Spatial, single-nucleus and pathological profiling of the invasive front in early hepatocellular carcinoma for characterizing specific leading-edge cell niche and improving recurrence modeling

By: Xicheng Wang · Xiaolan Mu · Yong Fu · Wei Dong · Wenfeng Lu · Xiuhua Li · Yanxiang Song · Changcheng Liu · Baoju Hou · Haibin Zhang · Xiong Chen · Yongchao Cai · Zhiying He

29 September 2026 at 18:00

Int J Biol Sci. 2026 Sep 10;22(14):8090-8118. doi: 10.7150/ijbs.137262. eCollection 2026.

ABSTRACT

The tumor leading edge (TLE) is a critical region where tumor cells interact with the microenvironment to drive invasion and metastasis; however, its cellular architecture in early hepatocellular carcinoma (HCC) remains poorly understood. Here, we integrated single-nucleus RNA-seq (snRNA-seq), spatial transcriptomics, and computational pathology to investigate TLE in early HCC. We annotated 35 cell subpopulations and identified STMN1-high tumor cells as a key malignant subset enriched at the invasive front, interacting with Treg, plasma B, LAMP3⁺ dendritic cells and SPP1⁺ macrophages. Spatial analysis revealed three co-localized cell pairs-(SPP1⁺ macrophages co-localized with Tip-like and inflammatory endothelial cells), (LAMP3⁺ DCs co-localized with naive T cells), and (plasma B cells co-localized with cancer-associated fibroblasts)-forming a leading-edge tumor microenvironment (L-TME) niche associated with early relapse. We developed an L-TME-related machine-learning benchmark framework incorporating 71 imaging features (65 deep-learning + 6 pathological) based on the snRNA-seq, spatial transcriptomics and pathomics. The pathology model achieved robust performance (mean C-index=0.77) and successfully predicted the recurrence of early HCC (log-rank p < 0.05) in TCGA (n=147) and an independent in-house cohort (n=123). This study delineates the TLE cellular ecosystem of early HCC, defines a spatially coordinated immunosuppressive L-TME niche, and provides a clinically applicable predictive tool for postoperative recurrence. Integrating multi-omics with computational pathology deepens our understanding of early HCC metastasis and offers insights into improved prognostication and therapeutic strategies.

PMID:42807944 | PMC:PMC13618224 | DOI:10.7150/ijbs.137262

Occamy-1.0: Open Pareto-frontier 35B Intelligence for Co-work

cs.AI, q-bio.NC updates on arXiv.org

By: Wenhui Chen · Shiwen Cheng · Hao Dong · Chenda Duan · Ruixiang Feng · Zhong Guan · Boqiang Guo · Xueyuan Han · Haojie Hao · Liangmeng Huang · Zhelong Huang · Xinke Kong · Hongyu Li · Jiazheng Li · Junbo Li · Qingchuan Li · Yukun Lian · Chang Liu · Tianyu Liu · Zicheng Liu · Shuyi Ouyang · Yijun Pan · Kunyu Shi · Xiaojun Tang · Bingquan Wang · Kesu Wang · Yuchen Wang · Sibo Wei · Sicong Xie · Xiaoying Xing · Yi Xu · Zhijun Xu · Hongwei Xue · Qingcheng Zeng · Di Zhang · Guannan Zhang · Haochen Zhang · Tianlong Zhang · Tianyu Zhao · Tianyu Zhao · Yanjun Zheng · Jialong Zhu · Zijian Zou

14 September 2026 at 12:00

arXiv:2609.11977v1 Announce Type: new Abstract: Co-work agents execute complex workflows that combine information gathering, tool use, coding, and file manipulation across many model invocations. Because cost and latency accumulate over the full episode, their practical value depends not only on peak capability but also on how efficiently that capability is delivered. Yet many steps in everyday work emphasize state tracking, coordination, recovery, and follow-through rather than frontier-scale reasoning. We present Occamy-1.0, a cost-efficient co-work model obtained by further training the post-trained Qwen3.6-35B-A3B checkpoint. We construct execution-grounded data and environments, capture replayable long-horizon trajectories across multiple harnesses, and use staged post-training to develop and consolidate complementary execution capabilities. Across a broad suite of co-work benchmarks, Occamy-1.0 is consistently among the strongest comparably sized models and remains competitive with substantially larger frontier systems on several tasks. Under our stated evaluation and pricing protocol, its aggregate performance across four representative benchmarks places it at the low-cost knee of the observed cost--performance Pareto frontier. Supporting evaluations in tool calling, coding, and instruction following further show that this specialization preserves broad agentic capability. We release the model weights and a subset of the training data to support research on practical co-work agents and agentic post-training.

