Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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RobustSGPO: Search-Space Control for Agent Harness Evolution
arXiv:2609.09646v1 Announce Type: new Abstract: Semantic-gradient-based prompt optimization (SGPO) improves agent harnesses using execution feedback, but its local update rule leaves the choice of edit scope and operation unresolved. We introduce RobustSGPO, which specifies the requested edit, constructs and checks the patch, and continues search from either the incumbent or retained snapshots. We evaluate permission scheduling, cumulative controls, and task-family transfer in the AgentX brains
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Nature Cancer
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SlideChat is a multimodal generative artificial intelligence assistant for whole-slide computational pathology across cancer types
Nature Cancer, Published online: 01 September 2026; doi:10.1038/s43018-026-01220-4Chen et al. have developed SlideChat, a multimodal generative artificial intelligence assistant, which they benchmark on 27 pathology tasks across 33 cancer types. Expert pathologists rated the assistant as clinically relevant and accurate.
SlideChat is a multimodal generative artificial intelligence assistant for whole-slide computational pathology across cancer types
Nature Cancer, Published online: 01 September 2026; doi:10.1038/s43018-026-01220-4
Chen et al. have developed SlideChat, a multimodal generative artificial intelligence assistant, which they benchmark on 27 pathology tasks across 33 cancer types. Expert pathologists rated the assistant as clinically relevant and accurate.-
cs.AI, q-bio.NC updates on arXiv.org
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LGMT: Logic-Grounded Metamorphic Testing for Evaluating the Reasoning Reliability of LLMs
arXiv:2605.23965v1 Announce Type: new Abstract: Large Language Models (LLMs) achieve strong performance on logical reasoning benchmarks, yet their reliability remains uncertain. Existing evaluations rely on static benchmarks, which fail to assess robustness under logically equivalent transformations and often overestimate reasoning capability. We propose LGMT (Logic-Grounded Metamorphic Testing), an oracle-free framework that leverages first-order logic (FOL) to evaluate LLM reasoning. By deriv
LGMT: Logic-Grounded Metamorphic Testing for Evaluating the Reasoning Reliability of LLMs
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cs.AI, q-bio.NC updates on arXiv.org
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Reason--Imagine--Act: Closed-Loop LLM Decision Making with World Models for Autonomous Driving
arXiv:2605.24004v1 Announce Type: new Abstract: Large language models (LLMs) are promising for autonomous driving, but semantics-only decision policies can yield physically unsafe behavior in dynamic traffic. Existing methods either perform online language reasoning without explicit dynamics verification or use world models mainly in offline pipelines, leaving a gap between semantic intent and physical feasibility at decision time. We propose Reason--Imagine--Act (RIA), a closed-loop framework
Reason--Imagine--Act: Closed-Loop LLM Decision Making with World Models for Autonomous Driving
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Nature Cancer
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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.-
Omics in Hepatocellular
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Multi-omics integration identifies ribosome biogenesis-active macrophage subpopulation and its key gene GNL2 in driving liver hepatocellular carcinoma progression and mechanisms
Cancer Cell Int. 2026 May 14. doi: 10.1186/s12935-026-04330-2. Online ahead of print.ABSTRACTBACKGROUND: Liver hepatocellular carcinoma (LIHC) is a common malignancy, yet the core genes driving its progression and potential therapeutic targets remain insufficiently explored. Ribosome biogenesis (RB) is a critical biological process linked to various cancers; however, its systematic role in LIHC remains unclear.METHODS: This study integrated LIHC single-cell RNA-Seq, bulk RNA-Seq, and spatial tra
Multi-omics integration identifies ribosome biogenesis-active macrophage subpopulation and its key gene GNL2 in driving liver hepatocellular carcinoma progression and mechanisms
Cancer Cell Int. 2026 May 14. doi: 10.1186/s12935-026-04330-2. Online ahead of print.
ABSTRACT
BACKGROUND: Liver hepatocellular carcinoma (LIHC) is a common malignancy, yet the core genes driving its progression and potential therapeutic targets remain insufficiently explored. Ribosome biogenesis (RB) is a critical biological process linked to various cancers; however, its systematic role in LIHC remains unclear.
