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Hera: Learning Long-Horizon Coordination for Device-Cloud Collaborative LLM Agents

arXiv:2605.24598v1 Announce Type: new Abstract: Large language model (LLM) agents excel at solving complex long-horizon tasks through autonomous interaction with environments. However, their real-world deployment faces a fundamental device--cloud dilemma: on-device models are efficient but often brittle, while cloud models are stronger but costly in computation. State-of-the-art LLM device--cloud routers usually make coarse task-level decisions, which cannot adapt to the changing difficulty of multi-step agent interactions. To address this issue, we present Hera, a step-level device--cloud LLM agent coordinator for long-horizon tasks achieving a strong performance--cost Pareto frontier. Hera adopts a novel two-stage training paradigm: (1) imitation learning for cold-start, followed by (2) reinforcement learning that jointly optimizes task success and cloud usage efficiency. The first stage casts step-level routing as a supervised classification problem: the device agent is replayed on cloud trajectories, with each state labeled by the agreement between device and cloud actions. In the second stage, we perform cost-aware reinforcement learning by grouping identical states across trajectories and updating Hera with labels favoring higher expected return and fewer future cloud calls. We evaluate Hera on ALFWorld, WebShop, and AppWorld, where it consistently outperforms prior methods, achieving 92.5% of the cloud-only success rate with cloud use in only 46.3% of steps.

NeurIPS: Neuro-anatomical Inductive Priors for Sphere-based Brain Decoding

arXiv:2605.24993v1 Announce Type: new Abstract: Current fMRI decoders face a performance-fidelity trade-off where efficient ID encoders outperform geometrically faithful surface-based models. We argue this is partly driven by inefficient surface tokenization and the failure to use anatomy as a predictive signal. We present NeurIPS, a framework that improves surface-based decoding by reframing anatomical variation from a nuisance to a powerful inductive prior. NeurIPS unites two innovations: a Selective ROI Spherical Tokenizer (SRST) for efficient geometric encoding, and a Structure-Guided Mixture of Experts (SG-MoE) that explicitly models individual anatomy using cortical features. On the Natural Scenes Dataset, NeurIPS establishes a new state-of-the-art for surface decoders and achieves performance comparable to strong 1D baselines. This is achieved with unprecedented efficiency, as the model converges dramatically faster (10 vs. 600 epochs). This efficiency enables rapid adaptation to new subjects using only 20% of data and ensures robust scalability as the training cohort is expanded. Ablations provide causal evidence that these gains are driven by the model's use of cortical features, not by memorizing subject IDs. By leveraging anatomical priors, NeurIPS provides a principled and scalable path toward robust, generalizable brain decoding.

A pathogen lncRNA secreted into rice sequesters a host miRNA for virulence

Nature, Published online: 20 May 2026; doi:10.1038/s41586-026-10572-x

A fungal long non-coding RNA from Magnaporthe oryzae translocates into rice cells to sequester a host microRNA that normally represses PKR1, a negative immunity regulator, thereby facilitating infection and revealing a widespread RNA-based pathogen–host interaction mechanism.

Integrative bioinformatics and experimental validation reveal quercetin as a potential multi-target therapeutic agent in hepatocellular carcinoma

Cytotechnology. 2026 Jun;78(3):119. doi: 10.1007/s10616-026-00993-x. Epub 2026 May 14.

ABSTRACT

Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer worldwide, with increasing incidence and mortality rates. Although several targeted therapies are currently available, the therapeutic outcomes remain unsatisfactory due to the high heterogeneity and drug resistance of HCC. Therefore, novel molecular mechanisms and therapeutic strategies urgently need to be explored. In this study, we obtained the GSE39791 dataset from the GEO database and identified 1,186 differentially expressed genes (DEGs). Weighted gene co-expression network analysis (WGCNA) was conducted to obtain 776 key module genes, which were intersected with 11,671 HCC-related genes from the GeneCards database, resulting in 226 candidate genes. A protein-protein interaction (PPI) network was constructed using the STRING database, and the top 20 hub genes were identified using the MNC algorithm in Cytoscape. Among these, the five most significant hub genes-RFC4, TOP2A, AURKA, HSP90AA1, and MCM4-were selected for further analysis. KEGG enrichment analysis was performed to explore their functional pathways. Potential therapeutic agents were predicted using the CMap database, and molecular docking was conducted via AutoDock Vina. To validate the computational predictions, a quercetin intervention model was established. The optimal dose was determined through CCK-8 assays in HepG2 cells, and the expression of the five hub genes was examined in normal liver cells (LO2), HepG2 cells, and HepG2 cells treated with quercetin using RT-qPCR. The five hub genes-RFC4, TOP2A, AURKA, HSP90AA1, and MCM4-were significantly overexpressed in both HCC tissues and cell lines. Enrichment analysis revealed that these genes were mainly involved in cancer-related pathways, including the cell cycle, p53 signaling pathway, and FoxO signaling pathway. Drug prediction analysis showed that quercetin exhibited a negative regulatory pattern with respect to HCC and displayed binding energies below - 5 kcal/mol with all five hub proteins. CCK-8 assays confirmed the dose-dependent inhibitory effect of quercetin on HepG2 cell viability. RT-qPCR results demonstrated that quercetin significantly downregulated the expression of the five hub genes, consistent with the bioinformatics predictions. This study integrated multi-omics analysis and experimental validation to identify five core genes closely associated with HCC and suggested that quercetin may exert anti-HCC effects partly associated with the regulation of these genes. Our findings offer new insights into the molecular mechanisms of HCC and provide a promising strategy for the development of targeted therapeutics.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10616-026-00993-x.

