ± 0.037 \n", "\n", " \n", " 8 \n", @@ -2138,7 +2968,7 @@ "text": [ "\n", "[0.662 0.639 0.633 0.578 0.576 0.609 0.582 0.59 0.64 0.605 0.63 0.629\n", - " 0.594 0.618]\n", + " 0.596 0.619]\n", "---- cyp3a4_substrate_carbonmangels ------\n", "---- roc-auc ------\n", " \n", @@ -2195,7 +3025,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.618 ± 0.030 \n", + " 0.619 ± 0.030 \n", "\n", " \n", " 8 \n", @@ -2219,7 +3049,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.594 ± 0.021 \n", + " 0.596 ± 0.018 \n", "\n", " \n", " 11 \n", @@ -2255,7 +3085,7 @@ "\n", "\n", "[0.038 0.184 0.329 0.177 0.085 0.129 0.151 0.239 0.392 0.438 0.544 0.547\n", - " 0.284 0.234]\n", + " 0.265 0.239]\n", "---- half_life_obach ------\n", "---- pcc ------\n", " \n", @@ -2304,10 +3134,18 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.284 ± 0.016 \n", + " 0.265 ± 0.032 \n", "\n", " \n", " 7 \n", + " Chemprop-RDKit \n", + " Kyle Swanson \n", + " GitHub, Paper \n", + " N/A \n", + " 0.239 ± 0.019 \n", + "\n", + " \n", + " 8 \n", " GCN \n", " Kexin Huang \n", " GitHub, Paper \n", @@ -2315,14 +3153,6 @@ " 0.239 ± 0.100 \n", "\n", " \n", - " 8 \n", - " Chemprop-RDKit \n", - " Kyle Swanson \n", - " GitHub, Paper \n", - " N/A \n", - " 0.234 ± 0.019 \n", - "\n", - " \n", " 9 \n", " RDKit2D + MLP (DeepPurpose) \n", " Kexin Huang \n", @@ -2377,7 +3207,7 @@ "output_type": "stream", "text": [ "\n", - "[0.235 0.382 0.272 0.401 0.289 0.439 0.413 0.366 0.44 0.424 0.432 0.427]\n", + "[0.235 0.382 0.272 0.401 0.289 0.439 0.413 0.366 0.44 0.424 0.431 0.43 ]\n", "---- clearance_hepatocyte_az ------\n", "---- pcc ------\n", " \n", @@ -2402,7 +3232,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.432 ± 0.008 \n", + " 0.431 ± 0.006 \n", "\n", " \n", " 4 \n", @@ -2410,7 +3240,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.427 ± 0.021 \n", + " 0.430 ± 0.021 \n", "\n", " \n", " 5 \n", @@ -2495,7 +3325,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.599 ± 0.026 \n", + " 0.599 ± 0.025 \n", "\n", " \n", " 3 \n", @@ -2543,7 +3373,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.555 ± 0.021 \n", + " 0.555 ± 0.022 \n", "\n", " \n", " 9 \n", @@ -2601,7 +3431,7 @@ "text": [ "\n", "[0.675 0.678 0.649 0.667 0.678 0.669 0.685 0.649 0.622 0.588 0.636 0.646\n", - " 0.552 0.617 0.63 ]\n", + " 0.552 0.606 0.625]\n", "---- ld50_zhu ------\n", "---- mae ------\n", " \n", @@ -2626,7 +3456,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.617 ± 0.021 \n", + " 0.606 ± 0.024 \n", "\n", " \n", " 4 \n", @@ -2642,7 +3472,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.630 ± 0.018 \n", + " 0.625 ± 0.022 \n", "\n", " \n", " 6 \n", @@ -2726,7 +3556,7 @@ "\n", "\n", "[0.754 0.841 0.736 0.722 0.825 0.756 0.778 0.738 0.874 0.715 0.856 0.749\n", - " 0.721 0.839]\n", + " 0.721 0.84 ]\n", "---- herg ------\n", "---- roc-auc ------\n", " \n", @@ -2759,7 +3589,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.839 ± 0.007 \n", + " 0.840 ± 0.007 \n", "\n", " \n", " 5 \n", @@ -2831,7 +3661,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.721 ± 0.046 \n", + " 0.721 ± 0.045 \n", "\n", " \n", " 14 \n", @@ -2848,8 +3678,8 @@ "output_type": "stream", "text": [ "\n", - "[0.776 0.823 0.794 0.823 0.814 0.837 0.842 0.818 0.716 0.871 0.755 0.849\n", - " 0.851]\n", + "[0.776 0.823 0.794 0.823 0.814 0.837 0.842 0.818 0.716 0.871 0.755 0.842\n", + " 0.85 ]\n", "---- ames ------\n", "---- roc-auc ------\n", " \n", @@ -2866,7 +3696,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.851 ± 0.004 \n", + " 0.850 ± 0.004 \n", "\n", " \n", " 3 \n", @@ -2874,7 +3704,7 @@ " Kyle Swanson \n", " GitHub, Paper \n", " N/A \n", - " 0.849 ± 0.006 \n", + " 0.842 ± 0.014 \n", "\n", " \n", " 4 \n", @@ -3074,13 +3904,6 @@ " 0.700 ± 0.000 \n", "\n" ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n" - ] } ], "source": [ diff --git a/benchmark/admet_group/01caco2/index.html b/benchmark/admet_group/01caco2/index.html index 65f2e260..57d90faf 100644 --- a/benchmark/admet_group/01caco2/index.html +++ b/benchmark/admet_group/01caco2/index.html @@ -367,24 +367,24 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.328 ± 0.024 + 0.330 ± 0.024 6 - Chemprop - Kyle Swanson - GitHub, Paper - N/A - 0.340 ± 0.016 - - - 7 Euclia ML model Euclia GitHub, Paper 50 0.341 ± 0.004 + + 7 + Chemprop + Kyle Swanson + GitHub, Paper + N/A + 0.344 ± 0.015 + 8 RDKit2D + MLP (DeepPurpose) diff --git a/benchmark/admet_group/03pgp/index.html b/benchmark/admet_group/03pgp/index.html index 3929dbc6..8c4a0349 100644 --- a/benchmark/admet_group/03pgp/index.html +++ b/benchmark/admet_group/03pgp/index.html @@ -407,7 +407,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.883 ± 0.016 + 0.886 ± 0.016 11 @@ -423,7 +423,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.858 ± 0.036 + 0.860 ± 0.036 13 diff --git a/benchmark/admet_group/04bioav/index.html b/benchmark/admet_group/04bioav/index.html index 218bb73c..65483bfb 100644 --- a/benchmark/admet_group/04bioav/index.html +++ b/benchmark/admet_group/04bioav/index.html @@ -367,7 +367,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.668 ± 0.069 + 0.667 ± 0.068 6 @@ -403,20 +403,20 @@

