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A Genetically Engineered Human Organoid Model Reveals Distinct Genetic and Epigenetic Barriers of Lineage Plasticity in Early PDAC Transformation

bioRxiv [Preprint]. 2026 Mar 11:2026.03.09.710586. doi: 10.64898/2026.03.09.710586.

ABSTRACT

The lack of accurate, human-based models recapitulating early-stage pancreatic ductal adenocarcinoma (PDAC) has hindered therapeutic development. Using pluripotent stem cell-derived pancreatic progenitor organoids, we established a human PDAC model that faithfully reproduces the genetic, epigenetic, and transcriptomic trajectory of tumor initiation and progression in vitro , validated against clinical datasets and histopathology. We demonstrate that CDKN2A loss, nearly universal in patients but dispensable in mouse models, is essential for neoplastic transformation when combined with KRAS and TP53 mutations, while SMAD4 loss promotes tumor progression. Multi-omics profiling reveals epigenetic repression of pancreatic lineage program during PDAC initiation, alongside oncogenic AP-1-driven chromatin remodeling. Notably, we identify TET1 suppression as a mechanistic link between oncogenic ERK signaling and the hypermethylation and silencing of essential pancreatic transcription factors. This model captures the genetic and epigenetic determinants of human PDAC, reveals antagonism between oncogenic and lineage restriction programs, and supports TET-based lineage restoration as a promising early intervention strategy for high-risk individuals.

PMID:41959451 | PMC:PMC13060829 | DOI:10.64898/2026.03.09.710586

The importance of competition and facilitation for global tree diversity

Nature, Published online: 08 April 2026; doi:10.1038/s41586-026-10349-2

Across 17 forest plots (2.7 million trees, 5,400 species), competition dominated overall, but facilitation was relatively stronger near the equator and declined towards higher latitudes, partly linked to temperature, legumes, mycorrhizal associations and canopy nursing effect.

TableVision: A Large-Scale Benchmark for Spatially Grounded Reasoning over Complex Hierarchical Tables

arXiv:2604.03660v1 Announce Type: new Abstract: Structured tables are essential for conveying high-density information in professional domains such as finance, healthcare, and scientific research. Despite the progress in Multimodal Large Language Models (MLLMs), reasoning performance remains limited for complex tables with hierarchical layouts. In this paper, we identify a critical Perception Bottleneck through quantitative analysis. We find that as task complexity scales, the number of involved discrete visual regions increases disproportionately. This processing density leads to an internal "Perceptual Overload," where MLLMs struggle to maintain accurate spatial attention during implicit generation. To address this bottleneck, we introduce TableVision, a large-scale, trajectory-aware benchmark designed for spatially grounded reasoning. TableVision stratifies tabular tasks into three cognitive levels (Perception, Reasoning, and Analysis) across 13 sub-categories. By utilizing a rendering-based deterministic grounding pipeline, the dataset explicitly couples multi-step logical deductions with pixel-perfect spatial ground truths, comprising 6,799 high-fidelity reasoning trajectories. Our empirical results, supported by diagnostic probing, demonstrate that explicit spatial constraints significantly recover the reasoning potential of MLLMs. Furthermore, our two-stage decoupled framework achieves a robust 12.3% overall accuracy improvement on the test set. TableVision provides a rigorous testbed and a fresh perspective on the synergy between perception and logic in document understanding.

XAttnRes: Cross-Stage Attention Residuals for Medical Image Segmentation

arXiv:2604.03297v1 Announce Type: cross Abstract: In the field of Large Language Models (LLMs), Attention Residuals have recently demonstrated that learned, selective aggregation over all preceding layer outputs can outperform fixed residual connections. We propose Cross-Stage Attention Residuals (XAttnRes), a mechanism that maintains a global feature history pool accumulating both encoder and decoder stage outputs. Through lightweight pseudo-query attention, each stage selectively aggregates from all preceding representations. To bridge the gap between the same-dimensional Transformer layers in LLMs and the multi-scale encoder-decoder stages in segmentation networks, XAttnRes introduces spatial alignment and channel projection steps that handle cross-resolution features with negligible overhead. When added to existing segmentation networks, XAttnRes consistently improves performance across four datasets and three imaging modalities. We further observe that XAttnRes alone, even without skip connections, achieves performance on par with the baseline, suggesting that learned aggregation can recover the inter-stage information flow traditionally provided by predetermined connections.

