❌

Reading view

RESample: A Robust Data Augmentation Framework via Exploratory Sampling for Robotic Manipulation

arXiv:2510.17640v2 Announce Type: replace-cross Abstract: Vision-Language-Action models (VLAs) have demonstrated remarkable performance on complex robotic manipulation tasks through imitation learning. However, existing imitation learning datasets contain only successful trajectories and lack failure or recovery data, especially for out-of-distribution (OOD) states where the robot deviates from the main policy due to minor perturbations or errors, leading VLA models to struggle with states deviating from the training distribution. To this end, we propose an automated OOD data augmentation framework named RESample through exploratory sampling. Specifically, we first leverage offline reinforcement learning to obtain an action-value network that accurately identifies sub-optimal actions under the current manipulation policy. We further sample potential OOD states from trajectories via rollout, and design an exploratory sampling mechanism that adaptively incorporates these action proxies into the training dataset to ensure efficiency. Subsequently, our framework explicitly encourages the VLAs to recover from OOD states and enhances their robustness against distributional shifts. We conduct extensive experiments on the LIBERO benchmark as well as real-world robotic manipulation tasks, demonstrating that RESample consistently improves the stability and generalization ability of VLA models.
  •  

Benchmarking GPT-5 for biomedical natural language processing

arXiv:2509.04462v2 Announce Type: replace-cross Abstract: Biomedical literature and clinical narratives pose multifaceted challenges for natural language understanding, from precise entity extraction and document synthesis to multi-step diagnostic reasoning. This study extends a unified benchmark to evaluate GPT-5 and GPT-4o under zero-, one-, and five-shot prompting across five core biomedical NLP tasks: named entity recognition, relation extraction, multi-label document classification, summarization, and simplification, and nine expanded biomedical QA datasets covering factual knowledge, clinical reasoning, and multimodal visual understanding. Using standardized prompts, fixed decoding parameters, and consistent inference pipelines, we assessed model performance, latency, and token-normalized cost under official pricing. GPT-5 consistently outperformed GPT-4o, with the largest gains on reasoning-intensive datasets such as MedXpertQA and DiagnosisArena and stable improvements in multimodal QA. In core tasks, GPT-5 achieved better chemical NER and ChemProt scores but remained below domain-tuned baselines for disease NER and summarization. Despite producing longer outputs, GPT-5 showed comparable latency and 30 to 50 percent lower effective cost per correct prediction. Fine-grained analyses revealed improvements in diagnosis, treatment, and reasoning subtypes, whereas boundary-sensitive extraction and evidence-dense summarization remain challenging. Overall, GPT-5 approaches deployment-ready performance for biomedical QA while offering a favorable balance of accuracy, interpretability, and economic efficiency. The results support a tiered prompting strategy: direct prompting for large-scale or cost-sensitive applications, and chain-of-thought scaffolds for analytically complex or high-stakes scenarios, highlighting the continued need for hybrid solutions where precision and factual fidelity are critical.
  •  

Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors

Nat Commun. 2025 Oct 17;16(1):9232. doi: 10.1038/s41467-025-64292-3.

ABSTRACT

Recent advancements in spatial transcriptomics technologies have significantly enhanced resolution and throughput, underscoring an urgent need for systematic benchmarking. Here, we generate serial tissue sections from colon adenocarcinoma, hepatocellular carcinoma, and ovarian cancer samples for systematic evaluation. Using these uniformly processed samples, we generate spatial transcriptomics data across four high-throughput platforms with subcellular resolution: Stereo-seq v1.3, Visium HD FFPE, CosMx 6K, and Xenium 5K. To establish ground truth datasets, we profile proteins on tissue sections adjacent to all platforms using CODEX and perform single-cell RNA sequencing on the same samples. Leveraging manual nuclear segmentation and detailed annotations, we systematically assess each platform's performance across capture sensitivity, specificity, diffusion control, cell segmentation, cell annotation, spatial clustering, and concordance with adjacent CODEX. The uniformly generated and processed multi-omics dataset could advance computational method development and biological discoveries. The dataset is accessible via SPATCH, a user-friendly web server for visualization and download.

PMID:41107232 | PMC:PMC12534522 | DOI:10.1038/s41467-025-64292-3

  •  

Targeting spermine metabolism to overcome immunotherapy resistance in pancreatic cancer

Nat Commun. 2025 Aug 22;16(1):7827. doi: 10.1038/s41467-025-63146-2.

ABSTRACT

While dysregulation of polyamine metabolism is frequently observed in cancer, it is unknown how polyamines alter the tumor microenvironment (TME) and contribute to therapeutic resistance. Analysis of polyamines in the plasma of pancreatic cancer patients reveals that spermine levels are significantly elevated and correlate with poor prognosis. Using a multi-omics approach, we identify Serpinb9 as a vulnerability in spermine metabolism in pancreatic cancer. Serpinb9, a serine protease inhibitor, directly interacts with spermine synthase (SMS), impeding its lysosome-mediated degradation and thereby augmenting spermine production and secretion. Mechanistically, the accumulation of spermine in the TME alters the metabolic landscape of immune cells, promoting CD8+ T cell dysfunction and pro-tumor polarization of macrophages, thus creating an immunosuppressive microenvironment. Small peptides that disrupt the Serpinb9-SMS interaction significantly enhance the efficacy of immune checkpoint blockade therapy. Together, our findings suggest that targeting spermine metabolism is a promising strategy to improve pancreatic cancer immunotherapy.

PMID:40846845 | PMC:PMC12373741 | DOI:10.1038/s41467-025-63146-2

  •  

A Novel Urine DNA Predictor for Noninvasive Early Diagnosis and Monitoring Minimal Residual Disease of Upper Tract Urothelial Carcinoma

Cancer Med. 2024 Oct;13(20):e70346. doi: 10.1002/cam4.70346.

ABSTRACT

BACKGROUND: For early detection and postoperative monitoring of upper tract urothelial carcinoma (UTUC), the traditional detection method was limited to its invasiveness and insufficient sensitivity. We aim to use urine tumour DNA (utDNA) for detecting minimal residual disease (MRD), early diagnosis and perioperative monitoring in UTUC.

METHOD: We previously established a utDNA multidimensional bioinformatic valuation model, named utLIFE, using low-coverage whole-genome sequencing and targeted deep sequencing. This prospective cohort enrolled 93 patients diagnosed with UTUC without metastasis. We collected morning urine samples on the day of surgery and the discharge day after the operation for utLIFE testing. In addition, we also enrolled 80 healthy controls to further validate the specificity of the utLIFE model in the study.

RESULTS: The utLIFE of preoperative samples could discriminate UTUC with high specificity (96.25%, 77/80), and high sensitivity (96.77%, 90/93) regardless of stage and grade. The sensitivity of utLIFE was significantly higher than urine cytology (p < 0.001) and fluorescence in situ hybridisation (FISH) (p < 0.001) (N = 19), especially in early-stage and low-grade UTUC. Postoperative utLIFE scores were significantly decreased compared with those of preoperative samples (79 vs. 36, p < 0.001), indicating its association with tumour burden. For special pathology types, utLIFE performed less well in sensitivity and perioperative alteration.

CONCLUSION: In conclusion, we established a bioinformatic utDNA valuation model, utLIFE, which was validated to be a rapid and noninvasive approach with high sensitivity for early detection and MRD monitoring for UTUC.

PMID:39440792 | PMC:PMC11497171 | DOI:10.1002/cam4.70346

  •  
❌