Dynamic Expert Quantization for Scalable Mixture-of-Experts Inference

cs.AI, q-bio.NC updates on arXiv.org

By: Kexin Chu · Dawei Xiang · Zixu Shen · Yiwei Yang · Zecheng Liu · Wei Zhang

14 September 2026 at 12:00

arXiv:2511.15015v4 Announce Type: replace-cross Abstract: Mixture-of-Experts (MoE) has become a practical architecture for scaling LLM capacity while keeping per-token compute modest, but deploying MoE models on a single, memory-limited GPU remains difficult because expert weights dominate the HBM footprint. Existing expert offloading and prefetching systems reduce the resident set, yet they often pay expert-loading costs on the critical path when activation becomes dense. Post-training quantization (PTQ) lowers the footprint without transfers, but prevailing pipelines fix expert bit-widths offline and assume routing remains stable, even though MoE expert utilization is heavy-tailed and the hot set can shift across workloads. We present DynaExq, a runtime-aware mixed-precision serving system that treats single-GPU MoE inference under a hard HBM envelope as an online, budget-constrained precision allocation problem. The key insight is to keep the experts that dominate runtime traffic resident at higher precision, while maintaining a low-precision fallback for the remaining experts, so the system can reduce transfer volume and avoid the waiting latency that limits offloading and prefetching under dense activation. DynaExq estimates long-horizon expert hotness from router traces, selects a per-layer high-precision resident set via a budget-feasible top-$n$ rule, and applies promotions and demotions asynchronously through stable expert handles so the forward pass always executes on a fully materialized expert version. Across Qwen3-MoE-30B/80B and six benchmarks, DynaExq improves accuracy over static PTQ on Qwen3-80B (73.09% to 77.57%) under comparable device-memory budgets and achieves up to 2.73x higher throughput than offloading/prefetch baselines at batch size 32.

Switchable single-atom catalysts for highly selective C–C coupling in direct methane oxidation

Nature Nanotechnology

By: Xiao Han · Peixin Cui · Geng Wu · Jinyan Cai · Chao Wang · Fanfei Sun · Panzhe Qiao · Xiaocheng Liu · Jiahao Zhuang · Huan Liu · Fabing Su · Gongming Wang · Wensheng Yan · Zeming Qi · Yue Lin · Xun Hong · Yadong Li

7 September 2026 at 08:00

Nature Nanotechnology, Published online: 07 September 2026; doi:10.1038/s41565-026-02271-5

Single copper atoms on boron nanosheets dynamically and reversibly switch to clusters, enabling the direct conversion of methane to acetic acid with 97% selectivity and high activity without the requirement for carbon monoxide.

The RNA-binding protein La/SSB is associated with HNSCC progression and TFAP2C/FSCN1-linked transcriptional regulation

Oncogene - Issue - nature.com science feeds

By: Shixian Liu · Deshang Chen · Wentao Zhang · Hui Li · Jie Peng · Xiaomin Wang · Mingjie Zhang · Weiwei Liu · Junjie Zhang · Mengjun Wang · Guoying Han · Changqi Cai · Shencheng Liu · Xiaoli You · Qun Xu · Yuefeng Han · Xiaojun Zha · Shiyin Ma

3 September 2026 at 08:00

Oncogene, Published online: 03 September 2026; doi:10.1038/s41388-026-03959-7

The RNA-binding protein La/SSB is associated with HNSCC progression and TFAP2C/FSCN1-linked transcriptional regulation

IndexMem: Learned KV-Cache Eviction with Latent Memory for Long-Context LLM Inference

cs.AI, q-bio.NC updates on arXiv.org

By: Xintong Yang · Hao Gu · Binxing Xu · Lujun Li · Bei Liu · Jiacheng Liu · Qiyuan Zhu · Sirui Han · Yike Guo

26 May 2026 at 12:00

arXiv:2605.25475v1 Announce Type: cross Abstract: Large Language Models (LLMs) are increasingly expected to operate over long contexts, yet standard softmax attention incurs a KV cache that grows linearly with sequence length, quickly becoming the bottleneck for long context inference. A practical remedy is to evict less important KV entries; however, existing eviction policies are largely heuristic and struggle to capture the rich, input-dependent distribution of token importance. In this work, we introduce a learnable indexer that predicts KV importance, enabling more accurate retention of critical tokens. Meanwhile, naively evicting tokens permanently discards their information, leading to irreversible forgetting and degraded retrieval over long ranges. To address this, we propose a lightweight latent memory module that compresses evicted tokens into a compact, online-updated state and provides residual readouts to compensate for the attention contributions lost through KV eviction. Collectively, our method enables accurate long-context inference under a bounded KV budget, delivering consistent improvements on RULER (4K/16K) across Qwen, Mistral, and Llama models (up to 25 points under aggressive eviction), markedly more stable Needle-in-a-Haystack retrieval, and superior LongBench scores and compression curves compared to existing eviction policies.

