Normal view
-
cs.AI, q-bio.NC updates on arXiv.org
-
Do LLMs Trust the Accuser or the Accusation? Measuring Belief Shifts in Werewolf
arXiv:2609.12446v1 Announce Type: new Abstract: Social-deduction games such as Werewolf are increasingly used to evaluate LLM agents, but existing evaluations often rely on final game outcomes. We propose a belief-shift evaluation benchmark in Werewolf for analyzing communication skills through belief updating. Using LLM-played games, we annotate suspicion and accusation messages and measure how an observing village-side model's beliefs change after each message. We evaluate 40 open-weight LLM
-
Molecular Therapy
-
A complement C5-targeted GalNAc-conjugated siRNA with sustained efficacy in a non-human primate model of IgA nephropathy
This study characterizes a GalNAc-C5 small interfering RNA with potent in vitro and in vivo activity. Single subcutaneous dosing sustains long-term C5 suppression in cynomolgus monkeys with IgA nephropathy, outperforming Nefecon in blocking glomerular complement deposition, supporting its standalone or combinational clinical application.
A complement C5-targeted GalNAc-conjugated siRNA with sustained efficacy in a non-human primate model of IgA nephropathy
-
Molecular Therapy
-
In vivo-directed evolution identifies AAV-WM04 as a next-generation vector for potent and sustained hearing restoration in DFNB9
AAV-WM04, an AAV vector identified through in-vivo-directed screening in the adult cochlea, enables highly efficient and selective inner hair cell transduction. Dual-AAV delivery of OTOF using AAV-WM04 restores hearing in a DFNA9 deafness mouse model at low doses, highlighting its translational potential for gene therapy.
In vivo-directed evolution identifies AAV-WM04 as a next-generation vector for potent and sustained hearing restoration in DFNB9
-
Omics in Hepatocellular
-
Integrative Multi-Omics Mendelian Randomization Analysis Identifies NIT2 as a Potential Metabolic Risk Gene in Hepatocellular Carcinoma
J Gene Med. 2026 Sep;28(9):e70111. doi: 10.1002/jgm.70111.ABSTRACTBACKGROUND: Metabolic pathways are crucial in hepatocellular carcinoma (HCC) pathogenesis, but causal metabolic genes remain unclear. This study used Summary data-based Mendelian Randomization (SMR) and colocalization to identify metabolism-related genetic loci influencing HCC risk.METHODS: Differentially expressed genes in hepatic malignancy phenotype versus normal tissues from TCGA and GTEx were analyzed. Metabolism-related cand
Integrative Multi-Omics Mendelian Randomization Analysis Identifies NIT2 as a Potential Metabolic Risk Gene in Hepatocellular Carcinoma
J Gene Med. 2026 Sep;28(9):e70111. doi: 10.1002/jgm.70111.
ABSTRACT
BACKGROUND: Metabolic pathways are crucial in hepatocellular carcinoma (HCC) pathogenesis, but causal metabolic genes remain unclear. This study used Summary data-based Mendelian Randomization (SMR) and colocalization to identify metabolism-related genetic loci influencing HCC risk.
METHODS: Differentially expressed genes in hepatic malignancy phenotype versus normal tissues from TCGA and GTEx were analyzed. Metabolism-related candidates were examined via SMR and colocalization using multi-omics data: methylation (mQTL), expression (eQTL), and protein (pQTL) quantitative trait loci.
RESULTS: Multi-omics integration identified NIT2 as a key metabolic regulator for HCC. The cg13016775 locus of NIT2 was associated with elevated HCC risk at gene (OR = 1.618, 95% CI: 1.199-2.182) and protein (OR = 4.432, 95% CI: 1.783-11.018) levels. Colocalization supported a shared causal variant (PPH4 > 0.6), linking NIT2 to hepatocarcinogenesis via metabolic regulation.
CONCLUSIONS: This study provides multi-omics evidence for NIT2 as a potential causal gene in HCC, enhancing understanding of metabolic contributions to HCC pathogenesis and highlighting integrative genomics for uncovering causal relationships.