METHODS: This study integrated LIHC single-cell RNA-Seq, bulk RNA-Seq, and spatial transcriptomic data with ribosome biogenesis-related gene sets to construct a single-cell atlas of LIHC. Weighted Gene Co-expression Network Analysis (WGCNA) was employed to characterize myeloid cell subsets. Furthermore, an LIHC prognostic risk model based on RB-related genes was developed using 117 machine-learning algorithm combinations. Key findings were subsequently corroborated through experimental validation and clinical sample analysis.
RESULTS: We identified a distinct macrophage subpopulation with high ribosome biogenesis activity, termed ribosome biogenesis-active macrophages (RAMs). These cells exhibited strong communication with inflammatory macrophages, potentially mediated by MIF-related receptor-ligand interactions. We further constructed an 8-gene prognostic model (PA2G4, GNL2, PWP1, DDX49, NOC4L, GDI2, CST7, and RCL1), which showed good predictive performance. Drug sensitivity analysis suggested that the high-risk group may be more responsive to several agents, including docetaxel. Among these genes, GNL2 was selected for further investigation. Elevated GNL2 expression was associated with increased stemness features in myeloid cells. Molecular docking analysis identified several candidate compounds with potential binding affinity to GNL2. Functionally, GNL2 knockdown in macrophages reduced TGF-β and TNF-α expression and was associated with decreased proliferation, migration, and invasion of LIHC cells.
CONCLUSION: We identified a highly active ribosome biogenesis-macrophage subpopulation (RAM), and constructed a robust risk model to aid in the diagnosis, prognosis, and treatment of LIHC. GNL2 is associated with increased expression of TGF-β and TNF-α and may contribute to LIHC progression.
PMID:42135716 | DOI:10.1186/s12935-026-04330-2
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Pulmonary nodule
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Integrating clinical and multiomics evidence based on disease module theory: deciphering the comorbidity network of psoriasis vulgaris via the Ising model for mechanistic insights
Front Immunol. 2026 Apr 14;17:1744789. doi: 10.3389/fimmu.2026.1744789. eCollection 2026.ABSTRACTPsoriasis vulgaris (PV), a chronic immune-mediated inflammatory dermatosis, is associated with a significant burden of systemic comorbidities. Traditional comorbidity research methods struggle to reveal its complex interconnectedness. Based on large-scale retrospective cohort data, we constructed a PV comorbidity network using the Ising model from statistical physics. Weighted network centrality anal
Integrating clinical and multiomics evidence based on disease module theory: deciphering the comorbidity network of psoriasis vulgaris via the Ising model for mechanistic insights
Front Immunol. 2026 Apr 14;17:1744789. doi: 10.3389/fimmu.2026.1744789. eCollection 2026.
ABSTRACT
Psoriasis vulgaris (PV), a chronic immune-mediated inflammatory dermatosis, is associated with a significant burden of systemic comorbidities. Traditional comorbidity research methods struggle to reveal its complex interconnectedness. Based on large-scale retrospective cohort data, we constructed a PV comorbidity network using the Ising model from statistical physics. Weighted network centrality analysis was used to identify core and hub nodes and elucidate shared molecular mechanisms at the multiomics level (nontargeted proteomics and lipid peroxidation metabolomics). Finally, the impact of IL-17A inhibition (IL-17Ai) on PV and atherosclerosis (assessed by carotid Doppler color ultrasound) was evaluated using a prospective intervention study. The Ising model identified atherosclerosis- coronary heart disease (CHD) as the core comorbidity (degree centrality >10), with pulmonary nodules, hypertension, and fatty liver serving as key hub nodes (betweenness centrality >60). Multiomics analysis revealed a core molecular mechanism in PV, involving immune inflammation, oxidative stress, lipid metabolism disorder, and coagulation abnormalities, where the oxidative stress molecule GPX3 acts as a critical hub. Following IL-17Ai intervention, both skin lesions and early atherosclerosis markers significantly improved, accompanied by downregulation of the proinflammatory peripheral blood factor S100A9 and upregulation of anti-inflammatory lipid peroxidation metabolites (e.g., 17(R)-RVD1). This study systematically revealed the modular hierarchical structure of PV comorbidities at the network topology and molecular mechanism levels, confirming the central role of the IL-17 signaling pathway in driving the comorbidity network. This conclusion was further clinically validated by IL-17Ai intervention outcomes. This research provides theoretical and clinical evidence for early identification, prioritized management, and "one drug, multiple targets" therapeutic strategies for treating PV comorbidities.