A SAUR gene enhances maize drought resilience by promoting silk elongation

Nature - Issue - nature.com science feeds

By: Chaohui Zhu · Zhirui Yang · Shiping Yang · Xueyan Zhou · Boxin Liu · Tian Tian · Bochen Zhao · Yingying Xie · Yujun Liu · Jinkui Cheng · Huaijun Tang · Yanjun Zhang · Xiaoqing Xie · Lei Zhang · Cheng Liu · Xingrong Wang · Shengxue Liu · Feng Qin

20 May 2026 at 08:00

Nature, Published online: 20 May 2026; doi:10.1038/s41586-026-10566-9

The Small Auxin Up RNA (SAUR) protein ZmSAUR72 in maize (Zea mays) promotes silk growth via regulation of H+-ATPase activity, and is a key determinant of the anthesis-silking interval and thus resilience to drought.

RDEx-CMOP: Feasibility-Aware Indicator-Guided Differential Evolution for Fixed-Budget Constrained Multiobjective Optimization

cs.AI, q-bio.NC updates on arXiv.org

By: Sichen Tao · Yifei Yang · Ruihan Zhao · Kaiyu Wang · Sicheng Liu · Shangce Gao

7 April 2026 at 12:00

arXiv:2604.03708v1 Announce Type: cross Abstract: Constrained multiobjective optimisation requires fast feasibility attainment together with stable convergence and diversity preservation under strict evaluation budgets. This report documents RDEx-CMOP, the differential evolution variant used in the IEEE CEC 2025 numerical optimisation competition (C06 special session) constrained multiobjective track. RDEx-CMOP integrates an {\epsilon}-level feasibility schedule, a SPEA2-style indicator-driven fitness assignment, and a fitness-oriented current-to-pbest/1 mutation operator. We evaluate RDEx-CMOP on the official CEC 2025 CMOP benchmark using the median-target U-score framework and the released trace data. Experimental results show that RDEx-CMOP achieves the highest total score and the best overall average rank among all released comparison algorithms, with strong target-attainment behaviour and near-zero final violation on most problems.

XModBench: Benchmarking Cross-Modal Capabilities and Consistency in Omni-Language Models

cs.AI, q-bio.NC updates on arXiv.org

By: Xingrui Wang · Jiang Liu · Chao Huang · Xiaodong Yu · Ze Wang · Ximeng Sun · Jialian Wu · Alan Yuille · Emad Barsoum · Zicheng Liu

7 April 2026 at 12:00

arXiv:2510.15148v2 Announce Type: replace-cross Abstract: Omni-modal large language models (OLLMs) aim to unify audio, vision, and text understanding within a single framework. While existing benchmarks primarily evaluate general cross-modal question-answering ability, it remains unclear whether OLLMs achieve modality-invariant reasoning or exhibit modality-specific biases. We introduce XModBench, a large-scale tri-modal benchmark explicitly designed to measure cross-modal consistency. XModBench comprises 60,828 multiple-choice questions spanning five task families and systematically covers all six modality compositions in question-answer pairs, enabling fine-grained diagnosis of an OLLM's modality-invariant reasoning, modality disparity, and directional imbalance. Experiments show that even the strongest model, Gemini 2.5 Pro, (i) struggles with spatial and temporal reasoning, achieving less than 60% accuracy, (ii) reveals persistent modality disparities, with performance dropping substantially when the same semantic content is conveyed through audio rather than text, and (iii) shows systematic directional imbalance, exhibiting lower consistency when vision serves as context compared to text. These findings indicate that current OLLMs remain far from truly modality-invariant reasoning and position XModBench as a fundamental diagnostic tool for evaluating and improving cross-modal competence. All data and evaluation tools will be available at https://xingruiwang.github.io/projects/XModBench/.

