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Activation of methionine metabolism mediated by HNF4α confers ferroptosis resistance in hepatocellular carcinoma

Cell Death Discovery, Published online: 26 May 2026; doi:10.1038/s41420-026-03165-0

Activation of methionine metabolism mediated by HNF4α confers ferroptosis resistance in hepatocellular carcinoma

FDX1 as a predictive biomarker and therapeutic target for lymph node metastasis in gastric cancer

Clin Exp Med. 2026 May 10. doi: 10.1007/s10238-026-02160-0. Online ahead of print.

ABSTRACT

The prognostic values of cuproptosis-related genes (CRGs) in gastric cancer with lymph node metastasis (GCLM), especially in the tumor immune microenvironment (TIME), remain unclear. We analyzed the expression, mutation, immunity, drug sensitivity, and prognostic value of CRGs in GCLM using TCGA and GEO cohorts. Consensus clustering was performed to identify CRG subtypes, with differences characterized by multi-omics analysis. A CRG-based prognostic risk score and immune score were constructed for individualized assessment, and the role of CRGs was validated through in vitro and in vivo experiments. Consensus clustering revealed that CRGs were significantly enriched in biological processes related to mitosis and energy metabolism, as well as in immune-related and cancer-associated pathways. Four distinct CRG subtypes were identified, showing marked differences in expression profiles, prognosis, genetic alterations, TIME, and chemotherapeutic drug sensitivity. We developed an exploratory CRG-based prognostic risk score for preliminary individualized assessment, and the functional relevance of CRGs in GCLM was further validated through in vitro experiments. Among these, FDX1, LIAS, DLAT, MTF1, and GLS were identified as key determinants of overall survival in patients with GCLM, with FDX1 emerging as a potential independent prognostic factor. Notably, upregulation of FDX1 significantly suppressed lymph node metastasis of gastric cancer cells in a mouse popliteal lymph node metastasis model. Our data uncovers FDX1 might be a potential favorable prognostic factors in GCLM patients. These findings may improve our understanding of CRGs in GCLM and provide new in-sights for assessing prognosis and developing more effective treatment strategies.

PMID:42107026 | DOI:10.1007/s10238-026-02160-0

Molecular basis for methylation-sensitive editing by Cas9

Nature, Published online: 15 April 2026; doi:10.1038/s41586-026-10384-z

ThermoCas9, a genome-editing enzyme that is sensitive to the DNA methylation status of the target locus, is characterized and shows promise for targeting hypomethylated DNA regions in cancer cells.

Beyond Retrieval: Modeling Confidence Decay and Deterministic Agentic Platforms in Generative Engine Optimization

arXiv:2604.03656v1 Announce Type: new Abstract: Generative Engine Optimization (GEO) is rapidly reshaping digital marketing paradigms in the era of Large Language Models (LLMs). However, current GEO strategies predominantly rely on Retrieval-Augmented Generation (RAG), which inherently suffers from probabilistic hallucinations and the "zero-click" paradox, failing to establish sustainable commercial trust. In this paper, we systematically deconstruct the probabilistic flaws of existing RAG-based GEO and propose a paradigm shift towards deterministic multi-agent intent routing. First, we mathematically formulate Semantic Entropy Drift (SED) to model the dynamic decay of confidence curves in LLMs over continuous temporal and contextual perturbations. To rigorously quantify optimization value in black-box commercial engines, we introduce the Isomorphic Attribution Regression (IAR) model, leveraging a Multi-Agent System (MAS) probe with strict human-in-the-loop physical isolation to enforce hallucination penalties. Furthermore, we architect the Deterministic Agent Handoff (DAH) protocol, conceptualizing an Agentic Trust Brokerage (ATB) ecosystem where LLMs function solely as intent routers rather than final answer generators. We empirically validate this architecture using EasyNote, an industrial AI meeting minutes product by Yishu Technology. By routing the intent of "knowledge graph mapping on an infinite canvas" directly to its specialized proprietary agent via DAH, we demonstrate the reduction of vertical task hallucination rates to near zero. This work establishes a foundational theoretical framework for next-generation GEO and paves the way for a well-ordered, deterministic human-AI collaboration ecosystem.

InsTraj: Instructing Diffusion Models with Travel Intentions to Generate Real-world Trajectories

arXiv:2604.04106v1 Announce Type: new Abstract: The generation of realistic and controllable GPS trajectories is a fundamental task for applications in urban planning, mobility simulation, and privacy-preserving data sharing. However, existing methods face a two-fold challenge: they lack the deep semantic understanding to interpret complex user travel intent, and struggle to handle complex constraints while maintaining the realistic diversity inherent in human behavior. To resolve this, we introduce InsTraj, a novel framework that instructs diffusion models to generate high-fidelity trajectories directly from natural language descriptions. Specifically, InsTraj first utilizes a powerful large language model to decipher unstructured travel intentions formed in natural language, thereby creating rich semantic blueprints and bridging the representation gap between intentions and trajectories. Subsequently, we proposed a multimodal trajectory diffusion transformer that can integrate semantic guidance to generate high-fidelity and instruction-faithful trajectories that adhere to fine-grained user intent. Comprehensive experiments on real-world datasets demonstrate that InsTraj significantly outperforms state-of-the-art methods in generating trajectories that are realistic, diverse, and semantically faithful to the input instructions.