CoopGuard: Stateful Cooperative Agents Safeguarding LLMs Against Evolving Multi-Round Attacks

arXiv:2604.04060v1 Announce Type: cross Abstract: As Large Language Models (LLMs) are increasingly deployed in complex applications, their vulnerability to adversarial attacks raises urgent safety concerns, especially those evolving over multi-round interactions. Existing defenses are largely reactive and struggle to adapt as adversaries refine strategies across rounds. In this work, we propose CoopGuard , a stateful multi-round LLM defense framework based on cooperative agents that maintains and updates an internal defense state to counter evolving attacks. It employs three specialized agents (Deferring Agent, Tempting Agent, and Forensic Agent) for complementary round-level strategies, coordinated by System Agent, which conditions decisions on the evolving defense state (interaction history) and orchestrates agents over time. To evaluate evolving threats, we introduce the EMRA benchmark with 5,200 adversarial samples across 8 attack types, simulating progressively LLM multi-round attacks. Experiments show that CoopGuard reduces attack success rate by 78.9% over state-of-the-art defenses, while improving deceptive rate by 186% and reducing attack efficiency by 167.9%, offering a more comprehensive assessment of multi-round defense. These results demonstrate that CoopGuard provides robust protection for LLMs in multi-round adversarial scenarios.

PRISM: Prompt-Refined In-Context System Modelling for Financial Retrieval

arXiv:2511.14130v2 Announce Type: replace Abstract: With the rapid progress of large language models (LLMs), financial information retrieval has become a critical industrial application. Extracting task-relevant information from lengthy financial filings is essential for both operational and analytical decision-making. We present PRISM, a training-free framework that integrates refined system prompting, in-context learning (ICL), and lightweight multi-agent coordination for document and chunk ranking tasks. Our primary contribution is a systematic empirical study of when each component provides value: prompt engineering delivers consistent performance with minimal overhead, ICL enhances reasoning for complex queries when applied selectively, and multi-agent systems show potential primarily with larger models and careful architectural design. Extensive ablation studies across FinAgentBench, FiQA-2018, and FinanceBench reveal that simpler configurations often outperform complex multi-agent pipelines, providing practical guidance for practitioners. Our best configuration achieves an NDCG@5 of 0.71818 on FinAgentBench, ranking third while being the only training-free approach in the top three. We provide comprehensive feasibility analyses covering latency, token usage, and cost trade-offs to support deployment decisions. The source code is released at https://bit.ly/prism-ailens.

Certified Training with Branch-and-Bound for Lyapunov-stable Neural Control

arXiv:2411.18235v3 Announce Type: replace-cross Abstract: We study the problem of learning verifiably Lyapunov-stable neural controllers that provably satisfy the Lyapunov asymptotic stability condition within a region-of-attraction (ROA). Unlike previous works that adopted counterexample-guided training without considering the computation of verification in training, we introduce Certified Training with Branch-and-Bound (CT-BaB), a new certified training framework that optimizes certified bounds, thereby reducing the discrepancy between training and test-time verification that also computes certified bounds. To achieve a relatively global guarantee on an entire input region-of-interest, we propose a training-time BaB technique that maintains a dynamic training dataset and adaptively splits hard input subregions into smaller ones, to tighten certified bounds and ease the training. Meanwhile, subregions created by the training-time BaB also inform test-time verification, for a more efficient training-aware verification. We demonstrate that CT-BaB yields verification-friendly models that can be more efficiently verified at test time while achieving stronger verifiable guarantees with larger ROA. On the largest output-feedback 2D Quadrotor system experimented, CT-BaB reduces verification time by over 11X relative to the previous state-of-the-art baseline using Counterexample Guided Inductive Synthesis (CEGIS), while achieving 164X larger ROA. Code is available at https://github.com/shizhouxing/CT-BaB.

AI-BAAM: AI-Driven Bank Statement Analytics as Alternative Data for Malaysian MSME Credit Scoring

arXiv:2510.16066v4 Announce Type: replace-cross Abstract: Despite accounting for 96.1% of all businesses in Malaysia, access to financing remains one of the most persistent challenges faced by Micro, Small, and Medium Enterprises (MSMEs). Newly established businesses are often excluded from formal credit markets as traditional underwriting approaches rely heavily on credit bureau data. This study investigates the potential of bank statement data as an alternative data source for credit assessment to promote financial inclusion in emerging markets. First, we propose a cash flow-based underwriting pipeline where we utilize bank statement data for end-to-end data extraction and machine learning credit scoring. Second, we introduce a novel dataset of 611 loan applicants from a Malaysian consulting firm. Third, we develop and evaluate credit scoring models based on application information and bank transaction-derived features. Empirical results demonstrate that incorporating bank statement features yields substantial improvements, with our best model achieving an AUROC of 0.806 on validation set, representing a 24.6% improvement over models using application information only. Finally, we will release the anonymized bank transaction dataset to facilitate further research on MSME financial inclusion within Malaysia's emerging economy.