Leaderboard

10 + Chemprop + Kyle Swanson + GitHub, Paper + N/A + 0.581 ± 0.024 + + + 11 Morgan + MLP (DeepPurpose) Kexin Huang GitHub, Paper 1,477,185 0.581 ± 0.086 - - 11 - Chemprop - Kyle Swanson - GitHub, Paper - N/A - 0.579 ± 0.023 - 12 AttrMasking diff --git a/benchmark/admet_group/05lipo/index.html b/benchmark/admet_group/05lipo/index.html index 2f98eba4..4863be8c 100644 --- a/benchmark/admet_group/05lipo/index.html +++ b/benchmark/admet_group/05lipo/index.html @@ -335,7 +335,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.466 ± 0.006 + 0.467 ± 0.006 2 @@ -343,7 +343,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.469 ± 0.005 + 0.470 ± 0.009 3 @@ -433,6 +433,7 @@

Leaderboard

226,625 0.743 ± 0.020 +

: The lower the better.

diff --git a/benchmark/admet_group/06aqsol/index.html b/benchmark/admet_group/06aqsol/index.html index b6ff72af..98befa93 100644 --- a/benchmark/admet_group/06aqsol/index.html +++ b/benchmark/admet_group/06aqsol/index.html @@ -335,7 +335,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.762 ± 0.020 + 0.761 ± 0.025 2 @@ -347,14 +347,6 @@

Leaderboard

3 - Chemprop - Kyle Swanson - GitHub, Paper - N/A - 0.818 ± 0.010 - - - 4 RDKit2D + MLP (DeepPurpose) Kexin Huang GitHub, Paper @@ -362,13 +354,21 @@

