Layki Soon

Farshad Noravesh, Reza Haffari, Layki Soon et al.

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.

Farshad Noravesh, Reza Haffari, Layki Soon et al.

Graph Neural Networks (GNNs) have emerged as a powerful tool for processing data represented in graph structures, achieving remarkable success across a wide range of applications. However, to further improve the performance on graph classification benchmarks, structural representation of each node that encodes rich local topological information in the neighbourhood of nodes is an important type of feature that is often overlooked in the modeling. The consequence of neglecting the structural information has resulted high number of layers to connect messages from distant nodes which by itself produces other problems such as oversmoothing. In the present paper, we leverage these structural information that are modeled by anonymous random walks (ARWs) and introduce graph structure attention network (GSAT) which is a generalization of graph attention network(GAT) to integrate the original attribute and the structural representation to enforce the model to automatically find patterns for attending to different edges in the node neighbourhood to enrich graph representation. Our experiments show GSAT slightly improves SOTA on some graph classification benchmarks.

Farshad Noravesh, Reza Haffari, Layki Soon et al.

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.

Farshad Noravesh, Reza Haffari, Ong Huey Fang et al.

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.