Conghao Wang

Yi Hao Chan, Deepank Girish, Sukrit Gupta et al.

Graph neural networks (GNN) have emerged as a popular tool for modelling functional magnetic resonance imaging (fMRI) datasets. Many recent studies have reported significant improvements in disorder classification performance via more sophisticated GNN designs and highlighted salient features that could be potential biomarkers of the disorder. However, existing methods of evaluating their robustness are often limited to cross-referencing with existing literature, which is a subjective and inconsistent process. In this review, we provide an overview of how GNN and model explainability techniques (specifically, feature attributors) have been applied to fMRI datasets for disorder prediction tasks, with an emphasis on evaluating the robustness of potential biomarkers produced for psychiatric disorders. Then, 65 studies using GNNs that reported potential fMRI biomarkers for psychiatric disorders (attention-deficit hyperactivity disorder, autism spectrum disorder, major depressive disorder, schizophrenia) published before 9 October 2024 were identified from 2 online databases (Scopus, PubMed). We found that while most studies have performant models, salient features highlighted in these studies (as determined by feature attribution scores) vary greatly across studies on the same disorder. Reproducibility of biomarkers is only limited to a small subset at the level of regions and few transdiagnostic biomarkers were identified. To address these issues, we suggest establishing new standards that are based on objective evaluation metrics to determine the robustness of these potential biomarkers. We further highlight gaps in the existing literature and put together a prediction-attribution-evaluation framework that could set the foundations for future research on discovering robust biomarkers of psychiatric disorders via GNNs.

Conghao Wang, Jagath C. Rajapakse

De novo design of bioactive drug molecules with potential to treat desired biological targets is a profound task in the drug discovery process. Existing approaches tend to leverage the pocket structure of the target protein to condition the molecule generation. However, even the pocket area of the target protein may contain redundant information since not all atoms in the pocket is responsible for the interaction with the ligand. In this work, we propose PharmacoBridge, a phamacophore-guided de novo design approach to generate drug candidates inducing desired bioactivity via diffusion bridge. Our method adapts the diffusion bridge to effectively convert pharmacophore arrangements in the spatial space into molecular structures under the manner of SE(3)-equivariant transformation, providing sophisticated control over optimal biochemical feature arrangements on the generated molecules. PharmacoBridge is demonstrated to generate hit candidates that exhibit high binding affinity with potential protein targets.

Beihao Xia, Conghao Wang, Qinmu Peng et al.

It remains challenging to automatically predict the multi-agent trajectory due to multiple interactions including agent to agent interaction and scene to agent interaction. Although recent methods have achieved promising performance, most of them just consider spatial influence of the interactions and ignore the fact that temporal influence always accompanies spatial influence. Moreover, those methods based on scene information always require extra segmented scene images to generate multiple socially acceptable trajectories. To solve these limitations, we propose a novel model named spatial-temporal attentive network with spatial continuity (STAN-SC). First, spatial-temporal attention mechanism is presented to explore the most useful and important information. Second, we conduct a joint feature sequence based on the sequence and instant state information to make the generative trajectories keep spatial continuity. Experiments are performed on the two widely used ETH-UCY datasets and demonstrate that the proposed model achieves state-of-the-art prediction accuracy and handles more complex scenarios.