Proposed Role of Circadian Clock Genes in Pathogenesis of HCC: Molecular Subtyping and Characterization

Omics in Hepatocellular

By: Zhikui Lu · Yi Zhou · Jian Luo · Zhicheng Liu · Zhenyu Xiao

28 March 2026 at 18:00

Biomedicines. 2026 Mar 12;14(3):645. doi: 10.3390/biomedicines14030645.

ABSTRACT

Background: Hepatocellular carcinoma (HCC) stands as a prevalent global health issue with increasing incidence and mortality rates. Hepatocellular carcinoma (HCC) exhibits profound molecular and clinical heterogeneity, which limits the effectiveness of current therapeutic strategies. Circadian rhythm disruption has been implicated in metabolic reprogramming, proliferation, and immune modulation in cancer, but its role in shaping HCC heterogeneity remains poorly defined. Methods: Four public HCC transcriptomic cohorts (TCGA-LIHC, CHCC, LIRI, LICA) were integrated using RMA normalization and ComBat for batch correction. Consensus clustering based on 31 core circadian clock genes (CCGs) identified robust molecular subtypes. Multi-omics characterization-including genomic alterations, pathway activity (GSEA/GSVA), immune microenvironment profiling (CIBERSORT, EPIC, MCP-counter, xCell), and drug-sensitivity prediction (pRRophetic/oncoPredict)-was performed to delineate subtype-specific biological properties. A nine-gene CCG-based RiskScore model was constructed using LASSO Cox regression to internally validate subtype robustness and intra-subtype risk stratification. Results: Using consensus clustering of 31 core CCGs in TCGA-LIHC and three independent validation cohorts (CHCC, LIRI, LICA), we identified three reproducible subtypes-Cluster-1 (metabolic-quiescent), Cluster-2 (transition-intermediate), and Cluster-3 (proliferation-inflammatory)-which were recapitulated across cohorts and showed distinct overall survival (Cluster-3 worst; log-rank p values significant across datasets). Multi-omic characterization revealed that Cluster-3 exhibits the highest tumor mutational burden and CNV burden with enrichment of TP53/AXIN1/TERT alterations, strong activation of cell-cycle, E2F, and G2M programs, and an immune-hot yet immunosuppressed microenvironment enriched for TAMs, Tregs and MDSCs. By contrast, Cluster-1 shows relative genomic stability, dominant hepatic metabolic signatures (fatty-acid oxidation, bile-acid and xenobiotic metabolism) and an immune-cold phenotype. Single-cell mapping linked ALAS1 expression to malignant hepatocytes predominating in Cluster-1, whereas NONO and CSNK1D localized to stromal (CAFs/TECs) and both malignant/immune compartments respectively in Cluster-3, providing a cellular mechanism for subtype-specific metabolism, angiogenesis and immune modulation. Finally, a nine-gene CCG-based RiskScore validated prognostic stratification and drug-sensitivity predictions indicated subtype-specific therapeutic vulnerabilities (notably increased predicted TKI sensitivity in Cluster-3). Conclusion: In conclusion, this study proposes a robust circadian rhythm-based molecular classification of hepatocellular carcinoma, revealing three biologically and clinically distinct subtypes characterized by divergent genomic alterations, metabolic programs, immune microenvironment states, and prognostic patterns. By integrating bulk and single-cell transcriptomic data, we identify subtype-specific roles of key circadian regulators-including ALAS1, NONO, and CSNK1D-in shaping tumor metabolism, proliferation, stromal remodeling, and immune suppression. These findings highlight circadian dysregulation as a potential upstream factor associated with HCC heterogeneity and provide a conceptual framework for developing subtype-tailored mechanistic studies and circadian-informed therapeutic strategies.

PMID:41898292 | PMC:PMC13024568 | DOI:10.3390/biomedicines14030645

Role-Aware Conditional Inference for Spatiotemporal Ecosystem Carbon Flux Prediction

cs.AI, q-bio.NC updates on arXiv.org

By: Yiming Sun · Runlong Yu · Rongchao Dong · Shuo Chen · Licheng Liu · Youmi Oh · Qianlai Zhuang · Yiqun Xie · Xiaowei Jia