InferenceEvolve: Towards Automated Causal Effect Estimators through Self-Evolving AI

arXiv:2604.04274v1 Announce Type: new Abstract: Causal inference is central to scientific discovery, yet choosing appropriate methods remains challenging because of the complexity of both statistical methodology and real-world data. Inspired by the success of artificial intelligence in accelerating scientific discovery, we introduce InferenceEvolve, an evolutionary framework that uses large language models to discover and iteratively refine causal methods. Across widely used benchmarks, InferenceEvolve yields estimators that consistently outperform established baselines: against 58 human submissions in a recent community competition, our best evolved estimator lay on the Pareto frontier across two evaluation metrics. We also developed robust proxy objectives for settings without semi-synthetic outcomes, with competitive results. Analysis of the evolutionary trajectories shows that agents progressively discover sophisticated strategies tailored to unrevealed data-generating mechanisms. These findings suggest that language-model-guided evolution can optimize structured scientific programs such as causal inference, even when outcomes are only partially observed.

Domain-Contextualized Inference: A Computable Graph Architecture for Explicit-Domain Reasoning

arXiv:2604.04344v1 Announce Type: new Abstract: We establish a computation-substrate-agnostic inference architecture in which domain is an explicit first-class computational parameter. This produces domain-scoped pruning that reduces per-query search space from O(N) to O(N/K), substrate-independent execution over symbolic, neural, vector, and hybrid substrates, and transparent inference chains where every step carries its evaluative context. The contribution is architectural, not logical. We formalize the computational theory across five dimensions: a five-layer architecture; three domain computation modes including chain indexing, path traversal as Kleisli composition, and vector-guided computation as a substrate transition; a substrate-agnostic interface with three operations Query, Extend, Bridge; reliability conditions C1 to C4 with three failure mode classes; and validation through a PHQ-9 clinical reasoning case study. The computational theory including operational semantics, complexity bounds, monad structure, substrate transitions, and boundary conditions is the contribution of this paper.

APPA: Adaptive Preference Pluralistic Alignment for Fair Federated RLHF of LLMs

arXiv:2604.04261v1 Announce Type: cross Abstract: Aligning large language models (LLMs) with diverse human preferences requires pluralistic alignment, where a single model must respect the values of multiple distinct groups simultaneously. In federated reinforcement learning from human feedback (FedRLHF), these groups align a shared policy without centralizing preference data, which makes fair reward aggregation essential. Existing aggregation methods exhibit clear trade offs: average based aggregation systematically under aligns worst performing groups, while min aggregation prioritizes worst group performance at the cost of overall alignment. We propose APPA, an Adaptive Preference Pluralistic Alignment framework that dynamically reweights group level rewards based on historical alignment rewards. Our approach prioritizes under aligned groups without degrading well aligned ones, while requiring no access to raw preference data. Integrated into a proximal policy optimization (PPO) based FedRLHF pipeline and evaluated on GLOBALQA and OQA across three model families (Gemma 2 2B, Llama 3.2 3B, Qwen3 0.6B), APPA achieves strong fairness alignment trade offs, improving worst group alignment by up to 28% over average aggregation while maintaining higher overall alignment than min aggregation across most configurations.

Pathogenesis and immune regulation of rheumatoid arthritis-associated interstitial lung disease: from basic research to clinical implications

Front Immunol. 2026 Mar 13;17:1770348. doi: 10.3389/fimmu.2026.1770348. eCollection 2026.

ABSTRACT

Interstitial lung disease (ILD) is one of the most common extra-articular manifestations of rheumatoid arthritis (RA). Some patients with RA-ILD may develop progressive pulmonary fibrosis, leading to severe impairment of lung function and respiratory failure, which impacts quality of life and can even be life-threatening. This review identified genetic susceptibility, environmental factors, and immune dysregulation as key contributors to the etiology and pathogenesis of RA-ILD. We highlight that autoantibodies, adaptive immune abnormalities, and tertiary lymphoid organ formation significantly drive pulmonary inflammation and fibrosis, while pro-inflammatory cytokines and epithelial-mesenchymal transition (EMT) further contribute to lung tissue injury. Current treatment options, including glucocorticoids, immunosuppressants, and antifibrotic agents such as nintedanib and pirfenidone, are often limited by substantial side effects. Additionally, emerging therapies like JAK inhibitors, CAR-T cells, and the upcoming phosphodiesterase-4B inhibitor, nerandomilast, show promise, but no curative treatment exists to date. Future research could focus on multi-omics technologies and conducting multicenter clinical trials to establish therapeutic targets and advance precision medicine for RA-ILD.

