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Received — 10 September 2026 ⏭

Rational and computation-assisted engineering of a compact and efficient CRISPR–Cas12f genome editor

✇Molecular Therapy
By: Jingtong Liu · Shengzhou Wang · Bei Wang · Tonglu Yu · Xuan Liu · Miaomiao Li · Min-Chi Ku · Rui Wang · Renjie Chai · Wei V. Zheng · Yongming Wang
31 August 2026 at 08:00
Structure-guided design combined with protein language model-guided engineering and sgRNA optimization enables the development of a compact and highly efficient CRISPR–Cas12f genome editor. This integrated strategy substantially improves genome-editing activity while preserving high specificity, expanding the therapeutic potential of compact CRISPR systems.

An operational perturbation proteomics-based virtual cell model

✇Nature - Issue - nature.com science feeds
By: Rui Sun · Liujia Qian · Yongge Li · Tong Liu · Honghan Cheng · Xuedong Zhang · Xueya Zhou · Yuecheng Zhan · Guangmei Zhang · Zhengchao Luo · Kunpeng Ma · Chunlong Wu · Dongchen Ji · Zhangzhi Xue · Hongxue Meng · Yuhang Xiang · Dingwei Lei · Qianhe Zhou · Wenbin Hu · Yuhan Deng · Lingling Tan · Qi Xiao · Zhiwei Liu · Lei Zeng · Liqin Qian · Xuan Zheng · Qiong Hu · Nianzi Luo · Weinan E · Peijie Zhou · Han Wen · Yi Zhu · Tiannan Guo
9 September 2026 at 08:00

Nature, Published online: 09 September 2026; doi:10.1038/s41586-026-11001-9

Temporal protein-abundance measurements from systematically perturbed breast cancer cell lines were generated to develop ProteinTalks, a virtual cell model that functions as an operational tool for diverse drug discovery tasks.
Received — 27 May 2026 ⏭

Generative AI impacts on intra-urban inequality and skill premium in Beijing

✇cs.AI, q-bio.NC updates on arXiv.org
By: Xiliu He · Haoxiang Zhao · Mingyi Ma · Edward Wen Chuan Lai · Koei Enomoto · Anni Hu · Jiatong Li · Lingyun Chu · Yuan Lai
26 May 2026 at 12:00
arXiv:2605.25505v1 Announce Type: cross Abstract: Generative artificial intelligence (GenAI) is the first automation wave to reach high-cognitive tasks at scale, yet its effects on intra-urban inequality remain largely unknown. Using 5 million job postings from Beijing (2018--2024), we construct a neighborhood-level GenAI Exposure Index by aggregating task-level assessments from five leading large language models. We examine the spatial, structural and causal mechanisms of this shock. We find that GenAI exposure is highly concentrated in the city's core districts, deepening the intra-urban AI divide. Since 2023, high-exposure neighborhoods have experienced wage stagnation even as they continue to attract high-skilled workers -- a "high-skill trap." This wage penalty is driven by task de-skilling and intensified labor-market crowding. A difference-in-differences design centered on ChatGPT's release supports a causal interpretation. These findings challenge the prevailing theory of skill-biased technological change and provide a basis for inclusive AI governance in global technology hubs.

Equip Pre-ranking with Target Attention by Residual Quantization

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yutong Li · Yu Zhu · Yichen Qiao · Ziyu Guan · Lv Shao · Tong Liu · Bo Zheng
26 May 2026 at 12:00
arXiv:2509.16931v3 Announce Type: replace-cross Abstract: The pre-ranking stage in industrial recommendation systems faces a fundamental conflict between efficiency and effectiveness. While powerful models like Target Attention (TA) excel at capturing complex feature interactions in the ranking stage, their high computational cost makes them infeasible for pre-ranking, which often relies on simplistic vector-product models. This disparity creates a significant performance bottleneck for the entire system. To bridge this gap, we propose TARQ, a novel pre-ranking framework. Inspired by generative models, TARQ's key innovation is to equip pre-ranking with an architecture approximate to TA by Residual Quantization. This allows us to bring the modeling power of TA into the latency-critical pre-ranking stage for the first time, establishing a new state-of-the-art trade-off between accuracy and efficiency. Extensive offline experiments and large-scale online A/B tests at Taobao demonstrate TARQ's significant improvements in ranking performance. Consequently, our model has been fully deployed in production, serving tens of millions of daily active users and yielding substantial business improvements. The code and data are available at https://github.com/zyody/tarq_sigir2026.

Multi-omics analysis of glutamine and fish collagen peptides in alleviating post-antibiotic Streptococcus pneumoniae injury in feline lung cells

✇Omics In Lung
By: Huasong Bai · Tong Liu · Hengyan Wang · Hongchen Jin · Yunliang Li · Zhanzhong Wang
16 April 2026 at 18:00

Exp Ther Med. 2026 Mar 30;31(6):148. doi: 10.3892/etm.2026.13143. eCollection 2026 Jun.

