arXiv:2604.03630v1 Announce Type: new Abstract: Spatial transcriptomics (ST) enables gene expression mapping within anatomical context but remains costly and low-throughput. Hematoxylin and eosin (H\&E) staining offers rich morphology yet lacks molecular resolution. We present \textbf{\ours} (\textbf{S}patial \textbf{T}ranscriptomics and hist\textbf{O}logy \textbf{R}epresentation \textbf{M}odel), a foundation model trained on 1.2 million spatially resolved transcriptomic profiles with matched histology across 18 organs. Using a hierarchical architecture integrating morphological features, gene expression, and spatial context, STORM bridges imaging and omics through robust molecular--morphological representations. STORM enhances spatial domain discovery, producing biologically coherent tissue maps, and outperforms existing methods in predicting spatial gene expression from H\&E images across 11 tumor types. The model is platform-agnostic, performing consistently across Visium, Xenium, Visium HD, and CosMx. Applied to 23 independent cohorts comprising 7,245 patients, STORM significantly improves immunotherapy response prediction and prognostication over established biomarkers, providing a scalable framework for spatially informed discovery and clinical precision medicine.

arXiv:2604.03925v1 Announce Type: cross Abstract: Large language models struggle to accumulate evidence across multiple rounds of user interaction, failing to update their beliefs in a manner consistent with Bayesian inference. Existing solutions require fine-tuning on sensitive user interaction data, limiting their applicability in privacy-conscious settings. We propose AdaptFuse, a training-free framework that externalizes probabilistic computation entirely from the LLM: a symbolic module maintains a Bayesian posterior over a discrete hypothesis set, while a frozen LLM contributes semantic reasoning via multi-sample Dirichlet aggregation. The two signals are combined through entropy-adaptive fusion, which automatically weights each source by its predictive confidence, shifting reliance from the LLM to the symbolic posterior as evidence accumulates. We evaluate across three domains: flight recommendation, hotel recommendation, and web shopping; on Gemma 2 9B, Llama 3 8B, and Qwen 2.5 7B. AdaptFuse consistently outperforms both prompting baselines and fine-tuned Bayesian Teaching models on all tasks, with accuracy improving monotonically over interaction rounds. These results demonstrate that principled inference-time algorithms can substitute for fine-tuning in personalized recommendation, without storing or training on sensitive user data. All the code and materials will be open-sourced.

arXiv:2509.12626v3 Announce Type: replace-cross Abstract: Aligning agentic AI with user intent is critical for delegating complex, socially embedded tasks, yet user preferences are often implicit, evolving, and difficult to specify upfront. We present DoubleAgents, a system for human-agent alignment in coordination tasks, grounded in distributed cognition. DoubleAgents integrates three components: (1) a coordination agent that maintains state and proposes plans and actions, (2) a dashboard visualization that makes the agent's reasoning legible for user evaluation, and (3) a policy module that transforms user edits into reusable alignment artifacts, including coordination policies, email templates, and stop hooks, which improve system behavior over time. We evaluate DoubleAgents through a two-day lab study (n=10), three real-world deployments, and a technical evaluation. Participants' comfort in offloading tasks and reliance on DoubleAgents both increased over time, correlating with the three distributed cognition components. Participants still required control at points of uncertainty - edge-case flagging and context-dependent actions. We contribute a distributed cognition approach to human-agent alignment in socially embedded tasks.

arXiv:2406.09031v5 Announce Type: replace-cross Abstract: Graph pooling has gained attention for its ability to obtain effective node and graph representations for various downstream tasks. Despite the recent surge in graph pooling approaches, there is a lack of standardized experimental settings and fair benchmarks to evaluate their performance. To address this issue, we have constructed a comprehensive benchmark that includes 17 graph pooling methods and 28 different graph datasets. This benchmark systematically assesses the performance of graph pooling methods in three dimensions, i.e., effectiveness, robustness, and generalizability. We first evaluate the performance of these graph pooling approaches across different tasks including graph classification, graph regression and node classification. Then, we investigate their performance under potential noise attacks and out-of-distribution shifts in real-world scenarios. We also involve detailed efficiency analysis, backbone analysis, parameter analysis and visualization to provide more evidence. Extensive experiments validate the strong capability and applicability of graph pooling approaches in various scenarios, which can provide valuable insights and guidance for deep geometric learning research. The source code of our benchmark is available at https://github.com/goose315/Graph_Pooling_Benchmark.

