Normal view
-
cs.AI, q-bio.NC updates on arXiv.org
-
The Anatomy and Boundary of Adaptation under Temporal Tabular Shift
arXiv:2609.12136v1 Announce Type: cross Abstract: Prequential adaptation of frozen tabular foundation models under temporal drift, with each label revealed only after prediction, helps some deployments and harms others, yet current practice does not predict which. We study the sources and limits of these gains. A diagnostic anatomy attributes gains to four recurring mechanisms under a streaming protocol that removes three optimistic biases and quantifies a fourth. Within an agnostic total-varia
-
cs.AI, q-bio.NC updates on arXiv.org
-
SCOPE-OPSD: Fisher-Conditioned Privileged Subspaces for On-Policy Self-Distillation
arXiv:2609.12579v1 Announce Type: cross Abstract: On-policy self-distillation (OPSD) scores student-generated prefixes with a solution-conditioned self-teacher, yet transfers supervision only through next-token probabilities. We ask whether the aligned final-layer discrepancy offers a useful second channel, and how to test that channel without confusing its geometry with auxiliary strength. SCOPE-OPSD projects the privileged teacher-student residual onto a frozen rank-64 factor estimated from r
SCOPE-OPSD: Fisher-Conditioned Privileged Subspaces for On-Policy Self-Distillation
-
Cell Death Discovery nature.com science feeds
-
Hepatic Usp2 orchestrates de novo lipogenesis through G3bp2 stabilization and β-catenin activation
Cell Death Discovery, Published online: 14 September 2026; doi:10.1038/s41420-026-03333-2Hepatic Usp2 orchestrates de novo lipogenesis through G3bp2 stabilization and β-catenin activation
Hepatic Usp2 orchestrates de novo lipogenesis through G3bp2 stabilization and β-catenin activation
Cell Death Discovery, Published online: 14 September 2026; doi:10.1038/s41420-026-03333-2
Hepatic Usp2 orchestrates de novo lipogenesis through G3bp2 stabilization and β-catenin activation-
Omics In Lung
-
Multi-omics approaches in idiopathic pulmonary fibrosis: from molecular mechanisms to therapeutic targets and precision medicine
Front Pharmacol. 2026 Aug 28;17:1899849. doi: 10.3389/fphar.2026.1899849. eCollection 2026.ABSTRACTIdiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease with limited therapeutic options and marked molecular heterogeneity. Despite available antifibrotic therapies, disease progression remains poorly predictable, highlighting the need for improved mechanistic understanding and therapeutic targeting. This review summarizes recent advances in multi-omics research to elucidate
Multi-omics approaches in idiopathic pulmonary fibrosis: from molecular mechanisms to therapeutic targets and precision medicine
Front Pharmacol. 2026 Aug 28;17:1899849. doi: 10.3389/fphar.2026.1899849. eCollection 2026.
ABSTRACT
Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease with limited therapeutic options and marked molecular heterogeneity. Despite available antifibrotic therapies, disease progression remains poorly predictable, highlighting the need for improved mechanistic understanding and therapeutic targeting. This review summarizes recent advances in multi-omics research to elucidate the molecular mechanisms underlying IPF and to identify potential biomarkers and pharmacological targets. Multi-omics studies, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiome profiling, and single-cell sequencing, have revealed key pathogenic mechanisms in IPF. Genetic susceptibility factors such as MUC5B promoter variants and telomere-related genes contribute to disease risk. Epigenetic regulation, including DNA methylation, histone modifications, and non-coding RNAs, plays a central role in fibrotic remodeling. Transcriptomic and proteomic analyses have identified dysregulated signaling pathways, including TGF-β, mTOR, cellular senescence, and extracellular matrix remodeling. Metabolomic alterations indicate disrupted lipid and amino acid metabolism. Importantly, integration of multi-omics datasets enables the identification of molecular endotypes, candidate biomarkers, and potential therapeutic targets. However, challenges including data integration, tissue heterogeneity, limited cohort size, and the need for functional validation remain important barriers to clinical translation. Continued development of multi-omics approaches may facilitate more accurate disease classification and support the development of personalized therapeutic strategies for IPF.