Leaderboard

0.827 ± 0.047 - 5 + 4 Basic ML Nilavo Boral GitHub, Paper N/A 0.828 ± 0.002 + + 5 + Chemprop + Kyle Swanson + GitHub, Paper + N/A + 0.829 ± 0.022 + 6 GCN diff --git a/benchmark/admet_group/07bbb/index.html b/benchmark/admet_group/07bbb/index.html index 459da91e..8785880c 100644 --- a/benchmark/admet_group/07bbb/index.html +++ b/benchmark/admet_group/07bbb/index.html @@ -334,24 +334,24 @@

Leaderboard

Lantern RADR Ensemble Rick Fontenot GitHub, Paper - 267,439 - 0.962 ± 0.003 + N/A + 0.915 ± 0.002 2 - Lantern RADR Logistic Regression + Lantern RADR Deep Neural Network Rick Fontenot GitHub, Paper - 456 - 0.956 ± 0.006 + N/A + 0.912 ± 0.003 3 - Lantern RADR Deep Neural Network - Rick Fontenot - GitHub, Paper - 266,881 - 0.949 ± 0.004 + ZairaChem + Gemma Turon + GitHub, Paper + N/A + 0.910 ± 0.024 4 @@ -359,18 +359,26 @@

Leaderboard

Rick Fontenot GitHub, Paper 319 - 0.928 ± 0.002 + 0.908 ± 0.002 5 - ZairaChem - Gemma Turon - GitHub, Paper - N/A - 0.910 ± 0.024 + Lantern RADR SVM + Rick Fontenot + GitHub, Paper + 241 + 0.905 ± 0.007 6 + Lantern RADR Logistic Regression + Rick Fontenot + GitHub, Paper + 456 + 0.903 ± 0.002 + + + 7 SimGCN Suman Kalyan Bera GitHub, Paper @@ -378,7 +386,7 @@

Leaderboard

0.901 ± 0.007 - 7 + 8 ContextPred Kexin Huang GitHub, Paper @@ -386,7 +394,7 @@

Leaderboard

0.897 ± 0.004 - 8 + 9 AttrMasking Kexin Huang GitHub, Paper @@ -394,7 +402,7 @@

Leaderboard

0.892 ± 0.012 - 9 + 10 RDKit2D + MLP (DeepPurpose) Kexin Huang GitHub, Paper @@ -402,15 +410,15 @@

Leaderboard

0.889 ± 0.016 - 10 + 11 Chemprop-RDKit Kyle Swanson GitHub, Paper N/A - 0.868 ± 0.027 + 0.869 ± 0.027 - 11 + 12 AttentiveFP Kexin Huang GitHub, Paper @@ -418,7 +426,7 @@

Leaderboard

0.855 ± 0.011 - 12 + 13 GCN Kexin Huang GitHub, Paper @@ -426,7 +434,7 @@

Leaderboard

0.842 ± 0.016 - 13 + 14 NeuralFP Kexin Huang GitHub, Paper @@ -434,7 +442,7 @@

Leaderboard

0.836 ± 0.009 - 14 + 15 Morgan + MLP (DeepPurpose) Kexin Huang GitHub, Paper @@ -442,15 +450,15 @@

Leaderboard

0.823 ± 0.015 - 15 + 16 Chemprop Kyle Swanson GitHub, Paper N/A - 0.820 ± 0.112 + 0.821 ± 0.112 - 16 + 17 Basic ML Nilavo Boral GitHub, Paper @@ -458,7 +466,7 @@

Leaderboard

0.811 ± 0.013 - 17 + 18 CNN (DeepPurpose) Kexin Huang GitHub, Paper @@ -466,7 +474,7 @@

Leaderboard

0.781 ± 0.030 - 18 + 19 Euclia ML model Euclia GitHub, Paper diff --git a/benchmark/admet_group/08ppbr/index.html b/benchmark/admet_group/08ppbr/index.html index fca6a7e1..51fff6cc 100644 --- a/benchmark/admet_group/08ppbr/index.html +++ b/benchmark/admet_group/08ppbr/index.html @@ -335,7 +335,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 7.811 ± 0.163 + 7.788 ± 0.210 2 @@ -351,7 +351,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 8.312 ± 0.180 + 8.288 ± 0.173 4 diff --git a/benchmark/admet_group/09vdss/index.html b/benchmark/admet_group/09vdss/index.html index fa8eb3f5..ebd5f0bd 100644 --- a/benchmark/admet_group/09vdss/index.html +++ b/benchmark/admet_group/09vdss/index.html @@ -379,20 +379,20 @@

