# Recent advances in interpretable machine learning using structure-based protein representations

arXiv: https://arxiv.org/abs/2409.17726 · HTML: https://mlsanity.com/paper/2409.17726/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 37 of its 97 references that are in the map.
- First posted on arXiv 26 Sep 2024.

## Builds on (most cited first, 30 of 37)

- [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)
- [Grad-CAM: Visual Explanations from Deep Networks via Gradient-based Localization](https://mlsanity.com/paper/1610.02391/) (2016)
- [A Unified Approach to Interpreting Model Predictions](https://mlsanity.com/paper/1705.07874/) (2017)
- ["Why Should I Trust You?": Explaining the Predictions of Any Classifier](https://mlsanity.com/paper/1602.04938/) (2016)
- [Neural Machine Translation by Jointly Learning to Align and Translate](https://mlsanity.com/paper/1409.0473/) (2014)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Relational inductive biases, deep learning, and graph networks](https://mlsanity.com/paper/1806.01261/) (2018)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [Fooling LIME and SHAP: Adversarial Attacks on Post hoc Explanation Methods](https://mlsanity.com/paper/1911.02508/) (2019)
- [Explainability in Graph Neural Networks: A Taxonomic Survey](https://mlsanity.com/paper/2012.15445/) (2020)
- [Interpretable machine learning: definitions, methods, and applications](https://mlsanity.com/paper/1901.04592/) (2019)
- [On Explainability of Graph Neural Networks via Subgraph Explorations](https://mlsanity.com/paper/2102.05152/) (2021)
- [SE(3) diffusion model with application to protein backbone generation](https://mlsanity.com/paper/2302.02277/) (2023)
- [XGNN: Towards Model-Level Explanations of Graph Neural Networks](https://mlsanity.com/paper/2006.02587/) (2020)
- [CatBoost: gradient boosting with categorical features support](https://mlsanity.com/paper/1810.11363/) (2018)
- [A Survey of the State of Explainable AI for Natural Language Processing](https://mlsanity.com/paper/2010.00711/) (2020)
- [Interpretable and Generalizable Graph Learning via Stochastic Attention Mechanism](https://mlsanity.com/paper/2201.12987/) (2022)
- [Protein Representation Learning by Geometric Structure Pretraining](https://mlsanity.com/paper/2203.06125/) (2022)
- [ProGen2: Exploring the Boundaries of Protein Language Models](https://mlsanity.com/paper/2206.13517/) (2022)
- [Interpreting Graph Neural Networks for NLP With Differentiable Edge Masking](https://mlsanity.com/paper/2010.00577/) (2020)
- [Generative Causal Explanations for Graph Neural Networks](https://mlsanity.com/paper/2104.06643/) (2021)
- [Graph Information Bottleneck for Subgraph Recognition](https://mlsanity.com/paper/2010.05563/) (2020)
- [Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders](https://mlsanity.com/paper/2203.12742/) (2022)
- [The Dangers of Post-hoc Interpretability: Unjustified Counterfactual Explanations](https://mlsanity.com/paper/1907.09294/) (2019)
- [ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts](https://mlsanity.com/paper/2301.12040/) (2023)
- [Explaining a Series of Models by Propagating Shapley Values](https://mlsanity.com/paper/2105.00108/) (2021)

## Built on by (most cited first, 1 of 1)

- [Protein Large Language Models: A Comprehensive Survey](https://mlsanity.com/paper/2502.17504/) (2025)

## Abstract (arXiv)

Recent advancements in machine learning (ML) are transforming the field of structural biology. For example, AlphaFold, a groundbreaking neural network for protein structure prediction, has been widely adopted by researchers. The availability of easy-to-use interfaces and interpretable outcomes from the neural network architecture, such as the confidence scores used to color the predicted structures, have made AlphaFold accessible even to non-ML experts. In this paper, we present various methods for representing protein 3D structures from low- to high-resolution, and show how interpretable ML methods can support tasks such as predicting protein structures, protein function, and protein-protein interactions. This survey also emphasizes the significance of interpreting and visualizing ML-based inference for structure-based protein representations that enhance interpretability and knowledge discovery. Developing such interpretable approaches promises to further accelerate fields including drug development and protein design.