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Received — 8 April 2026 ⏭

AdaptFuse: Training-Free Sequential Preference Learning via Externalized Bayesian Inference

✇cs.AI, q-bio.NC updates on arXiv.org
By: Fangzhou Lin · Peiran Li · Shuo Xing · Siyuan Yang · Qianwen Ge · Kazunori Yamada · Ziming Zhang · Haichong Zhang · Zhengzhong Tu
7 April 2026 at 12:00
arXiv:2604.03925v1 Announce Type: cross Abstract: Large language models struggle to accumulate evidence across multiple rounds of user interaction, failing to update their beliefs in a manner consistent with Bayesian inference. Existing solutions require fine-tuning on sensitive user interaction data, limiting their applicability in privacy-conscious settings. We propose AdaptFuse, a training-free framework that externalizes probabilistic computation entirely from the LLM: a symbolic module maintains a Bayesian posterior over a discrete hypothesis set, while a frozen LLM contributes semantic reasoning via multi-sample Dirichlet aggregation. The two signals are combined through entropy-adaptive fusion, which automatically weights each source by its predictive confidence, shifting reliance from the LLM to the symbolic posterior as evidence accumulates. We evaluate across three domains: flight recommendation, hotel recommendation, and web shopping; on Gemma 2 9B, Llama 3 8B, and Qwen 2.5 7B. AdaptFuse consistently outperforms both prompting baselines and fine-tuned Bayesian Teaching models on all tasks, with accuracy improving monotonically over interaction rounds. These results demonstrate that principled inference-time algorithms can substitute for fine-tuning in personalized recommendation, without storing or training on sensitive user data. All the code and materials will be open-sourced.

Preserving Forgery Artifacts: AI-Generated Video Detection at Native Scale

✇cs.AI, q-bio.NC updates on arXiv.org
By: Zhengcen Li · Chenyang Jiang · Hang Zhao · Shiyang Zhou · Yunyang Mo · Feng Gao · Fan Yang · Qiben Shan · Shaocong Wu · Jingyong Su
7 April 2026 at 12:00
arXiv:2604.04634v1 Announce Type: cross Abstract: The rapid advancement of video generation models has enabled the creation of highly realistic synthetic media, raising significant societal concerns regarding the spread of misinformation. However, current detection methods suffer from critical limitations. They rely on preprocessing operations like fixed-resolution resizing and cropping. These operations not only discard subtle, high-frequency forgery traces but also cause spatial distortion and significant information loss. Furthermore, existing methods are often trained and evaluated on outdated datasets that fail to capture the sophistication of modern generative models. To address these challenges, we introduce a comprehensive dataset and a novel detection framework. First, we curate a large-scale dataset of over 140K videos from 15 state-of-the-art open-source and commercial generators, along with Magic Videos benchmark designed specifically for evaluating ultra-realistic synthetic content. In addition, we propose a novel detection framework built on the Qwen2.5-VL Vision Transformer, which operates natively at variable spatial resolutions and temporal durations. This native-scale approach effectively preserves the high-frequency artifacts and spatiotemporal inconsistencies typically lost during conventional preprocessing. Extensive experiments demonstrate that our method achieves superior performance across multiple benchmarks, underscoring the critical importance of native-scale processing and establishing a robust new baseline for AI-generated video detection.

Discovering Failure Modes in Vision-Language Models using RL

✇cs.AI, q-bio.NC updates on arXiv.org
By: Kanishk Jain · Qian Yang · Shravan Nayak · Parisa Kordjamshidi · Nishanth Anand · Aishwarya Agrawal
7 April 2026 at 12:00
arXiv:2604.04733v1 Announce Type: cross Abstract: Vision-language Models (VLMs), despite achieving strong performance on multimodal benchmarks, often misinterpret straightforward visual concepts that humans identify effortlessly, such as counting, spatial reasoning, and viewpoint understanding. Previous studies manually identified these weaknesses and found that they often stem from deficits in specific skills. However, such manual efforts are costly, unscalable, and subject to human bias, which often overlooks subtle details in favor of salient objects, resulting in an incomplete understanding of a model's vulnerabilities. To address these limitations, we propose a Reinforcement Learning (RL)-based framework to automatically discover the failure modes or blind spots of any candidate VLM on a given data distribution without human intervention. Our framework trains a questioner agent that adaptively generates queries based on the candidate VLM's responses to elicit incorrect answers. Our approach increases question complexity by focusing on fine-grained visual details and distinct skill compositions as training progresses, consequently identifying 36 novel failure modes in which VLMs struggle. We demonstrate the broad applicability of our framework by showcasing its generalizability across various model combinations.