ABSTRACT

Streptococcus pneumoniae (SP) infection often leads to persistent lung injury even after antibiotic treatment. Despite this phenomenon, the mechanisms underlying host cell recovery remain poorly understood. Upon breaching the epithelial barrier, SP primarily targets the pulmonary interstitial cells, which constitute the major mesenchymal component of the lung. These cells serve as essential effectors of tissue repair, extracellular matrix remodeling and epithelial restoration. Therefore, a feline pulmonary interstitial cell (FCA-L2) model of SP infection was established to investigate the protective effects of glutamine (GLU) and fish collagen peptides (FCP) through integrated transcriptomic and metabolomic analyses. Cells were infected with SP (0.05 McFarland units for 4 h) and then treated with doxycycline (7.5 µg/ml for 18 h) followed by GLU (40 mM) or FCP (500 µg/ml). Notably, SP infection increased lactate dehydrogenase (LDH) release by 3.5-fold, induced secretion of IL-1β, TNF-α and IL-8, disrupted tight-junction proteins (claudin, ZO-1 and occludin) and caused oxidative imbalance and apoptosis despite antibiotic (doxycycline) treatment. However, treatment with GLU or FCP significantly reduced LDH release by ~40%, restored junctional proteins, suppressed inflammatory cytokines and enhanced antioxidant enzyme activities. Multi-omics analysis revealed that GLU promoted amino acid biosynthesis and energy metabolism and suppressed aminoacyl-tRNA synthetases and cell-cycle regulators, thereby enhancing metabolic adaptability. By contrast, FCP activated amino and nucleotide sugar metabolism, increased polyunsaturated fatty-acid synthesis and supported glycocalyx repair and membrane reconstruction. GLU and FCP provided complementary metabolic and structural protection, which mitigated post-infectious stress and promoted cellular recovery. The findings of the present study underscore the potential of bioactive food-derived compounds as adjunctive therapies that may accelerate lung tissue repair and enhance the efficacy of conventional antibiotics.

PMID:41988354 | PMC:PMC13077270 | DOI:10.3892/etm.2026.13143

EBV strain interacts with host HLA to drive nasopharyngeal carcinoma risk

✇Nature - Issue - nature.com science feeds
By: Yanhong Chen · Jingtong Liang · Wanlin Zhang · Xinyu Zhang · Xinyi Zhang · Ching-Yuan Wang · Fei Yao · Shanshan Zhang · Xiang Zhou · Weimin Ye · Ruimei Feng · Yonglin Cai · Zhe Zhang · Mingfang Ji · Qian Cui · Xihong Lin · Jiesen Li · Jialei Xu · Qiuting Zhang · Qinyao Huang · Yingying Cheng · Yanran Luo · Xiaoping Ye · Qisheng Feng · Minzhong Tang · Mu-Sheng Zeng · Yi-Xin Zeng · Zhonghua Liu · Weiwei Zhai · Jianjun Liu · Miao Xu
15 April 2026 at 08:00

Nature, Published online: 15 April 2026; doi:10.1038/s41586-026-10416-8

A genome-to-genome association study identifies host and viral risk factors that interact to drive nasopharyngeal carcinoma endemicity in southern China.
Received — 8 April 2026 ⏭

VitaTouch: Property-Aware Vision-Tactile-Language Model for Robotic Quality Inspection in Manufacturing

✇cs.AI, q-bio.NC updates on arXiv.org
By: Junyi Zong · Qingxuan Jia · Meixian Shi · Tong Li · Jiayuan Li · Zihang Lv · Gang Chen · Fang Deng
7 April 2026 at 12:00
arXiv:2604.03322v1 Announce Type: cross Abstract: Quality inspection in smart manufacturing requires identifying intrinsic material and surface properties beyond visible geometry, yet vision-only methods remain vulnerable to occlusion and reflection. We propose VitaTouch, a property-aware vision-tactile-language model for material-property inference and natural-language attribute description. VitaTouch uses modality-specific encoders and a dual Q-Former to extract language-relevant visual and tactile features, which are compressed into prefix tokens for a large language model. We align each modality with text and explicitly couple vision and touch through contrastive learning. We also construct VitaSet, a multimodal dataset with 186 objects, 52k images, and 5.1k human-verified instruction-answer pairs. VitaTouch achieves the best performance on HCT and the overall TVL benchmark, while remaining competitive on SSVTP. On VitaSet, it reaches 88.89% hardness accuracy, 75.13% roughness accuracy, and 54.81% descriptor recall; the material-description task further achieves a peak semantic similarity of 0.9009. With LoRA-based fine-tuning, VitaTouch attains 100.0%, 96.0%, and 92.0% accuracy for 2-, 3-, and 5-category defect recognition, respectively, and delivers 94.0% closed-loop recognition accuracy and 94.0% end-to-end sorting success in 100 laboratory robotic trials. More details are available at the project page: https://vitatouch.github.io/
Received — 4 April 2026 ⏭

