Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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HyperGuide: Hyperbolic Guidance for Efficient Multi-Step Reasoning in Large Language Models
arXiv:2605.24140v1 Announce Type: new Abstract: Multi-step reasoning remains a central challenge for large language models: single-pass generation is efficient but lacks accuracy; tree-search methods explore multiple paths but are computation-heavy. We address this gap by distilling reasoning progress into a hyperbolic geometric signal that guides step-by-step generation. Our approach is motivated by a structural observation: in combinatorial reasoning trees, solution-bearing states are few whi
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cs.AI, q-bio.NC updates on arXiv.org
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PHGNet: Prototype-Guided Hypergraph Construction for Heterogeneous Spatiotemporal Forecasting
arXiv:2605.25554v1 Announce Type: new Abstract: As a core task in intelligent transportation systems, traffic forecasting plays a critical role in urban traffic management. Accurate traffic forecasting relies on modeling complex spatiotemporal dependencies, which is inherently challenging due to spatial heterogeneity in traffic systems.Despite significant progress, most existing methods are still limited to pairwise spatial dependency modeling, making it difficult to capture dynamic high-order
PHGNet: Prototype-Guided Hypergraph Construction for Heterogeneous Spatiotemporal Forecasting
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cs.AI, q-bio.NC updates on arXiv.org
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STREAM: A Data-Centric Framework for Mining High-Value Task-Oriented Dialogues from Streaming Media
arXiv:2605.25162v1 Announce Type: cross Abstract: Large language models for vertical domains are bottlenecked by the scarcity of complex, domain-specific task-oriented dialogues. Existing data acquisition pipelines face a persistent trilemma: expert annotation is expensive, real-world service conversations are constrained by privacy and commercial restrictions, and static corpora quickly become temporally stale. We propose Stream, a data-centric framework that leverages publicly available strea
STREAM: A Data-Centric Framework for Mining High-Value Task-Oriented Dialogues from Streaming Media
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cs.AI, q-bio.NC updates on arXiv.org
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Reliable AI Needs to Externalize Implicit Knowledge: A Human-AI Collaboration Perspective
arXiv:2605.02010v2 Announce Type: replace Abstract: This position paper argues that reliable AI requires infrastructure for human validation of implicit knowledge. AI learns from both explicit knowledge (papers, documentation, structured databases) and implicit knowledge (reasoning patterns, debugging processes, intermediate steps). Implicit knowledge remains unexternalized because documentation cost exceeds perceived value -- yet AI learns from it indiscriminately, acquiring both beneficial pa
Reliable AI Needs to Externalize Implicit Knowledge: A Human-AI Collaboration Perspective
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cs.AI, q-bio.NC updates on arXiv.org
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SURGE: Surrogate Gradient Adaptation in Binary Neural Networks
arXiv:2605.10989v3 Announce Type: replace-cross Abstract: The training of Binary Neural Networks (BNNs) is fundamentally based on gradient approximation for non-differentiable binarization operations (e.g., sign function). However, prevailing methods including the Straight-Through Estimator (STE) and its improved variants, rely on hand-crafted designs that suffer from gradient mismatch problem and information loss induced by fixed-range gradient clipping. To address this, we propose SURrogate G
SURGE: Surrogate Gradient Adaptation in Binary Neural Networks
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npj Digital Medicine
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Personalized neoadjuvant treatment regimen selection in locally advanced rectal cancer based on regimen-specific response modeling
npj Digital Medicine, Published online: 26 May 2026; doi:10.1038/s41746-026-02798-wPersonalized neoadjuvant treatment regimen selection in locally advanced rectal cancer based on regimen-specific response modeling
Personalized neoadjuvant treatment regimen selection in locally advanced rectal cancer based on regimen-specific response modeling
npj Digital Medicine, Published online: 26 May 2026; doi:10.1038/s41746-026-02798-w
Personalized neoadjuvant treatment regimen selection in locally advanced rectal cancer based on regimen-specific response modeling-
(Multiomics OR Omics) AND (Pancreatic)
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Human pancreatic progenitor organoids define genetic and epigenetic barriers to early PDAC transformation
Dev Cell. 2026 May 19:S1534-5807(26)00159-0. doi: 10.1016/j.devcel.2026.04.012. Online ahead of print.ABSTRACTThe lack of accurate human models that recapitulate pancreatic ductal adenocarcinoma (PDAC) initiation 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 trajectories of tumor initiation and progression, validated against clinica
Human pancreatic progenitor organoids define genetic and epigenetic barriers to early PDAC transformation
Dev Cell. 2026 May 19:S1534-5807(26)00159-0. doi: 10.1016/j.devcel.2026.04.012. Online ahead of print.
