Correction: Integrative multi-omics and machine learning reveals the spatial niche distribution and role of CYP27A1+TAMs in immunotherapy response in non-small cell lung cancer

arXiv:2603.29176v1 Announce Type: new Abstract: Parkinson's disease (PD) affects over ten million people worldwide. Although temporal interference (TI) and deep brain stimulation (DBS) are promising therapies, inter-individual variability limits empirical treatment selection, increasing non-negligible surgical risk and cost. Previous explorations either resort to limited statistical biomarkers that are insufficient to characterize variability, or employ AI-driven methods which is prone to overfitting and opacity. We bridge this gap with a pretraining-finetuning framework to predict outcomes directly from resting-state fMRI. Critically, a generative virtual brain foundation model, pretrained on a collective dataset (2707 subjects, 5621 sessions) to capture universal disorder patterns, was finetuned on PD cohorts receiving TI (n=51) or DBS (n=55) to yield individualized virtual brains with high fidelity to empirical functional connectivity (r=0.935). By constructing counterfactual estimations between pathological and healthy neural states within these personalized models, we predicted clinical responses (TI: AUPR=0.853; DBS: AUPR=0.915), substantially outperforming baselines. External and prospective validations (n=14, n=11) highlight the feasibility of clinical translation. Moreover, our framework provides state-dependent regional patterns linked to response, offering hypothesis-generating mechanistic insights.

Route-Induced Density and Stability (RIDE): Controlled Intervention and Mechanism Analysis of Routing-Style Meta Prompts on LLM Internal States

cs.AI, q-bio.NC updates on arXiv.org

By: Dianxing Zhang · Gang Li · Sheng Li

1 April 2026 at 12:00

arXiv:2603.29206v1 Announce Type: new Abstract: Routing is widely used to scale large language models, from Mixture-of-Experts gating to multi-model/tool selection. A common belief is that routing to a task ``expert'' activates sparser internal computation and thus yields more certain and stable outputs (the Sparsity--Certainty Hypothesis). We test this belief by injecting routing-style meta prompts as a textual proxy for routing signals in front of frozen instruction-tuned LLMs. We quantify (C1) internal density via activation sparsity, (C2) domain-keyword attention, and (C3) output stability via predictive entropy and semantic variation. On a RouterEval subset with three instruction-tuned models (Qwen3-8B, Llama-3.1-8B-Instruct, and Mistral-7B-Instruct-v0.2), meta prompts consistently densify early/middle-layer representations rather than increasing sparsity; natural-language expert instructions are often stronger than structured tags. Attention responses are heterogeneous: Qwen/Llama reduce keyword attention, while Mistral reinforces it. Finally, the densification--stability link is weak and appears only in Qwen, with near-zero correlations in Llama and Mistral. We present RIDE as a diagnostic probe for calibrating routing design and uncertainty estimation.

iPoster: Content-Aware Layout Generation for Interactive Poster Design via Graph-Enhanced Diffusion Models

cs.AI, q-bio.NC updates on arXiv.org

By: Xudong Zhou · Jinyuan Liang · Qiuyi Guo · Guozheng Li

1 April 2026 at 12:00

arXiv:2603.29469v1 Announce Type: cross Abstract: We present iPoster, an interactive layout generation framework that empowers users to guide content-aware poster layout design by specifying flexible constraints. iPoster enables users to specify partial intentions within the intention module, such as element categories, sizes, positions, or coarse initial drafts. Then, the generation module instantly generates refined, context-sensitive layouts that faithfully respect these constraints. iPoster employs a unified graph-enhanced diffusion architecture that supports various design tasks under user-specified constraints. These constraints are enforced through masking strategies that precisely preserve user input at every denoising step. A cross content-aware attention module aligns generated elements with salient regions of the canvas, ensuring visual coherence. Extensive experiments show that iPoster not only achieves state-of-the-art layout quality, but offers a responsive and controllable framework for poster layout design with constraints.

MemFactory: Unified Inference & Training Framework for Agent Memory

cs.AI, q-bio.NC updates on arXiv.org

By: Ziliang Guo · Ziheng Li · Zhiyu Li

1 April 2026 at 12:00

arXiv:2603.29493v1 Announce Type: 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 both in-domain and out-of-distribution evaluation sets, MemFactory consistently improves performance over the corresponding base models, 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.

