arXiv subjects

Layki Soon

Publications and source records attributed to Layki Soon.

4 recordsLinked to original sources

arXiv2026

VQ-SAD: Vector Quantized Structure Aware Diffusion For Molecule Generation

Many diffusion based molecule generation methods ignore the symbolic information of molecules and represent the atom and bond type as one hot representation. Methods based on Morgan fingerprints produce hash collisions and are hard to embed into a continuous space without information loss and random fingerprints correspond to no valid molecule. To circumvent this issue we use another paradigm and consider atom and bond codes as latent variables of VQ-VAE. We introduce VQ-SAD which first trains a VQ-VAE and uses the frozen pretrained VQ-VAE model and considers the codebooks for both atom and bond types as tokenizers for the downstream diffusion process. VQ-SAD is a neuro-symbolic model that utilizes both symbolic and neural structural information for a diffusion based model with learnable forward process. The large discrete code space provides a more balanced atom and bond types which enhances the denoising process. VQ-VAE slightly outperforms SOTA models for diffusion based molecule generation on QM9 and ZINC250k datasets.

cs.LG↗

arXiv2025

Are Graph Attention Networks Able to Model Structural Information?

Graph Attention Networks (GATs) have emerged as powerful models for learning expressive representations from such data by adaptively weighting neighboring nodes through attention mechanisms. However, most existing approaches primarily rely on node attributes and direct neighborhood connections, often overlooking rich structural patterns that capture higher-order topological information crucial for many real-world datasets. In this work, we present the Graph Structure Attention Network (GSAT), a novel extension of GAT that jointly integrates attribute-based and structure-based representations for more effective graph learning. GSAT incorporates structural features derived from anonymous random walks (ARWs) and graph kernels to encode local topological information, enabling attention mechanisms to adapt based on the underlying graph structure. This design enhances the model's ability to discern meaningful relational dependencies within complex data. Comprehensive experiments on standard graph classification and regression benchmarks demonstrate that GSAT achieves consistent improvements over state-of-the-art graph learning methods, highlighting the value of incorporating structural context for representation learning on graphs.

cs.LG↗

arXiv2025

LGRPool: Hierarchical Graph Pooling Via Local-Global Regularisation

Hierarchical graph pooling(HGP) are designed to consider the fact that conventional graph neural networks(GNN) are inherently flat and are also not multiscale. However, most HGP methods suffer not only from lack of considering global topology of the graph and focusing on the feature learning aspect, but also they do not align local and global features since graphs should inherently be analyzed in a multiscale way. LGRPool is proposed in the present paper as a HGP in the framework of expectation maximization in machine learning that aligns local and global aspects of message passing with each other using a regularizer to force the global topological information to be inline with the local message passing at different scales through the representations at different layers of HGP. Experimental results on some graph classification benchmarks show that it slightly outperforms some baselines.

cs.LG↗

arXiv2025

Attending To Syntactic Information In Biomedical Event Extraction Via Graph Neural Networks

Many models are proposed in the literature on biomedical event extraction(BEE). Some of them use the shortest dependency path(SDP) information to represent the argument classification task. There is an issue with this representation since even missing one word from the dependency parsing graph may totally change the final prediction. To this end, the full adjacency matrix of the dependency graph is used to embed individual tokens using a graph convolutional network(GCN). An ablation study is also done to show the effect of the dependency graph on the overall performance. The results show a significant improvement when dependency graph information is used. The proposed model slightly outperforms state-of-the-art models on BEE over different datasets.

cs.CL↗