ABSTRACT
The lack of accurate human models that recapitulate pancreatic ductal adenocarcinoma (PDAC) initiation 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 trajectories of tumor initiation and progression, validated against clinical datasets and tumor histopathology. We demonstrate that CDKN2A loss, which is nearly universal in patients but dispensable in mouse models, is essential for neoplastic transformation when combined with KRAS and TP53 mutations, whereas SMAD4 loss promotes tumor progression. Multi-omics profiling reveals epigenetic repression of the pancreatic lineage program during PDAC initiation, alongside AP-1-driven chromatin remodeling. We identify TET1 suppression as a mechanistic link between oncogenic ERK signaling and hypermethylation of essential pancreatic transcription factors. This model captures genetic and epigenetic determinants of human PDAC, reveals antagonism between oncogenic and lineage restriction programs, and supports TET-based lineage restoration as a potential early intervention strategy.
PMID:42161274 | PMC:PMC13196429 | DOI:10.1016/j.devcel.2026.04.012
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Nature - Issue - nature.com science feeds
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Advancing solar and wind penetration in China through energy complementarity
Nature, Published online: 20 May 2026; doi:10.1038/s41586-026-10570-zUsing high-resolution satellite imagery combined with a deep-learning-based framework to build a national energy inventory enables a data-driven assessment of solar–wind complementarity strategies to reduce power variability and enhance renewable energy penetration across China.
Advancing solar and wind penetration in China through energy complementarity
Nature, Published online: 20 May 2026; doi:10.1038/s41586-026-10570-z
Using high-resolution satellite imagery combined with a deep-learning-based framework to build a national energy inventory enables a data-driven assessment of solar–wind complementarity strategies to reduce power variability and enhance renewable energy penetration across China.-
Omics In Lung
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GPNMB Drives Brain Metastasis by Sculpting a Pathological Endothelial-Immune Interactome
Cancer Discov. 2026 Apr 15. doi: 10.1158/2159-8290.CD-25-1663. Online ahead of print.ABSTRACTBrain metastases (BM) remain a devastating disease with dismal prognosis. How circulating tumor cells (CTCs) penetrate the blood brain barrier (BBB) and reprogram the brain microenvironment remain unclear. Using spatially resolved multi-omic profiling of CTCs and brain metastases, integrated with experimental and clinical analyses, we identified Glycoprotein Non-Metastatic Melanoma Protein B (GPNMB) as a
GPNMB Drives Brain Metastasis by Sculpting a Pathological Endothelial-Immune Interactome
Cancer Discov. 2026 Apr 15. doi: 10.1158/2159-8290.CD-25-1663. Online ahead of print.
ABSTRACT
Brain metastases (BM) remain a devastating disease with dismal prognosis. How circulating tumor cells (CTCs) penetrate the blood brain barrier (BBB) and reprogram the brain microenvironment remain unclear. Using spatially resolved multi-omic profiling of CTCs and brain metastases, integrated with experimental and clinical analyses, we identified Glycoprotein Non-Metastatic Melanoma Protein B (GPNMB) as a CTC-secreted driver of vascular disruption and brain colonization. CBX3 upregulation induced GPNMB expression, which bound endothelial EGFR, triggering CBL-mediated ubiquitination and degradation. Attenuated EGFR signaling suppressed FTO and disrupted endothelial junctions via YTHDF2-dependent TJP1 m6A methylation. Remarkably, GPNMB-induced BBB remodeling promoted immune infiltration via CXCL12-CXCR4 axis, and induced time course-dependent T cell exhaustion within the brain microenvironment. Clinically, elevated CBX3⁺GPNMB⁺ CTCs and plasma CXCL12 were significantly associated with BM progression in lung cancer and melanoma. Therapeutically, dual blockade of GPNMB and PD1 enhanced anti-BM efficacy in mice, unveiling GPNMB as a promising target for precision immunotherapy.
