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Normal view

Received today — 7 October 2026 ⏭

Immunotherapy for Digestive System Cancers: Progress, Challenges, and Future Directions

✇Omics in Hepatocellular
By: Keran Sun · Hongru Li · Hao Chi · Yuxuan Song · Yunze Niu · Jingyuan Ning · Hengrui Liu
26 September 2026 at 18:00

Biomedicines. 2026 Aug 27;14(9):1919. doi: 10.3390/biomedicines14091919.

ABSTRACT

Immune checkpoint blockade has changed the management of several digestive system cancers, but its impact is highly context dependent. This review evaluates evidence for esophageal, gastric and gastroesophageal junction, colorectal, hepatocellular, biliary tract and gallbladder, and pancreatic cancers. Randomized phase III trials have established chemoimmunotherapy or dual-checkpoint strategies in advanced esophageal cancer, biomarker- and regimen-dependent first-line therapy in gastric cancer, PD-1-based therapy for MSI-H/dMMR colorectal cancer, atezolizumab-bevacizumab and STRIDE for unresectable hepatocellular carcinoma, and chemoimmunotherapy for advanced biliary tract cancer. Recent results also expand perioperative treatment: neoadjuvant checkpoint blockade produces high pathological response rates in dMMR colon cancer, adjuvant atezolizumab plus mFOLFOX6 improves disease-free survival in stage III dMMR colon cancer, and perioperative serplulimab improves event-free survival in PD-L1-positive resectable gastric cancer. These advances coexist with important negative findings. Pembrolizumab-containing therapy did not meet superiority end points in KEYNOTE-062, the initial adjuvant signal in IMbrave050 was not sustained, and unselected pancreatic ductal adenocarcinoma remains largely resistant to checkpoint blockade. Early vaccine, cellular, TIGIT, radiomics, spatial, and multi-omics studies remain hypothesis-generating and require external or randomized validation. Clinical interpretation should integrate evidence maturity, biomarker validity, immune-related toxicity, patient-reported outcomes, cost, access, and manufacturing demands rather than response rate alone.

PMID:42792661 | PMC:PMC13604390 | DOI:10.3390/biomedicines14091919

Immunotherapy for Digestive System Cancers: Progress, Challenges, and Future Directions

✇(Multiomics OR Omics) AND (Pancreatic)
By: Keran Sun · Hongru Li · Hao Chi · Yuxuan Song · Yunze Niu · Jingyuan Ning · Hengrui Liu
26 September 2026 at 18:00

Biomedicines. 2026 Aug 27;14(9):1919. doi: 10.3390/biomedicines14091919.

ABSTRACT

Immune checkpoint blockade has changed the management of several digestive system cancers, but its impact is highly context dependent. This review evaluates evidence for esophageal, gastric and gastroesophageal junction, colorectal, hepatocellular, biliary tract and gallbladder, and pancreatic cancers. Randomized phase III trials have established chemoimmunotherapy or dual-checkpoint strategies in advanced esophageal cancer, biomarker- and regimen-dependent first-line therapy in gastric cancer, PD-1-based therapy for MSI-H/dMMR colorectal cancer, atezolizumab-bevacizumab and STRIDE for unresectable hepatocellular carcinoma, and chemoimmunotherapy for advanced biliary tract cancer. Recent results also expand perioperative treatment: neoadjuvant checkpoint blockade produces high pathological response rates in dMMR colon cancer, adjuvant atezolizumab plus mFOLFOX6 improves disease-free survival in stage III dMMR colon cancer, and perioperative serplulimab improves event-free survival in PD-L1-positive resectable gastric cancer. These advances coexist with important negative findings. Pembrolizumab-containing therapy did not meet superiority end points in KEYNOTE-062, the initial adjuvant signal in IMbrave050 was not sustained, and unselected pancreatic ductal adenocarcinoma remains largely resistant to checkpoint blockade. Early vaccine, cellular, TIGIT, radiomics, spatial, and multi-omics studies remain hypothesis-generating and require external or randomized validation. Clinical interpretation should integrate evidence maturity, biomarker validity, immune-related toxicity, patient-reported outcomes, cost, access, and manufacturing demands rather than response rate alone.