Excessive pyroptosis mediates the exacerbation of pneumonia caused by low-lethality influenza virus and secondary MRSA co-infection

✇Cell Death Discovery nature.com science feeds
By: Zi-Chen Tian · Yang Liu · Yi-Jun Niu · Xin Ai · Su-Ya Lao · Wei-Ming Xu · Xiao-Tong Lin · Cheng-Jie Xia · Zhi-Xuan Cai · Hai-Yan Zhu · Xun-Long Shi
2 April 2026 at 08:00

Cell Death Discovery, Published online: 02 April 2026; doi:10.1038/s41420-026-03031-z

Excessive pyroptosis mediates the exacerbation of pneumonia caused by low-lethality influenza virus and secondary MRSA co-infection
Received — 17 March 2026 ⏭

OpenSage: Self-programming Agent Generation Engine

✇cs.AI, q-bio.NC updates on arXiv.org
By: Hongwei Li · Zhun Wang · Qinrun Dai · Yuzhou Nie · Jinjun Peng · Ruitong Liu · Jingyang Zhang · Kaijie Zhu · Jingxuan He · Lun Wang · Yangruibo Ding · Yueqi Chen · Wenbo Guo · Dawn Song
16 March 2026 at 12:00
arXiv:2602.16891v2 Announce Type: replace Abstract: Agent development kits (ADKs) provide effective platforms and tooling for constructing agents, and their designs are critical to the constructed agents' performance, especially the functionality for agent topology, tools, and memory. However, current ADKs either lack sufficient functional support or rely on humans to manually design these components, limiting agents' generalizability and overall performance. We propose OpenSage, the first ADK that enables LLMs to automatically create agents with self-generated topology and toolsets while providing comprehensive and structured memory support. OpenSage offers effective functionality for agents to create and manage their own sub-agents and toolkits. It also features a hierarchical, graph-based memory system for efficient management and a specialized toolkit tailored to software engineering tasks. Extensive experiments across three state-of-the-art benchmarks with various backbone models demonstrate the advantages of OpenSage over existing ADKs. We also conduct rigorous ablation studies to demonstrate the effectiveness of our design for each component. We believe OpenSage can pave the way for the next generation of agent development, shifting the focus from human-centered to AI-centered paradigms.
Received — 11 March 2026 ⏭

Survey of Computerized Adaptive Testing: A Machine Learning Perspective

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yan Zhuang · Qi Liu · Haoyang Bi · Zhenya Huang · Weizhe Huang · Jiatong Li · Junhao Yu · Zirui Liu · Zirui Hu · Yuting Hong · Zachary A. Pardos · Haiping Ma · Mengxiao Zhu · Shijin Wang · Enhong Chen
10 March 2026 at 12:00
arXiv:2404.00712v3 Announce Type: replace-cross Abstract: Computerized Adaptive Testing (CAT) offers an efficient and personalized method for assessing examinee proficiency by dynamically adjusting test questions based on individual performance. Compared to traditional, non-personalized testing methods, CAT requires fewer questions and provides more accurate assessments. As a result, CAT has been widely adopted across various fields, including education, healthcare, sports, sociology, and the evaluation of AI models. While traditional methods rely on psychometrics and statistics, the increasing complexity of large-scale testing has spurred the integration of machine learning techniques. This paper aims to provide a machine learning-focused survey on CAT, presenting a fresh perspective on this adaptive testing paradigm. We delve into measurement models, question selection algorithm, bank construction, and test control within CAT, exploring how machine learning can optimize these components. Through an analysis of current methods, strengths, limitations, and challenges, we strive to develop robust, fair, and efficient CAT systems. By bridging psychometric-driven CAT research with machine learning, this survey advocates for a more inclusive and interdisciplinary approach to the future of adaptive testing.