PMID:41909710 | PMC:PMC13021622 | DOI:10.3389/fimmu.2026.1770348

Detecting Miscitation on the Scholarly Web through LLM-Augmented Text-Rich Graph Learning

arXiv:2603.12290v1 Announce Type: cross Abstract: Scholarly web is a vast network of knowledge connected by citations. However, this system is increasingly compromised by miscitation, where references do not support or even contradict the claims they are cited for. Current miscitation detection methods, which primarily rely on semantic similarity or network anomalies, struggle to capture the nuanced relationship between a citation's context and its place in the wider network. While large language models (LLMs) offer powerful capabilities in semantic reasoning for this task, their deployment is hindered by hallucination risks and high computational costs. In this work, we introduce LLM-Augmented Graph Learning-based Miscitation Detector (LAGMiD), a novel framework that leverages LLMs for deep semantic reasoning over citation graphs and distills this knowledge into graph neural networks (GNNs) for efficient and scalable miscitation detection. Specifically, LAGMiD introduces an evidence-chain reasoning mechanism, which uses chain-of-thought prompting, to perform multi-hop citation tracing and assess semantic fidelity. To reduce LLM inference costs, we design a knowledge distillation method aligning GNN embeddings with intermediate LLM reasoning states. A collaborative learning strategy further routes complex cases to the LLM while optimizing the GNN for structure-based generalization. Experiments on three real-world benchmarks show that LAGMiD achieves state-of-the-art miscitation detection with significantly reduced inference cost.

Towards AI Search Paradigm

arXiv:2506.17188v2 Announce Type: replace-cross Abstract: In this paper, we introduce the AI Search Paradigm, a comprehensive blueprint for next-generation search systems capable of emulating human information processing and decision-making. The paradigm employs a modular architecture of four LLM-powered agents (Master, Planner, Executor and Writer) that dynamically adapt to the full spectrum of information needs, from simple factual queries to complex multi-stage reasoning tasks. These agents collaborate dynamically through coordinated workflows to evaluate query complexity, decompose problems into executable plans, and orchestrate tool usage, task execution, and content synthesis. We systematically present key methodologies for realizing this paradigm, including task planning and tool integration, execution strategies, aligned and robust retrieval-augmented generation, and efficient LLM inference, spanning both algorithmic techniques and infrastructure-level optimizations. By providing an in-depth guide to these foundational components, this work aims to inform the development of trustworthy, adaptive, and scalable AI search systems.

LifeBench: A Benchmark for Long-Horizon Multi-Source Memory

arXiv:2603.03781v1 Announce Type: new Abstract: Long-term memory is fundamental for personalized agents capable of accumulating knowledge, reasoning over user experiences, and adapting across time. However, existing memory benchmarks primarily target declarative memory, specifically semantic and episodic types, where all information is explicitly presented in dialogues. In contrast, real-world actions are also governed by non-declarative memory, including habitual and procedural types, and need to be inferred from diverse digital traces. To bridge this gap, we introduce Lifebench, which features densely connected, long-horizon event simulation. It pushes AI agents beyond simple recall, requiring the integration of declarative and non-declarative memory reasoning across diverse and temporally extended contexts. Building such a benchmark presents two key challenges: ensuring data quality and scalability. We maintain data quality by employing real-world priors, including anonymized social surveys, map APIs, and holiday-integrated calendars, thus enforcing fidelity, diversity and behavioral rationality within the dataset. Towards scalability, we draw inspiration from cognitive science and structure events according to their partonomic hierarchy; enabling efficient parallel generation while maintaining global coherence. Performance results show that top-tier, state-of-the-art memory systems reach just 55.2\% accuracy, highlighting the inherent difficulty of long-horizon retrieval and multi-source integration within our proposed benchmark. The dataset and data synthesis code are available at https://github.com/1754955896/LifeBench.