PMID:42729333 | PMC:PMC13561894 | DOI:10.3389/fphar.2026.1899849
-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
-
Multi-omics approaches in idiopathic pulmonary fibrosis: from molecular mechanisms to therapeutic targets and precision medicine
Front Pharmacol. 2026 Aug 28;17:1899849. doi: 10.3389/fphar.2026.1899849. eCollection 2026.ABSTRACTIdiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease with limited therapeutic options and marked molecular heterogeneity. Despite available antifibrotic therapies, disease progression remains poorly predictable, highlighting the need for improved mechanistic understanding and therapeutic targeting. This review summarizes recent advances in multi-omics research to elucidate
Multi-omics approaches in idiopathic pulmonary fibrosis: from molecular mechanisms to therapeutic targets and precision medicine
Front Pharmacol. 2026 Aug 28;17:1899849. doi: 10.3389/fphar.2026.1899849. eCollection 2026.
ABSTRACT
Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease with limited therapeutic options and marked molecular heterogeneity. Despite available antifibrotic therapies, disease progression remains poorly predictable, highlighting the need for improved mechanistic understanding and therapeutic targeting. This review summarizes recent advances in multi-omics research to elucidate the molecular mechanisms underlying IPF and to identify potential biomarkers and pharmacological targets. Multi-omics studies, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiome profiling, and single-cell sequencing, have revealed key pathogenic mechanisms in IPF. Genetic susceptibility factors such as MUC5B promoter variants and telomere-related genes contribute to disease risk. Epigenetic regulation, including DNA methylation, histone modifications, and non-coding RNAs, plays a central role in fibrotic remodeling. Transcriptomic and proteomic analyses have identified dysregulated signaling pathways, including TGF-β, mTOR, cellular senescence, and extracellular matrix remodeling. Metabolomic alterations indicate disrupted lipid and amino acid metabolism. Importantly, integration of multi-omics datasets enables the identification of molecular endotypes, candidate biomarkers, and potential therapeutic targets. However, challenges including data integration, tissue heterogeneity, limited cohort size, and the need for functional validation remain important barriers to clinical translation. Continued development of multi-omics approaches may facilitate more accurate disease classification and support the development of personalized therapeutic strategies for IPF.
PMID:42729333 | PMC:PMC13561894 | DOI:10.3389/fphar.2026.1899849
-
Nature Medicine
-
A clinically-oriented foundation model for intraoperative pathology
Nature Medicine, Published online: 10 September 2026; doi:10.1038/s41591-026-04703-0CRISP, a vision-based pathology foundation model developed exclusively from frozen section slides, supports treatment decision-making throughout the surgical workflow with superior performance to current foundation models and extensive validation, including in a prospective cohort.
A clinically-oriented foundation model for intraoperative pathology
Nature Medicine, Published online: 10 September 2026; doi:10.1038/s41591-026-04703-0
CRISP, a vision-based pathology foundation model developed exclusively from frozen section slides, supports treatment decision-making throughout the surgical workflow with superior performance to current foundation models and extensive validation, including in a prospective cohort.-
cs.AI, q-bio.NC updates on arXiv.org
-
UnitBoost: Managing Compound LLM Systems with a Merge Operator, Not a Model
arXiv:2609.09815v1 Announce Type: new Abstract: Compound LLM systems often solve a coordination problem by adding a higher-level LLM. The resulting meta-agent reads workers' outputs, writes the final answer, allocates later calls, and decides when to stop. It is expressive, but it also concentrates three control decisions in an opaque, order-sensitive model call. We ask whether the manager needs to be generative at all. UnitBoost replaces that model with a defined meta-level operator: a task-gi
UnitBoost: Managing Compound LLM Systems with a Merge Operator, Not a Model
-
Cell
-
Genomics and social practices at Mogou and other Gansu sites during prehistoric trans-Eurasian exchange
Ancient DNA from 149 individuals at 11 sites in Gansu, China, dated to around 4,700–3,000 years ago, reveals human population history during early transcontinental exchanges of agriculture and technology, as well as contemporary social practices, at the large Mogou cemetery.
Genomics and social practices at Mogou and other Gansu sites during prehistoric trans-Eurasian exchange
-
Cell
-
Targeting peripheral 5-HT2AR enhances antitumor immunity in colorectal cancer
By selectively targeting peripheral 5-HT2AR without inducing psychedelic effects, a non-brain-penetrant agonist boosts antitumor CD8+ T cell immunity and improves immunotherapy responses in preclinical models of colorectal cancer.