More Bang for the Buck: Process Reward Modeling with Entropy-Driven Uncertainty

✇cs.AI, q-bio.NC updates on arXiv.org
By: Lang Cao · Renhong Chen · Yingtian Zou · Chao Peng · Huacong Xu · Yuxian Wang · Wu Ning · Qian Chen · Mofan Peng · Zijie Chen · Peishuo Su · Yitong Li
10 March 2026 at 12:00
arXiv:2503.22233v4 Announce Type: replace-cross Abstract: We introduce the Entropy-Driven Uncertainty Process Reward Model (EDU-PRM), a novel entropy-driven training framework for process reward modeling that enables dynamic, uncertainty-aligned segmentation of complex reasoning steps, eliminating the need for costly manual step annotations. Unlike previous Process Reward Models (PRMs) that rely on static partitioning and human labeling, EDU-PRM automatically anchors step boundaries at tokens with high predictive entropy, effectively capturing intrinsic logical transitions and facilitating efficient exploration of diverse reasoning paths. On the ProcessBench benchmark, EDU-PRM outperforms strong public PRM baselines, such as Math-Shepherd PRM and Omega PRM, and EDU-PRM achieves comparable results with SOTA models while only using 1.5% training data. Furthermore, by leveraging our proposed EDU sampling strategy, we observe accuracy boosts from 64.7% to 67.3% for generative reasoning tasks, accompanied by a reduction of 32% in token usage. These findings underscore the potential of EDU-PRM as a scalable and annotation-efficient paradigm for process supervision in mathematical reasoning, paving the way for more efficient and robust approaches to complex mathematical problem solving.
Received — 25 February 2026 ⏭

ToolSelf: Unifying Task Execution and Self-Reconfiguration via Tool-Driven Intrinsic Adaptation

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jingqi Zhou · Sheng Wang · DeZhao Deng · Junwen Lu · Junwei Su · Qintong Li · Jiahui Gao · Hao Wu · Jiyue Jiang · Lingpeng Kong · Chuan Wu
24 February 2026 at 13:00
arXiv:2602.07883v2 Announce Type: replace Abstract: Agentic systems powered by Large Language Models (LLMs) have demonstrated remarkable potential in tackling complex, long-horizon tasks. However, their efficacy is fundamentally constrained by static configurations governing agent behaviors, which are fixed prior to execution and fail to adapt to evolving task dynamics. Existing approaches, relying on manual orchestration or heuristic-based patches, often struggle with poor generalization and fragmented optimization. To transcend these limitations, we propose ToolSelf, a novel paradigm enabling tool-driven runtime self-reconfiguration. By abstracting configuration updates as a callable tool, ToolSelf unifies task execution and self-adjustment into a single action space, achieving a phase transition from external rules to intrinsic parameters. Agents can thereby autonomously update their sub-goals and context based on task progression, and correspondingly adapt their strategy and toolbox, transforming from passive executors into dual managers of both task and self. We further devise Configuration-Aware Two-stage Training (CAT), combining rejection sampling fine-tuning with trajectory-level reinforcement learning to internalize this meta-capability. Extensive experiments across diverse benchmarks demonstrate that ToolSelf rivals specialized workflows while generalizing to novel tasks, achieving a 24.1% average performance gain and illuminating a path toward truly self-adaptive agents.
Received — 17 February 2026 ⏭

LLM-Confidence Reranker: A Training-Free Approach for Enhancing Retrieval-Augmented Generation Systems

✇cs.AI, q-bio.NC updates on arXiv.org
By: Zhipeng Song · Xiangyu Kong · Xinrui Bao · Yizhi Zhou · Jiulong Jiao · Sitong Liu · Yuhang Zhou · Heng Qi
17 February 2026 at 13:00
arXiv:2602.13571v1 Announce Type: cross Abstract: Large language models (LLMs) have revolutionized natural language processing, yet hallucinations in knowledge-intensive tasks remain a critical challenge. Retrieval-augmented generation (RAG) addresses this by integrating external knowledge, but its efficacy depends on accurate document retrieval and ranking. Although existing rerankers demonstrate effectiveness, they frequently necessitate specialized training, impose substantial computational expenses, and fail to fully exploit the semantic capabilities of LLMs, particularly their inherent confidence signals. We propose the LLM-Confidence Reranker (LCR), a training-free, plug-and-play algorithm that enhances reranking in RAG systems by leveraging black-box LLM confidence derived from Maximum Semantic Cluster Proportion (MSCP). LCR employs a two-stage process: confidence assessment via multinomial sampling and clustering, followed by binning and multi-level sorting based on query and document confidence thresholds. This approach prioritizes relevant documents while preserving original rankings for high-confidence queries, ensuring robustness. Evaluated on BEIR and TREC benchmarks with BM25 and Contriever retrievers, LCR--using only 7--9B-parameter pre-trained LLMs--consistently improves NDCG@5 by up to 20.6% across pre-trained LLM and fine-tuned Transformer rerankers, without degradation. Ablation studies validate the hypothesis that LLM confidence positively correlates with document relevance, elucidating LCR's mechanism. LCR offers computational efficiency, parallelism for scalability, and broad compatibility, mitigating hallucinations in applications like medical diagnosis.
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