# MUBen: Benchmarking the Uncertainty of Molecular Representation Models

arXiv: https://arxiv.org/abs/2306.10060 · HTML: https://mlsanity.com/paper/2306.10060/

## Key facts

- Cited by 11 papers in the map (data through 14 Oct 2026).
- Builds on 57 of its 102 references that are in the map.
- First posted on arXiv 14 Jun 2023.

## Builds on (most cited first, 30 of 57)

- [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)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [On Calibration of Modern Neural Networks](https://mlsanity.com/paper/1706.04599/) (2017)
- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [HuggingFace's Transformers: State-of-the-art Natural Language Processing](https://mlsanity.com/paper/1910.03771/) (2019)
- [Averaging Weights Leads to Wider Optima and Better Generalization](https://mlsanity.com/paper/1803.05407/) (2018)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [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)
- [Selective Classification for Deep Neural Networks](https://mlsanity.com/paper/1705.08500/) (2017)
- [Deep Bayesian Active Learning with Image Data](https://mlsanity.com/paper/1703.02910/) (2017)
- [A Gentle Introduction to Conformal Prediction and Distribution-Free Uncertainty Quantification](https://mlsanity.com/paper/2107.07511/) (2021)
- [Evidential Deep Learning to Quantify Classification Uncertainty](https://mlsanity.com/paper/1806.01768/) (2018)
- [A Survey of Uncertainty in Deep Neural Networks](https://mlsanity.com/paper/2107.03342/) (2021)
- [A Simple Baseline for Bayesian Uncertainty in Deep Learning](https://mlsanity.com/paper/1902.02476/) (2019)
- [Weight Uncertainty in Neural Networks](https://mlsanity.com/paper/1505.05424/) (2015)
- [Variational Dropout and the Local Reparameterization Trick](https://mlsanity.com/paper/1506.02557/) (2015)
- [Deep Ensembles: A Loss Landscape Perspective](https://mlsanity.com/paper/1912.02757/) (2019)
- [InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization](https://mlsanity.com/paper/1908.01000/) (2019)
- [Accurate Uncertainties for Deep Learning Using Calibrated Regression](https://mlsanity.com/paper/1807.00263/) (2018)
- [BatchEnsemble: An Alternative Approach to Efficient Ensemble and Lifelong Learning](https://mlsanity.com/paper/2002.06715/) (2020)

## Built on by (most cited first, 11 of 11)

- [Diffusion Models as Constrained Samplers for Optimization with Unknown Constraints](https://mlsanity.com/paper/2402.18012/) (2024)
- [Language Model Uncertainty Quantification with Attention Chain](https://mlsanity.com/paper/2503.19168/) (2025)
- [Kermut: Composite kernel regression for protein variant effects](https://mlsanity.com/paper/2407.00002/) (2024)
- [Towards Foundation-model-based Multiagent System to Accelerate AI for Social Impact](https://mlsanity.com/paper/2412.07880/) (2024)
- [Ensembles of Low-Rank Expert Adapters](https://mlsanity.com/paper/2502.00089/) (2025)
- [Composite Flow Matching for Reinforcement Learning with Shifted-Dynamics Data](https://mlsanity.com/paper/2505.23062/) (2025)
- [Robust Optimization with Diffusion Models for Green Security](https://mlsanity.com/paper/2503.05730/) (2025)
- [Asymmetric Duos: Sidekicks Improve Uncertainty](https://mlsanity.com/paper/2505.18636/) (2025)
- [Reliable OOD Virtual Screening with Extrapolatory Pseudo-Label Matching](https://mlsanity.com/paper/2406.01825/) (2024)
- [LLM-based Agent Simulation for Maternal Health Interventions: Uncertainty Estimation and Decision-focused Evaluation](https://mlsanity.com/paper/2503.22719/) (2025)
- [Two Birds with One Stone: Enhancing Uncertainty Quantification and Interpretability with Graph Functional Neural Process](https://mlsanity.com/paper/2508.17097/) (2025)

## Abstract (arXiv)

Large molecular representation models pre-trained on massive unlabeled data have shown great success in predicting molecular properties. However, these models may tend to overfit the fine-tuning data, resulting in over-confident predictions on test data that fall outside of the training distribution. To address this issue, uncertainty quantification (UQ) methods can be used to improve the models' calibration of predictions. Although many UQ approaches exist, not all of them lead to improved performance. While some studies have included UQ to improve molecular pre-trained models, the process of selecting suitable backbone and UQ methods for reliable molecular uncertainty estimation remains underexplored. To address this gap, we present MUBen, which evaluates different UQ methods for state-of-the-art backbone molecular representation models to investigate their capabilities. By fine-tuning various backbones using different molecular descriptors as inputs with UQ methods from different categories, we assess the influence of architectural decisions and training strategies. Our study offers insights for selecting UQ for backbone models, which can facilitate research on uncertainty-critical applications in fields such as materials science and drug discovery.