Xinming Zhang

Ji Shi, Chengxun Xie, Zhonghao Li et al.

The discovery of new molecules based on the original chemical molecule distributions is of great importance in medicine. The graph transformer, with its advantages of high performance and scalability compared to traditional graph networks, has been widely explored in recent research for applications of graph structures. However, current transformer-based graph decoders struggle to effectively utilize graph information, which limits their capacity to leverage only sequences of nodes rather than the complex topological structures of molecule graphs. This paper focuses on building a graph transformer-based framework for molecular generation, which we call \textbf{JTreeformer} as it transforms graph generation into junction tree generation. It combines GCN parallel with multi-head attention as the encoder. It integrates a directed acyclic GCN into a graph-based Transformer to serve as a decoder, which can iteratively synthesize the entire molecule by leveraging information from the partially constructed molecular structure at each step. In addition, a diffusion model is inserted in the latent space generated by the encoder, to enhance the efficiency and effectiveness of sampling further. The empirical results demonstrate that our novel framework outperforms existing molecule generation methods, thus offering a promising tool to advance drug discovery (https://anonymous.4open.science/r/JTreeformer-C74C).

Zhonghao Li, Ji Shi, Xinming Zhang et al.

Graph Transformers (GTs) have demonstrated superior performance compared to traditional message-passing graph neural networks in many studies, especially in processing graph data with long-range dependencies. However, GTs tend to suffer from weak inductive bias, overfitting and over-globalizing problems due to the dense attention. In this paper, we introduce SFi-attention, a novel attention mechanism designed to learn sparse pattern by minimizing an energy function based on network flows with l1-norm regularization, to relieve those issues caused by dense attention. Furthermore, SFi-Former is accordingly devised which can leverage the sparse attention pattern of SFi-attention to generate sparse network flows beyond adjacency matrix of graph data. Specifically, SFi-Former aggregates features selectively from other nodes through flexible adaptation of the sparse attention, leading to a more robust model. We validate our SFi-Former on various graph datasets, especially those graph data exhibiting long-range dependencies. Experimental results show that our SFi-Former obtains competitive performance on GNN Benchmark datasets and SOTA performance on LongRange Graph Benchmark (LRGB) datasets. Additionally, our model gives rise to smaller generalization gaps, which indicates that it is less prone to over-fitting. Click here for codes.

Xinming Zhang, Ling Ma

From the viewpoint of inverse problem, the optimization of drug release based on the multi-laminated drug controlled release devices has been regarded as the solution problem of the diffusion equation initial value inverse problem. In view of the ill-posedness of the corresponding inverse problem, a modified Tikhonov regularization method is proposed by constructing a new regularizing filter function based on the singular value theory of compact operator. The convergence and the optimal asymptotic order of the regularized solution are obtained. Then the classical Tikhonov regularization method and the modified Tikhonov regularization method are applied to the optimization problem of the initial drug concentration distribution. For three various desired release profiles (constant release, linear decrease release and linear increase followed by a constant release profiles), better results can be obtained by using the modified Tikhonov regularization method. The numerical results demonstrate that the modified Tikhonov regularization method not only has the optimal asymptotic order, but also is suitable for the optimization and design of multi-laminated drug controlled release devices.