PMID:42792661 | PMC:PMC13604390 | DOI:10.3390/biomedicines14091919

Received — 15 September 2026 ⏭

Recommendation Retrievers Need Verifiers: Universal Generative Reranking for Sequential Recommendations

✇cs.AI, q-bio.NC updates on arXiv.org
By: Benyu Zhang · Qiang Zhang · Rui Li · Qunshu Zhang · Devansh Tandon · Neeraj Bhatia
14 September 2026 at 12:00
arXiv:2609.12270v1 Announce Type: cross Abstract: First-stage recommenders in multi-stage systems produce a ranked candidate list from which a limited prefix is forwarded to downstream rankers. Because each forwarded item must be processed by more expensive ranking stages, this shortlist cannot be arbitrarily large. The first-stage objective is therefore high coverage of relevant items within the forwarded prefix, commonly measured by Recall@$k$. A relevant item may be available deeper in the retrieved list but absent from the shorter prefix that is actually consumed. This paper studies post-hoc verification for promoting such candidates into the consumed shortlist without retraining or replacing the retriever. We introduce a lightweight generative verifier for retrieval models. Given a retriever state and a candidate item, the verifier scores the item through the likelihood of its identifier tokens. It is trained post hoc with next-token cross entropy, requires no sampled negatives or candidate pool during training, and scores only the retriever's top-$K$ candidates at inference. The interface is minimal: the retriever supplies a query state and candidate items, and the item representation can use any fixed tokenization. Across Amazon product recommendation and YaMBDa music recommendation, the same verifier training recipe improves Recall@10 for SASRec, GRU4Rec, NextItNet, and MiniOneRec. Ablations show that the improvements are not explained solely by injecting item-content features into the retriever, supporting verification as a post-hoc output-side adaptation mechanism.
Received — 13 September 2026 ⏭

The effect of unique molecular identifier family size using tumor-informed circulating tumor-DNA analysis in childhood cancers

✇MRD
By: Tobias Österlund · Daniel Andersson · Raghda R Ibrahim · Elisabeth Mellström · Jenny Lundmark · Junrui Li · Stefan Filges · Peter Micallef · Manuel Luna Santamaría · Mandy Escobar · Pia Mouhanna · Firaol Tamiru Kebede · Christoffer Vannas · Ida Rahmqvist · Fani Pujol Calderón · Agnes Dahlstrand Rudin · Wilma Franssila · Åsa Torinsson Naluai · Serik Sagitov · Joakim Håkansson · Henrik Fagman · Martin Dalin · Anders Ståhlberg
11 September 2026 at 18:00

J Mol Diagn. 2026 Sep 11:S1525-1578(26)00156-X. doi: 10.1016/j.jmoldx.2026.08.002. Online ahead of print.

ABSTRACT

Analysis of circulating tumor-DNA (ctDNA) provides a molecular assessment that can complement routine imaging in childhood cancer management. Detailed monitoring of ctDNA levels may provide information on treatment efficacy and resistance, minimal residual disease and allows for early detection of relapse. Here, tumor-informed ctDNA analysis was applied to 90 blood plasma samples collected from eight children with malignant tumors. Four to ten tumor-specific mutations per patient were assessed using SiMSen-Seq, a digital sequencing approach utilizing unique molecular identifiers (UMIs). The effects of individual SiMSen-Seq assays and plasma samples were evaluated in relation to their impact on background error rate, number of detected target molecules and mutant calling using different UMI family size cutoff settings. The use of at least two sequencing reads per UMI provided the best overall performance by generating the highest number of detected target molecules and hence the optimal chance to detect low-frequent mutations. Data were consistent between SiMSen-Seq assays and plasma samples, providing robust ctDNA profiling over time for all patients. In conclusion, the results show that optimal use of UMIs in tumor-informed ctDNA analysis enables sensitive molecular readout that can assist in management of childhood cancers.