ContextDrag: Precise Drag-Based Image Editing via Context-Preserving Token Injection and Position-Aligned Attention

✇cs.AI, q-bio.NC updates on arXiv.org
By: Huiguo He · Pengyu Yan · Ziqi Yi · Weizhi Zhong · Zheng Liu · Yejun Tang · Huan Yang · Guanbin Li · Lianwen Jin
7 April 2026 at 12:00
arXiv:2512.08477v2 Announce Type: replace-cross Abstract: Drag-based image editing enables intuitive visual manipulation through point-based drag operations. Existing methods mainly rely on diffusion inversion or pixel-space warping with inpainting. However, inversion inherently introduces approximation errors that degrade texture fidelity, whereas rigid pixel-space operations discard semantic context and produce unnatural deformations. To address these issues, we introduce ContextDrag, to our knowledge the first framework that brings drag-based manipulation into the in-context image editing paradigm. By leveraging the in-context capabilities of editing models (e.g., FLUX-Kontext), ContextDrag enables precise drag editing without inversion or fine-tuning. Specifically, we first propose Context-preserving Token Injection (CTI), which injects VAE-encoded reference features into attention layers at spatially aligned target positions, guided by latent-space correspondences estimated directly from user-specified control points. By operating on clean, directly encoded features rather than noisy inversion outputs, CTI preserves rich texture details and enables precise drag control. Second, we propose Position-Aligned Attention (PAA) to eliminate interference caused by spatial displacement of reference features. PAA re-encodes positional embeddings of displaced reference tokens to match their target locations, and masks overlapping regions between source and destination to prevent conflicting features from degrading visual consistency. Experiments on DragBench-SR and DragBench-DR demonstrate that ContextDrag achieves SOTA editing accuracy and overall quality, and comprehensive ablations validate the effectiveness of each proposed component. Code will be publicly available.

GPA: Learning GUI Process Automation from Demonstrations

✇cs.AI, q-bio.NC updates on arXiv.org
By: Zirui Zhao · Jun Hao Liew · Yan Yang · Wenzhuo Yang · Ziyang Luo · Doyen Sahoo · Silvio Savarese · Junnan Li
7 April 2026 at 12:00
arXiv:2604.01676v2 Announce Type: replace-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.

Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation

✇(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
By: Zhengyu Hu · Jiaqi Wang · Jialin Yu · Zheqing Hu · Jing Xue · Zhanbing Ma · Miaomiao Nian · Ruixin Qi · Tingting Zhao · Xia Cao · Hongxia Xin · Xiuyan Wang · Guilan Yang · Zhenzhen Gui · Xiaoming Liu · Juan Chen
6 April 2026 at 18:00

Front Immunol. 2026 Mar 19;17:1730289. doi: 10.3389/fimmu.2026.1730289. eCollection 2026.

ABSTRACT

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with limited treatment options and a poor prognosis. Recent studies suggest a critical role for the gut-immune-lung axis in IPF, yet the underlying molecular mechanisms remain unclear.

METHODS: The current study performed in silico multi-omics integration of publicly available datasets, including bulk RNA-seq, single-cell and spatial transcriptomics, as well as peripheral blood multi-omics data to uncover key molecular signatures in IPF. Furthermore, machine learning techniques were utilized to identify core genes, whereas functional analyses and Mendelian randomization were conducted to evaluate the causal relationships among gut microbiota, immune cells, and IPF. Additionally, experimental validation using qPCR and ELISA assays was conducted in vitro, in vivo, and in patient plasma to confirm the expression patterns of key genes.

RESULTS: Across integrated public bulk, single-cell, spatial, and blood multi-omics, CXCL13, IL33, TLR4, and IGF1 were identified as core IPF genes consistently linked to immune infiltration and fibrotic remodeling. Deconvolution, scRNA-seq, and spatial mapping localized their dysregulation to fibroblasts and immune compartments (notably B-cell, macrophage, and mast-cell axes), highlighting fibroblast-immune crosstalk in fibrotic foci. A four-gene model robustly distinguished IPF from controls across cohorts. Mendelian randomization supported a gut-immune-lung axis, indicating causal effects of specific gut taxa on IPF risk via immune phenotypes. qPCR/ELISA in TGF-β1-stimulated fibroblasts, bleomycin mouse lungs, and patient plasma corroborated upregulation of IL33, CXCL13, IGF1 and downregulation of TLR4. Drug-signature reversal nominated cucurbitacin I and temsirolimus; molecular docking was performed as a preliminary in silico, computer-simulation-based assessment of potential ligand-protein interactions between these compounds and the four core targets.

