# Identifying Semantic Component for Robust Molecular Property Prediction

arXiv: https://arxiv.org/abs/2311.04837 · HTML: https://mlsanity.com/paper/2311.04837/

## Key facts

- Cited by 10 papers in the map (data through 14 Oct 2026).
- Builds on 57 of its 105 references that are in the map.
- First posted on arXiv 8 Nov 2023.

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

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Categorical Reparameterization with Gumbel-Softmax](https://mlsanity.com/paper/1611.01144/) (2016)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Relational inductive biases, deep learning, and graph networks](https://mlsanity.com/paper/1806.01261/) (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)
- [Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations](https://mlsanity.com/paper/1811.12359/) (2018)
- [Representation Learning on Graphs with Jumping Knowledge Networks](https://mlsanity.com/paper/1806.03536/) (2018)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [Variational Autoencoders and Nonlinear ICA: A Unifying Framework](https://mlsanity.com/paper/1907.04809/) (2019)
- [Towards Out-Of-Distribution Generalization: A Survey](https://mlsanity.com/paper/2108.13624/) (2021)
- [Self-Supervised Learning with Data Augmentations Provably Isolates Content from Style](https://mlsanity.com/paper/2106.04619/) (2021)
- [Nonlinear ICA Using Auxiliary Variables and Generalized Contrastive Learning](https://mlsanity.com/paper/1805.08651/) (2018)
- [Unsupervised Feature Extraction by Time-Contrastive Learning and Nonlinear ICA](https://mlsanity.com/paper/1605.06336/) (2016)
- [Variational Inference of Disentangled Latent Concepts from Unlabeled Observations](https://mlsanity.com/paper/1711.00848/) (2017)
- [Contrastive Learning Inverts the Data Generating Process](https://mlsanity.com/paper/2102.08850/) (2021)
- [Discovering Invariant Rationales for Graph Neural Networks](https://mlsanity.com/paper/2201.12872/) (2022)
- [Interpretable and Generalizable Graph Learning via Stochastic Attention Mechanism](https://mlsanity.com/paper/2201.12987/) (2022)
- [Motif-based Graph Self-Supervised Learning for Molecular Property Prediction](https://mlsanity.com/paper/2110.00987/) (2021)
- [Deep Stable Learning for Out-Of-Distribution Generalization](https://mlsanity.com/paper/2104.07876/) (2021)
- [3D Infomax improves GNNs for Molecular Property Prediction](https://mlsanity.com/paper/2110.04126/) (2021)
- [Learning Causally Invariant Representations for Out-of-Distribution Generalization on Graphs](https://mlsanity.com/paper/2202.05441/) (2022)
- [GOOD: A Graph Out-of-Distribution Benchmark](https://mlsanity.com/paper/2206.08452/) (2022)
- [Graph Information Bottleneck for Subgraph Recognition](https://mlsanity.com/paper/2010.05563/) (2020)

## Built on by (most cited first, 10 of 10)

- [On the Identification of Temporally Causal Representation with Instantaneous Dependence](https://mlsanity.com/paper/2405.15325/) (2024)
- [Empowering Graph Invariance Learning with Deep Spurious Infomax](https://mlsanity.com/paper/2407.11083/) (2024)
- [Towards Identifiability of Hierarchical Temporal Causal Representation Learning](https://mlsanity.com/paper/2510.18310/) (2025)
- [CausalGame: Benchmarking Causal Thinking of LLM Agents in Games](https://mlsanity.com/paper/2607.04293/) (2026)
- [From Orthogonality to Dependency: Learning Disentangled Representation for Multi-Modal Time-Series Sensing Signals](https://mlsanity.com/paper/2405.16083/) (2024)
- [Nonstationary Time Series Forecasting via Unknown Distribution Adaptation](https://mlsanity.com/paper/2402.12767/) (2024)
- [Online Time Series Forecasting with Theoretical Guarantees](https://mlsanity.com/paper/2510.18281/) (2025)
- [Time Series Domain Adaptation via Latent Invariant Causal Mechanism](https://mlsanity.com/paper/2502.16637/) (2025)
- [Causal View of Time Series Imputation: Some Identification Results on Missing Mechanism](https://mlsanity.com/paper/2505.07180/) (2025)
- [Hierarchical Action Learning for Weakly-Supervised Action Segmentation](https://mlsanity.com/paper/2602.24275/) (2026)

## Abstract (arXiv)

Although graph neural networks have achieved great success in the task of molecular property prediction in recent years, their generalization ability under out-of-distribution (OOD) settings is still under-explored. Different from existing methods that learn discriminative representations for prediction, we propose a generative model with semantic-components identifiability, named SCI. We demonstrate that the latent variables in this generative model can be explicitly identified into semantic-relevant (SR) and semantic-irrelevant (SI) components, which contributes to better OOD generalization by involving minimal change properties of causal mechanisms. Specifically, we first formulate the data generation process from the atom level to the molecular level, where the latent space is split into SI substructures, SR substructures, and SR atom variables. Sequentially, to reduce misidentification, we restrict the minimal changes of the SR atom variables and add a semantic latent substructure regularization to mitigate the variance of the SR substructure under augmented domain changes. Under mild assumptions, we prove the block-wise identifiability of the SR substructure and the comment-wise identifiability of SR atom variables. Experimental studies achieve state-of-the-art performance and show general improvement on 21 datasets in 3 mainstream benchmarks. Moreover, the visualization results of the proposed SCI method provide insightful case studies and explanations for the prediction results. The code is available at: https://github.com/DMIRLAB-Group/SCI.