PMID:42727690 | DOI:10.1016/j.jmoldx.2026.08.002

Received — 10 September 2026 ⏭

No Free Checker: A Survey of Verifiers for Robot Policies

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yang Wan · Xihang Yue · Zhirui Liu · Ziyuan Chu · Shuxun Wang · Yuhan Chen · Xiaonan Jiang · Xukun Zhu · Yubo Dong · Linchao Zhu
10 September 2026 at 12:00
arXiv:2609.09250v1 Announce Type: cross Abstract: A verifier for robot policies reads a candidate behavior and returns a score for how well it did, used both to evaluate vision-language-action policies and to train them. Verifiers range from success detectors and reward models to runtime monitors, safety filters, and temporal-logic specifications. We survey roughly 150 verifiers and compare them along two properties. Availability is how much a verdict costs, how early in a rollout the verdict arrives, and how often a verdict can be asked for. Availability rises as verdicts get cheaper, earlier, and denser. Credibility is how much a high score tells us about the task. Credibility falls as the judgment becomes gameable and self-serving. We group the verifiers by who supplies the judgment: human verifiers, rule-based and formal verifiers, learned and pretrained verifiers, and model-intrinsic verifiers. Across the four families, we find that credibility falls as availability rises. Regardless of who supplies the judgment, there is no free checker. We then examine what validates a verifier itself, and how much a high score tells us. Three measures appear in the literature: agreement with human labels, the performance of the policy it trains, and behavior under reward hacking. We close with nine metrics that make a verifier claim checkable, and coordinates for the verifiers still to be built.

Hierarchical and Permutation-Invariant Feature Transformation Learning via Policy-Guided Embedding Search

✇cs.AI, q-bio.NC updates on arXiv.org
By: Rui Liu · Tao Zhe · Yanyong Huang · Sankha Narayan Guria · Xiao Luo · Wei Fan · Yanjie Fu · Dongjie Wang
10 September 2026 at 12:00
arXiv:2609.10225v1 Announce Type: cross Abstract: Feature transformation improves predictive performance on tabular data by constructing informative abstractions from raw features. Recent generative approaches encode transformation knowledge into continuous embedding spaces for efficient exploration of candidate strategies, but face three key limitations: (1) overlooking hierarchical relationships between low-level features, operations, and high-level abstractions; (2) enforcing order-sensitive embeddings on inherently permutation-invariant transformation sequences, thereby introducing systematic bias; and (3) relying on gradient-based search, which is ill-suited to non-convex transformation spaces. We propose a framework with two complementary components. First, a permutation-invariant hierarchical module captures interactions across features, operations, and abstraction levels, with a self-attention pooling mechanism that maps semantically equivalent structures to consistent embeddings aligned with downstream performance. Second, a policy-guided multi-objective reinforcement learning strategy initializes the search from empirically strong seeds and jointly optimizes predictive accuracy and transformation efficiency. Extensive experiments on diverse tabular benchmarks demonstrate the effectiveness and robustness of our framework against strong baselines. Our code and data are publicly available at: https://github.com/RayLiu1103/PHER.

Synergistic Vision-Language Reinforcement Enables Scalable On-Demand Analysis across Diverse Clinical Tasks

