Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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AdaRoPE: Not All Attention Heads Should Rotate and Scale Equally
arXiv:2607.19363v3 Announce Type: replace Abstract: Rotary Position Embedding (RoPE) is widely adopted in Transformers to encode positional information, yet standard implementations enforce a uniform frequency schedule and scaling across all attention heads. Using simplified retrieval tasks and length generalization scenarios, we show -- both empirically and theoretically -- that heads with different functional roles require distinct frequency ranges and attention scaling factors to operate eff
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cs.AI, q-bio.NC updates on arXiv.org
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When Bias Pretends to Be Truth: How Spurious Correlations Undermine Hallucination Detection in LLMs
arXiv:2511.07318v3 Announce Type: replace-cross Abstract: Despite substantial advances, large language models (LLMs) continue to exhibit hallucinations, generating plausible yet incorrect responses. In this paper, we highlight a critical yet previously underexplored class of hallucinations driven by spurious correlations -- superficial but statistically prominent associations between features (e.g., surnames) and attributes (e.g., nationality) present in the training data. We demonstrate that t
When Bias Pretends to Be Truth: How Spurious Correlations Undermine Hallucination Detection in LLMs
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npj Digital Medicine
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Deep learning predicts gene rearrangements from histopathology in large B-cell lymphoma
npj Digital Medicine, Published online: 12 September 2026; doi:10.1038/s41746-026-03238-5Deep learning predicts gene rearrangements from histopathology in large B-cell lymphoma
Deep learning predicts gene rearrangements from histopathology in large B-cell lymphoma
npj Digital Medicine, Published online: 12 September 2026; doi:10.1038/s41746-026-03238-5
Deep learning predicts gene rearrangements from histopathology in large B-cell lymphoma-
cs.AI, q-bio.NC updates on arXiv.org
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Distilling Image Prototypes for Guided Test-Time Adaptation
arXiv:2609.09737v1 Announce Type: cross Abstract: Test-Time Adaptation (TTA) enhances the robustness of models against distribution shifts but faces two critical challenges: error accumulation from noisy pseudo-labels and catastrophic forgetting of source knowledge. Uncertainty-based approaches designed to mitigate error accumulation often yield overconfident or computationally expensive estimates, while strategies intended to prevent forgetting via prototype replay rely on static representatio
Distilling Image Prototypes for Guided Test-Time Adaptation
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cs.AI, q-bio.NC updates on arXiv.org
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GlobalDentBench: A Multinational Benchmark for Evaluating LLM Clinical Reasoning in Dentistry with Expert Calibration
arXiv:2605.24636v2 Announce Type: new Abstract: While large language models (LLMs) hold transformative potential for medicine, their reasoning robustness and safety in real-world clinical scenarios remain critically underexplored, particularly in dentistry. Here we introduce GlobalDentBench, the first multinational dental benchmark, featuring a taxonomy that encompasses 14 dental specialties across 88 countries and regions spanning six continents. The benchmark comprises 8,978 expert-validated
GlobalDentBench: A Multinational Benchmark for Evaluating LLM Clinical Reasoning in Dentistry with Expert Calibration
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cs.AI, q-bio.NC updates on arXiv.org
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CUA-Gym: Scaling Verifiable Training Environments and Tasks for Computer-Use Agents
arXiv:2605.25624v1 Announce Type: new Abstract: Reinforcement learning with verifiable rewards (RLVR) has driven breakthroughs in domains such as math, tool-use, and software engineering, yet its extension to computer-use agents (CUAs) has been bottlenecked by the scarcity of scalable training data with deterministic rewards. Constructing such data for CUAs requires consistent task instruction, executable environment, and verifiable reward. However, hand-curated benchmarks achieve high reward f
CUA-Gym: Scaling Verifiable Training Environments and Tasks for Computer-Use Agents
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cs.AI, q-bio.NC updates on arXiv.org
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Small Models, Strong Priors: Architectural Inductive Bias for Parameter-Efficient Neural PDE Solvers
arXiv:2605.25949v1 Announce Type: cross Abstract: Neural PDE solvers have followed the scaling trajectory of vision and language, with recent foundation models reaching billions of parameters. We argue that scale is a poor substitute for architectural inductive bias in this domain: structured priors deliver outsized parameter efficiency, and the pattern of where they succeed and fail is itself informative about what they capture. We instantiate this argument in WaveLiT, an architecture combinin
Small Models, Strong Priors: Architectural Inductive Bias for Parameter-Efficient Neural PDE Solvers
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cs.AI, q-bio.NC updates on arXiv.org
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SentGraph: Hierarchical Sentence Graph for Multi-hop Retrieval-Augmented Question Answering
arXiv:2601.03014v3 Announce Type: replace-cross Abstract: Traditional Retrieval-Augmented Generation (RAG) effectively supports single-hop question answering with large language models but faces significant limitations in multi-hop question answering tasks, which require combining evidence from multiple documents. Existing chunk-based retrieval often provides irrelevant and logically incoherent context, leading to incomplete evidence chains and incorrect reasoning during answer generation. To a
SentGraph: Hierarchical Sentence Graph for Multi-hop Retrieval-Augmented Question Answering
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Nature - Issue - nature.com science feeds
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Nonlinear atomic tunnelling boosted by bright squeezed vacuum
Nature, Published online: 20 May 2026; doi:10.1038/s41586-026-10485-9Bright squeezed vacuum light boosts nonlinear atomic tunnelling ionization more than 20-fold compared with coherent light, enabling quantum control of strong-field processes without increasing classical intensity.