arXiv:2603.22779v2 Announce Type: replace-cross Abstract: Large Language Models (LLMs) are equipped with profound semantic knowledge, making them a natural choice for injecting semantic generalization into personalized search systems. However, in practice we find that directly fine-tuning LLMs on industrial personalized tasks (e.g. next item prediction) often yields suboptimal results. We attribute this bottleneck to a critical Knowledge--Action Gap: the inherent conflict between preserving pre-trained semantic knowledge and aligning with specific personalized actions by discriminative objectives. Empirically, action-only training objectives induce Semantic Collapse, such as attention "sinks". This degradation severely cripples the LLM's generalization, failing to bring improvements to personalized search systems. We propose KARMA (Knowledge--Action Regularized Multimodal Alignment), a unified framework that treats semantic reconstruction as a train-only regularizer. KARMA optimizes a next-interest embedding for retrieval (Action) while enforcing semantic decodability (Knowledge) through two complementary objectives: (i) history-conditioned semantic generation, which anchors optimization to the LLM's native next-token distribution, and (ii) embedding-conditioned semantic reconstruction, which constrains the interest embedding to remain semantically recoverable. On Taobao search system, KARMA mitigates semantic collapse (attention-sink analysis) and improves both action metrics and semantic fidelity. In ablations, semantic decodability yields up to +22.5 HR@200. With KARMA, we achieve +0.25 CTR AUC in ranking, +1.86 HR in pre-ranking and +2.51 HR in recalling. Deployed online with low inference overhead at ranking & pre-ranking stage, KARMA drives +0.9% increase in GMV.

arXiv:2603.22978v1 Announce Type: new Abstract: In the maintenance of complex systems, fault trees are used to locate problems and provide targeted solutions. To enable fault trees stored as images to be directly processed by large language models, which can assist in tracking and analyzing malfunctions, we propose a novel textual representation of fault trees. Building on it, we construct a benchmark for multi-turn dialogue systems that emphasizes robust interaction in complex environments, evaluating a model's ability to assist in malfunction localization, which contains $3130$ entries and $40.75$ turns per entry on average. We train an end-to-end model to generate vague information to reflect user behavior and introduce long-range rollback and recovery procedures to simulate user error scenarios, enabling assessment of a model's integrated capabilities in task tracking and error recovery, and Gemini 2.5 pro archives the best performance.

arXiv:2603.22369v1 Announce Type: cross Abstract: Accurate prediction of synthetic lethality (SL) is important for guiding the development of cancer drugs and therapies. SL prediction faces significant challenges in the effective fusion of heterogeneous multi-source data. Existing multimodal methods often suffer from "modality laziness" due to disparate convergence speeds, which hinders the exploitation of complementary information. This is also one reason why most existing SL prediction models cannot perform well on both pan-cancer and single-cancer SL pair prediction. In this study, we propose SynLeaF, a dual-stage multimodal fusion framework for SL prediction across pan- and single-cancer contexts. The framework employs a VAE-based cross-encoder with a product of experts mechanism to fuse four omics data types (gene expression, mutation, methylation, and CNV), while simultaneously utilizing a relational graph convolutional network to capture structured gene representations from biomedical knowledge graphs. To mitigate modality laziness, SynLeaF introduces a dual-stage training mechanism employing featurelevel knowledge distillation with adaptive uni-modal teacher and ensemble strategies. In extensive experiments across eight specific cancer types and a pancancer dataset, SynLeaF achieves superior performance in 17 out of 19 scenarios. Ablation studies and gradient analyses further validate the critical contributions of the proposed fusion and distillation mechanisms to model robustness and generalization. To facilitate community use, a web server is available at https://synleaf.bioinformatics-lilab.cn.

