arXiv:2603.06618v1 Announce Type: cross Abstract: Multiplex Biological Networks (MBNs), which represent multiple interaction types between entities, are crucial for understanding complex biological systems. Yet, existing methods often inadequately model multiplexity, struggle to integrate structural and sequence information, and face difficulties in zero-shot prediction for unseen entities with no prior neighbourhood information. To address these limitations, we propose a novel framework for zero-shot interaction prediction in MBNs by leveraging context-aware representation learning and knowledge distillation. Our approach leverages domain-specific foundation models to generate enriched embeddings, introduces a topology-aware graph tokenizer to capture multiplexity and higher-order connectivity, and employs contrastive learning to align embeddings across modalities. A teacher-student distillation strategy further enables robust zero-shot generalization. Experimental results demonstrate that our framework outperforms state-of-the-art methods in interaction prediction for MBNs, providing a powerful tool for exploring various biological interactions and advancing personalized therapeutics.

arXiv:2505.19371v2 Announce Type: replace Abstract: Top-$k$ decoding is a widely used method for sampling from LLMs: at each token, only the largest $k$ next-token-probabilities are kept, and the next token is sampled after re-normalizing them to sum to unity. Top-$k$ and other sampling methods are motivated by the intuition that true next-token distributions are sparse, and the noisy LLM probabilities need to be truncated. However, to our knowledge, a precise theoretical motivation for the use of top-$k$ decoding is missing. In this work, we develop a theoretical framework that both explains and generalizes top-$k$ decoding. We view decoding at a fixed token as the recovery of a sparse probability distribution. We consider \emph{Bregman decoders} obtained by minimizing a separable Bregman divergence (for both the \emph{primal} and \emph{dual} cases) with a sparsity-inducing $\ell_0$ regularization. Despite the combinatorial nature of the objective, we show how to optimize it efficiently for a large class of divergences. We show that the optimal decoding strategies are greedy, and further that the loss function is discretely convex in $k$, so that binary search provably and efficiently finds the optimal $k$. We show that top-$k$ decoding arises as a special case for the KL divergence, and identify new decoding strategies that have distinct behaviors (e.g., non-linearly up-weighting larger probabilities after re-normalization).