ML Research Wiki / Benchmarks / Drug Discovery / Tox21

Tox21

Drug Discovery Benchmark

Performance Over Time

📊 Showing 10 results | 📏 Metric: AUC

Top Performing Models

Rank	Model	Paper	AUC	Date	Code
1	elEmBERT-V1	Structure to Property: Chemical Element Embeddings and a Deep Learning Approach for Accurate Prediction of Chemical Properties	0.96	2023-09-17	📦 dmamur/elembert
2	TrimNet + Perforated Backpropagation	Perforated Backpropagation: A Neuroscience Inspired Extension to Artificial Neural Networks	0.89	2025-01-29	📦 PerforatedAI/PerforatedAI-API
3	SSVAE with multiple SMILES	All SMILES Variational Autoencoder	0.87	2019-05-30	-
4	Ensemble predictor	ToxicBlend: Virtual Screening of Toxic Compounds with Ensemble Predictors	0.86	2018-06-12	-
5	GraphConv + dummy super node	Learning Graph-Level Representation for Drug Discovery	0.85	2017-09-12	📦 microljy/graph_level_drug_discovery 📦 ZJULearning/graph_level_drug_discovery
6	GraphConv	Convolutional Networks on Graphs for Learning Molecular Fingerprints	0.85	2015-09-30	📦 HIPS/neural-fingerprint 📦 debbiemarkslab/neural-fingerprint-theano 📦 nrel/m2p
7	SNN (SELU Network)	Self-Normalizing Neural Networks	0.85	2017-06-08	📦 bioinf-jku/SNNs 📦 MaximeVandegar/Papers-in-100-Lines-of-Code 📦 mshunshin/SegNetCMR
8	ContextPred	Strategies for Pre-training Graph Neural Networks	0.78	2019-05-29	📦 snap-stanford/pretrain-gnns 📦 snap-stanford/pretrain-gnns 📦 gnn4dr/DRKG
9	GIT-Mol(G+S)	GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text	0.76	2023-08-14	📦 ai-hpc-research-team/git-mol
10	RNN-DFS	Relational Pooling for Graph Representations	0.75	2019-03-06	📦 PurdueMINDS/RelationalPooling

All Papers (10)

Structure to Property: Chemical Element Embeddings and a Deep Learning Approach for Accurate Prediction of Chemical Properties

2023

elEmBERT-V1

dmamur/elembert

Perforated Backpropagation: A Neuroscience Inspired Extension to Artificial Neural Networks

2025

TrimNet + Perforated Backpropagation

PerforatedAI/PerforatedAI-API

All SMILES Variational Autoencoder

2019

SSVAE with multiple SMILES

ToxicBlend: Virtual Screening of Toxic Compounds with Ensemble Predictors

2018

Ensemble predictor

Learning Graph-Level Representation for Drug Discovery

2017

GraphConv + dummy super node

microljy/graph_level_drug_discovery ZJULearning/graph_level_drug_discovery

Convolutional Networks on Graphs for Learning Molecular Fingerprints

2015

GraphConv

HIPS/neural-fingerprint debbiemarkslab/neural-fingerprint-theano

Self-Normalizing Neural Networks

2017

SNN (SELU Network)

bioinf-jku/SNNs MaximeVandegar/Papers-in-100-Lines-of-Code

Strategies for Pre-training Graph Neural Networks

2019

ContextPred

snap-stanford/pretrain-gnns snap-stanford/pretrain-gnns

GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text

2023

GIT-Mol(G+S)

ai-hpc-research-team/git-mol

Relational Pooling for Graph Representations

2019

RNN-DFS

PurdueMINDS/RelationalPooling

Tox21

Performance Over Time

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Top Performing Models

All Papers (10)

Structure to Property: Chemical Element Embeddings and a Deep Learning Approach for Accurate Prediction of Chemical Properties

Perforated Backpropagation: A Neuroscience Inspired Extension to Artificial Neural Networks

All SMILES Variational Autoencoder

ToxicBlend: Virtual Screening of Toxic Compounds with Ensemble Predictors

Learning Graph-Level Representation for Drug Discovery

Convolutional Networks on Graphs for Learning Molecular Fingerprints

Self-Normalizing Neural Networks

Strategies for Pre-training Graph Neural Networks

GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text

Relational Pooling for Graph Representations

Model	Paper	AUC	Date
elEmBERT-V1	Structure to Property: Chemical Element Embedding…	0.96	2023-09-17
TrimNet + Perforated Backpropagation	Perforated Backpropagation: A Neuroscience Inspir…	0.89	2025-01-29
SSVAE with multiple SMILES	All SMILES Variational Autoencoder	0.87	2019-05-30
Ensemble predictor	ToxicBlend: Virtual Screening of Toxic Compounds …	0.86	2018-06-12
GraphConv + dummy super node	Learning Graph-Level Representation for Drug Disc…	0.85	2017-09-12
GraphConv	Convolutional Networks on Graphs for Learning Mol…	0.85	2015-09-30
SNN (SELU Network)	Self-Normalizing Neural Networks	0.85	2017-06-08
ContextPred	Strategies for Pre-training Graph Neural Networks	0.78	2019-05-29
GIT-Mol(G+S)	GIT-Mol: A Multi-modal Large Language Model for M…	0.76	2023-08-14
RNN-DFS	Relational Pooling for Graph Representations	0.75	2019-03-06