PMID:42058202 | PMC:PMC13121148 | DOI:10.3389/fimmu.2026.1744789
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cs.AI, q-bio.NC updates on arXiv.org
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RaPA: Enhancing Transferable Targeted Attacks via Random Parameter Pruning
arXiv:2504.18594v3 Announce Type: replace-cross Abstract: Compared to untargeted attacks, targeted transfer-based attack is still suffering from much lower Attack Success Rates (ASRs), although significant improvements have been achieved by kinds of methods, such as diversifying input, stabilizing the gradient, and re-training surrogate models. In this paper, we find that adversarial examples generated by existing methods rely heavily on a small subset of surrogate model parameters, which in tu
RaPA: Enhancing Transferable Targeted Attacks via Random Parameter Pruning
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cs.AI, q-bio.NC updates on arXiv.org
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ContextDrag: Precise Drag-Based Image Editing via Context-Preserving Token Injection and Position-Aligned Attention
arXiv:2512.08477v2 Announce Type: replace-cross Abstract: Drag-based image editing enables intuitive visual manipulation through point-based drag operations. Existing methods mainly rely on diffusion inversion or pixel-space warping with inpainting. However, inversion inherently introduces approximation errors that degrade texture fidelity, whereas rigid pixel-space operations discard semantic context and produce unnatural deformations. To address these issues, we introduce ContextDrag, to our
ContextDrag: Precise Drag-Based Image Editing via Context-Preserving Token Injection and Position-Aligned Attention
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Cell Death Discovery nature.com science feeds
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Programmed cell death in cancer: targeting necroptosis to kill tumor cell
Cell Death Discovery, Published online: 06 April 2026; doi:10.1038/s41420-026-03002-4Programmed cell death in cancer: targeting necroptosis to kill tumor cell
Programmed cell death in cancer: targeting necroptosis to kill tumor cell
Cell Death Discovery, Published online: 06 April 2026; doi:10.1038/s41420-026-03002-4
Programmed cell death in cancer: targeting necroptosis to kill tumor cell-
cs.AI, q-bio.NC updates on arXiv.org
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ContextBudget: Budget-Aware Context Management for Long-Horizon Search Agents
arXiv:2604.01664v1 Announce Type: new Abstract: LLM-based agents show strong potential for long-horizon reasoning, yet their context size is limited by deployment factors (e.g., memory, latency, and cost), yielding a constrained context budget. As interaction histories grow, this induces a trade-off between retaining past information and staying within the context limit. To address this challenge, we propose Budget-Aware Context Management (BACM), which formulates context management as a sequen
ContextBudget: Budget-Aware Context Management for Long-Horizon Search Agents
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cs.AI, q-bio.NC updates on arXiv.org
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X-World: Controllable Ego-Centric Multi-Camera World Models for Scalable End-to-End Driving
arXiv:2603.19979v2 Announce Type: replace-cross Abstract: Scalable and reliable evaluation is increasingly critical in the end-to-end era of autonomous driving, where vision--language--action (VLA) policies directly map raw sensor streams to driving actions. Yet, current evaluation pipelines still rely heavily on real-world road testing, which is costly, biased toward limited scenario coverage, and difficult to reproduce. These challenges motivate a real-world simulator that can generate realis
X-World: Controllable Ego-Centric Multi-Camera World Models for Scalable End-to-End Driving
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Nature - Issue - nature.com science feeds
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Nanoscale transfer-printed full-colour ultrahigh-resolution quantum dot LEDs