Rewriting Video: Text-Driven Reauthoring of Video Footage

arXiv:2601.08565v2 Announce Type: replace-cross Abstract: Video is a powerful medium for communication and storytelling, yet reauthoring existing footage remains challenging. Even simple edits often demand expertise, time, and careful planning, constraining how creators envision and shape their narratives. Recent advances in generative AI suggest a new paradigm: what if editing a video were as straightforward as rewriting text? To investigate this, we present a tech probe and a study on text-driven video reauthoring. Our approach involves two technical contributions: (1) a generative reconstruction algorithm that reverse-engineers video into an editable text prompt, and (2) an interactive probe, Rewrite Kit, that allows creators to manipulate these prompts. A technical evaluation of the algorithm reveals a critical human-AI perceptual gap. A probe study with 12 creators surfaced novel use cases such as virtual reshooting, synthetic continuity, and aesthetic restyling. It also highlighted key tensions around coherence, control, and creative alignment in this new paradigm. Our work contributes empirical insights into the opportunities and challenges of text-driven video reauthoring, offering design implications for future co-creative video tools.

Vision-as-Inverse-Graphics Agent via Interleaved Multimodal Reasoning

arXiv:2601.11109v3 Announce Type: replace-cross Abstract: Vision-as-inverse-graphics, the concept of reconstructing images into editable programs, remains challenging for Vision-Language Models (VLMs), which inherently lack fine-grained spatial grounding in one-shot settings. To address this, we introduce VIGA (Vision-as-Inverse-Graphics Agent), an interleaved multimodal reasoning framework where symbolic logic and visual perception actively cross-verify each other. VIGA operates through a tightly coupled code-render-inspect loop: synthesizing symbolic programs, projecting them into visual states, and inspecting discrepancies to guide iterative edits. Equipped with high-level semantic skills and an evolving multimodal memory, VIGA sustains evidence-based modifications over long horizons. This training-free, task-agnostic framework seamlessly supports 2D document generation, 3D reconstruction, multi-step 3D editing, and 4D physical interaction. Finally, we introduce BlenderBench, a challenging visual-to-code benchmark. Empirically, VIGA substantially improves accuracy compared with one-shot baselines in BlenderGym (35.32%), SlideBench (117.17%) and our proposed BlenderBench (124.70%).

InfoTok: Information-Theoretic Regularization for Capacity-Constrained Shared Visual Tokenization in Unified MLLMs

arXiv:2602.01554v2 Announce Type: replace-cross Abstract: Unified multimodal large language models (MLLMs) aim to unify image understanding and image generation within a single framework, where a shared visual tokenizer serves as the sole interface that maps high-dimensional images into a limited token budget for downstream multimodal reasoning and synthesis. However, existing shared-token designs are largely architecture-driven and lack an explicit criterion for what information should be preserved to simultaneously support semantic abstraction and visual detail. In this paper, we adopt a capacity-constrained perspective, viewing the shared tokenizer as a compute-bounded learner whose finite representational budget should prioritize reusable structure over hard-to-exploit high-entropy variations and redundancy. Motivated by this view, we propose \textbf{\textit{InfoTok}}, an information-regularized tokenization mechanism grounded in the Information Bottleneck (IB) principle. InfoTok explicitly controls information flow from images to shared tokens to multimodal outputs by imposing mutual-information (MI) constraints that enforce a principled trade-off between compression and task relevance, while also encouraging cross-modal consistency. Because MI is intractable for high-dimensional visual representations, we instantiate InfoTok with practical, differentiable dependence estimators, including a variational IB formulation and a Hilbert Schmidt Independence Criterion (HSIC) based alternative. Integrated into three representative unified MLLMs without introducing any additional training data, InfoTok consistently improves both image understanding and generation performance. These results support information-regularized visual tokenization as a sound basis for token learning in unified MLLMs.

Infeasibility Aware Large Language Models for Combinatorial Optimization

arXiv:2604.01455v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly explored for NP-hard combinatorial optimization problems, but most existing methods emphasize feasible-instance solution generation and do not explicitly address infeasibility detection. We propose an infeasibility-aware framework that combines certifiable dataset construction, supervised fine-tuning, and LLM-assisted downstream search. For the minor-embedding problem, we introduce a new mathematical programming formulation together with provable zero-phase infeasibility screening, which enables scalable construction of training instances labeled either as feasible with structured certificates or as certifiably infeasible. Using training data generated through this exact optimization pipeline, we show that an 8B-parameter LLM can be fine-tuned to jointly perform solution generation and infeasibility detection. We further utilize LLM outputs as warm starts for downstream local search, providing a practical way to accelerate optimization even when the LLM outputs are imperfect. Experiments show that our fine-tuned model improves overall accuracy by up to 30\% over GPT-5.2; meanwhile LLM-guided warm starts provide up to $2\times$ speedup compared with starting from scratch in downstream local search.