PMID:41973996 | DOI:10.1158/2159-8290.CD-25-1663
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Cell
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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
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(Multiomics OR Omics) AND (Pancreatic)
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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.ABSTRACTThe 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 data
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
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Nature - Issue - nature.com science feeds
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The importance of competition and facilitation for global tree diversity
Nature, Published online: 08 April 2026; doi:10.1038/s41586-026-10349-2Across 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.
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.-
cs.AI, q-bio.NC updates on arXiv.org
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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 f
XAttnRes: Cross-Stage Attention Residuals for Medical Image Segmentation
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cs.AI, q-bio.NC updates on arXiv.org
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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 p
Infeasibility Aware Large Language Models for Combinatorial Optimization
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cs.AI, q-bio.NC updates on arXiv.org
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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 trans
Four Generations of Quantum Biomedical Sensors
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cs.AI, q-bio.NC updates on arXiv.org
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Four Generations of Quantum Biomedical Sensors
arXiv:2603.29944v1 Announce Type: 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
Four Generations of Quantum Biomedical Sensors
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cs.AI, q-bio.NC updates on arXiv.org
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InfiniteVL: Synergizing Linear and Sparse Attention for Highly-Efficient, Unlimited-Input Vision-Language Models
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
InfiniteVL: Synergizing Linear and Sparse Attention for Highly-Efficient, Unlimited-Input Vision-Language Models
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Nature - Issue - nature.com science feeds
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Gene regulatory landscape dissected by single-cell four-omics sequencing
Nature, Published online: 01 April 2026; doi:10.1038/s41586-026-10322-zCombining single-cell parallel profiling of genome conformation, histone modifications, chromatin accessibility and gene expression reveals dynamics and intranuclear spatial clustering of epigenome profiles, enabling sophisticated analysis of the regulatory landscape across cell types and tissues.
Gene regulatory landscape dissected by single-cell four-omics sequencing
Nature, Published online: 01 April 2026; doi:10.1038/s41586-026-10322-z
Combining single-cell parallel profiling of genome conformation, histone modifications, chromatin accessibility and gene expression reveals dynamics and intranuclear spatial clustering of epigenome profiles, enabling sophisticated analysis of the regulatory landscape across cell types and tissues.-
cs.AI, q-bio.NC updates on arXiv.org
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TDATR: Improving End-to-End Table Recognition via Table Detail-Aware Learning and Cell-Level Visual Alignment
arXiv:2603.22819v1 Announce Type: cross Abstract: Tables are pervasive in diverse documents, making table recognition (TR) a fundamental task in document analysis. Existing modular TR pipelines separately model table structure and content, leading to suboptimal integration and complex workflows. End-to-end approaches rely heavily on large-scale TR data and struggle in data-constrained scenarios. To address these issues, we propose TDATR (Table Detail-Aware Table Recognition) improves end-to-end
TDATR: Improving End-to-End Table Recognition via Table Detail-Aware Learning and Cell-Level Visual Alignment
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cs.AI, q-bio.NC updates on arXiv.org
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BIRD-INTERACT: Re-imagining Text-to-SQL Evaluation for Large Language Models via Lens of Dynamic Interactions
arXiv:2510.05318v3 Announce Type: replace Abstract: Large language models (LLMs) have demonstrated remarkable performance on single-turn text-to-SQL tasks, but real-world database applications predominantly require multi-turn interactions to handle ambiguous queries, execution errors, and evolving user requirements. Existing multi-turn benchmarks fall short by treating conversation histories as static context or limiting evaluation to read-only operations, failing to reflect production-grade da