From Efficiency to Adaptivity: A Deeper Look at Adaptive Reasoning in Large Language Models

cs.AI, q-bio.NC updates on arXiv.org

By: Chao Wu · Baoheng Li · Mingchen Gao · Yu Tian · Zhenyi Wang

1 April 2026 at 12:00

arXiv:2511.10788v3 Announce Type: replace Abstract: Recent advances in large language models (LLMs) have made reasoning a central benchmark for evaluating intelligence. While prior surveys focus on efficiency by examining how to shorten reasoning chains or reduce computation, this view overlooks a fundamental challenge: current LLMs apply uniform reasoning strategies regardless of task complexity, generating long traces for trivial problems while failing to extend reasoning for difficult tasks. This survey reframes reasoning through the lens of {adaptivity}: the capability to allocate reasoning effort based on input characteristics such as difficulty and uncertainty. We make three contributions. First, we formalize deductive, inductive, and abductive reasoning within the LLM context, connecting these classical cognitive paradigms with their algorithmic realizations. Second, we formalize adaptive reasoning as a control-augmented policy optimization problem balancing task performance with computational cost, distinguishing learned policies from inference-time control mechanisms. Third, we propose a systematic taxonomy organizing existing methods into training-based approaches that internalize adaptivity through reinforcement learning, supervised fine-tuning, and learned controllers, and training-free approaches that achieve adaptivity through prompt conditioning, feedback-driven halting, and modular composition. This framework clarifies how different mechanisms realize adaptive reasoning in practice and enables systematic comparison across diverse strategies. We conclude by identifying open challenges in self-evaluation, meta-reasoning, and human-aligned reasoning control.

QuestA: Expanding Reasoning Capacity in LLMs via Question Augmentation

cs.AI, q-bio.NC updates on arXiv.org

By: Jiazheng Li · Hongzhou Lin · Hong Lu · Kaiyue Wen · Zaiwen Yang · Jiaxuan Gao · Yi Wu · Jingzhao Zhang

1 April 2026 at 12:00

arXiv:2507.13266v4 Announce Type: replace-cross Abstract: Reinforcement learning (RL) has emerged as a central paradigm for training large language models (LLMs) in reasoning tasks. Yet recent studies question RL's ability to incentivize reasoning capacity beyond the base model. This raises a key challenge: how can RL be adapted to solve harder reasoning problems more effectively? To address this challenge, we propose a simple yet effective strategy via Question Augmentation: introduce partial solutions during training to reduce problem difficulty and provide more informative learning signals. Our method, QuestA, when applied during RL training on math reasoning tasks, not only improves pass@1 but also pass@k-particularly on problems where standard RL struggles to make progress. This enables continual improvement over strong open-source models such as DeepScaleR and OpenMath Nemotron, further enhancing their reasoning capabilities. We achieve new state-of-the-art results on math benchmarks using 1.5B-parameter models: 72.50% (+10.73%) on AIME24, 62.29% (+12.79%) on AIME25, and 41.67% (+10.11%) on HMMT25. Code, data and model are available at https://github.com/foreverlasting1202/QuestA.

InfiniteVL: Synergizing Linear and Sparse Attention for Highly-Efficient, Unlimited-Input Vision-Language Models

cs.AI, q-bio.NC updates on arXiv.org

By: Hongyuan Tao · Bencheng Liao · Shaoyu Chen · Haoran Yin · Qian Zhang · Wenyu Liu · Xinggang Wang

1 April 2026 at 12:00

arXiv:2512.08829v2 Announce Type: replace-cross Abstract: Vision-Language Models (VLMs) are increasingly tasked with ultra-long multimodal understanding. While linear architectures offer constant computation and memory footprints, they often struggle with high-frequency visual perception compared to standard Transformers. To bridge this gap, we introduce \textbf{InfiniteVL}. We first develop a hybrid base model called \textbf{InfiniteVL-Base} that interleaves a small fraction of Full Attention layers with Gated DeltaNet. Empowered by a tailored distillation and fine-tuning strategy, InfiniteVL-Base matches the fundamental multimodal performance of equivalent Transformers while achieving a \textbf{1.7$\times$} decoding speedup. However, the quadratic complexity of the retained Full Attention inevitably becomes an efficiency bottleneck when scaling to ultra long context. To break this barrier, we propose a novel Long-Sequence Architectural Fine-Tuning strategy that seamlessly transforms the dense attention into vision-specific sparse mechanisms. This yields two specialized variants: \textbf{InfiniteVL-Offline} for offline retrieval and \textbf{InfiniteVL-Online} for online streaming. By eliminating the computation explosion of global attention without sacrificing high-frequency visual recall, InfiniteVL-Offline achieves Transformer-level length generalization with a \textbf{5x} prefill acceleration at 256K context. Concurrently, InfiniteVL-Online delivers robust streaming perception with a constant memory footprint and a real-time throughput of \textbf{25} FPS. Code and models are available at https://github.com/hustvl/InfiniteVL.