PMID:42145839 | PMC:PMC13176377 | DOI:10.1007/s10616-026-00993-x

HoloTrauma 3X Triadic AI Co reasoning for robot assisted emergency maxillofacial reconstruction

npj Digital Medicine, Published online: 04 April 2026; doi:10.1038/s41746-026-02573-x

HoloTrauma 3X Triadic AI Co reasoning for robot assisted emergency maxillofacial reconstruction

Integrated proteomics and metabolomics analysis reveals mechanisms by which SFYC decoction regulates airway inflammation in asthma

J Ethnopharmacol. 2026 Mar 30;365:121612. doi: 10.1016/j.jep.2026.121612. Online ahead of print.

ABSTRACT

ETHNOPHARMACOLOGICAL RELEVANCE: Airway inflammation is one of the primary pathological characteristics of asthma. Soufeng Yuchuan (SFYC) decoction, a compound formula derived from multiple traditional Chinese medicine prescriptions, is widely applied clinically and exhibits significant therapeutic efficacy against asthma. However, its anti-asthmatic mechanisms remain incompletely understood.

MATERIALS AND METHODS: Asthmatic rat models induced by ovalbumin (OVA) and ferroptosis models induced by erastin in BEAS-2B cells were established. Proteomics and metabolomics analyses were conducted on lung tissues and serum. Key ferroptosis-related targets (GPX4, SLC7A11/SLC3A2, GCLC, GSS, and VDAC2) were validated using Western blotting, RT-qPCR, and biochemical assays. The direct anti-ferroptosis effects of SFYC-containing serum were compared with ferrostatin-1 and blank serum in vitro.

RESULTS: Integrated omics analysis revealed that ferroptosis, glutathione metabolism, and ROS signaling pathways were the core targets modulated by SFYC. In vivo, SFYC significantly reduced airway inflammation and ROS accumulation, restored pulmonary GSH levels, upregulated the expression of GPX4, GCLC, GSS, SLC7A11, and SLC3A2, and downregulated VDAC2 expression (P < 0.05). In vitro, SFYC-containing serum effectively reversed erastin-induced lipid peroxidation, iron overload, GSH depletion, ROS elevation, and apoptosis in BEAS-2B cells, demonstrating comparable or superior efficacy to ferrostatin-1.

CONCLUSION: SFYC alleviates airway inflammation in asthma primarily by inhibiting ferroptosis. This study provides evidence that SFYC exerts anti-asthmatic effects, at least in part, via the regulation of ferroptosis pathways.

PMID:41921764 | DOI:10.1016/j.jep.2026.121612

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 intelligence across chip design, GPU kernel optimization, embedded systems, compiler optimization, and 3D modeling. By adopting an efficient architecture, we train InCoder-32B from scratch with general code pre-training, curated industrial code annealing, mid-training that progressively extends context from 8K to 128K tokens with synthetic industrial reasoning data, and post-training with execution-grounded verification. We conduct extensive evaluation on 14 mainstream general code benchmarks and 9 industrial benchmarks spanning 4 specialized domains. Results show InCoder-32B achieves highly competitive performance on general tasks while establishing strong open-source baselines across industrial domains.

Integrative Multi-omics Analysis of Buti Huatan Tang in Chronic Obstructive Pulmonary Disease

J Vis Exp. 2026 Mar 13;(229). doi: 10.3791/70383.

