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Integration of multi-omics and machine learning to identify core genes in PANoptosisof lung adenocarcinoma and their mechanisms in the tumor microenvironment and therapeutic potential

Naunyn Schmiedebergs Arch Pharmacol. 2026 Apr 5. doi: 10.1007/s00210-026-05251-7. Online ahead of print.

ABSTRACT

Lung adenocarcinoma (LUAD) is one of the leading causes of cancer-related deaths worldwide, and its complex tumor microenvironment (TME) is a key barrier to treatment. PANoptosis is a novel programmed cell death mechanism that integrates features of pyroptosis, apoptosis, and necroptosis. However, its core regulatory network and cell specific role in LUAD are still unclear. This study integrated three LUAD transcriptome datasets, screened differentially expressed genes through bioinformatics analysis, and intersected with PANoptosis-related genes to construct a protein interaction network, using a combination of 113 machine learning algorithms to screen and validate core genes and using CIBERSORT and single-cell transcriptome data to analyze the spatial expression characteristics of immune cell infiltration and core genes. Finally, the intervention mechanism of core targets and ginsenosides was validated through molecular docking, immunohistochemistry, and cell experiments (CCK-8, Western Blot). Six core genes of LUAD PANoptosis, including IRF1, NLRP3, CASP1, TIMP1, S100A8, and TLR4, were identified in the study. Single-cell analysis revealed that these genes were significantly enriched in M2 macrophages. Functional enrichment indicates that they jointly regulate death- and inflammation-related pathways such as NF-ΞΊB signaling and NOD-like receptor signaling. In vitro experiments have confirmed that ginsenosides can induce PANoptosis, promote tumor cell death, or inhibit LUAD cell proliferation by upregulating the ZBP1/AIM2/RIPK3/CASP1 death complex and inhibiting the TLR4/NLRP3 survival signaling axis. This study systematically revealed a PANoptosis core gene network centered on M2 macrophages in LUAD, elucidating a new mechanism by which ginsenosides induce integrated cell death by regulating this network. This provides new potential targets and theoretical basis for the immunotherapy of LUAD and the development of traditional Chinese medicine monomers.

PMID:41935997 | DOI:10.1007/s00210-026-05251-7

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Integration of multi-omics and machine learning to identify core genes in PANoptosisof lung adenocarcinoma and their mechanisms in the tumor microenvironment and therapeutic potential

Naunyn Schmiedebergs Arch Pharmacol. 2026 Apr 5. doi: 10.1007/s00210-026-05251-7. Online ahead of print.

ABSTRACT

Lung adenocarcinoma (LUAD) is one of the leading causes of cancer-related deaths worldwide, and its complex tumor microenvironment (TME) is a key barrier to treatment. PANoptosis is a novel programmed cell death mechanism that integrates features of pyroptosis, apoptosis, and necroptosis. However, its core regulatory network and cell specific role in LUAD are still unclear. This study integrated three LUAD transcriptome datasets, screened differentially expressed genes through bioinformatics analysis, and intersected with PANoptosis-related genes to construct a protein interaction network, using a combination of 113 machine learning algorithms to screen and validate core genes and using CIBERSORT and single-cell transcriptome data to analyze the spatial expression characteristics of immune cell infiltration and core genes. Finally, the intervention mechanism of core targets and ginsenosides was validated through molecular docking, immunohistochemistry, and cell experiments (CCK-8, Western Blot). Six core genes of LUAD PANoptosis, including IRF1, NLRP3, CASP1, TIMP1, S100A8, and TLR4, were identified in the study. Single-cell analysis revealed that these genes were significantly enriched in M2 macrophages. Functional enrichment indicates that they jointly regulate death- and inflammation-related pathways such as NF-ΞΊB signaling and NOD-like receptor signaling. In vitro experiments have confirmed that ginsenosides can induce PANoptosis, promote tumor cell death, or inhibit LUAD cell proliferation by upregulating the ZBP1/AIM2/RIPK3/CASP1 death complex and inhibiting the TLR4/NLRP3 survival signaling axis. This study systematically revealed a PANoptosis core gene network centered on M2 macrophages in LUAD, elucidating a new mechanism by which ginsenosides induce integrated cell death by regulating this network. This provides new potential targets and theoretical basis for the immunotherapy of LUAD and the development of traditional Chinese medicine monomers.

