Most discussions about Large Language Model (LLM) safety have focused on single-agent settings but multi-agent LLM systems now create novel adversarial risks because their behavior depends on communication between agents and decentralized reasoning. In this work, we innovatively focus on attacking pragmatic systems that have constrains such as limited token bandwidth, latency between message delivery, and defense mechanisms. We design a permutation-invariant adversarial attack that optimizes prompt distribution across latency and bandwidth-constraint network topologies to bypass distributed safety mechanisms within the system. Formulating the attack path as a problem of maximum-flow minimum-cost, coupled with the novel Permutation-Invariant Evasion Loss (PIEL), we leverage graph-based optimization to maximize attack success rate while minimizing detection risk. Evaluating across models including Llama, Mistral, Gemma, DeepSeek and other variants on various datasets like JailBreakBench and AdversarialBench, our method outperforms conventional attacks by up to 7×, exposing critical vulnerabilities in multi-agent systems. Moreover, we demonstrate that existing defenses, including variants of Llama-Guard and PromptGuard, fail to prohibit our attack, emphasizing the urgent need for multi-agent specific safety mechanisms.

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: 3.6\\% increase in drug response prediction correlation, 9.6\\% improvement in single-cell drug classification AUC, and 1.1\\% average gain in gene perturbation prediction accuracy.

Image mass cytometry (IMC) enables high-dimensional spatial profiling by combining mass cytometry’s analytical power with spatial distributions of cell phenotypes. Recent studies leverage large language models (LLMs) to extract cell states by translating gene or protein expression into biological context. However, existing single-cell LLMs face two major challenges: (1) Integration of spatial information—they struggle to generalize spatial coordinates and effectively encode spatial context as text, and (2) Treating each cell independently—they overlook cell-cell interactions, limiting their ability to capture biological relationships. To address these limitations, we propose Spatial2Sentence, a novel framework that integrates both single-cell expression and spatial information into natural language using a multi-sentence approach. Given an expression matrix and spatial coordinates, Spatial2Sentence constructs expression similarity and distance matrices, pairing spatially adjacent and expressionally similar cells as positive pairs while using distant and dissimilar cells as negatives. These multi-sentence representations are processed by LLMs, enabling them to learn cellular interactions in both expression and spatial contexts. Equipped with multi-task learning, Spatial2Sentence outperforms existing single-cell LLMs on preprocessed IMC datasets for diabetes and brain tumors, improving cell-type classification by 5.98% and clinical status prediction by 4.18% on the diabetes dataset while enhancing interpretability. The source code can be found here: https://github.com/UNITES-Lab/Spatial2Sentence.

Recent advancements in large language models (LLMs) have achieved promising performances across various applications. Nonetheless, the ongoing challenge of integrating long-tail knowledge continues to impede the seamless adoption of LLMs in specialized domains. In this work, we introduce DALK, a.k.a. Dynamic Co-Augmentation of LLMs and KG, to address this limitation and demonstrate its ability on studying Alzheimer’s Disease (AD), a specialized sub-field in biomedicine and a global health priority. With a synergized framework of LLM and KG mutually enhancing each other, we first leverage LLM to construct an evolving AD-specific knowledge graph (KG) sourced from AD-related scientific literature, and then we utilize a coarse-to-fine sampling method with a novel self-aware knowledge retrieval approach to select appropriate knowledge from the KG to augment LLM inference capabilities. The experimental results, conducted on our constructed AD question answering (ADQA) benchmark, underscore the efficacy of DALK. Additionally, we perform a series of detailed analyses that can offer valuable insights and guidelines for the emerging topic of mutually enhancing KG and LLM.