# PCEvo: Path-Consistent Molecular Representation via Virtual Evolutionary

arXiv: https://arxiv.org/abs/2601.19257 · HTML: https://mlsanity.com/paper/2601.19257/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 27 of its 59 references that are in the map.
- First posted on arXiv 27 Jan 2026.

## Builds on (most cited first, 27 of 27)

- [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)
- [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)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [Learning Local Equivariant Representations for Large-Scale Atomistic Dynamics](https://mlsanity.com/paper/2204.05249/) (2022)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [Rademacher Complexity for Adversarially Robust Generalization](https://mlsanity.com/paper/1810.11914/) (2018)
- [The Design Space of E(3)-Equivariant Atom-Centered Interatomic Potentials](https://mlsanity.com/paper/2205.06643/) (2022)
- [N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules](https://mlsanity.com/paper/1806.09206/) (2018)
- [Does GNN Pretraining Help Molecular Representation?](https://mlsanity.com/paper/2207.06010/) (2022)
- [MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction](https://mlsanity.com/paper/2406.12950/) (2024)
- [DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery](https://mlsanity.com/paper/2505.13940/) (2025)
- [Text-guided multi-property molecular optimization with a diffusion language model](https://mlsanity.com/paper/2410.13597/) (2024)
- [Collaborative Expert LLMs Guided Multi-Objective Molecular Optimization](https://mlsanity.com/paper/2503.03503/) (2025)
- [GraphCL: Graph-based Clustering for Semi-Supervised Medical Image Segmentation](https://mlsanity.com/paper/2411.13147/) (2024)
- [Antibody Design and Optimization with Multi-scale Equivariant Graph Diffusion Models for Accurate Complex Antigen Binding](https://mlsanity.com/paper/2506.20957/) (2025)
- [Can Molecular Evolution Mechanism Enhance Molecular Representation?](https://mlsanity.com/paper/2501.15799/) (2025)
- [Graph-structured Small Molecule Drug Discovery Through Deep Learning: Progress, Challenges, and Opportunities](https://mlsanity.com/paper/2502.08975/) (2025)
- [Bridging Molecular Graphs and Large Language Models](https://mlsanity.com/paper/2503.03135/) (2025)
- [Equivariant Masked Position Prediction for Efficient Molecular Representation](https://mlsanity.com/paper/2502.08209/) (2025)
- [Zero-Shot Learning with Subsequence Reordering Pretraining for Compound-Protein Interaction](https://mlsanity.com/paper/2507.20925/) (2025)

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

- [When Molecular Similarity Works: Property Cliffs Reveal Hidden Errors](https://mlsanity.com/paper/2605.17265/) (2026)

## Abstract (arXiv)

Molecular representation learning aims to learn vector embeddings that capture molecular structure and geometry, thereby enabling property prediction and downstream scientific applications. In many AI for science tasks, labeled data are expensive to obtain and therefore limited in availability. Under the few-shot setting, models trained with scarce supervision often learn brittle structure-property relationships, resulting in substantially higher prediction errors and reduced generalization to unseen molecules. To address this limitation, we propose PCEvo, a path-consistent representation method that learns from virtual paths through dynamic structural evolution. PCEvo enumerates multiple chemically feasible edit paths between retrieved similar molecular pairs under topological dependency constraints. It transforms the labels of the two molecules into stepwise supervision along each virtual evolutionary path. It introduces a path-consistency objective that enforces prediction invariance across alternative paths connecting the same two molecules. Comprehensive experiments on the QM9 and MoleculeNet datasets demonstrate that PCEvo substantially improves the few-shot generalization performance of baseline methods. The code is available at https://anonymous.4open.science/r/PCEvo-4BF2.