Proposed Role of Circadian Clock Genes in Pathogenesis of HCC: Molecular Subtyping and Characterization

Omics in Hepatocellular

By: Zhikui Lu · Yi Zhou · Jian Luo · Zhicheng Liu · Zhenyu Xiao

28 March 2026 at 18:00

Biomedicines. 2026 Mar 12;14(3):645. doi: 10.3390/biomedicines14030645.

ABSTRACT

Background: Hepatocellular carcinoma (HCC) stands as a prevalent global health issue with increasing incidence and mortality rates. Hepatocellular carcinoma (HCC) exhibits profound molecular and clinical heterogeneity, which limits the effectiveness of current therapeutic strategies. Circadian rhythm disruption has been implicated in metabolic reprogramming, proliferation, and immune modulation in cancer, but its role in shaping HCC heterogeneity remains poorly defined. Methods: Four public HCC transcriptomic cohorts (TCGA-LIHC, CHCC, LIRI, LICA) were integrated using RMA normalization and ComBat for batch correction. Consensus clustering based on 31 core circadian clock genes (CCGs) identified robust molecular subtypes. Multi-omics characterization-including genomic alterations, pathway activity (GSEA/GSVA), immune microenvironment profiling (CIBERSORT, EPIC, MCP-counter, xCell), and drug-sensitivity prediction (pRRophetic/oncoPredict)-was performed to delineate subtype-specific biological properties. A nine-gene CCG-based RiskScore model was constructed using LASSO Cox regression to internally validate subtype robustness and intra-subtype risk stratification. Results: Using consensus clustering of 31 core CCGs in TCGA-LIHC and three independent validation cohorts (CHCC, LIRI, LICA), we identified three reproducible subtypes-Cluster-1 (metabolic-quiescent), Cluster-2 (transition-intermediate), and Cluster-3 (proliferation-inflammatory)-which were recapitulated across cohorts and showed distinct overall survival (Cluster-3 worst; log-rank p values significant across datasets). Multi-omic characterization revealed that Cluster-3 exhibits the highest tumor mutational burden and CNV burden with enrichment of TP53/AXIN1/TERT alterations, strong activation of cell-cycle, E2F, and G2M programs, and an immune-hot yet immunosuppressed microenvironment enriched for TAMs, Tregs and MDSCs. By contrast, Cluster-1 shows relative genomic stability, dominant hepatic metabolic signatures (fatty-acid oxidation, bile-acid and xenobiotic metabolism) and an immune-cold phenotype. Single-cell mapping linked ALAS1 expression to malignant hepatocytes predominating in Cluster-1, whereas NONO and CSNK1D localized to stromal (CAFs/TECs) and both malignant/immune compartments respectively in Cluster-3, providing a cellular mechanism for subtype-specific metabolism, angiogenesis and immune modulation. Finally, a nine-gene CCG-based RiskScore validated prognostic stratification and drug-sensitivity predictions indicated subtype-specific therapeutic vulnerabilities (notably increased predicted TKI sensitivity in Cluster-3). Conclusion: In conclusion, this study proposes a robust circadian rhythm-based molecular classification of hepatocellular carcinoma, revealing three biologically and clinically distinct subtypes characterized by divergent genomic alterations, metabolic programs, immune microenvironment states, and prognostic patterns. By integrating bulk and single-cell transcriptomic data, we identify subtype-specific roles of key circadian regulators-including ALAS1, NONO, and CSNK1D-in shaping tumor metabolism, proliferation, stromal remodeling, and immune suppression. These findings highlight circadian dysregulation as a potential upstream factor associated with HCC heterogeneity and provide a conceptual framework for developing subtype-tailored mechanistic studies and circadian-informed therapeutic strategies.

PMID:41898292 | PMC:PMC13024568 | DOI:10.3390/biomedicines14030645

High-resolution metagenome assembly for modern long reads with myloasm

Nature Biotechnology - Issue - nature.com science feeds

By: Jim Shaw · Maximillian G. Marin · Heng Li

27 March 2026 at 08:00

Nature Biotechnology, Published online: 27 March 2026; doi:10.1038/s41587-026-03053-z

A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

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