ABSTRACT

This study utilized a multi-omics and computational biology framework to investigate the therapeutic potential of the Traditional Chinese Medicine (TCM) formula Buti Huatan Tang (BTHTT) against chronic obstructive pulmonary disease (COPD). Significant physiological improvements were observed in a rat model following BTHTT intervention. Histological analysis showed a reversal of lung pathological damage, while biochemical assays, and transcriptomics confirmed the normalization of IL-1β and IL-1R2 levels. Additionally, metabolic profiling revealed that BTHTT corrected disruptions in T3 and T4 thyroid hormone levels. A negative correlation was observed between the IL-1β/IL-1R2 axis and these thyroid hormones, indicating that their regulation is associated with the formula's therapeutic effect. Beyond direct measurements, machine learning algorithms identified ten COPD signature genes from clinical databases. Pathway enrichment analysis suggests that BTHTT may act through cytokine-cytokine-receptor interactions and thyroid hormone synthesis pathways. Furthermore, while 283 components were identified in vivo, compounds such as tanshinone IIA and cryptotanshinone are currently considered candidate active substances. Their role as primary drivers is supported by a model in which they stably bind to IL-1R2; this inference is based on molecular docking and molecular dynamics (MD) simulations rather than direct experimental isolation. Overall, the data support a model in which BTHTT exerts a multi-target effect on COPD by modulating inflammation and metabolic homeostasis. This integrated approach provides a refined scientific basis for the clinical application of BTHTT and highlights specific pathways for future experimental validation.

PMID:41911070 | DOI:10.3791/70383

Integrative Multi-omics Analysis of Buti Huatan Tang in Chronic Obstructive Pulmonary Disease

J Vis Exp. 2026 Mar 13;(229). doi: 10.3791/70383.

ABSTRACT

This study utilized a multi-omics and computational biology framework to investigate the therapeutic potential of the Traditional Chinese Medicine (TCM) formula Buti Huatan Tang (BTHTT) against chronic obstructive pulmonary disease (COPD). Significant physiological improvements were observed in a rat model following BTHTT intervention. Histological analysis showed a reversal of lung pathological damage, while biochemical assays, and transcriptomics confirmed the normalization of IL-1β and IL-1R2 levels. Additionally, metabolic profiling revealed that BTHTT corrected disruptions in T3 and T4 thyroid hormone levels. A negative correlation was observed between the IL-1β/IL-1R2 axis and these thyroid hormones, indicating that their regulation is associated with the formula's therapeutic effect. Beyond direct measurements, machine learning algorithms identified ten COPD signature genes from clinical databases. Pathway enrichment analysis suggests that BTHTT may act through cytokine-cytokine-receptor interactions and thyroid hormone synthesis pathways. Furthermore, while 283 components were identified in vivo, compounds such as tanshinone IIA and cryptotanshinone are currently considered candidate active substances. Their role as primary drivers is supported by a model in which they stably bind to IL-1R2; this inference is based on molecular docking and molecular dynamics (MD) simulations rather than direct experimental isolation. Overall, the data support a model in which BTHTT exerts a multi-target effect on COPD by modulating inflammation and metabolic homeostasis. This integrated approach provides a refined scientific basis for the clinical application of BTHTT and highlights specific pathways for future experimental validation.

PMID:41911070 | DOI:10.3791/70383

VLM-CAD: VLM-Optimized Collaborative Agent Design Workflow for Analog Circuit Sizing

arXiv:2601.07315v4 Announce Type: replace-cross Abstract: Vision Language Models (VLMs) have demonstrated remarkable potential in multimodal reasoning, yet they inherently suffer from spatial blindness and logical hallucinations when interpreting densely structured engineering content, such as analog circuit schematics. To address these challenges, we propose a Vision Language Model-Optimized Collaborative Agent Design Workflow for Analog Circuit Sizing (VLM-CAD) designed for robust, step-by-step reasoning over multimodal evidence. VLM-CAD bridges the modality gap by integrating a neuro-symbolic structural parsing module, Image2Net, which transforms raw pixels into explicit topological graphs and structured JSON representations to anchor VLM interpretation in deterministic facts. To ensure the reliability required for engineering decisions, we further propose ExTuRBO, an Explainable Trust Region Bayesian Optimization method. ExTuRBO serves as an explainable grounding engine, employing agent-generated semantic seeds to warm-start local searches and utilizing Automatic Relevance Determination to provide quantified evidence for the VLM's decisions. Experimental results on two complex circuit benchmarks demonstrate that VLM-CAD significantly enhances spatial reasoning accuracy and maintains physics-based explainability. VLM-CAD consistently satisfies complex specification requirements while achieving low power consumption, with a total runtime under 66 minutes, marking a significant step toward robust, explainable multimodal reasoning in specialized technical domains.