Nature, Published online: 01 April 2026; doi:10.1038/s41586-026-10333-wA dual-action force dynamics strategy using a hard silicon template as a nanoimprinting stamp combined with inverted transfer printing is described for the manufacture of high-performance full-colour ultrahigh-resolution quantum dot light-emitting diodes (LEDs) for active-matrix displays, while revealing electric-field reconstruction in nanoscale arrays and introducing dielectric matching to mitigate field concentration and p
Nanoscale transfer-printed full-colour ultrahigh-resolution quantum dot LEDs
Nature, Published online: 01 April 2026; doi:10.1038/s41586-026-10333-w
A dual-action force dynamics strategy using a hard silicon template as a nanoimprinting stamp combined with inverted transfer printing is described for the manufacture of high-performance full-colour ultrahigh-resolution quantum dot light-emitting diodes (LEDs) for active-matrix displays, while revealing electric-field reconstruction in nanoscale arrays and introducing dielectric matching to mitigate field concentration and performance degradation.-
Cell Death Discovery nature.com science feeds
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Doxorubicin promotes the production of inflammatory cytokines in tumor-associated macrophages through activating lactate dehydrogenase A
Cell Death Discovery, Published online: 31 March 2026; doi:10.1038/s41420-026-03014-0Doxorubicin promotes the production of inflammatory cytokines in tumor-associated macrophages through activating lactate dehydrogenase A
Doxorubicin promotes the production of inflammatory cytokines in tumor-associated macrophages through activating lactate dehydrogenase A
Cell Death Discovery, Published online: 31 March 2026; doi:10.1038/s41420-026-03014-0
Doxorubicin promotes the production of inflammatory cytokines in tumor-associated macrophages through activating lactate dehydrogenase A-
cs.AI, q-bio.NC updates on arXiv.org
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Learning to Trust: How Humans Mentally Recalibrate AI Confidence Signals
arXiv:2603.22634v1 Announce Type: cross Abstract: Productive human-AI collaboration requires appropriate reliance, yet contemporary AI systems are often miscalibrated, exhibiting systematic overconfidence or underconfidence. We investigate whether humans can learn to mentally recalibrate AI confidence signals through repeated experience. In a behavioral experiment (N = 200), participants predicted the AI's correctness across four AI calibration conditions: standard, overconfidence, underconfide
Learning to Trust: How Humans Mentally Recalibrate AI Confidence Signals
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Omics in Hepatocellular
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Hypoxia-related and immune phenotype-related fusion model for non-invasive prognostication of hepatocellular carcinoma treated by TACE: a multicentre study
Gut. 2026 Mar 30:gutjnl-2025-337938. doi: 10.1136/gutjnl-2025-337938. Online ahead of print.ABSTRACTBACKGROUND: Survival outcomes after transarterial chemoembolisation (TACE) vary in hepatocellular carcinoma (HCC) patients, and existing prognostic scores and imaging models often lack generalisability and biological interpretability.OBJECTIVE: To develop and validate a multimodal prognostication model for HCC that allows for a precise assessment of survival outcomes of HCC patients receiving TACE
Hypoxia-related and immune phenotype-related fusion model for non-invasive prognostication of hepatocellular carcinoma treated by TACE: a multicentre study
Gut. 2026 Mar 30:gutjnl-2025-337938. doi: 10.1136/gutjnl-2025-337938. Online ahead of print.
ABSTRACT
BACKGROUND: Survival outcomes after transarterial chemoembolisation (TACE) vary in hepatocellular carcinoma (HCC) patients, and existing prognostic scores and imaging models often lack generalisability and biological interpretability.
OBJECTIVE: To develop and validate a multimodal prognostication model for HCC that allows for a precise assessment of survival outcomes of HCC patients receiving TACE therapy.
