# Uni-QSAR: an Auto-ML Tool for Molecular Property Prediction

arXiv: https://arxiv.org/abs/2304.12239 · HTML: https://mlsanity.com/paper/2304.12239/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 22 of its 73 references that are in the map.
- First posted on arXiv 24 Apr 2023.

## Builds on (most cited first, 22 of 22)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [data2vec: A General Framework for Self-supervised Learning in Speech, Vision and Language](https://mlsanity.com/paper/2202.03555/) (2022)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development](https://mlsanity.com/paper/2102.09548/) (2021)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [3D Infomax improves GNNs for Molecular Property Prediction](https://mlsanity.com/paper/2110.04126/) (2021)
- [Gradient Harmonized Single-stage Detector](https://mlsanity.com/paper/1811.05181/) (2018)
- [Molecular representation learning with language models and domain-relevant auxiliary tasks](https://mlsanity.com/paper/2011.13230/) (2020)
- [N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules](https://mlsanity.com/paper/1806.09206/) (2018)
- [Molecule Attention Transformer](https://mlsanity.com/paper/2002.08264/) (2020)
- [SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery](https://mlsanity.com/paper/1911.04738/) (2019)
- [KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction](https://mlsanity.com/paper/2206.03364/) (2022)

## Built on by (most cited first, 4 of 4)

- [Bohrium + SciMaster: Building the Infrastructure and Ecosystem for Agentic Science at Scale](https://mlsanity.com/paper/2512.20469/) (2025)
- [An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning](https://mlsanity.com/paper/2402.12714/) (2024)
- [Suiren-1.0 Technical Report: A Family of Molecular Foundation Models](https://mlsanity.com/paper/2603.21942/) (2026)
- [A Systematic Evaluation of Co-folding Model Representations for Small-Molecule Learning](https://mlsanity.com/paper/2602.13249/) (2026)

## Abstract (arXiv)

Recently deep learning based quantitative structure-activity relationship (QSAR) models has shown surpassing performance than traditional methods for property prediction tasks in drug discovery. However, most DL based QSAR models are restricted to limited labeled data to achieve better performance, and also are sensitive to model scale and hyper-parameters. In this paper, we propose Uni-QSAR, a powerful Auto-ML tool for molecule property prediction tasks. Uni-QSAR combines molecular representation learning (MRL) of 1D sequential tokens, 2D topology graphs, and 3D conformers with pretraining models to leverage rich representation from large-scale unlabeled data. Without any manual fine-tuning or model selection, Uni-QSAR outperforms SOTA in 21/22 tasks of the Therapeutic Data Commons (TDC) benchmark under designed parallel workflow, with an average performance improvement of 6.09%. Furthermore, we demonstrate the practical usefulness of Uni-QSAR in drug discovery domains.