5 March 2026 at 13:00

arXiv:2603.03531v1 Announce Type: cross Abstract: Accurate prediction of terrestrial ecosystem carbon fluxes (e.g., CO$_2$, GPP, and CH$_4$) is essential for understanding the global carbon cycle and managing its impacts. However, prediction remains challenging due to strong spatiotemporal heterogeneity: ecosystem flux responses are constrained by slowly varying regime conditions, while short-term fluctuations are driven by high-frequency dynamic forcings. Most existing learning-based approaches treat environmental covariates as a homogeneous input space, implicitly assuming a global response function, which leads to brittle generalization across heterogeneous ecosystems. In this work, we propose Role-Aware Conditional Inference (RACI), a process-informed learning framework that formulates ecosystem flux prediction as a conditional inference problem. RACI employs hierarchical temporal encoding to disentangle slow regime conditioners from fast dynamic drivers, and incorporates role-aware spatial retrieval that supplies functionally similar and geographically local context for each role. By explicitly modeling these distinct functional roles, RACI enables a model to adapt its predictions across diverse environmental regimes without training separate local models or relying on fixed spatial structures. We evaluate RACI across multiple ecosystem types (wetlands and agricultural systems), carbon fluxes (CO$_2$, GPP, CH$_4$), and data sources, including both process-based simulations and observational measurements. Across all settings, RACI consistently outperforms competitive spatiotemporal baselines, demonstrating improved accuracy and spatial generalization under pronounced environmental heterogeneity.

DUET-VLM: Dual stage Unified Efficient Token reduction for VLM Training and Inference

cs.AI, q-bio.NC updates on arXiv.org

By: Aditya Kumar Singh · Hitesh Kandala · Pratik Prabhanjan Brahma · Zicheng Liu · Emad Barsoum

24 February 2026 at 13:00

arXiv:2602.18846v1 Announce Type: cross Abstract: Vision-language models (VLMs) have achieved remarkable multimodal understanding and reasoning capabilities, yet remain computationally expensive due to dense visual tokenization. Existing efficiency approaches either merge redundant visual tokens or drop them progressively in language backbone, often trading accuracy for speed. In this work, we propose DUET-VLM, a versatile plug-and-play dual compression framework that consists of (a) vision-only redundancy aware compression of vision encoder's output into information-preserving tokens, followed by (b) layer-wise, salient text-guided dropping of visual tokens within the language backbone to progressively prune less informative tokens. This coordinated token management enables aggressive compression while retaining critical semantics. On LLaVA-1.5-7B, our approach maintains over 99% of baseline accuracy with 67% fewer tokens, and still retains >97% even at 89% reduction. With this dual-stage compression during training, it achieves 99.7% accuracy at 67% and 97.6% at 89%, surpassing prior SoTA visual token reduction methods across multiple benchmarks. When integrated into Video-LLaVA-7B, it even surpasses the baseline -- achieving >100% accuracy with a substantial 53.1% token reduction and retaining 97.6% accuracy under an extreme 93.4% setting. These results highlight end-to-end training with DUET-VLM, enabling robust adaptation to reduced visual (image/video) input without sacrificing accuracy, producing compact yet semantically rich representations within the same computational budget. Our code is available at https://github.com/AMD-AGI/DUET-VLM.

ALOE: Action-Level Off-Policy Evaluation for Vision-Language-Action Model Post-Training

cs.AI, q-bio.NC updates on arXiv.org

By: Rushuai Yang · Hecheng Wang · Chiming Liu · Xiaohan Yan · Yunlong Wang · Xuan Du · Shuoyu Yue · Yongcheng Liu · Chuheng Zhang · Lizhe Qi · Yi Chen · Wei Shan · Maoqing Yao

24 February 2026 at 13:00

arXiv:2602.12691v2 Announce Type: replace-cross Abstract: We study how to improve large foundation vision-language-action (VLA) systems through online reinforcement learning (RL) in real-world settings. Central to this process is the value function, which provides learning signals to guide VLA learning from experience. In practice, the value function is estimated from trajectory fragments collected from different data sources, including historical policies and intermittent human interventions. Estimating the value function of current behavior quality from the mixture data is inherently an off-policy evaluation problem. However, prior work often adopts conservative on-policy estimation for stability, which avoids direct evaluation of the current high-capacity policy and limits learning effectiveness. In this paper, we propose ALOE, an action-level off-policy evaluation framework for VLA post-training. ALOE applies chunking-based temporal-difference bootstrapping to evaluate individual action sequences instead of predicting final task outcomes. This design improves effective credit assignment to critical action chunks under sparse rewards and supports stable policy improvement. We evaluate our method on three real-world manipulation tasks, including smartphone packing as a high-precision task, laundry folding as a long-horizon deformable-object task, and bimanual pick-and-place involving multi-object perception. Across all tasks, ALOE improves learning efficiency without compromising execution speed, showing that off-policy RL can be reintroduced in a reliable manner for real-world VLA post-training. Videos and additional materials are available at our project website.

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