arXiv:2603.22779v1 Announce Type: cross Abstract: Large Language Models (LLMs) are equipped with profound semantic knowledge, making them a natural choice for injecting semantic generalization into personalized search systems. However, in practice we find that directly fine-tuning LLMs on industrial personalized tasks (e.g. next item prediction) often yields suboptimal results. We attribute this bottleneck to a critical Knowledge--Action Gap: the inherent conflict between preserving pre-trained semantic knowledge and aligning with specific personalized actions by discriminative objectives. Empirically, action-only training objectives induce Semantic Collapse, such as attention ``sinks''. This degradation severely cripples the LLM's generalization, failing to bring improvements to personalized search systems. We propose KARMA (Knowledge--Action Regularized Multimodal Alignment), a unified framework that treats semantic reconstruction as a train-only regularizer. KARMA optimizes a next-interest embedding for retrieval (Action) while enforcing semantic decodability (Knowledge) through two complementary objectives: (i) history-conditioned semantic generation, which anchors optimization to the LLM's native next-token distribution, and (ii) embedding-conditioned semantic reconstruction, which constrains the interest embedding to remain semantically recoverable. On Taobao search system, KARMA mitigates semantic collapse (attention-sink analysis) and improves both action metrics and semantic fidelity. In ablations, semantic decodability yields up to +22.5 HR@200. With KARMA, we achieve +0.25 CTR AUC in ranking, +1.86 HR in pre-ranking and +2.51 HR in recalling. Deployed online with low inference overhead at ranking stage, KARMA drives +0.5% increase in Item Click.

arXiv:2603.01875v2 Announce Type: replace-cross Abstract: Knowledge distillation (KD) is an essential technique to compress large language models (LLMs) into smaller ones. However, despite the distinct roles of the student model and the teacher model in KD, most existing frameworks still use a homogeneous training backend (e.g., FSDP and DeepSpeed) for both models, leading to suboptimal training efficiency. In this paper, we present a novel framework for LLM distillation, termed \textbf{KDFlow}, which features a decoupled architecture and employs SGLang for teacher inference. By bridging the training efficiency of FSDP2 and the inference efficiency of SGLang, KDFlow achieves full utilization of both advantages in a unified system. Moreover, instead of transferring full logits across different processes, our framework only transmits the teacher's hidden states using zero-copy data transfer and recomputes the logits on the student side, effectively balancing the communication cost and KD performance. Furthermore, our framework supports both off-policy and on-policy distillation and incorporates KD algorithms for cross-tokenizer KD through highly extensible and user-friendly APIs. Experiments show that KDFlow can achieve \textbf{1.44$\times$ to 6.36$\times$} speedup compared to current KD frameworks, enabling researchers to rapidly prototype and scale LLM distillation with minimal engineering overhead. Code is available at: https://github.com/songmzhang/KDFlow

Nature, Published online: 25 March 2026; doi:10.1038/s41586-026-10258-4

Colonic stem cells retain a memory of inflammation following disease resolution and there is a mechanistic link between chronic inflammation and malignancy, suggesting potential strategies to mitigate cancer risk in patients with chronic inflammatory conditions.

arXiv:2603.12612v1 Announce Type: cross Abstract: Scaling Maximum Entropy Reinforcement Learning (RL) to high-dimensional humanoid control remains a formidable challenge, as the ``curse of dimensionality'' induces severe exploration inefficiency and training instability in expansive action spaces. Consequently, recent high-throughput paradigms have largely converged on deterministic policy gradients combined with massive parallel simulation. We challenge this compromise with FastDSAC, a framework that effectively unlocks the potential of maximum entropy stochastic policies for complex continuous control. We introduce Dimension-wise Entropy Modulation (DEM) to dynamically redistribute the exploration budget and enforce diversity, alongside a continuous distributional critic tailored to ensure value fidelity and mitigate high-dimensional value overestimation. Extensive evaluations on HumanoidBench and other continuous control tasks demonstrate that rigorously designed stochastic policies can consistently match or outperform deterministic baselines, achieving notable gains of 180\% and 400\% on the challenging \textit{Basketball} and \textit{Balance Hard} tasks.

arXiv:2603.06651v1 Announce Type: cross Abstract: Euclidean gradient descent algorithms barely capture the geometry of objective function-induced hypersurfaces and risk driving update trajectories off the hypersurfaces. Riemannian gradient descent algorithms address these issues but fail to represent complex hypersurfaces via a single classic manifold. We propose geodesic gradient descent (GGD), a generic and learning-rate-free Riemannian gradient descent algorithm. At each iteration, GGD uses an n-dimensional sphere to approximate a local neighborhood on the objective function-induced hypersurface, adapting to arbitrarily complex geometries. A tangent vector derived from the Euclidean gradient is projected onto the sphere to form a geodesic, ensuring the update trajectory stays on the hypersurface. Parameter updates are performed using the endpoint of the geodesic. The maximum step size of the gradient in GGD is equal to a quarter of the arc length on the n-dimensional sphere, thus eliminating the need for a learning rate. Experimental results show that compared with the classic Adam algorithm, GGD achieves test MSE reductions ranging from 35.79% to 48.76% for fully connected networks on the Burgers' dataset, and cross-entropy loss reductions ranging from 3.14% to 11.59% for convolutional neural networks on the MNIST dataset.