PMID:41935997 | DOI:10.1007/s00210-026-05251-7

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Stronger Normalization-Free Transformers

arXiv:2512.10938v2 Announce Type: replace-cross Abstract: Although normalization layers have long been viewed as indispensable components of deep learning architectures, the recent introduction of Dynamic Tanh (DyT) has demonstrated that alternatives are possible. The point-wise function DyT constrains extreme values for stable convergence and reaches normalization-level performance; this work seeks further for function designs that can surpass it. We first study how the intrinsic properties of point-wise functions influence training and performance. Building on these findings, we conduct a large-scale search for a more effective function design. Through this exploration, we introduce $\mathrm{Derf}(x) = \mathrm{erf}(\alpha x + s)$, where $\mathrm{erf}(x)$ is the rescaled Gaussian cumulative distribution function, and identify it as the most performant design. Derf outperforms LayerNorm, RMSNorm, and DyT across a wide range of domains, including visual recognition and generation, speech representation, and DNA sequence modeling. Our analysis also suggests that the performance gains of Derf largely stem from its improved generalization rather than stronger fitting capacity. Its simplicity and stronger performance make Derf a practical choice for normalization-free Transformer architectures.
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Functional-based multi-omics early prediction of radiation pneumonitis in NSCLC using AI-generated perfusion and ventilation from planning CT

Phys Med Biol. 2026 Mar 13. doi: 10.1088/1361-6560/ae5209. Online ahead of print.

ABSTRACT

ObjectiveThis study aims to develop a functional-based multi-omics model for early prediction of radiation pneumonitis (RP) by extracting radiomic and dosiomic features from functionally defined lung regions, using generated perfusion (Q) and ventilation (V) from pre-radiotherapy planning computed tomography (CT).
ApproachWe retrospectively analyzed data from 121 patients with locally advanced non-small cell lung cancer (NSCLC) treated with curative-intent IMRT between 2015 and 2019, including pre-treatment CT and dose maps. Q and V maps were generated from CT with deep learning-based and supervoxel-based approaches, respectively. Regions of interest (ROIs) combined the planning target volume (PTV) with each of three functional lung regions-high functional lung (HFL), low functional lung (LFL), and whole lung (WL)-defined by thresholds on Q and V maps. Radiomic and dosiomic features were extracted from CT and dose distributions within each ROI. For each ROI, For each ROI, three methods-radiomics (R), dosiomics (D), and dual-omics (RD)-were constructed. 13 machine learning algorithms were trained and evaluated using 10-fold cross-validation, and model performance was assessed by the average area under the receiver operating characteristic curve (AUC), accuracy, precision, recall, and F1 score. RP was defined as CTCAE grade β‰₯ 2.
Main resultsOf the 35 selected features, 20 were from HFL. In dual-omics models, using HFL features improved predictive performance for RP (AUC 0.879Β±0.105) compared to WL (AUC 0.778 Β± 0.100). In HFL, the RD method outperformed both R (AUC 0.786Β± 0.076) and D (AUC 0.791 Β± 0.107) methods. Decision curve analysis showed the dual-omics model based on HFL provided the highest net benefit across threshold probabilities.
SignificanceThis study is the first to systematically demonstrate that features extracted from CT-derived HFL capture important functional differences and provide strong predictive value for RP. Compared to conventional methods, integrating radiomics, dosiomics, and CT-based functional information further improves predictive performance.&#xD.

PMID:41825133 | DOI:10.1088/1361-6560/ae5209

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Functional-based multi-omics early prediction of radiation pneumonitis in NSCLC using AI-generated perfusion and ventilation from planning CT

Phys Med Biol. 2026 Mar 13. doi: 10.1088/1361-6560/ae5209. Online ahead of print.

