7 papers
Can Tabular In-Context Learners Generalize to Biomolecular Property Prediction?
Davy Guan, Lu Zhang, Asiri Wijesinghe +7
Predicting biomolecular properties from limited labeled data is a central bottleneck in protein engineering and small-molecule design. As strong pretrained encoders now supply rich…
Flowette: Flow Matching with Graphette Priors for Graph Generation
Asiri Wijesinghe, Sevvandi Kandanaarachchi, Daniel M. Steinberg +1
We study generative modeling of graphs with recurring subgraph motifs. We propose Flowette, a continuous flow matching framework that employs a graph neural network-based transform…
Invariant-Stratified Propagation for Expressive Graph Neural Networks
Asela Hevapathige, Ahad N. Zehmakan, Asiri Wijesinghe +1
Graph Neural Networks (GNNs) face fundamental limitations in expressivity and capturing structural heterogeneity. Standard message-passing architectures are constrained by the 1-di…
Amortized Active Generation of Pareto Sets
Daniel M. Steinberg, Asiri Wijesinghe, Rafael Oliveira +3
We introduce active generation of Pareto sets (A-GPS), a new framework for online discrete black-box multi-objective optimization (MOO). A-GPS learns a generative model of the Pare…
Beyond Fixed Depth: Adaptive Graph Neural Networks for Node Classification Under Varying Homophily
Asela Hevapathige, Asiri Wijesinghe, Ahad N. Zehmakan
Graph Neural Networks (GNNs) have achieved significant success in addressing node classification tasks. However, the effectiveness of traditional GNNs degrades on heterophilic grap…
Graph Neural Diffusion via Generalized Opinion Dynamics
Asela Hevapathige, Asiri Wijesinghe, Ahad N. Zehmakan
There has been a growing interest in developing diffusion-based Graph Neural Networks (GNNs), building on the connections between message passing mechanisms in GNNs and physical di…