Leaderboard

7 + Chemprop + Kyle Swanson + GitHub, Paper + N/A + 0.491 ± 0.046 + + + 8 ContextPred Kexin Huang GitHub, Paper 2,067,053 0.485 ± 0.092 - - 8 - Chemprop - Kyle Swanson - GitHub, Paper - N/A - 0.474 ± 0.048 - 9 GCN @@ -407,7 +407,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.394 ± 0.076 + 0.389 ± 0.075 11 diff --git a/benchmark/admet_group/10cyp2c9i/index.html b/benchmark/admet_group/10cyp2c9i/index.html index fd9c5185..6f278734 100644 --- a/benchmark/admet_group/10cyp2c9i/index.html +++ b/benchmark/admet_group/10cyp2c9i/index.html @@ -360,7 +360,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.780 ± 0.001 + 0.777 ± 0.003 5 @@ -376,7 +376,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.750 ± 0.004 + 0.754 ± 0.002 7 diff --git a/benchmark/admet_group/11cyp2d6i/index.html b/benchmark/admet_group/11cyp2d6i/index.html index 92845e99..49eab00b 100644 --- a/benchmark/admet_group/11cyp2d6i/index.html +++ b/benchmark/admet_group/11cyp2d6i/index.html @@ -351,24 +351,24 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.672 ± 0.008 + 0.673 ± 0.007 4 + Chemprop + Kyle Swanson + GitHub, Paper + N/A + 0.649 ± 0.016 + + + 5 AttentiveFP Kexin Huang GitHub, Paper 300,806 0.646 ± 0.014 - - 5 - Chemprop - Kyle Swanson - GitHub, Paper - N/A - 0.645 ± 0.018 - 6 ZairaChem @@ -433,7 +433,6 @@

Leaderboard

50 0.348 ± 0.004 -

: The lower the better.

diff --git a/benchmark/admet_group/12cyp3a4i/index.html b/benchmark/admet_group/12cyp3a4i/index.html index 11a14d12..9e072565 100644 --- a/benchmark/admet_group/12cyp3a4i/index.html +++ b/benchmark/admet_group/12cyp3a4i/index.html @@ -347,19 +347,19 @@

Leaderboard

3 - ZairaChem - Gemma Turon - GitHub, Paper + Chemprop-RDKit + Kyle Swanson + GitHub, Paper N/A - 0.875 ± 0.002 + 0.876 ± 0.003 4 - Chemprop-RDKit - Kyle Swanson - GitHub, Paper + ZairaChem + Gemma Turon + GitHub, Paper N/A - 0.874 ± 0.004 + 0.875 ± 0.002 5 @@ -367,7 +367,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.862 ± 0.004 + 0.862 ± 0.003 6 diff --git a/benchmark/admet_group/13cyp2c9s/index.html b/benchmark/admet_group/13cyp2c9s/index.html index 3fe27cf9..3a5658e2 100644 --- a/benchmark/admet_group/13cyp2c9s/index.html +++ b/benchmark/admet_group/13cyp2c9s/index.html @@ -359,7 +359,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.407 ± 0.020 + 0.400 ± 0.008 5 @@ -375,7 +375,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.387 ± 0.012 + 0.382 ± 0.019 7 diff --git a/benchmark/admet_group/14cyp2d6s/index.html b/benchmark/admet_group/14cyp2d6s/index.html index a8cfdfd8..2a771611 100644 --- a/benchmark/admet_group/14cyp2d6s/index.html +++ b/benchmark/admet_group/14cyp2d6s/index.html @@ -347,19 +347,19 @@

Leaderboard

3 - ZairaChem - Gemma Turon - GitHub, Paper + Chemprop-RDKit + Kyle Swanson + GitHub, Paper N/A - 0.685 ± 0.029 + 0.686 ± 0.031 4 - Chemprop-RDKit - Kyle Swanson - GitHub, Paper + ZairaChem + Gemma Turon + GitHub, Paper N/A - 0.684 ± 0.029 + 0.685 ± 0.029 5 @@ -383,7 +383,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.624 ± 0.046 + 0.632 ± 0.037 8 diff --git a/benchmark/admet_group/15cyp3a4s/index.html b/benchmark/admet_group/15cyp3a4s/index.html index bd5e3466..2523f294 100644 --- a/benchmark/admet_group/15cyp3a4s/index.html +++ b/benchmark/admet_group/15cyp3a4s/index.html @@ -383,7 +383,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.618 ± 0.030 + 0.619 ± 0.030 8 @@ -407,7 +407,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.594 ± 0.021 + 0.596 ± 0.018 11 diff --git a/benchmark/admet_group/16halflife/index.html b/benchmark/admet_group/16halflife/index.html index b471f20f..0ac74ade 100644 --- a/benchmark/admet_group/16halflife/index.html +++ b/benchmark/admet_group/16halflife/index.html @@ -329,7 +329,7 @@