✇cs.AI, q-bio.NC updates on arXiv.org
By: Haonan Wang · Jiaji Mao · Lehan Wang · Qixiang Zhang · Marawan Elbatel · Yi Qin · Huijun Hu · Baoxun Li · Wenhui Deng · Weifeng Qin · Hongrui Li · Jialin Liang · Jun Shen · Xiaomeng Li
10 September 2026 at 12:00
arXiv:2505.03380v2 Announce Type: replace-cross Abstract: Accurate delineation of tumors and surrounding organs-at-risk is essential for radiotherapy, surgery and treatment response assessment, yet remains time-consuming and expertise-intensive. Existing artificial intelligence systems often require manual spatial prompts or task-specific retraining, while generic class labels provide limited semantic grounding for heterogeneous disease targets. Here we present SyRe, a promptable segmentation foundation model based on Synergistic vision-language Reinforcement. SyRe strengthens bidirectional interaction between visual and linguistic representations to improve semantically grounded spatial understanding. To support large-scale training, we introduce the Color Region Description strategy and construct SyReData, comprising 20 million image-mask-description triplets across 9 modalities and 229 segmentation tasks. Training with diversified prompt forms further enables open-ended prompting, invalid-prompt rejection and flexible switching between single- and multi-target analysis. SyRe achieves accurate text-prompted segmentation across diverse clinical scenarios, with particularly strong performance on disease-related targets. Across 28 unseen external datasets, including 20 cancer types and multinational in-house cohorts, SyRe generalizes robustly under real-world distribution shifts. SyRe-generated masks also preserve clinically relevant quantitative information in pathology and yield radiomics features that stratify survival and improve prognostic modeling across five retrospective CT and MRI tumor cohorts. Finally, clinician-in-the-loop refinement enables efficient case-level correction when greater precision is required. These results establish SyRe as a generalizable foundation for scalable quantitative oncology and clinician-guided segmentation refinement.

City Editing: Hierarchical Agentic Execution for Dependency-Aware Urban Geospatial Modification

✇cs.AI, q-bio.NC updates on arXiv.org
By: Rui Liu · Steven Jige Quan · Zhong-Ren Peng · Zijun Yao · Han Wang · Pengyang Wang · Kunpeng Liu · Yanjie Fu · Dongjie Wang
10 September 2026 at 12:00
arXiv:2602.19326v3 Announce Type: replace-cross Abstract: Urban renewal requires incremental modifications to existing geospatial plans, yet manually updating complex layouts under spatial constraints is labor-intensive and error-prone. To tackle this, we propose CEAE, a hierarchical agentic framework that formulates urban renewal as machine-executable GeoJSON editing from natural-language instructions. CEAE decomposes instructions into hierarchical geometric intents, executing edits from coarse to fine while preserving spatial consistency through a self-reflective execution-validation loop. Experimental results show that CEAE outperforms baselines in execution validity, robustness, and geometric accuracy.

Reconstituting human primitive streak formation through extra-embryonic cell coordination

✇Cell
By: Qiaoyan Shen · Xin Zhang · Naixin Chen · Xiaodi Yan · Hongan Ren · Xizhuang Sun · Linjie Xu · Jianchao Zhao · Rong Li · Sirui Lin · Xiaojie Jia · Leqian Yu · Yulei Wei
24 June 2026 at 08:00
Tissue patterning events of early human embryo development, including an embryo-disc with primitive streak-like structures, are captured using an in vitro model where embryonic stem cells are cultured with extra-embryonic cell types.
Received — 27 May 2026 ⏭

A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development

✇(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
By: Qian Tang · Chen Lian · Xinyan Han · Xuhan Zhang · Zihan Wang · Boyu Wang · Taoyu Zhu · Xinrui Lin · Xiaolei Wang · Yaping Xu · Manyu Xiao · Zijin Wang · Junming Li · Silin Chen · Yunze Wang · Yufei Liu · Songsong Li · Zuolin Shen · Xi Lu · Xueqi Han · Yilu Zhou · Mingyang Xiao · Jiayi Ran · Xiaoran Cao · Xinyi Xu · Hugo Sámano-Sánchez · Alfredo Rodríguez · Lian Wang · Shuifang Chen · Zhanyu Xu · Shirong Zhang · Nuo Yang · Yong Tang · Jian Liu
26 May 2026 at 18:00

Adv Sci (Weinh). 2026 May 26:e75839. doi: 10.1002/advs.75839. Online ahead of print.

ABSTRACT

Lung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datasets, genetically engineered mouse models, human and murine LUSC cell lines, and multi-omics analyses, we demonstrate that SMAD4 deficiency promotes LUSC progression by unleashing EP300-mediated enhancer-promoter looping at the SOX2 locus. Mechanistically, SMAD4 does not directly bind SOX2 regulatory elements but instead constrains chromatin looping by sequestering EP300 away from loop anchor regions. Loss of SMAD4 leads to enhanced H3K27ac deposition, aberrant SOX2 activation, and increased LUSC tumor cell proliferation. Together, these findings reveal a non-canonical role for a transcription factor (e.g., SMAD4) in regulating dysregulated 3D genome architecture to inhibit tumor development.