ABSTRACT

ObjectiveThis study aims to develop a functional-based multi-omics model for early prediction of radiation pneumonitis (RP) by extracting radiomic and dosiomic features from functionally defined lung regions, using generated perfusion (Q) and ventilation (V) from pre-radiotherapy planning computed tomography (CT).
ApproachWe retrospectively analyzed data from 121 patients with locally advanced non-small cell lung cancer (NSCLC) treated with curative-intent IMRT between 2015 and 2019, including pre-treatment CT and dose maps. Q and V maps were generated from CT with deep learning-based and supervoxel-based approaches, respectively. Regions of interest (ROIs) combined the planning target volume (PTV) with each of three functional lung regions-high functional lung (HFL), low functional lung (LFL), and whole lung (WL)-defined by thresholds on Q and V maps. Radiomic and dosiomic features were extracted from CT and dose distributions within each ROI. For each ROI, For each ROI, three methods-radiomics (R), dosiomics (D), and dual-omics (RD)-were constructed. 13 machine learning algorithms were trained and evaluated using 10-fold cross-validation, and model performance was assessed by the average area under the receiver operating characteristic curve (AUC), accuracy, precision, recall, and F1 score. RP was defined as CTCAE grade β‰₯ 2.
Main resultsOf the 35 selected features, 20 were from HFL. In dual-omics models, using HFL features improved predictive performance for RP (AUC 0.879Β±0.105) compared to WL (AUC 0.778 Β± 0.100). In HFL, the RD method outperformed both R (AUC 0.786Β± 0.076) and D (AUC 0.791 Β± 0.107) methods. Decision curve analysis showed the dual-omics model based on HFL provided the highest net benefit across threshold probabilities.
SignificanceThis study is the first to systematically demonstrate that features extracted from CT-derived HFL capture important functional differences and provide strong predictive value for RP. Compared to conventional methods, integrating radiomics, dosiomics, and CT-based functional information further improves predictive performance.&#xD.

PMID:41825133 | DOI:10.1088/1361-6560/ae5209

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FinToolBench: Evaluating LLM Agents for Real-World Financial Tool Use

arXiv:2603.08262v1 Announce Type: new Abstract: The integration of Large Language Models (LLMs) into the financial domain is driving a paradigm shift from passive information retrieval to dynamic, agentic interaction. While general-purpose tool learning has witnessed a surge in benchmarks, the financial sector, characterized by high stakes, strict compliance, and rapid data volatility, remains critically underserved. Existing financial evaluations predominantly focus on static textual analysis or document-based QA, ignoring the complex reality of tool execution. Conversely, general tool benchmarks lack the domain-specific rigor required for finance, often relying on toy environments or a negligible number of financial APIs. To bridge this gap, we introduce FinToolBench, the first real-world, runnable benchmark dedicated to evaluating financial tool learning agents. Unlike prior works limited to a handful of mock tools, FinToolBench establishes a realistic ecosystem coupling 760 executable financial tools with 295 rigorous, tool-required queries. We propose a novel evaluation framework that goes beyond binary execution success, assessing agents on finance-critical dimensions: timeliness, intent type, and regulatory domain alignment. Furthermore, we present FATR, a finance-aware tool retrieval and reasoning baseline that enhances stability and compliance. By providing the first testbed for auditable, agentic financial execution, FinToolBench sets a new standard for trustworthy AI in finance. The tool manifest, execution environment, and evaluation code will be open-sourced to facilitate future research.
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PaLMR: Towards Faithful Visual Reasoning via Multimodal Process Alignment

arXiv:2603.06652v1 Announce Type: cross Abstract: Reinforcement learning has recently improved the reasoning ability of Large Language Models and Multimodal LLMs, yet prevailing reward designs emphasise final-answer correctness and consequently tolerate process hallucinations--cases where models reach the right answer while misperceiving visual evidence. We address this process-level misalignment with PaLMR, a framework that aligns not only outcomes but also the reasoning process itself. PaLMR comprises two complementary components: a perception-aligned data layer that constructs process-aware reasoning data with structured pseudo-ground-truths and verifiable visual facts, and a process-aligned optimisation layer that constructs a hierarchical reward fusion scheme with a process-aware scoring function to encourage visually faithful chains-of-thought and improve training stability. Experiments on Qwen2.5-VL-7B show that our approach substantially reduces reasoning hallucinations and improves visual reasoning fidelity, achieving state-of-the-art results on HallusionBench while maintaining strong performance on MMMU, MathVista, and MathVerse. These findings indicate that PaLMR offers a principled and practical route to process-aligned multimodal reasoning, advancing the reliability and interpretability of MLLMs.
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Qute: Towards Quantum-Native Database

arXiv:2602.14699v1 Announce Type: cross Abstract: This paper envisions a quantum database (Qute) that treats quantum computation as a first-class execution option. Unlike prior simulation-based methods that either run quantum algorithms on classical machines or adapt existing databases for quantum simulation, Qute instead (i) compiles an extended form of SQL into gate-efficient quantum circuits, (ii) employs a hybrid optimizer to dynamically select between quantum and classical execution plans, (iii) introduces selective quantum indexing, and (iv) designs fidelity-preserving storage to mitigate current qubit constraints. We also present a three-stage evolution roadmap toward quantum-native database. Finally, by deploying Qute on a real quantum processor (origin_wukong), we show that it outperforms a classical baseline at scale, and we release an open-source prototype at https://github.com/weAIDB/Qute.
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