arXiv:2602. 17162v3 Announce Type: replace Abstract: Genomic Foundation Models (GFMs) typically rely on Masked Language Modeling (MLM) or Next-Token Prediction (NTP) to learn the "Laws of Nature".
arXiv:2607. 11374v1 Announce Type: new Abstract: Graph Foundation Models (GFMs) have emerged as a promising paradigm for learning transferable representations across diverse graph domains.
HyPE-GT introduces a framework that generates learnable hyperbolic positional encodings for Graph Transformers, enabling the capture of complex hierarchical relationships in graph-structured data. Unlike traditional Euclidean encodings, HyPE’s hyperbolic encodings can be selected to suit specific downstream tasks and help mitigate oversmoothing in deep Graph Neural Networks. Experiments on molecular benchmarks and large-scale Open Graph Benchmark datasets demonstrate improved performance, while additional tests on Coauthor and Copurchase networks confirm HyPE’s effectiveness in controlling oversmoothing.
Graph Foundation Models (GFMs) have emerged as a promising paradigm for learning transferable representations across diverse graph domains. Recent advancements in GFMs have been largely dominated by two paradigms: Graph Neural Network and Large Language Model (LLM) based methods.
arXiv:2509.24367v2 Announce Type: replace Abstract: Deepfake generators evolve rapidly, making exhaustive data collection and repeated retraining impractical. Unlike generic multi-task settings, deep...
The paper investigates how the choice of graph tokenization affects transformer expressivity. It analyzes three tokenization families—spectral, random‑walk, and adjacency—showing that each induces different depth requirements and that some tokenizations are inherently lossy or ill‑conditioned for certain tasks. The authors prove lower bounds and impossibility results for converting between tokenizations and validate these findings with experiments on synthetic and real‑world data.
arXiv:2607. 19083v1 Announce Type: new Abstract: Equivariant graph neural networks provide a powerful modeling language for three-dimensional scientific data, but their reuse is often limited by implementations tied to specific tasks, outputs, and training regimes.
arXiv:2606. 20382v1 Announce Type: new Abstract: MultiModal Federated Graph Learning (MM-FGL) offers a natural collaborative training paradigm, but its practical deployment is challenged by two granularities of modality imbalance.
arXiv:2608. 12906v1 Announce Type: cross Abstract: RNA-Protein Interactions (RPIs) are critical for regulating cellular functions.
arXiv:2606. 10461v1 Announce Type: cross Abstract: Text-attributed Graphs (TAGs) incorporate textual node attributes with graph structures to describe rich relational semantics.
JEPAMatch introduces a new semi‑supervised learning framework that replaces traditional output‑thresholding with explicit geometric shaping of latent representations. By combining the FlexMatch loss with a latent‑space regularization inspired by LeJEPA, the method encourages isotropic Gaussian structure in the embedding space, mitigating class imbalance and noisy pseudo‑labels. Experiments on CIFAR‑100, STL‑10, and Tiny‑ImageNet show consistent performance gains and faster convergence compared to existing FixMatch‑based baselines.
arXiv:2606. 16112v1 Announce Type: cross Abstract: Residual architectures are ubiquitous in deep learning, but they suffer from a subtle structural limitation: the norm of the residual stream can grow rapidly with depth.