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Decipher-MR: a vision-language foundation model for 3D MRI representations
npj Digital Medicine, Published online: 04 April 2026; doi:10.1038/s41746-026-02596-4
Decipher-MR: a vision-language foundation model for 3D MRI representations
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GPA: Learning GUI Process Automation from Demonstrations
arXiv:2604.01676v1 Announce Type: cross
Abstract: GUI Process Automation (GPA) is a lightweight but general vision-based Robotic Process Automation (RPA), which enables fast and stable process replay with only a single demo. Addressing the fragility of traditional RPA and the non-deterministic risks of current vision language model-based GUI agents, GPA introduces three core benefits: (1) Robustness via Sequential Monte Carlo-based localization to handle rescaling and detection uncertainty; (2) Deterministic and Reliability safeguarded by readiness calibration; and (3) Privacy through fast, fully local execution. This approach delivers the adaptability, robustness, and security required for enterprise workflows. It can also be used as an MCP/CLI tool by other agents with coding capabilities so that the agent only reasons and orchestrates while GPA handles the GUI execution. We conducted a pilot experiment to compare GPA with Gemini 3 Pro (with CUA tools) and found that GPA achieves higher success rate with 10 times faster execution speed in finishing long-horizon GUI tasks.
Development and multi-center evaluation of domain-adapted speech recognition for human-AI teaming in real-world gastrointestinal endoscopy
arXiv:2604.01705v1 Announce Type: cross
Abstract: Automatic speech recognition (ASR) is a critical interface for human-AI interaction in gastrointestinal endoscopy, yet its reliability in real-world clinical settings is limited by domain-specific terminology and complex acoustic conditions. Here, we present EndoASR, a domain-adapted ASR system designed for real-time deployment in endoscopic workflows. We develop a two-stage adaptation strategy based on synthetic endoscopy reports, targeting domain-specific language modeling and noise robustness. In retrospective evaluation across six endoscopists, EndoASR substantially improves both transcription accuracy and clinical usability, reducing character error rate (CER) from 20.52% to 14.14% and increasing medical term accuracy (Med ACC) from 54.30% to 87.59%. In a prospective multi-center study spanning five independent endoscopy centers, EndoASR demonstrates consistent generalization under heterogeneous real-world conditions. Compared with the baseline Paraformer model, CER is reduced from 16.20% to 14.97%, while Med ACC is improved from 61.63% to 84.16%, confirming its robustness in practical deployment scenarios. Notably, EndoASR achieves a real-time factor (RTF) of 0.005, significantly faster than Whisper-large-v3 (RTF 0.055), while maintaining a compact model size of 220M parameters, enabling efficient edge deployment. Furthermore, integration with large language models demonstrates that improved ASR quality directly enhances downstream structured information extraction and clinician-AI interaction. These results demonstrate that domain-adapted ASR can serve as a reliable interface for human-AI teaming in gastrointestinal endoscopy, with consistent performance validated across multi-center real-world clinical settings.
DIVER: A Multi-Stage Approach for Reasoning-intensive Information Retrieval
arXiv:2508.07995v5 Announce Type: replace-cross
Abstract: Retrieval-augmented generation has achieved strong performance on knowledge-intensive tasks where query-document relevance can be identified through direct lexical or semantic matches. However, many real-world queries involve abstract reasoning, analogical thinking, or multi-step inference, which existing retrievers often struggle to capture. To address this challenge, we present DIVER, a retrieval pipeline designed for reasoning-intensive information retrieval. It consists of four components. The document preprocessing stage enhances readability and preserves content by cleaning noisy texts and segmenting long documents. The query expansion stage leverages large language models to iteratively refine user queries with explicit reasoning and evidence from retrieved documents. The retrieval stage employs a model fine-tuned on synthetic data spanning medical and mathematical domains, along with hard negatives, enabling effective handling of reasoning-intensive queries. Finally, the reranking stage combines pointwise and listwise strategies to produce both fine-grained and globally consistent rankings. On the BRIGHT benchmark, DIVER achieves state-of-the-art nDCG@10 scores of 46.8 overall and 31.9 on original queries, consistently outperforming competitive reasoning-aware models. These results demonstrate the effectiveness of reasoning-aware retrieval strategies in complex real-world tasks.