Targeting peripheral 5-HT2AR enhances antitumor immunity in colorectal cancer
-
cs.AI, q-bio.NC updates on arXiv.org
-
MindAlign: Bridging EEG, Vision, and Language for Zero-Shot Visual Decoding
arXiv:2605.24523v1 Announce Type: cross Abstract: Visual decoding from brain signals is a key challenge at the intersection of computer vision and neuroscience, requiring methods that bridge neural representations and computational models of vision. We introduce a tri-modal contrastive framework for EEG-based visual decoding that aligns EEG, visual, and textual representations within a unified latent space. Our approach follows a two-stage design. First, we pre-train an EEG encoder via masked r
MindAlign: Bridging EEG, Vision, and Language for Zero-Shot Visual Decoding
-
cs.AI, q-bio.NC updates on arXiv.org
-
What Are We Actually Decoding? Source Attribution for Non-Invasive Brain-to-Language Retrieval
arXiv:2605.24524v1 Announce Type: cross Abstract: In non-invasive neural language decoding, results can be inflated by sources that are not stimulus-evoked neural evidence: decoder priors, embedding-based metrics, and non-neural structural nuisances such as signal duration. The methodological challenge is therefore attribution: a reported gain is more informative when it can be traced to a specific source. We recast stimulus-locked MEG-to-audio retrieval as an auditing framework that separates
What Are We Actually Decoding? Source Attribution for Non-Invasive Brain-to-Language Retrieval
-
(Multiomics OR Omics) AND (Pancreatic)
-
Multi-omics Analysis Reveals the Protection of a Quadruple Probiotic Mixture in Experimental Autoimmune Hepatitis
Probiotics Antimicrob Proteins. 2026 May 23. doi: 10.1007/s12602-026-11062-2. Online ahead of print.ABSTRACTAutoimmune hepatitis (AIH) is a chronic progressive inflammatory liver disease with a rising global incidence. The treatment of AIH remains challenging because first-line drugs show limited efficacy and systemic side effects. Gut microbiota plays a crucial role in the pathogenesis of AIH, leading to growing interest in developing probiotic-based therapies. In this study, we used multi-omic
Multi-omics Analysis Reveals the Protection of a Quadruple Probiotic Mixture in Experimental Autoimmune Hepatitis
Probiotics Antimicrob Proteins. 2026 May 23. doi: 10.1007/s12602-026-11062-2. Online ahead of print.
ABSTRACT
Autoimmune hepatitis (AIH) is a chronic progressive inflammatory liver disease with a rising global incidence. The treatment of AIH remains challenging because first-line drugs show limited efficacy and systemic side effects. Gut microbiota plays a crucial role in the pathogenesis of AIH, leading to growing interest in developing probiotic-based therapies. In this study, we used multi-omics analysis to investigate the therapeutic effects of a quadruple probiotic mixture (Probiotic-quad) consisting of Bifidobacterium infantis, Lactobacillus acidophilus, Enterococcus faecalis, and Bacillus cereus in a well-established chronic AIH murine model. Our results showed that Probiotic-quad treatment significantly alleviated AIH progression, as evidenced by lower serum liver enzyme levels, ameliorated hepatic inflammatory infiltration and histopathological damage. Metagenomic sequencing results showed that gut dysbiosis in AIH mice was partially reversed after Probiotic-quad administration. Additionally, the integrity of the intestinal epithelial barrier was restored, accompanied by a reduction in serum lipopolysaccharide levels. Untargeted metabolomic and transcriptomic analysis revealed that Probiotic-quad treatment was linked to alterations in hepatic metabolism, including the citrate cycle and tryptophan metabolism, and was associated with reduced activation of the NF-κB and NOD-like receptor signaling pathways. These findings suggest that Probiotic-quad treatment ameliorates AIH severity and is potentially associated with changes in hepatic immune responses, metabolism, gut microbiota, and intestinal barrier function, highlighting its potential as an adjuvant therapy for AIH.
PMID:42176246 | DOI:10.1007/s12602-026-11062-2
-
Nature Cancer
-
CD300ld on pathologically activated neutrophils promotes tumor immune suppression by binding phosphatidylserine on CD8<sup>+</sup> T cells
Nature Cancer, Published online: 15 May 2026; doi:10.1038/s43018-026-01169-4Zhao and colleagues show that CD300ld, upregulated in pathologically activated neutrophils, mediates contact-dependent suppression of cytotoxic CD8+ T cells by binding to phosphatidylserine, inhibiting antitumor immune responses.