DESIGN: This study enrolled 1448 HCC patients, including a TACE cohort (n=1349), a biomarker subset from a randomised trial (n=41), a single-cell RNA sequencing cohort and The Cancer Genome Atlas (TCGA) HCC cohort (n=50). Pre-treatment contrast-enhanced CT images were used to construct deep learning and conventional radiomic models. The early-fusion and late-fusion models (LFMs) were compared, and a clinical-radiologic model (CRM) was formed by integrating the better-performing LFM with clinical variables. Using TCGA data and single-cell transcriptomic profiles, the differences between high-score and low-score groups in tumour immune microenvironment, cellular functional states and key signalling pathways were investigated.
RESULTS: The CRM effectively stratified patients' survival across multiple independent cohorts and achieved more granular risk stratification than the existing clinical models. Multi-omic analyses revealed that in the LFM high-score group, myelocytomatosis oncogene was activated, epithelial-mesenchymal transition enhanced, glycolysis upregulated and hypoxia pathway activated. Single-cell transcriptomic data confirmed that virtually all cell types in high-risk patients scored high in hypoxia, and cytotoxic T cells had a reduced cytotoxic activity.
CONCLUSION: The CRM model can non-invasively predict the prognosis of HCC patients treated by TACE therapy.
PMID:41856522 | DOI:10.1136/gutjnl-2025-337938
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cs.AI, q-bio.NC updates on arXiv.org
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RetroReasoner: A Reasoning LLM for Strategic Retrosynthesis Prediction
arXiv:2603.12666v1 Announce Type: cross Abstract: Retrosynthesis prediction is a core task in organic synthesis that aims to predict reactants for a given product molecule. Traditionally, chemists select a plausible bond disconnection and derive corresponding reactants, which is time-consuming and requires substantial expertise. While recent advancements in molecular large language models (LLMs) have made progress, many methods either predict reactants without strategic reasoning or conduct onl
RetroReasoner: A Reasoning LLM for Strategic Retrosynthesis Prediction
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Nature - Issue - nature.com science feeds
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Author Correction: SLAMF6 as a drug-targetable suppressor of T cell immunity against cancer
Nature, Published online: 13 March 2026; doi:10.1038/s41586-026-10376-zAuthor Correction: SLAMF6 as a drug-targetable suppressor of T cell immunity against cancer
Author Correction: SLAMF6 as a drug-targetable suppressor of T cell immunity against cancer
Nature, Published online: 13 March 2026; doi:10.1038/s41586-026-10376-z
Author Correction: SLAMF6 as a drug-targetable suppressor of T cell immunity against cancer-
Nature - Issue - nature.com science feeds
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Structures of Marburgvirus glycoprotein and its complex with NPC1 receptor
Nature, Published online: 11 March 2026; doi:10.1038/s41586-026-10240-0Marburgvirus glycoprotein binds to the endosomal receptor NPC1 in a distinct orientation with higher affinity compared with Ebola virus glycoprotein, accompanied by fusion-relevant rearrangements, enabling more efficient viral entry.
Structures of Marburgvirus glycoprotein and its complex with NPC1 receptor
Nature, Published online: 11 March 2026; doi:10.1038/s41586-026-10240-0
Marburgvirus glycoprotein binds to the endosomal receptor NPC1 in a distinct orientation with higher affinity compared with Ebola virus glycoprotein, accompanied by fusion-relevant rearrangements, enabling more efficient viral entry.-
Nature - Issue - nature.com science feeds
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Risk-adaptive therapy guided by dynamic ctDNA in nasopharyngeal carcinoma
Nature, Published online: 11 March 2026; doi:10.1038/s41586-026-10244-wA clinical trial testing whether monitoring ctDNA clearance during treatment for nasopharyngeal cancer could be used to inform decisions about an individual’s subsequent therapeutic programme shows promising results.
Risk-adaptive therapy guided by dynamic ctDNA in nasopharyngeal carcinoma
Nature, Published online: 11 March 2026; doi:10.1038/s41586-026-10244-w
A clinical trial testing whether monitoring ctDNA clearance during treatment for nasopharyngeal cancer could be used to inform decisions about an individual’s subsequent therapeutic programme shows promising results.