When Should a Robot Think? Resource-Aware Reasoning via Reinforcement Learning for Embodied Robotic Decision-Making
arXiv:2603.16673v3 Announce Type: replace-cross
Abstract: Embodied robotic systems increasingly rely on large language model (LLM)-based agents to support high-level reasoning, planning, and decision-making during interactions with the environment. However, invoking LLM reasoning introduces substantial computational latency and resource overhead, which can interrupt action execution and reduce system reliability. Excessive reasoning may delay actions, while insufficient reasoning often leads to incorrect decisions and task failures. This raises a fundamental question for embodied agents: when should the agent reason, and when should it act? In this work, we propose RARRL (Resource-Aware Reasoning via Reinforcement Learning), a hierarchical framework for resource-aware orchestration of embodied agents. Rather than learning low-level control policies, RARRL learns a high-level orchestration policy that operates at the agent's decision-making layer. This policy enables the agent to adaptively determine whether to invoke reasoning, which reasoning role to employ, and how much computational budget to allocate based on current observations, execution history, and remaining resources. Extensive experiments, including evaluations with empirical latency profiles derived from the ALFRED benchmark, show that RARRL consistently improves task success rates while reducing execution latency and enhancing robustness compared with fixed or heuristic reasoning strategies. These results demonstrate that adaptive reasoning control is essential for building reliable and efficient embodied robotic agents.
Metabolite-gated vascular contractility switch: OXGR1 activation mechanism enables agonist therapy for rosacea erythema
Xiao et al. identify α-KG as a rosacea-associated metabolite that activates the OXGR1-Gq-MYL9 axis in the vascular smooth muscle cells to boost contractility and suppress pathological vasodilation underlying erythema. Cryo-EM reveals a bipartite-acid pocket of OXGR1 that enables structure-guided development of A-1, a selective agonist that alleviates erythema in rosacea-like models.
CREST: Constraint-Release Execution for Multi-Robot Warehouse Shelf Rearrangement
arXiv:2603.28803v1 Announce Type: cross
Abstract: Double-Deck Multi-Agent Pickup and Delivery (DD-MAPD) models the multi-robot shelf rearrangement problem in automated warehouses. MAPF-DECOMP is a recent framework that first computes collision-free shelf trajectories with a MAPF solver and then assigns agents to execute them. While efficient, it enforces strict trajectory dependencies, often leading to poor execution quality due to idle agents and unnecessary shelf switching. We introduce CREST, a new execution framework that achieves more continuous shelf carrying by proactively releasing trajectory constraints during execution. Experiments on diverse warehouse layouts show that CREST consistently outperforms MAPF-DECOMP, reducing metrics related to agent travel, makespan, and shelf switching by up to 40.5\%, 33.3\%, and 44.4\%, respectively, with even greater benefits under lift/place overhead. These results underscore the importance of execution-aware constraint release for scalable warehouse rearrangement. Code and data are available at https://github.com/ChristinaTan0704/CREST.
SecureVibeBench: Evaluating Secure Coding Capabilities of Code Agents with Realistic Vulnerability Scenarios
arXiv:2509.22097v2 Announce Type: replace-cross
Abstract: Large language model-powered code agents are rapidly transforming software engineering, yet the security risks of their generated code have become a critical concern. Existing benchmarks have provided valuable insights, but they fail to capture scenarios in which vulnerabilities are actually introduced by human developers, making fair comparisons between humans and agents infeasible. We therefore introduce SecureVibeBench, a benchmark of 105 C/C++ secure coding tasks sourced from 41 projects in OSS-Fuzz for code agents. SecureVibeBench has the following features: (i) realistic task settings that require multi-file edits in large repositories, (ii)~aligned contexts based on real-world open-source vulnerabilities with precisely identified vulnerability introduction points, and (iii) comprehensive evaluation that combines functionality testing and security checking with both static and dynamic oracles. We evaluate 5 popular code agents like OpenHands, supported by 5 LLMs (e.g., Claude sonnet 4.5) on SecureVibeBench. Results show that current agents struggle to produce both correct and secure code, as even the best-performing one, produces merely 23.8\% correct and secure solutions on SecureVibeBench.