Leaderboard

Spearman - + 1 Euclia ML model Euclia @@ -375,24 +375,24 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.284 ± 0.016 + 0.265 ± 0.032 7 + Chemprop-RDKit + Kyle Swanson + GitHub, Paper + N/A + 0.239 ± 0.019 + + + 8 GCN Kexin Huang GitHub, Paper 191,810 0.239 ± 0.100 - - 8 - Chemprop-RDKit - Kyle Swanson - GitHub, Paper - N/A - 0.234 ± 0.019 - 9 RDKit2D + MLP (DeepPurpose) diff --git a/benchmark/admet_group/17clhepa/index.html b/benchmark/admet_group/17clhepa/index.html index 8f216ca3..97445382 100644 --- a/benchmark/admet_group/17clhepa/index.html +++ b/benchmark/admet_group/17clhepa/index.html @@ -351,7 +351,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.432 ± 0.008 + 0.431 ± 0.006 4 @@ -359,7 +359,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.427 ± 0.021 + 0.430 ± 0.021 5 diff --git a/benchmark/admet_group/18clmicro/index.html b/benchmark/admet_group/18clmicro/index.html index 410609ab..50e03080 100644 --- a/benchmark/admet_group/18clmicro/index.html +++ b/benchmark/admet_group/18clmicro/index.html @@ -343,7 +343,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.599 ± 0.026 + 0.599 ± 0.025 3 @@ -391,7 +391,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.555 ± 0.021 + 0.555 ± 0.022 9 diff --git a/benchmark/admet_group/19ld50/index.html b/benchmark/admet_group/19ld50/index.html index 30dfbbbe..d3850ed8 100644 --- a/benchmark/admet_group/19ld50/index.html +++ b/benchmark/admet_group/19ld50/index.html @@ -351,7 +351,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.617 ± 0.021 + 0.606 ± 0.024 4 @@ -367,7 +367,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.630 ± 0.018 + 0.625 ± 0.022 6 diff --git a/benchmark/admet_group/20herg/index.html b/benchmark/admet_group/20herg/index.html index f4b72716..2f8eaad2 100644 --- a/benchmark/admet_group/20herg/index.html +++ b/benchmark/admet_group/20herg/index.html @@ -359,7 +359,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.839 ± 0.007 + 0.840 ± 0.007 5 @@ -431,7 +431,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.721 ± 0.046 + 0.721 ± 0.045 14 diff --git a/benchmark/admet_group/21ames/index.html b/benchmark/admet_group/21ames/index.html index a68c02e7..166290e2 100644 --- a/benchmark/admet_group/21ames/index.html +++ b/benchmark/admet_group/21ames/index.html @@ -343,7 +343,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.851 ± 0.004 + 0.850 ± 0.004 3 @@ -351,7 +351,7 @@

Leaderboard

Kyle Swanson GitHub, Paper N/A - 0.849 ± 0.006 + 0.842 ± 0.014 4 diff --git a/benchmark/admet_group/22dili/index.html b/benchmark/admet_group/22dili/index.html index 77410ac8..0c6443b7 100644 --- a/benchmark/admet_group/22dili/index.html +++ b/benchmark/admet_group/22dili/index.html @@ -441,7 +441,6 @@

Leaderboard

N/A 0.700 ± 0.000 -

: The higher the better.

diff --git a/feed.xml b/feed.xml index e0060a8a..079d1526 100644 --- a/feed.xml +++ b/feed.xml @@ -1,2 +1,2 @@ -Jekyll2023-07-10T22:55:51-07:00http://localhost:4000/feed.xmlTDCArtificial intelligence foundation for therapeutic science +Jekyll2023-10-01T10:47:18-07:00http://localhost:4000/feed.xmlTDCArtificial intelligence foundation for therapeutic science \ No newline at end of file