PMID:42681890 | PMC:PMC13534973 | DOI:10.1002/jgm.70111
-
cs.AI, q-bio.NC updates on arXiv.org
-
Mitigating Object Hallucinations in Vision-Language Models through Region-Aware Attention Recalibration
arXiv:2605.24957v1 Announce Type: new Abstract: The generation of factually incorrect objects, commonly known as object hallucination, remains a persistent challenge in Large Vision-Language Models (LVLMs). Current approaches to address this issue - ranging from expensive data-driven fine-tuning and high-latency contrastive decoding to rigid attention head truncation - frequently compromise either computational efficiency or the continuity of the model's feature space. To overcome these limitat
Mitigating Object Hallucinations in Vision-Language Models through Region-Aware Attention Recalibration
-
cs.AI, q-bio.NC updates on arXiv.org
-
NeurIPS: Neuro-anatomical Inductive Priors for Sphere-based Brain Decoding
arXiv:2605.24993v1 Announce Type: new Abstract: Current fMRI decoders face a performance-fidelity trade-off where efficient ID encoders outperform geometrically faithful surface-based models. We argue this is partly driven by inefficient surface tokenization and the failure to use anatomy as a predictive signal. We present NeurIPS, a framework that improves surface-based decoding by reframing anatomical variation from a nuisance to a powerful inductive prior. NeurIPS unites two innovations: a S
NeurIPS: Neuro-anatomical Inductive Priors for Sphere-based Brain Decoding
-
cs.AI, q-bio.NC updates on arXiv.org
-
Cascade-KDE: Robust Time-Series Restoration under Out-of-Distribution Impulse Corruptions
arXiv:2605.24055v1 Announce Type: cross Abstract: Real-world time-series data in industrial sensing, healthcare, and energy systems is often corrupted by a mixture of Gaussian noise and occasional large-magnitude impulse outliers. For tasks that depend on local shape, such as ECG morphology analysis and battery degradation monitoring, the main requirement is not only low reconstruction error but also preservation of derivative peaks and task-critical features. We propose Cascade-KDE, a training
Cascade-KDE: Robust Time-Series Restoration under Out-of-Distribution Impulse Corruptions
-
cs.AI, q-bio.NC updates on arXiv.org
-
Cross-Domain Energy-Guided Diffusion Generation for Off-Dynamics Reinforcement Learning
arXiv:2605.24810v1 Announce Type: cross Abstract: Off-dynamics offline reinforcement learning seeks to learn a target-domain policy from a large source dataset and a limited target dataset under mismatched transition dynamics. Existing approaches such as reward augmentation and data filtering are constrained to the source dataset and cannot synthesize new target behavior to improve coverage beyond the collected source trajectories. While recent model-based methods attempt to address this by lea
Cross-Domain Energy-Guided Diffusion Generation for Off-Dynamics Reinforcement Learning
-
cs.AI, q-bio.NC updates on arXiv.org
-
Inference-Time Alignment of Diffusion Models via Trust-Region Iterative Twisted Sequential Monte Carlo
arXiv:2605.25123v1 Announce Type: cross Abstract: We study inference-time alignment for diffusion-based generative models, aiming to steer a base model toward high-reward outputs without updating its weights. Recent Sequential Monte Carlo (SMC)-based steering methods approximate reward-tilted target distributions in a principled way, but their proposals remain largely tied to the base sampler. Since reward information is mainly used after propagation through particle reweighting and resampling,
Inference-Time Alignment of Diffusion Models via Trust-Region Iterative Twisted Sequential Monte Carlo
-
cs.AI, q-bio.NC updates on arXiv.org
-
AutoResearchClaw: Self-Reinforcing Autonomous Research with Human-AI Collaboration
arXiv:2605.20025v2 Announce Type: replace Abstract: Automating scientific discovery requires more than generating papers from ideas. Real research is iterative: hypotheses are challenged from multiple perspectives, experiments fail and inform the next attempt, and lessons accumulate across cycles. Existing autonomous research systems often model this process as a linear pipeline: they rely on single-agent reasoning, stop when execution fails, and do not carry experience across runs. We present
AutoResearchClaw: Self-Reinforcing Autonomous Research with Human-AI Collaboration
-
cs.AI, q-bio.NC updates on arXiv.org
-
Memorize Theorems, Not Instances: Probing SFT Generalization through Mathematical Reasoning
arXiv:2605.09270v2 Announce Type: replace-cross Abstract: Supervised Fine-Tuning (SFT) is widely used for task-specific adaptation, yet recent work shows it systematically undermines reasoning generalization. We argue the root cause is not memorization itself, but its target: vanilla SFT drives models to exploit and memorize spurious surface correlations in problem-solution pairs, leaving them brittle to superficial input variations. To address this, we propose Theorem-SFT, which reorients supe
Memorize Theorems, Not Instances: Probing SFT Generalization through Mathematical Reasoning
-
Omics In Lung
-
Epigenome-wide Mendelian randomization with multi-omics validation identifies epigenetic drivers of idiopathic pulmonary fibrosis
Commun Biol. 2026 Apr 11. doi: 10.1038/s42003-026-10033-1. Online ahead of print.ABSTRACTIdiopathic pulmonary fibrosis (IPF) is a complex disease without clear etiology or effective therapy. While DNA methylation has been implicated in IPF pathogenesis, the tissue-specific causal effects of the epigenetic factors on IPF remain undetermined. Here, we perform epigenome-wide Mendelian randomization using blood-based methylation quantitative trait loci of 420,509 CpG sites and genome-wide associatio
Epigenome-wide Mendelian randomization with multi-omics validation identifies epigenetic drivers of idiopathic pulmonary fibrosis
Commun Biol. 2026 Apr 11. doi: 10.1038/s42003-026-10033-1. Online ahead of print.