Fairness Begins with State: Purifying Latent Preferences for Hierarchical Reinforcement Learning in Interactive Recommendation

arXiv:2603.03820v1 Announce Type: cross Abstract: Interactive recommender systems (IRS) are increasingly optimized with Reinforcement Learning (RL) to capture the sequential nature of user-system dynamics. However, existing fairness-aware methods often suffer from a fundamental oversight: they assume the observed user state is a faithful representation of true preferences. In reality, implicit feedback is contaminated by popularity-driven noise and exposure bias, creating a distorted state that misleads the RL agent. We argue that the persistent conflict between accuracy and fairness is not merely a reward-shaping issue, but a state estimation failure. In this work, we propose \textbf{DSRM-HRL}, a framework that reformulates fairness-aware recommendation as a latent state purification problem followed by decoupled hierarchical decision-making. We introduce a Denoising State Representation Module (DSRM) based on diffusion models to recover the low-entropy latent preference manifold from high-entropy, noisy interaction histories. Built upon this purified state, a Hierarchical Reinforcement Learning (HRL) agent is employed to decouple conflicting objectives: a high-level policy regulates long-term fairness trajectories, while a low-level policy optimizes short-term engagement under these dynamic constraints. Extensive experiments on high-fidelity simulators (KuaiRec, KuaiRand) demonstrate that DSRM-HRL effectively breaks the "rich-get-richer" feedback loop, achieving a superior Pareto frontier between recommendation utility and exposure equity.

REVISION:Reflective Intent Mining and Online Reasoning Auxiliary for E-commerce Visual Search System Optimization

arXiv:2510.22739v2 Announce Type: replace-cross Abstract: In Taobao e-commerce visual search, user behavior analysis reveals a large proportion of no-click requests, suggesting diverse and implicit user intents. These intents are expressed in various forms and are difficult to mine and discover, thereby leading to the limited adaptability and lag in platform strategies. This greatly restricts users' ability to express diverse intents and hinders the scalability of the visual search system. This mismatch between user implicit intent expression and system response defines the User-SearchSys Intent Discrepancy. To alleviate the issue, we propose a novel framework REVISION. This framework integrates offline reasoning mining with online decision-making and execution, enabling adaptive strategies to solve implicit user demands. In the offline stage, we construct a periodic pipeline to mine discrepancies from historical no-click requests. Leveraging large models, we analyze implicit intent factors and infer optimal suggestions by jointly reasoning over query and product metadata. These inferred suggestions serve as actionable insights for refining platform strategies. In the online stage, REVISION-R1-3B, trained on the curated offline data, performs holistic analysis over query images and associated historical products to generate optimization plans and adaptively schedule strategies across the search pipeline. Our framework offers a streamlined paradigm for integrating large models with traditional search systems, enabling end-to-end intelligent optimization across information aggregation and user interaction. Experimental results demonstrate that our approach improves the efficiency of implicit intent mining from large-scale search logs and significantly reduces the no-click rate.

Generalization of RLVR Using Causal Reasoning as a Testbed

arXiv:2512.20760v2 Announce Type: replace-cross Abstract: Reinforcement learning with verifiable rewards (RLVR) has emerged as a promising paradigm for post-training large language models (LLMs) on complex reasoning tasks. Yet, the conditions under which RLVR yields robust generalization remain underexplored. This paper provides an empirical study of RLVR generalization in the setting of probabilistic inference over causal graphical models. This setting offers two natural axes along which to examine generalization: (i) the level of the probabilistic query -- associational, interventional, or counterfactual -- and (ii) the structural complexity of the query, measured by the size of its relevant subgraph. We construct a dataset of causal graphs and queries spanning these difficulty axes and fine-tune Qwen-2.5-Instruct models using RLVR or supervised fine-tuning (SFT). We vary both the model scale (3B-32B) and the query level included in training. We find that RLVR yields stronger within-level and across-level generalization than SFT, but only for specific combinations of model size and training query level. Further analysis shows that RLVR's effectiveness depends on the model's initial reasoning competence. With sufficient initial competence, RLVR improves an LLM's marginalization strategy and reduces errors in intermediate probability calculations, producing substantial accuracy gains, particularly on more complex queries. These results show that RLVR can improve specific causal reasoning subskills, with its benefits emerging only when the model has sufficient initial competence. Our code and data is available at https://github.com/zhichul/rlcausal.

Social-JEPA: Emergent Geometric Isomorphism

arXiv:2603.02263v1 Announce Type: cross Abstract: World models compress rich sensory streams into compact latent codes that anticipate future observations. We let separate agents acquire such models from distinct viewpoints of the same environment without any parameter sharing or coordination. After training, their internal representations exhibit a striking emergent property: the two latent spaces are related by an approximate linear isometry, enabling transparent translation between them. This geometric consensus survives large viewpoint shifts and scant overlap in raw pixels. Leveraging the learned alignment, a classifier trained on one agent can be ported to the other with no additional gradient steps, while distillation-like migration accelerates later learning and markedly reduces total compute. The findings reveal that predictive learning objectives impose strong regularities on representation geometry, suggesting a lightweight path to interoperability among decentralized vision systems. The code is available at https://anonymous.4open.science/r/Social-JEPA-5C57.

Doxing via the Lens: Revealing Location-related Privacy Leakage on Multi-modal Large Reasoning Models

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.
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