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.
The 1000 Chinese Pangenome empowers medical and population genetics
Nature, Published online: 01 April 2026; doi:10.1038/s41586-026-10315-y
Development of the pangenome-informed genome assembly (PIGA) workflow enabled the generation of 1,116 diploid genome assemblies (55 de novo and 1,061 pangenome-informed), representing an extensive resource of medically relevant genic variations.
Surgery-centered integrated strategies for personalized hepatocellular carcinoma care
Cancer Biol Med. 2026 Mar 30:j.issn.2095-3941.2026.0045. doi: 10.20892/j.issn.2095-3941.2026.0045. Online ahead of print.
ABSTRACT
Hepatocellular carcinoma (HCC) remains a major global health burden characterized by late-stage diagnosis and high postoperative recurrence rates. This review presents a surgery-centered precision management framework integrating 3 synergistic components: early detection, precision surgery, and recurrence prevention. Early detection strategies incorporate multiparameter risk models including the gender, age, AFP-L3, AFP, and DCP (GALAD) as well as age, sex, AFP, and PIVKA-II (ASAP) scores, alongside circulating tumor DNA methylation-based liquid biopsy, thus enabling tumor identification at stages amenable to curative resection. Precision surgery optimizes patient selection through refined staging systems including the Chinese liver cancer staging (CNLC), and functional assessments including the albumin-bilirubin (ALBI) grade, whereas conversion therapy and minimally invasive approaches extend surgical eligibility to selected patients with intermediate-stage disease. To mitigate the risk of postoperative recurrence, distinguishing between early and late recurrence patterns and monitoring minimal residual disease are critical strategies. Perioperative systemic therapies, particularly immune checkpoint inhibitor-based combinations, show promise for eradicating micrometastatic disease. This integrated framework provides a cohesive, evidence-based approach to personalized HCC management aimed at maximizing curative potential and long-term survival.
PMID:41913379 | DOI:10.20892/j.issn.2095-3941.2026.0045
Dynamic Targetable Extracellular Vesicle Surface Proteins Monitor Depth of Response to CAR T Therapy
Res Sq [Preprint]. 2026 Mar 18:rs.3.rs-8913641. doi: 10.21203/rs.3.rs-8913641/v1.
ABSTRACT
Extracellular vesicles (EVs) represent a promising liquid biopsy platform in multiple myeloma (MM). We developed an MM EV Surface Protein Assay to quantify and dynamically monitor four MM EV subpopulations defined by targetable MM surface proteins (BCMA, CD38, GPRC5D, and CD319) across 336 serial blood samples from 45 relapsed/refractory MM (RRMM) patients treated with anti-BCMA chimeric antigen receptor (CAR) T-cell therapy. All four MM EV subpopulations significantly decreased in 43 patients with initial response, while BCMA+, GPRC5D+, and CD319+ MM EVs increased in 19 patients with progression, and antigen escape was detected by BCMA+ MM EVs. MM EV subpopulations differentiated minimal residual disease (MRD) status and complemented MRD for detecting early relapse before clinical progression. Notably, CD319+ MM EVs were early predictors of progression-free and overall survival in MRD-negative patients. This assay enables noninvasive monitoring of deep response, progression, and antigen escape, and stratifies survival in MRD-negative patients with RRMM.
PMID:41890853 | PMC:PMC13015583 | DOI:10.21203/rs.3.rs-8913641/v1
Ran Score: a LLM-based Evaluation Score for Radiology Report Generation
arXiv:2603.22935v1 Announce Type: new
Abstract: Chest X-ray report generation and automated evaluation are limited by poor recognition of low-prevalence abnormalities and inadequate handling of clinically important language, including negation and ambiguity. We develop a clinician-guided framework combining human expertise and large language models for multi-label finding extraction from free-text chest X-ray reports and use it to define Ran Score, a finding-level metric for report evaluation. Using three non-overlapping MIMIC-CXR-EN cohorts from a public chest X-ray dataset and an independent ChestX-CN validation cohort, we optimize prompts, establish radiologist-derived reference labels and evaluate report generation models. The optimized framework improves the macro-averaged score from 0.753 to 0.956 on the MIMIC-CXR-EN development cohort, exceeds the CheXbert benchmark by 15.7 percentage points on directly comparable labels, and shows robust generalization on the ChestX-CN validation cohort. Here we show that clinician-guided prompt optimization improves agreement with a radiologist-derived reference standard and that Ran Score enables finding-level evaluation of report fidelity, particularly for low-prevalence abnormalities.