Nonlinear atomic tunnelling boosted by bright squeezed vacuum
Nature, Published online: 20 May 2026; doi:10.1038/s41586-026-10485-9
Bright squeezed vacuum light boosts nonlinear atomic tunnelling ionization more than 20-fold compared with coherent light, enabling quantum control of strong-field processes without increasing classical intensity.-
Omics In Lung
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Pulmonary-Intestinal Axis: Shared Genetic Basis and Mediating Factors Identified Through Multi-Omics Analysis
Int J Chron Obstruct Pulmon Dis. 2026 Apr 7;21:561645. doi: 10.2147/COPD.S561645. eCollection 2026.ABSTRACTBACKGROUND: Chronic obstructive pulmonary disease (COPD) is a systemic condition with comorbidities beyond the lung (eg, cardiovascular and metabolic disorders), and gastrointestinal (GI) disorders are also common. The shared genetic basis of COPD-GI comorbidity and its mediating factors remain unclear. We hypothesized that COPD and GI diseases share pleiotropic genetic architecture implica
Pulmonary-Intestinal Axis: Shared Genetic Basis and Mediating Factors Identified Through Multi-Omics Analysis
Int J Chron Obstruct Pulmon Dis. 2026 Apr 7;21:561645. doi: 10.2147/COPD.S561645. eCollection 2026.
ABSTRACT
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a systemic condition with comorbidities beyond the lung (eg, cardiovascular and metabolic disorders), and gastrointestinal (GI) disorders are also common. The shared genetic basis of COPD-GI comorbidity and its mediating factors remain unclear. We hypothesized that COPD and GI diseases share pleiotropic genetic architecture implicating lipid-metabolic pathways, with smoking mediating part of the association.
METHODS: We analyzed publicly available European-ancestry GWAS summary statistics for COPD (Global Biobank Meta-analysis Initiative), 15 GI diseases (FinnGen), and smoking phenotypes (UK Biobank). Genetic correlation was estimated using linkage disequilibrium score regression (LDSC) and high-definition likelihood (HDL). Multi-trait analysis of GWAS (MTAG) boosted COPD discovery by leveraging genetically correlated GI traits. We integrated locus-to-gene mapping with multi-tissue expression quantitative trait loci (eQTL) and plasma protein quantitative trait loci (pQTL) evidence to prioritize shared loci, genes, and proteins. Bidirectional two-sample Mendelian randomization (MR) tested causal directions, and two-step mediation MR evaluated smoking.
RESULTS: COPD showed significant genetic correlation with nine GI diseases. We identified six comorbidity-associated loci (three with CADD > 12.37) and 13 unique candidate pleiotropic genes; APOE was supported by proteomic evidence. Enrichment analyses highlighted lipid-metabolism pathways. MR suggested COPD increases risk of gastroesophageal reflux disease (GERD), irritable bowel syndrome (IBS), acute appendicitis, and gastric ulcer, while diverticular disease showed reverse causality toward COPD. Smoking partially mediated the COPD effect on GERD, acute appendicitis, and gastric ulcer.
CONCLUSION: COPD and multiple GI disorders share a distributed pleiotropic genetic basis within the broader systemic comorbidity spectrum of COPD. Multi-omics evidence supports a genomic pulmonary-intestinal axis in which lipid metabolism and smoking-related mechanisms contribute to COPD and GI comorbidity, providing targets for risk stratification and potential intervention.