arXiv:2603.06859v1 Announce Type: cross Abstract: Cooperative multi-agent reinforcement learning (MARL) systems powered by large language models (LLMs) are frequently optimized via sparse terminal-only feedback. This shared signal entangles upstream decisions, obstructing accurate decision-level credit assignment. To address this trajectory-level diffusion, we introduce Contextual Counterfactual Credit Assignment (\textbf{\texttt{C3}}). Instead of distributing rewards across an entire episode, \textbf{\texttt{C3}} isolates the causal impact of individual messages by freezing the exact transcript-derived context, evaluating context-matched alternatives via fixed-continuation replay, and applying a leave-one-out (LOO) baseline. This localized intervention extracts unbiased, low-variance marginal advantages for standard policy-gradient optimization. Evaluated across five mathematical and coding benchmarks under matched budgets, \textbf{\texttt{C3}} improves terminal performance over established baselines. Mechanistic diagnostics further show that these gains are accompanied by higher credit fidelity, lower contextual variance, and stronger inter-agent causal dependence. Our code is available at https://github.com/EIT-EAST-Lab/C3.

arXiv:2510.05699v3 Announce Type: replace-cross Abstract: Membership inference attacks (MIAs) are widely used to assess the privacy risks associated with machine learning models. However, when these attacks are applied to pre-trained large language models (LLMs), they encounter significant challenges, including mislabeled samples, distribution shifts, and discrepancies in model size between experimental and real-world settings. To address these limitations, we introduce tokenizers as a new attack vector for membership inference. Specifically, a tokenizer converts raw text into tokens for LLMs. Unlike full models, tokenizers can be efficiently trained from scratch, thereby avoiding the aforementioned challenges. In addition, the tokenizer's training data is typically representative of the data used to pre-train LLMs. Despite these advantages, the potential of tokenizers as an attack vector remains unexplored. To this end, we present the first study on membership leakage through tokenizers and explore five attack methods to infer dataset membership. Extensive experiments on millions of Internet samples reveal the vulnerabilities in the tokenizers of state-of-the-art LLMs. To mitigate this emerging risk, we further propose an adaptive defense. Our findings highlight tokenizers as an overlooked yet critical privacy threat, underscoring the urgent need for privacy-preserving mechanisms specifically designed for them.

arXiv:2603.03331v1 Announce Type: cross Abstract: Photoplethysmography (PPG) is a widely used non-invasive sensing modality for continuous cardiovascular and physiological monitoring across clinical, laboratory, and wearable settings. While existing PPG datasets support a broad range of downstream tasks, they typically provide supervision in the form of numerical measurements or task-specific labels, limiting their suitability for language-based physiological reasoning and multimodal foundation models. In this work, we introduce PulseLM, a large-scale PPG-text dataset designed to bridge raw PPG waveforms and natural language through a unified, closed-ended question answering (QA) formulation. PulseLM aggregates PPG recordings from fifteen publicly available sources and harmonizes heterogeneous annotations into twelve common physiologically QA tasks. The dataset comprises 1.31 million standardized 10-second PPG segments, associated with 3.15 million question-answer pairs. We further define reproducible preprocessing, supervision, and evaluation protocols and establish baseline benchmarks using multimodal PPG-aware large language models. PulseLM provides a standardized foundation for studying multimodal physiological reasoning, cross-dataset generalization, and scalable benchmarking of PPG-based language models. The data and code can be found publicly available at: https://github.com/manhph2211/PulseLM.