OmniDiT: Extending Diffusion Transformer to Omni-VTON Framework
arXiv:2603.19643v2 Announce Type: replace-cross
Abstract: Despite the rapid advancement of Virtual Try-On (VTON) and Try-Off (VTOFF) technologies, existing VTON methods face challenges with fine-grained detail preservation, generalization to complex scenes, complicated pipeline, and efficient inference. To tackle these problems, we propose OmniDiT, an omni Virtual Try-On framework based on the Diffusion Transformer, which combines try-on and try-off tasks into one unified model. Specifically, we first establish a self-evolving data curation pipeline to continuously produce data, and construct a large VTON dataset Omni-TryOn, which contains over 380k diverse and high-quality garment-model-tryon image pairs and detailed text prompts. Then, we employ the token concatenation and design an adaptive position encoding to effectively incorporate multiple reference conditions. To relieve the bottleneck of long sequence computation, we are the first to introduce Shifted Window Attention into the diffusion model, thus achieving a linear complexity. To remedy the performance degradation caused by local window attention, we utilize multiple timestep prediction and an alignment loss to improve generation fidelity. Experiments reveal that, under various complex scenes, our method achieves the best performance in both the model-free VTON and VTOFF tasks and a performance comparable to current SOTA methods in the model-based VTON task.
The dual regulatory role of METTL14-mediated m<sup>6</sup>A modification in tumorigenesis and its underlying mechanisms
Front Oncol. 2026 Mar 4;16:1771313. doi: 10.3389/fonc.2026.1771313. eCollection 2026.
ABSTRACT
N6-methyladenosine (m6A), as the most abundant RNA epitranscriptional modification in eukaryotes, its key component of the methyltransferase complex, METTL14, not only cooperates in catalyzing m6A deposition but also has functions independent of methyltransferase activity. This article systematically reviews the dual regulatory role of METTL14 in tumors and its molecular mechanisms, mainly organizing the relevant research in a logical sequence of "tumor suppressive effect - tumor promoting effect - controversial or context-dependent". Studies have shown that METTL14 often plays a tumor suppressive role in tumors such as hepatocellular carcinoma and colorectal cancer, while in pancreatic cancer and nasopharyngeal carcinoma, it mostly promotes malignant progression, showing a high degree of context dependence. This article focuses on two key mechanisms: on the one hand, METTL14 precisely regulates the processing, stability, and function of non-coding RNAs (including miRNAs, lncRNAs, and circRNAs) through m6A modification, reshaping the competitive endogenous RNA (ceRNA) network; on the other hand, it shapes an immunosuppressive tumor microenvironment by directly upregulating immune checkpoints such as PD-L1, mediating metabolism-immune interactions, and regulating the function of immune cells. Its functional duality also stems from the selective regulation of key pathways such as PI3K/AKT, as well as the differential interpretation by different m6A readers (such as YTHDF2 and IGF2BPs). Given the close association of these mechanisms with clinical prognosis, the expression level of METTL14 shows significant potential as a prognostic marker and therapeutic target; in the future, it is necessary to combine single-cell multi-omics and other technologies to analyze its dynamic regulatory network in specific tumor contexts and explore precise treatment strategies based on synthetic lethality or targeting downstream effector molecules.
PMID:41858346 | PMC:PMC12995618 | DOI:10.3389/fonc.2026.1771313
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
Tuning the sensitivity of mechanosensory receptors through histidine scanning
Histidine scanning represents a broadly applicable technique for the identification of critical interaction sites within TCRs and other mechanosensory receptors to enhance receptor signaling strength and augment therapeutic efficacy via the catch bond mechanism.