Inactivating <i>SnRK1β1A</i> promotes broad-spectrum disease resistance in rice

Nature, Published online: 25 March 2026; doi:10.1038/s41586-026-10273-5

SnRK1β1A in rice promotes susceptibility to multiple fungal diseases, and disrupting this infection-inducible gene confers broad-spectrum resistance without compromising growth or yield under normal field conditions.

Single-cell multiomics uncovers an endothelial mechanosensitive PIEZO1-IL-33 axis driving pulmonary fibrosis

Nat Commun. 2026 Mar 20;17(1):2655. doi: 10.1038/s41467-026-70193-w.

ABSTRACT

Pulmonary fibrosis represents a progressive interstitial lung disease marked by excessive extracellular matrix deposition and architectural distortion. Vascular endothelial cells critically contribute to fibrogenesis through paracrine secretion of pro-fibrotic mediators, yet their mechanobiological regulation remains elusive. Using integrated single-cell multi-omics profiling of human pulmonary fibrosis specimens and experimental fibrosis models induced by bleomycin or silica, we identify mechanosensitive Piezo1 upregulation in Endothelial cells as a hallmark of fibrotic progression. Endothelial-specific Piezo1 knockout significantly attenuates Bleomycin-induced fibrotic remodeling in male mice, establishing its pathogenic necessity. Mechanistically, PIEZO1 activation promotes pulmonary fibrosis development via CAPN2-mediated STAT3 phosphorylation, which may regulate the secretion of the pro-fibrotic molecule interleukin-33. These findings suggest that the endothelial PIEZO1-CAPN2-STAT3-IL33 axis is a potential therapeutic target for PF intervention.

PMID:41862476 | PMC:PMC13004862 | DOI:10.1038/s41467-026-70193-w

A multiomics Mendelian randomization study on PANoptosis-related genes and gastric cancer risk

J Int Med Res. 2026 Mar;54(3):3000605261430163. doi: 10.1177/03000605261430163. Epub 2026 Mar 16.

ABSTRACT

ObjectiveTo explore the potential involvement of PANoptosis-related genes in gastric cancer susceptibility through multiomics analyses.MethodsSummary-data-based Mendelian randomization was performed by integrating blood-derived methylation, gene expression, and protein quantitative trait loci data with genome-wide association study results. The findings were further evaluated in The Cancer Genome Atlas cohort, followed by protein-protein interaction analysis, drug prediction, and molecular docking.ResultsSummary-data-based Mendelian randomization and colocalization analyses identified several traits suggestively associated with gastric cancer risk. Genetically predicted higher expression of apoptosis and caspase activation inhibitor (AVEN) and hepatocyte growth factor (HGF) as well as higher HGF protein levels were associated with increased risk, whereas higher levels of protein phosphatase 2 regulatory subunit B beta (PPP2R2B) appeared to be protective. Multiomics integration suggested epigenetic regulation of HGF and PPP2R2B. The Cancer Genome Atlas analysis corroborated the dysregulation of these candidates, with high AVEN expression associated with poorer survival. Protein-protein interaction and drug prediction analyses highlighted functional networks and potential therapeutics, supported by molecular docking demonstrating strong HGF-binding affinities. However, these associations did not reach statistical significance in the independent validation cohort, possibly due to limited statistical power.ConclusionsThis study identified AVEN, HGF, and PPP2R2B as potential candidate genes for gastric cancer. These findings require further validation in larger cohorts.

PMID:41840829 | DOI:10.1177/03000605261430163

Partially Recentralization Softmax Loss for Vision-Language Models Robustness

arXiv:2402.03627v4 Announce Type: replace-cross Abstract: As Large Language Models make a breakthrough in natural language processing tasks (NLP), multimodal technique becomes extremely popular. However, it has been shown that multimodal NLP are vulnerable to adversarial attacks, where the outputs of a model can be dramatically changed by a perturbation to the input. While several defense techniques have been proposed both in computer vision and NLP models, the multimodal robustness of models have not been fully explored. In this paper, we study the adversarial robustness provided by modifying loss function of pre-trained multimodal models, by restricting top K softmax outputs. Based on the evaluation and scoring, our experiments show that after a fine-tuning, adversarial robustness of pre-trained models can be significantly improved, against popular attacks. Further research should be studying, such as output diversity, generalization and the robustness-performance trade-off of this kind of loss functions. Our code will be available after this paper is accepted