PMID:41978582 | PMC:PMC13070119 | DOI:10.2147/COPD.S561645
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Omics In Lung
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Integrin β3 deficiency unleashes spontaneous pulmonary inflammation by promoting B cell hyperactivation via the CD40-CD40L axis
Front Immunol. 2026 Mar 24;17:1796926. doi: 10.3389/fimmu.2026.1796926. eCollection 2026.ABSTRACTBACKGROUND: Pulmonary immune homeostasis requires tight control of adaptive responses. Integrin β3 is a well-known mediator of cell adhesion and platelet function. However, its role in adaptive immunity, especially in B cell responses, remains unclear.METHODS: We defined the pulmonary phenotype of constitutive β3-deficient (β3-/-) mice by histopathology. We performed integrated transcriptomic and pro
Integrin β3 deficiency unleashes spontaneous pulmonary inflammation by promoting B cell hyperactivation via the CD40-CD40L axis
Front Immunol. 2026 Mar 24;17:1796926. doi: 10.3389/fimmu.2026.1796926. eCollection 2026.
ABSTRACT
BACKGROUND: Pulmonary immune homeostasis requires tight control of adaptive responses. Integrin β3 is a well-known mediator of cell adhesion and platelet function. However, its role in adaptive immunity, especially in B cell responses, remains unclear.
METHODS: We defined the pulmonary phenotype of constitutive β3-deficient (β3-/-) mice by histopathology. We performed integrated transcriptomic and proteomic profiling of lung tissue to map the molecular signature of spontaneous pulmonary inflammation. We further probed the underlying mechanisms with additional histology and functional assays and tested for biological significance using transcriptomics data from auto-immune disease patients.
RESULTS: β3-/- mice developed spontaneous pulmonary inflammation marked by B cell activation and in situ immune-complex deposition within alveoli. Multi-omics integration implicated the CD40-CD40 Ligand (CD40L) axis as a central driver of this pathology. Mechanistically, loss of β3 enhanced CD40L-CD40 engagement on B cells, resulting in NF-κB pathway hyperactivation. Consistent with our murine data, reduced ITGB3 expression in patients with autoimmune disease correlated with transcriptional signatures of B cell activation and inflammation.
CONCLUSIONS: These results reframe integrin β3 as a threshold regulator of B cell activation. The β3-CD40L-CD40 axis therefore represents a potential therapeutic target for B cell-mediated autoimmune diseases.
PMID:41953039 | PMC:PMC13055533 | DOI:10.3389/fimmu.2026.1796926
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Integrin β3 deficiency unleashes spontaneous pulmonary inflammation by promoting B cell hyperactivation via the CD40-CD40L axis
Front Immunol. 2026 Mar 24;17:1796926. doi: 10.3389/fimmu.2026.1796926. eCollection 2026.ABSTRACTBACKGROUND: Pulmonary immune homeostasis requires tight control of adaptive responses. Integrin β3 is a well-known mediator of cell adhesion and platelet function. However, its role in adaptive immunity, especially in B cell responses, remains unclear.METHODS: We defined the pulmonary phenotype of constitutive β3-deficient (β3-/-) mice by histopathology. We performed integrated transcriptomic and pro
Integrin β3 deficiency unleashes spontaneous pulmonary inflammation by promoting B cell hyperactivation via the CD40-CD40L axis
Front Immunol. 2026 Mar 24;17:1796926. doi: 10.3389/fimmu.2026.1796926. eCollection 2026.
ABSTRACT
BACKGROUND: Pulmonary immune homeostasis requires tight control of adaptive responses. Integrin β3 is a well-known mediator of cell adhesion and platelet function. However, its role in adaptive immunity, especially in B cell responses, remains unclear.
METHODS: We defined the pulmonary phenotype of constitutive β3-deficient (β3-/-) mice by histopathology. We performed integrated transcriptomic and proteomic profiling of lung tissue to map the molecular signature of spontaneous pulmonary inflammation. We further probed the underlying mechanisms with additional histology and functional assays and tested for biological significance using transcriptomics data from auto-immune disease patients.
RESULTS: β3-/- mice developed spontaneous pulmonary inflammation marked by B cell activation and in situ immune-complex deposition within alveoli. Multi-omics integration implicated the CD40-CD40 Ligand (CD40L) axis as a central driver of this pathology. Mechanistically, loss of β3 enhanced CD40L-CD40 engagement on B cells, resulting in NF-κB pathway hyperactivation. Consistent with our murine data, reduced ITGB3 expression in patients with autoimmune disease correlated with transcriptional signatures of B cell activation and inflammation.