ABSTRACT
Idiopathic pulmonary fibrosis (IPF) is a complex disease without clear etiology or effective therapy. While DNA methylation has been implicated in IPF pathogenesis, the tissue-specific causal effects of the epigenetic factors on IPF remain undetermined. Here, we perform epigenome-wide Mendelian randomization using blood-based methylation quantitative trait loci of 420,509 CpG sites and genome-wide association study for IPF to elucidate the causal effects of the CpG sites on IPF. Totally, 452 CpG sites has shown putative causal effects on IPF risk after Bonferroni correction. Among them, 13 CpG sites have shown strong colocalization evidence with genetic factors associated with IPF. Specifically, DNA methylation at CpG sites within MAN2A2 and TRIM27 shows significant differences between IPF lungs and controls, correlating with altered mRNA expressions of these genes in lung tissues. The CpG site in MAN2A2 is a binding site of ZNF384 according to transcription factor databases. RNA sequencing in the TGFβ1-induced alveolar epithelia confirms significantly reduced expression of MAN2A2 and ZNF384 comparing to the controls. Collectively, our study suggests a putative causal link between DNA methylation within MAN2A2 and IPF risk, wherein lung-specific DNA methylation in MAN2A2 may perturb the interaction between ZNF384 and MAN2A2, revealing novel roles for these genes in IPF pathogenesis.
PMID:41965819 | DOI:10.1038/s42003-026-10033-1
-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
-
Epigenome-wide Mendelian randomization with multi-omics validation identifies epigenetic drivers of idiopathic pulmonary fibrosis
Commun Biol. 2026 Apr 11. doi: 10.1038/s42003-026-10033-1. Online ahead of print.ABSTRACTIdiopathic pulmonary fibrosis (IPF) is a complex disease without clear etiology or effective therapy. While DNA methylation has been implicated in IPF pathogenesis, the tissue-specific causal effects of the epigenetic factors on IPF remain undetermined. Here, we perform epigenome-wide Mendelian randomization using blood-based methylation quantitative trait loci of 420,509 CpG sites and genome-wide associatio
Epigenome-wide Mendelian randomization with multi-omics validation identifies epigenetic drivers of idiopathic pulmonary fibrosis
Commun Biol. 2026 Apr 11. doi: 10.1038/s42003-026-10033-1. Online ahead of print.
ABSTRACT
Idiopathic pulmonary fibrosis (IPF) is a complex disease without clear etiology or effective therapy. While DNA methylation has been implicated in IPF pathogenesis, the tissue-specific causal effects of the epigenetic factors on IPF remain undetermined. Here, we perform epigenome-wide Mendelian randomization using blood-based methylation quantitative trait loci of 420,509 CpG sites and genome-wide association study for IPF to elucidate the causal effects of the CpG sites on IPF. Totally, 452 CpG sites has shown putative causal effects on IPF risk after Bonferroni correction. Among them, 13 CpG sites have shown strong colocalization evidence with genetic factors associated with IPF. Specifically, DNA methylation at CpG sites within MAN2A2 and TRIM27 shows significant differences between IPF lungs and controls, correlating with altered mRNA expressions of these genes in lung tissues. The CpG site in MAN2A2 is a binding site of ZNF384 according to transcription factor databases. RNA sequencing in the TGFβ1-induced alveolar epithelia confirms significantly reduced expression of MAN2A2 and ZNF384 comparing to the controls. Collectively, our study suggests a putative causal link between DNA methylation within MAN2A2 and IPF risk, wherein lung-specific DNA methylation in MAN2A2 may perturb the interaction between ZNF384 and MAN2A2, revealing novel roles for these genes in IPF pathogenesis.