PMID:42189071 | DOI:10.1002/advs.75839

A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development

✇Omics In Lung
By: Qian Tang · Chen Lian · Xinyan Han · Xuhan Zhang · Zihan Wang · Boyu Wang · Taoyu Zhu · Xinrui Lin · Xiaolei Wang · Yaping Xu · Manyu Xiao · Zijin Wang · Junming Li · Silin Chen · Yunze Wang · Yufei Liu · Songsong Li · Zuolin Shen · Xi Lu · Xueqi Han · Yilu Zhou · Mingyang Xiao · Jiayi Ran · Xiaoran Cao · Xinyi Xu · Hugo Sámano-Sánchez · Alfredo Rodríguez · Lian Wang · Shuifang Chen · Zhanyu Xu · Shirong Zhang · Nuo Yang · Yong Tang · Jian Liu
26 May 2026 at 18:00

Adv Sci (Weinh). 2026 May 26:e75839. doi: 10.1002/advs.75839. Online ahead of print.

ABSTRACT

Lung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datasets, genetically engineered mouse models, human and murine LUSC cell lines, and multi-omics analyses, we demonstrate that SMAD4 deficiency promotes LUSC progression by unleashing EP300-mediated enhancer-promoter looping at the SOX2 locus. Mechanistically, SMAD4 does not directly bind SOX2 regulatory elements but instead constrains chromatin looping by sequestering EP300 away from loop anchor regions. Loss of SMAD4 leads to enhanced H3K27ac deposition, aberrant SOX2 activation, and increased LUSC tumor cell proliferation. Together, these findings reveal a non-canonical role for a transcription factor (e.g., SMAD4) in regulating dysregulated 3D genome architecture to inhibit tumor development.

PMID:42189071 | DOI:10.1002/advs.75839

DRIVE: Modeling Skills at the Reasoning and Interaction Levels for Web Agents under Continual Learning

✇cs.AI, q-bio.NC updates on arXiv.org
By: Xirui Liu · Sihang Zhou · Yanning Hou · Rong Zhou · Haoyuan Chen · Maolin He · Siwei Wang · Hao Chen · Jian Huang
26 May 2026 at 12:00
arXiv:2605.23939v1 Announce Type: new Abstract: Web agents require both high-level reasoning (for task decomposition) and low-level interactions (for page elements manipulation) to conduct different tasks. However, these knowledge types differ fundamentally: reasoning knowledge (e.g., booking a flight requires first searching for routes) is abstract and transferable across websites, while interaction knowledge (e.g., clicking the Search button at a specific coordinate on Site A) depends heavily on page-specific contexts. Existing methods store experiences uniformly. This creates a dilemma: abstract representations lose executability on concrete pages, while concrete representations fail to generalize across domains. This entanglement limits capability accumulation: on new websites, agents either fail to recognize reusable task logic due to surface-level differences or attempt infeasible actions from outdated page structures. To disentangle them, we propose DRIVE, a dual-level skill modeling framework separating historical experience into natural language reasoning skills, which capture transferable task logic, and programmatic interaction skills, grounding abstract actions to executable operations. A scene-aware coordination mechanism adaptively retrieves and invokes these dual-level skills based on task semantics. DRIVE also uses skill-level reflection to identify hierarchy-specific failure modes, enabling targeted skill library expansion and refinement. Experiments across five WebArena domains show DRIVE attains an average task success rate of 52.8%, exceeding the skill-free baseline by 7.3 percentage points. Further ablations show reasoning and interaction skills provide distinct, complementary benefits, supporting separation of transferable task logic from executable page-level operations.

