Yong Li

Can Rong, Jingtao Ding, Zhicheng Liu et al.

The Origin-Destination~(OD) networks provide an estimation of the flow of people from every region to others in the city, which is an important research topic in transportation, urban simulation, etc. Given structural regional urban features, generating the OD network has become increasingly appealing to many researchers from diverse domains. However, existing works are limited in independent generation of each OD pair, i.e., flow of people from one region to another, overlooking the relations within the overall network. In this paper, we instead propose to generate the OD network, and design a graph denoising diffusion method to learn the conditional joint probability distribution of the nodes and edges within the OD network given city characteristics at region level. To overcome the learning difficulty of the OD networks covering over thousands of regions, we decompose the original one-shot generative modeling of the diffusion model into two cascaded stages, corresponding to the generation of network topology and the weights of edges, respectively. To further reproduce important network properties contained in the city-wide OD network, we design an elaborated graph denoising network structure including a node property augmentation module and a graph transformer backbone. Empirical experiments on data collected in three large US cities have verified that our method can generate OD matrices for new cities with network statistics remarkably similar with the ground truth, further achieving superior outperformance over competitive baselines in terms of the generation realism.

Jiang Li, Yuan-Ting Li

Identifying protein-protein interactions (PPI) is crucial for gaining in-depth insights into numerous biological processes within cells and holds significant guiding value in areas such as drug development and disease treatment. Currently, most PPI prediction methods focus primarily on the study of protein sequences, neglecting the critical role of the internal structure of proteins. This paper proposes a novel PPI prediction method named MgslaPPI, which utilizes graph attention to mine protein structural information and enhances the expressive power of the protein encoder through multitask learning strategy. Specifically, we decompose the end-to-end PPI prediction process into two stages: amino acid residue reconstruction (A2RR) and protein interaction prediction (PIP). In the A2RR stage, we employ a graph attention-based residue reconstruction method to explore the internal relationships and features of proteins. In the PIP stage, in addition to the basic interaction prediction task, we introduce two auxiliary tasks, i.e., protein feature reconstruction (PFR) and masked interaction prediction (MIP). The PFR task aims to reconstruct the representation of proteins in the PIP stage, while the MIP task uses partially masked protein features for PPI prediction, with both working in concert to prompt MgslaPPI to capture more useful information. Experimental results demonstrate that MgslaPPI significantly outperforms existing state-of-the-art methods under various data partitioning schemes.