arXiv:2603.02281v1 Announce Type: cross Abstract: Recent studies show that quantum neural networks (QNNs) generalize well in few-shot regimes. To extend this advantage to large-scale tasks, we propose Q-LoRA, a quantum-enhanced fine-tuning scheme that integrates lightweight QNNs into the low-rank adaptation (LoRA) adapter. Applied to AI-generated content (AIGC) detection, Q-LoRA consistently outperforms standard LoRA under few-shot settings. We analyze the source of this improvement and identify two possible structural inductive biases from QNNs: (i) phase-aware representations, which encode richer information across orthogonal amplitude-phase components, and (ii) norm-constrained transformations, which stabilize optimization via inherent orthogonality. However, Q-LoRA incurs non-trivial overhead due to quantum simulation. Motivated by our analysis, we further introduce H-LoRA, a fully classical variant that applies the Hilbert transform within the LoRA adapter to retain similar phase structure and constraints. Experiments on few-shot AIGC detection show that both Q-LoRA and H-LoRA outperform standard LoRA by over 5% accuracy, with H-LoRA achieving comparable accuracy at significantly lower cost in this task.

arXiv:2504.19373v5 Announce Type: replace-cross Abstract: Recent advances in multi-modal large reasoning models (MLRMs) have shown significant ability to interpret complex visual content. While these models enable impressive reasoning capabilities, they also introduce novel and underexplored privacy risks. In this paper, we identify a novel category of privacy leakage in MLRMs: Adversaries can infer sensitive geolocation information, such as a user's home address or neighborhood, from user-generated images, including selfies captured in private settings. To formalize and evaluate these risks, we propose a three-level visual privacy risk framework that categorizes image content based on contextual sensitivity and potential for location inference. We further introduce DoxBench, a curated dataset of 500 real-world images reflecting diverse privacy scenarios. Our evaluation across 11 advanced MLRMs and MLLMs demonstrates that these models consistently outperform non-expert humans in geolocation inference and can effectively leak location-related private information. This significantly lowers the barrier for adversaries to obtain users' sensitive geolocation information. We further analyze and identify two primary factors contributing to this vulnerability: (1) MLRMs exhibit strong reasoning capabilities by leveraging visual clues in combination with their internal world knowledge; and (2) MLRMs frequently rely on privacy-related visual clues for inference without any built-in mechanisms to suppress or avoid such usage. To better understand and demonstrate real-world attack feasibility, we propose GeoMiner, a collaborative attack framework that decomposes the prediction process into two stages: clue extraction and reasoning to improve geolocation performance while introducing a novel attack perspective. Our findings highlight the urgent need to reassess inference-time privacy risks in MLRMs to better protect users' sensitive information.

arXiv:2602.14010v1 Announce Type: cross Abstract: Pathology foundation models (PFMs) have enabled robust generalization in computational pathology through large-scale datasets and expansive architectures, but their substantial computational cost, particularly for gigapixel whole slide images, limits clinical accessibility and scalability. Here, we present LitePath, a deployment-friendly foundational framework designed to mitigate model over-parameterization and patch level redundancy. LitePath integrates LiteFM, a compact model distilled from three large PFMs (Virchow2, H-Optimus-1 and UNI2) using 190 million patches, and the Adaptive Patch Selector (APS), a lightweight component for task-specific patch selection. The framework reduces model parameters by 28x and lowers FLOPs by 403.5x relative to Virchow2, enabling deployment on low-power edge hardware such as the NVIDIA Jetson Orin Nano Super. On this device, LitePath processes 208 slides per hour, 104.5x faster than Virchow2, and consumes 0.36 kWh per 3,000 slides, 171x lower than Virchow2 on an RTX3090 GPU. We validated accuracy using 37 cohorts across four organs and 26 tasks (26 internal, 9 external, and 2 prospective), comprising 15,672 slides from 9,808 patients disjoint from the pretraining data. LitePath ranks second among 19 evaluated models and outperforms larger models including H-Optimus-1, mSTAR, UNI2 and GPFM, while retaining 99.71% of the AUC of Virchow2 on average. To quantify the balance between accuracy and efficiency, we propose the Deployability Score (D-Score), defined as the weighted geometric mean of normalized AUC and normalized FLOP, where LitePath achieves the highest value, surpassing Virchow2 by 10.64%. These results demonstrate that LitePath enables rapid, cost-effective and energy-efficient pathology image analysis on accessible hardware while maintaining accuracy comparable to state-of-the-art PFMs and reducing the carbon footprint of AI deployment.