CD300ld on pathologically activated neutrophils promotes tumor immune suppression by binding phosphatidylserine on CD8<sup>+</sup> T cells
Nature Cancer, Published online: 15 May 2026; doi:10.1038/s43018-026-01169-4
Zhao and colleagues show that CD300ld, upregulated in pathologically activated neutrophils, mediates contact-dependent suppression of cytotoxic CD8+ T cells by binding to phosphatidylserine, inhibiting antitumor immune responses.-
Cell
-
Pan-neurodegeneration proteomics reveals disease subtypes and molecular signatures
A pan-neurodegeneration atlas built from multilayer, deep proteomics of 2,279 brain samples across 6 major diseases integrates whole proteome, detergent-insoluble proteome, and posttranslational modifications to enable intra- and inter-disease comparisons to reveal disease-specific subtypes and dysregulated pathways, while identifying shared changes such as GPNMB upregulation and NPTX2 downregulation.
Pan-neurodegeneration proteomics reveals disease subtypes and molecular signatures
-
cs.AI, q-bio.NC updates on arXiv.org
-
BAAI Cardiac Agent: An intelligent multimodal agent for automated reasoning and diagnosis of cardiovascular diseases from cardiac magnetic resonance imaging
arXiv:2604.04078v1 Announce Type: cross Abstract: Cardiac magnetic resonance (CMR) is a cornerstone for diagnosing cardiovascular disease. However, it remains underutilized due to complex, time-consuming interpretation across multi-sequences, phases, quantitative measures that heavily reliant on specialized expertise. Here, we present BAAI Cardiac Agent, a multimodal intelligent system designed for end-to-end CMR interpretation. The agent integrates specialized cardiac expert models to perform
BAAI Cardiac Agent: An intelligent multimodal agent for automated reasoning and diagnosis of cardiovascular diseases from cardiac magnetic resonance imaging
-
cs.AI, q-bio.NC updates on arXiv.org
-
ATLAS: A Layered Constraint-Guided Framework for Structured Artifact Generation in LLM-Assisted MDE
arXiv:2510.25890v3 Announce Type: replace-cross Abstract: ATLAS is a constraint-guided generation framework for structured engineering artifacts whose outputs must satisfy explicit schemas, domain rules, and audit requirements. Rather than treating a large language model as a standalone generator, ATLAS places generation inside a model-driven workflow that separates domain representation, constraint compilation, and post-generation validation. ATLAS combines three components. A metamodel-integr
ATLAS: A Layered Constraint-Guided Framework for Structured Artifact Generation in LLM-Assisted MDE
-
cs.AI, q-bio.NC updates on arXiv.org
-
RASA: Routing-Aware Safety Alignment for Mixture-of-Experts Models
arXiv:2602.04448v2 Announce Type: replace-cross Abstract: Mixture-of-Experts (MoE) language models introduce unique challenges for safety alignment due to their sparse routing mechanisms, which can enable degenerate optimization behaviors under standard full-parameter fine-tuning. In our preliminary experiments, we observe that naively applying full-parameter safety fine-tuning to MoE models can reduce attack success rates through routing or expert dominance effects, rather than by directly rep
RASA: Routing-Aware Safety Alignment for Mixture-of-Experts Models
-
cs.AI, q-bio.NC updates on arXiv.org
-
HISA: Efficient Hierarchical Indexing for Fine-Grained Sparse Attention
arXiv:2603.28458v3 Announce Type: replace-cross Abstract: Token-level sparse attention mechanisms, exemplified by DeepSeek Sparse Attention (DSA), achieve fine-grained key selection by scoring every historical key for each query through a lightweight indexer, then computing attention only on the selected subset. While the downstream sparse attention itself scales favorably, the indexer must still scan the entire prefix for every query, introducing an per-layer bottleneck that grows prohibitivel
HISA: Efficient Hierarchical Indexing for Fine-Grained Sparse Attention
-
cs.AI, q-bio.NC updates on arXiv.org
-
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
Owl-AuraID 1.0: An Intelligent System for Autonomous Scientific Instrumentation and Scientific Data Analysis
-
cs.AI, q-bio.NC updates on arXiv.org
-
JFTA-Bench: Evaluate LLM's Ability of Tracking and Analyzing Malfunctions Using Fault Trees
arXiv:2603.22978v1 Announce Type: new Abstract: In the maintenance of complex systems, fault trees are used to locate problems and provide targeted solutions. To enable fault trees stored as images to be directly processed by large language models, which can assist in tracking and analyzing malfunctions, we propose a novel textual representation of fault trees. Building on it, we construct a benchmark for multi-turn dialogue systems that emphasizes robust interaction in complex environments, ev