CONCLUSION: This study provides new insights into the importance of gut-immune-lung axis in IPF and identifies CXCL13, IL33, TLR4, and IGF1 as diagnostic signatures and therapeutic targets. By integrating public multi-omics resources with experimental validation, our findings offer a foundation for future diagnostic and treatment strategies aimed at modulating the gut microbiota and immune system in IPF.

PMID:41939867 | PMC:PMC13043422 | DOI:10.3389/fimmu.2026.1730289

Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation

✇Omics In Lung
By: Zhengyu Hu · Jiaqi Wang · Jialin Yu · Zheqing Hu · Jing Xue · Zhanbing Ma · Miaomiao Nian · Ruixin Qi · Tingting Zhao · Xia Cao · Hongxia Xin · Xiuyan Wang · Guilan Yang · Zhenzhen Gui · Xiaoming Liu · Juan Chen
6 April 2026 at 18:00

Front Immunol. 2026 Mar 19;17:1730289. doi: 10.3389/fimmu.2026.1730289. eCollection 2026.

ABSTRACT

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with limited treatment options and a poor prognosis. Recent studies suggest a critical role for the gut-immune-lung axis in IPF, yet the underlying molecular mechanisms remain unclear.

METHODS: The current study performed in silico multi-omics integration of publicly available datasets, including bulk RNA-seq, single-cell and spatial transcriptomics, as well as peripheral blood multi-omics data to uncover key molecular signatures in IPF. Furthermore, machine learning techniques were utilized to identify core genes, whereas functional analyses and Mendelian randomization were conducted to evaluate the causal relationships among gut microbiota, immune cells, and IPF. Additionally, experimental validation using qPCR and ELISA assays was conducted in vitro, in vivo, and in patient plasma to confirm the expression patterns of key genes.

RESULTS: Across integrated public bulk, single-cell, spatial, and blood multi-omics, CXCL13, IL33, TLR4, and IGF1 were identified as core IPF genes consistently linked to immune infiltration and fibrotic remodeling. Deconvolution, scRNA-seq, and spatial mapping localized their dysregulation to fibroblasts and immune compartments (notably B-cell, macrophage, and mast-cell axes), highlighting fibroblast-immune crosstalk in fibrotic foci. A four-gene model robustly distinguished IPF from controls across cohorts. Mendelian randomization supported a gut-immune-lung axis, indicating causal effects of specific gut taxa on IPF risk via immune phenotypes. qPCR/ELISA in TGF-β1-stimulated fibroblasts, bleomycin mouse lungs, and patient plasma corroborated upregulation of IL33, CXCL13, IGF1 and downregulation of TLR4. Drug-signature reversal nominated cucurbitacin I and temsirolimus; molecular docking was performed as a preliminary in silico, computer-simulation-based assessment of potential ligand-protein interactions between these compounds and the four core targets.

CONCLUSION: This study provides new insights into the importance of gut-immune-lung axis in IPF and identifies CXCL13, IL33, TLR4, and IGF1 as diagnostic signatures and therapeutic targets. By integrating public multi-omics resources with experimental validation, our findings offer a foundation for future diagnostic and treatment strategies aimed at modulating the gut microbiota and immune system in IPF.

PMID:41939867 | PMC:PMC13043422 | DOI:10.3389/fimmu.2026.1730289

Received — 6 April 2026 ⏭
Received — 4 April 2026 ⏭

GPA: Learning GUI Process Automation from Demonstrations

✇cs.AI, q-bio.NC updates on arXiv.org
By: Zirui Zhao · Jun Hao Liew · Yan Yang · Wenzhuo Yang · Ziyang Luo · Doyen Sahoo · Silvio Savarese · Junnan Li
3 April 2026 at 12:00
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

✇cs.AI, q-bio.NC updates on arXiv.org
By: Ruijie Yang · Yan Zhu · Peiyao Fu · Te Luo · Zhihua Wang · Xian Yang · Quanlin Li · Pinghong Zhou · Shuo Wang
3 April 2026 at 12:00
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

✇cs.AI, q-bio.NC updates on arXiv.org
By: Duolin Sun · Meixiu Long · Dan Yang · Junjie Wang · Yecheng Luo · Yue Shen · Jian Wang · Hualei Zhou · Chunxiao Guo · Peng Wei · Jiahai Wang · Jinjie Gu
3 April 2026 at 12:00
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