GlobalDentBench: A Multinational Benchmark for Evaluating LLM Clinical Reasoning in Dentistry with Expert Calibration

✇cs.AI, q-bio.NC updates on arXiv.org
By: Junjie Zhao · Jingyi Liang · Zhenyang Cai · Jiaming Zhang · Zhenwei Wen · Shuzhi Deng · Wenjing Yi · Chunfeng Luo · Hexian Zhang · Junying Chen · Tianrui Liu · Zhuhui Bai · Zixu Zhang · Pradeep Singh · Xiang Liu · Jianquan Li · Nhan L Tran · Falk Schwendicke · Zuolin Jin · Lijian Jin · Liangyi Chen · Wei-fa Yang · Benyou Wang · Junwen Wang · Shan Jiang
26 May 2026 at 12:00
arXiv:2605.24636v2 Announce Type: new Abstract: While large language models (LLMs) hold transformative potential for medicine, their reasoning robustness and safety in real-world clinical scenarios remain critically underexplored, particularly in dentistry. Here we introduce GlobalDentBench, the first multinational dental benchmark, featuring a taxonomy that encompasses 14 dental specialties across 88 countries and regions spanning six continents. The benchmark comprises 8,978 expert-validated questions across three formats (multiple-choice, short-answer, and case-based questions) and assesses three progressive reasoning levels: knowledge recall (L1), routine reasoning (L2), and individualized reasoning (L3). To ensure data quality, the automated construction framework was calibrated by six senior dentists, achieving expert agreement rates of 99.98% for multiple-choice and short-answer questions and 96.78% for the more complex case-based questions. Evaluation of 12 frontier LLMs on GlobalDentBench revealed a sharp, stepwise performance degradation with increasing reasoning complexity. Specifically, accuracy plummeted from 81.34% on multiple-choice to 64.53% on short-answer and 22.34% on case-based questions, while declining markedly from 74.01% at L1 to 55.64% at L2 and 35.71% at L3. More critically, risk analysis of real-world dental cases demonstrated an alarming overall unsafe rate of 31.01% in LLM-generated clinical recommendations, with 4.51% posing risks of irreversible patient harm and risks particularly pronounced in specialties such as orthodontics. These findings expose fundamental limitations in the medical reasoning and safety of current LLMs. Consequently, GlobalDentBench provides a scalable foundation for trustworthy clinical AI evaluation, underscoring the urgent need for rigorous validation before the safe deployment of these models in healthcare.

Towards Multi-Turn Dialog Systems for Industrial Asset Operations and Maintenance

✇cs.AI, q-bio.NC updates on arXiv.org
By: Chengrui Li · Rujing Li · Yitong Bai · Rui Li
26 May 2026 at 12:00
arXiv:2605.24953v1 Announce Type: new Abstract: Industrial asset operations and maintenance question answering is inherently multi-turn, iterative, and highly dependent on external tool invocation. However, the conventional plan-execute single-agent architecture exhibits clear limitations in maintaining cross-turn context, and reusing intermediate results. In this paper, we present a multi-turn dialog system designed for industrial scenarios based on a supervisor-specialist multi-agent architecture. To alleviate tool invocation bottlenecks, the system incorporates structured artifact reuse, dynamic replanning, and parallel tool execution. Evaluation results show that our system achieves better response quality compared with the baseline, with planning effectiveness increasing by 54.5% and task completion improving by 37.8%. System profiling further shows that cross-turn artifact reuse effectively reduces redundant tool invocation, decreasing the tool-time share from 47.3% to 26.3% and making turns 2-5 approximately 4.2x faster than the first turn.

FrontierOR: Benchmarking LLMs' Capacity for Efficient Algorithm Design in Large-Scale Optimization