PMID:41965819 | DOI:10.1038/s42003-026-10033-1
-
cs.AI, q-bio.NC updates on arXiv.org
-
Unifying Group-Relative and Self-Distillation Policy Optimization via Sample Routing
arXiv:2604.02288v1 Announce Type: cross Abstract: Reinforcement learning with verifiable rewards (RLVR) has become a standard paradigm for post-training large language models. While Group Relative Policy Optimization (GRPO) is widely adopted, its coarse credit assignment uniformly penalizes failed rollouts, lacking the token-level focus needed to efficiently address specific deviations. Self-Distillation Policy Optimization (SDPO) addresses this by providing denser, more targeted logit-level su
Unifying Group-Relative and Self-Distillation Policy Optimization via Sample Routing
-
cs.AI, q-bio.NC updates on arXiv.org
-
When Models Judge Themselves: Unsupervised Self-Evolution for Multimodal Reasoning
arXiv:2603.21289v2 Announce Type: replace-cross Abstract: Recent progress in multimodal large language models has led to strong performance on reasoning tasks, but these improvements largely rely on high-quality annotated data or teacher-model distillation, both of which are costly and difficult to scale. To address this, we propose an unsupervised self-evolution training framework for multimodal reasoning that achieves stable performance improvements without using human-annotated answers or ex
When Models Judge Themselves: Unsupervised Self-Evolution for Multimodal Reasoning
-
Cell Death Discovery nature.com science feeds
-
Lysine attenuates acute lung injury by restoring α-tubulin acetylation and ciliary activity
Cell Death Discovery, Published online: 16 March 2026; doi:10.1038/s41420-026-03025-xLysine attenuates acute lung injury by restoring α-tubulin acetylation and ciliary activity
Lysine attenuates acute lung injury by restoring α-tubulin acetylation and ciliary activity
Cell Death Discovery, Published online: 16 March 2026; doi:10.1038/s41420-026-03025-x
Lysine attenuates acute lung injury by restoring α-tubulin acetylation and ciliary activity-
cs.AI, q-bio.NC updates on arXiv.org
-
Deconstructing Multimodal Mathematical Reasoning: Towards a Unified Perception-Alignment-Reasoning Paradigm
arXiv:2603.08291v1 Announce Type: new Abstract: Multimodal Mathematical Reasoning (MMR) has recently attracted increasing attention for its capability to solve mathematical problems that involve both textual and visual modalities. However, current models still face significant challenges in real-world visual math tasks. They often misinterpret diagrams, fail to align mathematical symbols with visual evidence, and produce inconsistent reasoning steps. Moreover, existing evaluations mainly focus
Deconstructing Multimodal Mathematical Reasoning: Towards a Unified Perception-Alignment-Reasoning Paradigm
-
cs.AI, q-bio.NC updates on arXiv.org
-
\$OneMillion-Bench: How Far are Language Agents from Human Experts?
arXiv:2603.07980v1 Announce Type: cross Abstract: As language models (LMs) evolve from chat assistants to long-horizon agents capable of multi-step reasoning and tool use, existing benchmarks remain largely confined to structured or exam-style tasks that fall short of real-world professional demands. To this end, we introduce \$OneMillion-Bench \$OneMillion-Bench, a benchmark of 400 expert-curated tasks spanning Law, Finance, Industry, Healthcare, and Natural Science, built to evaluate agents a
\$OneMillion-Bench: How Far are Language Agents from Human Experts?
-
cs.AI, q-bio.NC updates on arXiv.org
-
Performance of Conventional EEG Biomarkers Across Different Clinical Phases of Major Depressive Disorder: A Comprehensive Evaluation
arXiv:2603.03864v1 Announce Type: new Abstract: While EEG features differentiate Major Depressive Disorder (MDD) from healthy controls (HC), their clinical utility as biomarkers depends on a monotonic trajectory across the disease spectrum, from the acute (AC) phase to the maintenance (MA) phase and finally to the healthy baseline. However, the progression of the MA phase remains poorly understood in traditional marker analysis. Analyzing EEG data from 74 individuals (24 AC, 23 MA, and 27 HC),
Performance of Conventional EEG Biomarkers Across Different Clinical Phases of Major Depressive Disorder: A Comprehensive Evaluation
-
cs.AI, q-bio.NC updates on arXiv.org
-
Pushing the Limits of Inverse Lithography with Generative Reinforcement Learning
arXiv:2602.19027v1 Announce Type: cross Abstract: Inverse lithography (ILT) is critical for modern semiconductor manufacturing but suffers from highly non-convex objectives that often trap optimization in poor local minima. Generative AI has been explored to warm-start ILT, yet most approaches train deterministic image-to-image translators to mimic sub-optimal datasets, providing limited guidance for escaping non-convex traps during refinement. We reformulate mask synthesis as conditional sampl