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jun Liu · Pu Zhao · Zhenglun Kong · Xuan Shen · Peiyan Dong · Fan Yang · Lin Cui · Hao Tang · Geng Yuan · Wei Niu · Wenbin Zhang · Xue Lin · Gaowen Liu · Yanzhi Wang · Dong Huang
3 April 2026 at 12:00
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

✇Cell
By: Wenqin Xiao · Yan Zhu · Xinjie Tang · Kongkai Zhu · Weifeng Zhang · Mengting Chen · Kui Cai · San Xu · Zheng Wu · Mei Wang · Jiayi Liu · Linglong Long · Zixin Tan · Aike Wu · Songqi Zhou · Zhixiang Zhao · Yan Tang · Yingxue Huang · Ben Wang · Fangfen Liu · Qian Wang · Fan Yang · Dan Jian · Wei Shi · Hongfu Xie · Xiang Chen · Lulu Guo · Zhili Deng · Jinpeng Sun · Ji Li
5 March 2026 at 08:00
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.
Received — 2 April 2026 ⏭

CREST: Constraint-Release Execution for Multi-Robot Warehouse Shelf Rearrangement

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jiaqi Tan · Yudong Luo · Sophia Huang · Yifan Yang · Hang Ma
1 April 2026 at 12:00
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

✇cs.AI, q-bio.NC updates on arXiv.org
By: Junkai Chen · Huihui Huang · Yunbo Lyu · Junwen An · Jieke Shi · Chengran Yang · Ting Zhang · Haoye Tian · Yikun Li · Zhenhao Li · Xin Zhou · Xing Hu · David Lo
1 April 2026 at 12:00
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

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jian Yang · Wei Zhang · Jiajun Wu · Junhang Cheng · Shawn Guo · Haowen Wang · Weicheng Gu · Yaxin Du · Joseph Li · Fanglin Xu · Yizhi Li · Lin Jing · Yuanbo Wang · Yuhan Gao · Ruihao Gong · Chuan Hao · Ran Tao · Aishan Liu · Tuney Zheng · Ganqu Cui · Zhoujun Li · Mingjie Tang · Chenghua Lin · Wayne Xin Zhao · Xianglong Liu · Ming Zhou · Bryan Dai · Weifeng Lv
1 April 2026 at 12:00
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 - Issue - nature.com science feeds
By: Yifei Wang · Zhongqu Duan · Dan Chen · Dandan Shi · Yi Ding · Zhibin Wang · Baoqing Li · Zhiyi Wang · Minmin Guo · Wen Yang · Junren Hou · Wenhao Chen · Yazhou Guo · Wenjie Wei · Yujie Cao · Xiwei Sun · Weiyang Bai · Mingdong Lu · Ting Qi · Xian Shen · Jian Yang
1 April 2026 at 08:00

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

✇MRD
By: Yuhan Cui · Zuchao Du · Jiahao Xu · Lihui Gu · Jiaqi Du · Mingda Wang · Tian Yang
31 March 2026 at 18:00

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

✇MRD
By: Chen Zhao · Lei Qiu · Ning An · Yong Ju · Jacqueline Ziqian Yang · Hyoyong Kim · Ryan Y Zhang · Junseok Lee · Jingjing He · Liang-Yan Chen · Yaya Xu · Yue Ma · Emily Ren · Sophie Pan · Pranay Sashikanth · Jina Kim · Di Wang · Peiling Zhang · Jianlin Hu · Yang Gao · Yuhan Bao · Yanhua Tu · Li Wang · Zhili Wang · Zhicheng Zhang · Renjun Pei · Edwin M Posadas · Sungyong You · Wanxing Chai-Ho · Tasha L Lin · Sarah M Larson · Dinesh S Rao · Hsian-Rong Tseng · Na Sun · Chunrui Li · Yazhen Zhu
27 March 2026 at 18:00

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

Received — 26 March 2026 ⏭

Ran Score: a LLM-based Evaluation Score for Radiology Report Generation

✇cs.AI, q-bio.NC updates on arXiv.org
By: Ran Zhang · Yucong Lin · Zhaoli Su · Bowen Liu · Danni Ai · Tianyu Fu · Deqiang Xiao · Jingfan Fan · Yuanyuan Wang · Mingwei Gao · Yuwan Hu · Shuya Gao · Jingtao Li · Jian Yang · Hong Song · Hongliang Sun
25 March 2026 at 12:00
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.
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