How to Build a Quantum Supercomputer: Scaling from Hundreds to Millions of Qubits

arXiv:2411.10406v3 Announce Type: replace-cross Abstract: In the span of four decades, quantum computation has evolved from an intellectual curiosity to a potentially realizable technology. Today, small-scale demonstrations have become possible for quantum algorithmic primitives on hundreds of physical qubits. Nevertheless, there are significant outstanding challenges in quantum hardware, fabrication, software architecture, and algorithms on the path towards a full-stack scalable quantum computing technology. Here, we provide a comprehensive review of these scaling challenges. We show how to facilitate scaling by adopting existing semiconductor technology to build much higher-quality qubits, employing systems engineering approaches, and performing distributed heterogeneous quantum-classical computing. We provide a detailed resource and sensitivity analysis for quantum applications on surface-code error-corrected quantum computers given current, target, and desired hardware specifications based on superconducting qubits, accounting for a realistic distribution of errors. We provide comprehensive resource estimates for several utility-scale applications including quantum chemistry calculations, catalyst design, NMR spectroscopy, and Fermi-Hubbard simulation. We show that orders of magnitude enhancement in performance could be obtained by a combination of hardware improvements and tight quantum-HPC integration. Furthermore, we introduce high-performance architectures for quantum-probabilistic computing with custom-designed accelerators to tackle today's industry-scale classical optimization, machine learning, and quantum simulation tasks in a cost-effective manner.

Contact-Guided 3D Genome Structure Generation of E. coli via Diffusion Transformers

arXiv:2603.07472v1 Announce Type: cross Abstract: In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure, we formulate genome reconstruction as a conditional generative modeling problem that samples heterogeneous conformations whose ensemble-averaged contacts are consistent with the input Hi-C data. A synthetic dataset is constructed using coarse-grained molecular dynamics simulations to generate chromatin ensembles and corresponding Hi-C maps under circular topology. Our models operate in a latent diffusion setting with a variational autoencoder that preserves per-bin alignment and supports replication-aware representations. Hi-C information is injected through a transformer-based encoder and cross-attention, enforcing a physically interpretable one-way constraint from Hi-C to structure. The model is trained using a flow-matching objective for stable optimization. On held-out ensembles, generated structures reproduce the input Hi-C distance-decay and structural correlation metrics while maintaining substantial conformational diversity, demonstrating the effectiveness of diffusion-based generative modeling for ensemble-level 3D genome reconstruction.

CrystaL: Spontaneous Emergence of Visual Latents in MLLMs

arXiv:2602.20980v2 Announce Type: replace-cross Abstract: Multimodal Large Language Models (MLLMs) have achieved remarkable performance by integrating powerful language backbones with large-scale visual encoders. Among these, latent Chain-of-Thought (CoT) methods enable implicit reasoning in continuous hidden states, facilitating seamless vision-language integration and faster inference. However, existing heuristically predefined supervision signals in latent CoT provide limited guidance for preserving critical visual information in intermediate latent states. To address this limitation, we propose CrystaL (Crystallized Latent Reasoning), a single-stage framework with two paths to process intact and corrupted images, respectively. By explicitly aligning the attention patterns and prediction distributions across the two paths, CrystaL crystallizes latent representations into task-relevant visual semantics, without relying on auxiliary annotations or external modules. Extensive experiments on perception-intensive benchmarks demonstrate that CrystaL consistently outperforms state-of-the-art baselines, achieving substantial gains in fine-grained visual understanding while maintaining robust reasoning capabilities.

IntPro: A Proxy Agent for Context-Aware Intent Understanding via Retrieval-conditioned Inference

arXiv:2603.03325v1 Announce Type: cross Abstract: Large language models (LLMs) have become integral to modern Human-AI collaboration workflows, where accurately understanding user intent serves as a crucial step for generating satisfactory responses. Context-aware intent understanding, which involves inferring user intentions from situational environments, is inherently challenging because it requires reasoning over both the immediate context and the user's underlying motivations that drive their behavior. Moreover, existing approaches often treat intent understanding as a static recognition task, overlooking users' accumulated intent patterns that could provide valuable references for more accurate and generalizable understanding. To address this gap, we propose IntPro, a proxy agent that learns to adapt to individual users via retrieval-conditioned intent inference. We design intent explanations that abstract how contextual signals connect to expressed intents, and store them in an individual intent history library for retrieval. We train IntPro through supervised fine-tuning on retrieval-conditioned trajectories and multi-turn Group Relative Policy Optimization (GRPO) with tool-aware reward functions, enabling the agent to learn when to leverage historical intent patterns and when to infer directly. Experiments across three diverse scenarios (Highlight-Intent, MIntRec2.0, and Weibo Post-Sync) demonstrate that IntPro achieves strong intent understanding performance with effective context-aware reasoning capabilities across different scenarios and model types.
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