Diagnosing Retrieval Bias Under Multiple In-Context Knowledge Updates in Large Language Models
arXiv:2603.12271v1 Announce Type: cross
Abstract: LLMs are widely used in knowledge-intensive tasks where the same fact may be revised multiple times within context. Unlike prior work focusing on one-shot updates or single conflicts, multi-update scenarios contain multiple historically valid versions that compete at retrieval, yet remain underexplored. This challenge resembles the AB-AC interference paradigm in cognitive psychology: when the same cue A is successively associated with B and C, the old and new associations compete during retrieval, leading to bias. Inspired by this, we introduce a Dynamic Knowledge Instance (DKI) evaluation framework, modeling multi-updates of the same fact as a cue paired with a sequence of updated values, and assess models via endpoint probing of the earliest (initial) and latest (current) states. Across diverse LLMs, we observe that retrieval bias intensifies as updates increase, earliest-state accuracy stays high while latest-state accuracy drops substantially. Diagnostic analyses of attention, hidden-state similarity, and output logits further reveal that these signals become flatter and weakly discriminative on errors, providing little stable basis for identifying the latest update. Finally, cognitively inspired heuristic intervention strategies yield only modest gains and do not eliminate the bias. Our results reveal a persistent challenge in tracking and following knowledge updates in long contexts.
SRAM-Based Compute-in-Memory Accelerator for Linear-decay Spiking Neural Networks
arXiv:2603.12739v1 Announce Type: cross
Abstract: Spiking Neural Networks (SNNs) have emerged as a biologically inspired alternative to conventional deep networks, offering event-driven and energy-efficient computation. However, their throughput remains constrained by the serial update of neuron membrane states. While many hardware accelerators and Compute-in-Memory (CIM) architectures efficiently parallelize the synaptic operation (W x I) achieving O(1) complexity for matrix-vector multiplication, the subsequent state update step still requires O(N) time to refresh all neuron membrane potentials. This mismatch makes state update the dominant latency and energy bottleneck in SNN inference. To address this challenge, we propose an SRAM-based CIM for SNN with Linear Decay Leaky Integrate-and-Fire (LD-LIF) Neuron that co-optimizes algorithm and hardware. At the algorithmic level, we replace the conventional exponential membrane decay with a linear decay approximation, converting costly multiplications into simple additions while accuracy drops only around 1%. At the architectural level, we introduce an in-memory parallel update scheme that performs in-place decay directly within the SRAM array, eliminating the need for global sequential updates. Evaluated on benchmark SNN workloads, the proposed method achieves a 1.1 x to 16.7 x reduction of SOP energy consumption, while providing 15.9 x to 69 x more energy efficiency, with negligible accuracy loss relative to original decay models. This work highlights that beyond accelerating the (W x I) computation, optimizing state-update dynamics within CIM architectures is essential for scalable, low-power, and real-time neuromorphic processing.
SortScrews: A Dataset and Baseline for Real-time Screw Classification
arXiv:2603.13027v1 Announce Type: cross
Abstract: Automatic identification of screw types is important for industrial automation, robotics, and inventory management. However, publicly available datasets for screw classification are scarce, particularly for controlled single-object scenarios commonly encountered in automated sorting systems. In this work, we introduce $\textbf{SortScrews}$, a dataset for casewise visual classification of screws. The dataset contains 560 RGB images at $512\times512$ resolution covering six screw types and a background class. Images are captured using a standardized acquisition setup and include mild variations in lighting and camera perspective across four capture settings.
To facilitate reproducible research and dataset expansion, we also provide a reusable data collection script that allows users to easily construct similar datasets for custom hardware components using inexpensive camera setups.
We establish baseline results using transfer learning with EfficientNet-B0 and ResNet-18 classifiers pretrained on ImageNet. In addition, we conduct a well-explored failure analysis. Despite the limited dataset size, these lightweight models achieve strong classification accuracy, demonstrating that controlled acquisition conditions enable effective learning even with relatively small datasets. The dataset, collection pipeline, and baseline training code are publicly available at https://github.com/ATATC/SortScrews.