✇cs.AI, q-bio.NC updates on arXiv.org
By: Minwei Kong · Chonghe Jiang · Ao Qu · Wenbin Ouyang · Zhaoming Zeng · Xiaotong Guo · Zhekai Li · Junyi Li · Yi Fan · Xinshou Zheng · Xi Jing · Yikai Zhang · Zhiwei Liang · Seonghoo Kim · Runqing Yang · Zijian Zhou · Sirui Li · Han Zheng · Wangyang Ying · Ou Zheng · Chonghuan Wang · Jinglong Zhao · Hanzhang Qin · Cathy Wu · Paul Pu Liang · Jinhua Zhao · Hai Wang
26 May 2026 at 12:00
arXiv:2605.25246v2 Announce Type: new Abstract: Large language models (LLMs) are increasingly used for optimization modeling and solver-code generation, yet practical operations research and optimization problems often require a harder capability: designing scalable algorithms that exploit problem structure and outperform direct formulation-and-solve baselines. Existing benchmarks are limited to small or simplified examples far below real-world scale and complexity. We introduce FrontierOR, among the first benchmarks to systematically evaluate LLM-based efficient algorithm design for realistic large-scale optimization problems. FrontierOR includes 180 tasks derived from methodologically diverse papers published in top-tier operations research venues, each with standardized instances and a hidden, expert-verified evaluation suite. We evaluate seven LLMs spanning frontier, cost-effective, and open-source models both in one-shot and test-time evolution settings. The results reveal that frontier models still struggle to move from executable formulations to efficient optimization algorithms: the strongest one-shot model outperforms Gurobi in only 31% of cases in both solution quality and computational efficiency, and even strong coding agents with test-time evolution achieve only 50% on selected hard tasks. FrontierOR establishes a practical evaluation platform for LLM-based optimization algorithm design, which enables future LLMs and agents to be systematically tested on whether they can move beyond correct formulation toward a feasible, high-quality, and efficient algorithm.

AutoResearchClaw: Self-Reinforcing Autonomous Research with Human-AI Collaboration

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jiaqi Liu · Shi Qiu · Mairui Li · Bingzhou Li · Haonian Ji · Siwei Han · Xinyu Ye · Peng Xia · Zihan Dong · Meng Chen · Congyu Zhang · Letian Zhang · Guiming Chen · Haoqin Tu · Xinyu Yang · Lu Feng · Xujiang Zhao · Haifeng Chen · Jiawei Zhou · Xiao Wang · Weitong Zhang · Hongtu Zhu · Yun Li · Jieru Mei · Hongliang Fei · Jiaheng Zhang · Linjie Li · Linjun Zhang · Yuyin Zhou · Sheng Wang · Caiming Xiong · James Zou · Zeyu Zheng · Cihang Xie · Mingyu Ding · Huaxiu Yao
26 May 2026 at 12:00
arXiv:2605.20025v2 Announce Type: replace Abstract: Automating scientific discovery requires more than generating papers from ideas. Real research is iterative: hypotheses are challenged from multiple perspectives, experiments fail and inform the next attempt, and lessons accumulate across cycles. Existing autonomous research systems often model this process as a linear pipeline: they rely on single-agent reasoning, stop when execution fails, and do not carry experience across runs. We present AutoResearchClaw, a multi-agent autonomous research pipeline built on five mechanisms: structured multi-agent debate for hypothesis generation and result analysis, a self-healing executor with a \textsc{Pivot}/\textsc{Refine} decision loop that transforms failures into information, verifiable result reporting that prevents fabricated numbers and hallucinated citations, human-in-the-loop collaboration with seven intervention modes spanning full autonomy to step-by-step oversight, and cross-run evolution that converts past mistakes into future safeguards. On ARC-Bench, a 25-topic experiment-stage benchmark, AutoResearchClaw outperforms AI Scientist v2 by 54.7%. A human-in-the-loop ablation across seven intervention modes reveals that precise, targeted collaboration at high-leverage decision points consistently outperforms both full autonomy and exhaustive step-by-step oversight. We position AutoResearchClaw as a research amplifier that augments rather than replaces human scientific judgment. Code is available at https://github.com/aiming-lab/AutoResearchClaw.