CONCLUSIONS: These results reframe integrin β3 as a threshold regulator of B cell activation. The β3-CD40L-CD40 axis therefore represents a potential therapeutic target for B cell-mediated autoimmune diseases.
PMID:41953039 | PMC:PMC13055533 | DOI:10.3389/fimmu.2026.1796926
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cs.AI, q-bio.NC updates on arXiv.org
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InCoder-32B: Code Foundation Model for Industrial Scenarios
arXiv:2603.16790v3 Announce Type: replace-cross Abstract: Recent code large language models have achieved remarkable progress on general programming tasks. Nevertheless, their performance degrades significantly in industrial scenarios that require reasoning about hardware semantics, specialized language constructs, and strict resource constraints. To address these challenges, we introduce InCoder-32B (Industrial-Coder-32B), the first 32B-parameter code foundation model unifying code intelligenc
InCoder-32B: Code Foundation Model for Industrial Scenarios
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cs.AI, q-bio.NC updates on arXiv.org
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How Long Can Unified Multimodal Models Generate Images Reliably? Taming Long-Horizon Interleaved Image Generation via Context Curation
arXiv:2603.07540v1 Announce Type: cross Abstract: Unified multimodal models hold the promise of generating extensive, interleaved narratives, weaving text and imagery into coherent long-form stories. However, current systems suffer from a critical reliability gap: as sequences grow, generation quality rapidly collapses. In this work, we investigate the mechanism behind this failure and argue that it is distinct from standard long-context challenges. We reveal that in generation, accumulated vis
How Long Can Unified Multimodal Models Generate Images Reliably? Taming Long-Horizon Interleaved Image Generation via Context Curation
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cs.AI, q-bio.NC updates on arXiv.org
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BoxMind: Closed-loop AI strategy optimization for elite boxing validated in the 2024 Olympics
arXiv:2601.11492v2 Announce Type: replace Abstract: Competitive sports require sophisticated tactical analysis, yet combat disciplines like boxing remain underdeveloped in AI-driven analytics due to the complexity of action dynamics and the lack of structured tactical representations. To address this, we present BoxMind, a closed-loop AI expert system validated in elite boxing competition. By defining atomic punch events with precise temporal boundaries and spatial and technical attributes, we
BoxMind: Closed-loop AI strategy optimization for elite boxing validated in the 2024 Olympics
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cs.AI, q-bio.NC updates on arXiv.org
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Efficient Self-Evaluation for Diffusion Language Models via Sequence Regeneration
arXiv:2603.02760v1 Announce Type: cross Abstract: Diffusion large language models (dLLMs) have recently attracted significant attention for their ability to enhance diversity, controllability, and parallelism. However, their non-sequential, bidirectionally masked generation makes quality assessment difficult, underscoring the need for effective self-evaluation. In this work, we propose DiSE, a simple yet effective self-evaluation confidence quantification method for dLLMs. DiSE quantifies confi
Efficient Self-Evaluation for Diffusion Language Models via Sequence Regeneration
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cs.AI, q-bio.NC updates on arXiv.org
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HSSBench: Benchmarking Humanities and Social Sciences Ability for Multimodal Large Language Models
arXiv:2506.03922v3 Announce Type: replace-cross Abstract: Multimodal Large Language Models (MLLMs) have demonstrated significant potential to advance a broad range of domains. However, current benchmarks for evaluating MLLMs primarily emphasize general knowledge and vertical step-by-step reasoning typical of STEM disciplines, while overlooking the distinct needs and potential of the Humanities and Social Sciences (HSS). Tasks in the HSS domain require more horizontal, interdisciplinary thinking
HSSBench: Benchmarking Humanities and Social Sciences Ability for Multimodal Large Language Models
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cs.AI, q-bio.NC updates on arXiv.org
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Generative Reasoning Re-ranker
arXiv:2602.07774v4 Announce Type: replace-cross Abstract: Recent studies increasingly explore Large Language Models (LLMs) as a new paradigm for recommendation systems due to their scalability and world knowledge. However, existing work has three key limitations: (1) most efforts focus on retrieval and ranking, while the reranking phase, critical for refining final recommendations, is largely overlooked; (2) LLMs are typically used in zero-shot or supervised fine-tuning settings, leaving their