Aleksandar Stanković

Aleksandar Stanković

We present FuseSampleAgg, a CUDA operator that fuses neighbor sampling and mean aggregation into a single pass for one and two hop GraphSAGE. By eliminating block materialization and extra kernel launches, FuseSampleAgg reduces memory traffic and overhead while preserving GraphSAGE mean semantics via saved index replay. Across the Reddit, ogbn-arxiv, and ogbn-products benchmarks (batch size 1024, automatic mixed precision enabled), we observe step time speedups up to 51x on ogbn-products, about 4x on Reddit with fanouts 10-10 and 15-10, and about 3.3x on ogbn-arxiv at larger fanouts, with peak GPU memory reductions up to 100x, 36x, and about 3.5x, respectively. The operator is deterministic, integrates with standard PyTorch optimizers, and ships with scripts that reproduce all tables and figures from CSV logs. Code and scripts are available at https://github.com/SV25-22/FuseSampleAgg.

Aleksandar Stanković, Dejan Lisica

We present reproducible, edge-aware baselines for ogbn-proteins in PyTorch Geometric (PyG). We study two system choices that dominate practice: (i) how 8-dimensional edge evidence is aggregated into node inputs, and (ii) how edges are used inside message passing. Our strongest baseline is GraphSAGE with sum-based edge-to-node features. We compare LayerNorm (LN), BatchNorm (BN), and a species-aware Conditional LayerNorm (CLN), and report compute cost (time, VRAM, parameters) together with accuracy (ROC-AUC) and decision quality. In our primary experimental setup (hidden size 512, 3 layers, 3 seeds), sum consistently beats mean and max; BN attains the best AUC, while CLN matches the AUC frontier with better thresholded F1. Finally, post-hoc per-label temperature scaling plus per-label thresholds substantially improves micro-F1 and expected calibration error (ECE) with negligible AUC change, and light label-correlation smoothing yields small additional gains. We release standardized artifacts and scripts used for all of the runs presented in the paper.