A Role-Based LLM Framework for Structured Information Extraction from Healthy Food Policies

arXiv:2604.01529v1 Announce Type: new Abstract: Current Large Language Model (LLM) approaches for information extraction (IE) in the healthy food policy domain are often hindered by various factors, including misinformation, specifically hallucinations, misclassifications, and omissions that result from the structural diversity and inconsistency of policy documents. To address these limitations, this study proposes a role-based LLM framework that automates the IE from unstructured policy data by assigning specialized roles: an LLM policy analyst for metadata and mechanism classification, an LLM legal strategy specialist for identifying complex legal approaches, and an LLM food system expert for categorizing food system stages. This framework mimics expert analysis workflows by incorporating structured domain knowledge, including explicit definitions of legal mechanisms and classification criteria, into role-specific prompts. We evaluate the framework using 608 healthy food policies from the Healthy Food Policy Project (HFPP) database, comparing its performance against zero-shot, few-shot, and chain-of-thought (CoT) baselines using Llama-3.3-70B. Our proposed framework demonstrates superior performance in complex reasoning tasks, offering a reliable and transparent methodology for automating IE from health policies.

ATBench: A Diverse and Realistic Trajectory Benchmark for Long-Horizon Agent Safety

arXiv:2604.02022v1 Announce Type: new Abstract: Evaluating the safety of LLM-based agents is increasingly important because risks in realistic deployments often emerge over multi-step interactions rather than isolated prompts or final responses. Existing trajectory-level benchmarks remain limited by insufficient interaction diversity, coarse observability of safety failures, and weak long-horizon realism. We introduce ATBench, a trajectory-level benchmark for structured, diverse, and realistic evaluation of agent safety. ATBench organizes agentic risk along three dimensions: risk source, failure mode, and real-world harm. Based on this taxonomy, we construct trajectories with heterogeneous tool pools and a long-context delayed-trigger protocol that captures realistic risk emergence across multiple stages. The benchmark contains 1,000 trajectories (503 safe and 497 unsafe), averaging 9.01 turns and 3.95k tokens, with 1,954 invoked tools drawn from pools spanning 2,084 available tools. Data quality is supported by rule-based and LLM-based filtering plus full human audit. Experiments on frontier LLMs, open-source models, and specialized guard systems show that ATBench is challenging even for strong evaluators, while enabling taxonomy-stratified analysis, cross-benchmark comparison, and diagnosis of long-horizon failure patterns.

TRACE-Bot: Detecting Emerging LLM-Driven Social Bots via Implicit Semantic Representations and AIGC-Enhanced Behavioral Patterns

arXiv:2604.02147v1 Announce Type: new Abstract: Large Language Model-driven (LLM-driven) social bots pose a growing threat to online discourse by generating human-like content that evades conventional detection. Existing methods suffer from limited detection accuracy due to overreliance on single-modality signals, insufficient sensitivity to the specific generative patterns of Artificial Intelligence-Generated Content (AIGC), and a failure to adequately model the interplay between linguistic patterns and behavioral dynamics. To address these limitations, we propose TRACE-Bot, a unified dual-channel framework that jointly models implicit semantic representations and AIGC-enhanced behavioral patterns. TRACE-Bot constructs fine-grained representations from heterogeneous sources, including personal information data, interaction behavior data and tweet data. A dual-channel architecture captures linguistic representations via a pretrained language model and behavioral irregularities via multidimensional activity features augmented with signals from state-of-the-art (SOTA) AIGC detectors. The fused representations are then classified through a lightweight prediction head. Experiments on two public LLM-driven social bot datasets demonstrate SOTA performance, achieving accuracies of 98.46% and 97.50%, respectively. The results further indicate strong robustness against advanced bot strategies, highlighting the effectiveness of jointly leveraging implicit semantic representations and AIGC-enhanced behavioral patterns for emerging LLM-driven social bot detection.

