Victor Liang

Suwei Yang, Victor C. Liang, Kuldeep S. Meel

Inference and prediction of routes have become of interest over the past decade owing to a dramatic increase in package delivery and ride-sharing services. Given the underlying combinatorial structure and the incorporation of probabilities, route prediction involves techniques from both formal methods and machine learning. One promising approach for predicting routes uses decision diagrams that are augmented with probability values. However, the effectiveness of this approach depends on the size of the compiled decision diagrams. The scalability of the approach is limited owing to its empirical runtime and space complexity. In this work, our contributions are two-fold: first, we introduce a relaxed encoding that uses a linear number of variables with respect to the number of vertices in a road network graph to significantly reduce the size of resultant decision diagrams. Secondly, instead of a stepwise sampling procedure, we propose a single pass sampling-based route prediction. In our evaluations arising from a real-world road network, we demonstrate that the resulting system achieves around twice the quality of suggested routes while being an order of magnitude faster compared to state-of-the-art.

Yingxu Wang, Victor Liang, Nan Yin et al.

Classifying antimicrobial peptides(AMPs) from the vast array of peptides mined from metagenomic sequencing data is a significant approach to addressing the issue of antibiotic resistance. However, current AMP classification methods, primarily relying on sequence-based data, neglect the spatial structure of peptides, thereby limiting the accurate classification of AMPs. Additionally, the number of known AMPs is significantly lower than that of non-AMPs, leading to imbalanced datasets that reduce predictive accuracy for AMPs. To alleviate these two limitations, we first employ Omegafold to predict the three-dimensional spatial structures of AMPs and non-AMPs, constructing peptide graphs based on the amino acids' C$_α$ positions. Building upon this, we propose a novel classification model named Spatial GNN-based AMP Classifier (SGAC). Our SGAC model employs a graph encoder based on Graph Neural Networks (GNNs) to process peptide graphs, generating high-dimensional representations that capture essential features from the three-dimensional spatial structure of amino acids. Then, to address the inherent imbalanced datasets, SGAC first incorporates Weight-enhanced Contrastive Learning, which clusters similar peptides while ensuring separation between dissimilar ones, using weighted contributions to emphasize AMP-specific features. Furthermore, SGAC employs Weight-enhanced Pseudo-label Distillation to dynamically generate high-confidence pseudo labels for ambiguous peptides, further refining predictions and promoting balanced learning between AMPs and non-AMPs. Experiments on publicly available AMP and non-AMP datasets demonstrate that SGAC significantly outperforms traditional sequence-based methods and achieves state-of-the-art performance among graph-based models, validating its effectiveness in AMP classification.