Ferroptosis and macrophage polarization: mechanisms, interplay, and implications for medical applications

✇Cell Death Discovery nature.com science feeds
By: Yajuan Zhao · Jianbin Fu · Ping Zhao · Yuan Jiang · Yuhan Wang · Yaopeng Zhang · Zhaorui Li · Yongjun Zhao · Niannian Li · Bao Lang · Yanhua Luo
23 May 2026 at 08:00

Cell Death Discovery, Published online: 23 May 2026; doi:10.1038/s41420-026-03147-2

Ferroptosis and macrophage polarization: mechanisms, interplay, and implications for medical applications

PRXL2B facilitates the progression of hepatocellular carcinoma and the therapeutic efficacy of oncolytic adenovirus H101 through the PI3K/AKT/PD-L1 axis

✇Omics in Hepatocellular
By: Ziqi Zhang · Hongli Chen · Yangming Liu · Hao Wang · You Yan · Yanxi Yu · Zuotian Huang · Yanyao Liu · Wei Li · Zhongjun Wu · Meiqing Kang · Xiaoyong Luo · Ping Che · Rui Liao
20 May 2026 at 18:00

Biosci Trends. 2026 May 21. doi: 10.5582/bst.2026.01000. Online ahead of print.

ABSTRACT

Oncolytic adenovirus H101 has shown antitumor activity in hepatocellular carcinoma (HCC), but the molecular determinants of treatment response remain unclear. In this study, a Hepa1-6 subcutaneous tumor model was established in C57BL/6 mice and treated with intratumoral H101, followed by integrated transcriptomic and proteomic analyses to identify candidate genes associated with H101 response. PRXL2B was selected for further investigation using public multi-omics datasets, tissue microarray-based immunohistochemistry, in vitro functional assays, mechanistic analyses, and in vivo validation experiments. Integrated multi-omics analyses identified PRXL2B as a candidate gene downregulated after H101 treatment. Public datasets and tissue-based validation further showed that PRXL2B was upregulated in HCC tissues. In MHCC97H and HCCLM3 cells, PRXL2B knockdown inhibited proliferation, migration, and invasion, promoted apoptosis and cell-cycle arrest, and enhanced the antitumor effect of H101. Mechanistically, PRXL2B silencing reduced AKT phosphorylation and PD-L1 expression. In vivo, PRXL2B knockdown suppressed tumor growth, and the combination of PRXL2B knockdown and H101 produced the strongest antitumor effect. These findings indicate that PRXL2B promotes malignant phenotypes in HCC and may modulate H101 efficacy through the PI3K/AKT/PD-L1 axis. Targeting PRXL2B may therefore represent a potential strategy to enhance the therapeutic efficacy of oncolytic virus therapy in HCC.

PMID:42161529 | DOI:10.5582/bst.2026.01000

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

✇Nature - Issue - nature.com science feeds
By: Min He · Jia Su · Xiaogang Zhou · Tuo Qi · Jiazheng Wang · Tianxin Zhang · Jinhua Chen · Mawsheng Chern · Youpin Xu · Xiang Lu · Qingqing Hou · Hongrui Liu · Wenfang Huang · Jiawei Liu · Shiying Li · Yunfei Zhu · Xue Chen · Senyu Ran · Han Li · Renju Liu · Mingliang Lei · Guosong Shu · Haicheng Liao · Junjie Yin · Xiaobo Zhu · Yongyan Tang · Li Song · Long Wang · Qing Xiong · Jiali Liu · Yu Bi · Yihua Yang · Hai Qing · Bingtian Ma · Yan Li · Jing Fan · Peng Qin · Yuping Wang · Jianming Wu · Wenming Wang · Shigui Li · Weitao Li · Jing Wang · Xuewei Chen
20 May 2026 at 08:00

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.

Pixelated quantum-dot superlattice LEDs

✇Nature - Issue - nature.com science feeds
By: Chengxi Zhang · Qingsen Zeng · Hui Li · Renjun Guo · Yue Yu · Linjie Dai · Lyudmila Turyanska · Zirui Liu · Jun Dai · Yingguo Yang · Yue Zhao · Jun Lu · Lin Wang · Lingmei Kong · Tze Chien Sum · Yuchen Wu · Tae-Woo Lee · Xuyong Yang
15 April 2026 at 08:00

Nature, Published online: 15 April 2026; doi:10.1038/s41586-026-10392-z

Scalable fabrication of ordered perovskite quantum dot superlattices enables high-efficiency, ultrahigh-resolution LEDs and active-matrix displays with greatly improved brightness, stability and device lifetime.
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