# Why Physics Still Matters: Improving Machine Learning Prediction of Material Properties with Phonon-Informed Datasets

arXiv: https://arxiv.org/abs/2511.15222 · HTML: https://mlsanity.com/paper/2511.15222/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 8 of its 48 references that are in the map.
- First posted on arXiv 19 Nov 2025.

## Builds on (most cited first, 8 of 8)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [A Survey of Large Language Models](https://mlsanity.com/paper/2303.18223/) (2023)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks](https://mlsanity.com/paper/1810.02244/) (2018)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [GraphFramEx: Towards Systematic Evaluation of Explainability Methods for Graph Neural Networks](https://mlsanity.com/paper/2206.09677/) (2022)
- [A practical guide to machine learning interatomic potentials -- Status and future](https://mlsanity.com/paper/2503.09814/) (2025)
- [Accurate Crystal Structure Prediction of New 2D Hybrid Organic Inorganic Perovskites](https://mlsanity.com/paper/2403.06955/) (2024)

## Abstract (arXiv)

Machine learning (ML) methods have become powerful tools for predicting material properties with near first-principles accuracy and vastly reduced computational cost. However, the performance of ML models critically depends on the quality, size, and diversity of the training dataset. In materials science, this dependence is particularly important for learning from low-symmetry atomistic configurations that capture thermal excitations, structural defects, and chemical disorder, features that are ubiquitous in real materials but underrepresented in most datasets. The absence of systematic strategies for generating representative training data may therefore limit the predictive power of ML models in technologically critical fields such as energy conversion and photonics. In this work, we assess the effectiveness of graph neural network (GNN) models trained on two fundamentally different types of datasets: one composed of randomly generated atomic configurations and another constructed using physically informed sampling based on lattice vibrations. As a case study, we address the challenging task of predicting electronic and mechanical properties of a prototypical family of optoelectronic materials under realistic finite-temperature conditions. We find that the phonons-informed model consistently outperforms the randomly trained counterpart, despite relying on fewer data points. Explainability analyses further reveal that high-performing models assign greater weight to chemically meaningful bonds that control property variations, underscoring the importance of physically guided data generation. Overall, this work demonstrates that larger datasets do not necessarily yield better GNN predictive models and introduces a simple and general strategy for efficiently constructing high-quality training data in materials informatics.