MemFactory: Unified Inference & Training Framework for Agent Memory

arXiv:2603.29493v3 Announce Type: replace-cross Abstract: Memory-augmented Large Language Models (LLMs) are essential for developing capable, long-term AI agents. Recently, applying Reinforcement Learning (RL) to optimize memory operations, such as extraction, updating, and retrieval, has emerged as a highly promising research direction. However, existing implementations remain highly fragmented and task-specific, lacking a unified infrastructure to streamline the integration, training, and evaluation of these complex pipelines. To address this gap, we present MemFactory, the first unified, highly modular training and inference framework specifically designed for memory-augmented agents. Inspired by the success of unified fine-tuning frameworks like LLaMA-Factory, MemFactory abstracts the memory lifecycle into atomic, plug-and-play components, enabling researchers to seamlessly construct custom memory agents via a "Lego-like" architecture. Furthermore, the framework natively integrates Group Relative Policy Optimization (GRPO) to fine-tune internal memory management policies driven by multi-dimensional environmental rewards. MemFactory provides out-of-the-box support for recent cutting-edge paradigms, including Memory-R1, RMM, and MemAgent. We empirically validate MemFactory on the open-source MemAgent architecture using its publicly available training and evaluation data. Across the evaluation sets, MemFactory improves performance over the corresponding base models on average, with relative gains of up to 14.8%. By providing a standardized, extensible, and easy-to-use infrastructure, MemFactory significantly lowers the barrier to entry, paving the way for future innovations in memory-driven AI agents.

Four Generations of Quantum Biomedical Sensors

arXiv:2603.29944v2 Announce Type: replace-cross Abstract: Quantum sensing technologies offer transformative potential for ultra-sensitive biomedical sensing, yet their clinical translation remains constrained by classical noise limits and a reliance on macroscopic ensembles. We propose a unifying generational framework to organize the evolving landscape of quantum biosensors based on their utilization of quantum resources. First-generation devices utilize discrete energy levels for signal transduction but follow classical scaling laws. Second-generation sensors exploit quantum coherence to reach the standard quantum limit, while third-generation architectures leverage entanglement and spin squeezing to approach Heisenberg-limited precision. We further define an emerging fourth generation characterized by the end-to-end integration of quantum sensing with quantum learning and variational circuits, enabling adaptive inference directly within the quantum domain. By analyzing critical parameters such as bandwidth matching and sensor-tissue proximity, we identify key technological bottlenecks and propose a roadmap for transitioning from measuring physical observables to extracting structured biological information with quantum-enhanced intelligence.

PAR$^2$-RAG: Planned Active Retrieval and Reasoning for Multi-Hop Question Answering

arXiv:2603.29085v1 Announce Type: new Abstract: Large language models (LLMs) remain brittle on multi-hop question answering (MHQA), where answering requires combining evidence across documents through retrieval and reasoning. Iterative retrieval systems can fail by locking onto an early low-recall trajectory and amplifying downstream errors, while planning-only approaches may produce static query sets that cannot adapt when intermediate evidence changes. We propose \textbf{Planned Active Retrieval and Reasoning RAG (PAR$^2$-RAG)}, a two-stage framework that separates \emph{coverage} from \emph{commitment}. PAR$^2$-RAG first performs breadth-first anchoring to build a high-recall evidence frontier, then applies depth-first refinement with evidence sufficiency control in an iterative loop. Across four MHQA benchmarks, PAR$^2$-RAG consistently outperforms existing state-of-the-art baselines, compared with IRCoT, PAR$^2$-RAG achieves up to \textbf{23.5\%} higher accuracy, with retrieval gains of up to \textbf{10.5\%} in NDCG.

Owl-AuraID 1.0: An Intelligent System for Autonomous Scientific Instrumentation and Scientific Data Analysis

arXiv:2603.29828v1 Announce Type: new Abstract: Scientific discovery increasingly depends on high-throughput characterization, yet automation is hindered by proprietary GUIs and the limited generalizability of existing API-based systems. We present Owl-AuraID, a software-hardware collaborative embodied agent system that adopts a GUI-native paradigm to operate instruments through the same interfaces as human experts. Its skill-centric framework integrates Type-1 (GUI operation) and Type-2 (data analysis) skills into end-to-end workflows, connecting physical sample handling with scientific interpretation. Owl-AuraID demonstrates broad coverage across ten categories of precision instruments and diverse workflows, including multimodal spectral analysis, microscopic imaging, and crystallographic analysis, supporting modalities such as FTIR, NMR, AFM, and TGA. Overall, Owl-AuraID provides a practical, extensible foundation for autonomous laboratories and illustrates a path toward evolving laboratory intelligence through reusable operational and analytical skills. The code are available at https://github.com/OpenOwlab/AuraID.
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