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Received — 17 March 2026 ⏭

Tumor-informed liquid biopsy detection of structural variants in high grade serous ovarian cancer

✇MRD
By: Jian Li · Shiro Takamatsu · Allison L Brodsky · Thomas Welte · Katherine Calzoncinth · Veena K Vuttaradhi · Joseph Celestino · Barrett Lawson · R Tyler Hillman
16 March 2026 at 18:00

Oncoscience. 2026 Mar 5;13:44-54. doi: 10.18632/oncoscience.645. eCollection 2026.

ABSTRACT

BACKGROUND: High grade serous ovarian cancer (HGSOC) recurs frequently and commercial tests have emerged for tumor-informed, cell-free DNA (cfDNA)-based detection of minimal residual disease. These tests are based on somatic single nucleotide variants prevalent in many cancers and thus are not well matched to HGSOC, which is dominated by structural genomic rearrangements. The purpose of this study was to evaluate the feasibility of a structural-variant (SV)-informed, cfDNA-based method for detecting clonal and subclonal HGSOC disease burden.

METHODS: A method was developed for detecting patient-specific SV breakpoints using digital droplet PCR (ddPCR) with custom tumor-informed primer/probe pairs. Test parameters were first estimated using synthetic cfDNA generated by ultrasonication of genomic DNA from ovarian cancer cell lines. The optimized workflow was implemented in which whole genome sequencing of multisite pre-treatment HGSOC biopsies performed and high confidence SVs were called by multiple published SV callers. Real-time PCR and ddPCR were used for assay development.

RESULTS: Following the optimized workflow, tumor-specific SV breakpoint-spanning primers/probe sets of four HGSOC patients' multisite biopsies were designed and validated by real-time PCR and ddPCR. Together with four HGSOCs, a total of 29 SVs breakpoints-spanning tumor-informed primers/probe sets were designed and validated in multisite biopsies. 15 validated tumor-specific SVs were selected for quantification in their corresponding liquid biopsies using the validated ddPCR, and 9 had measurements in liquid biopsies.

CONCLUSIONS: Our result shows the detection of SVs from pre-treatment cfDNA using tumor-informed breakpoints-spanning ddPCR is feasible and may enable a novel and sensitive method for monitoring on-treatment disease burden.

PMID:41835357 | PMC:PMC12981705 | DOI:10.18632/oncoscience.645

  • ✇cs.AI, q-bio.NC updates on arXiv.org
  • The Economics of AI Supply Chain Regulation Sihan Qian · Amit Mehra · Dengpan Liu
    arXiv:2603.12630v1 Announce Type: cross Abstract: The rise of foundation models has driven the emergence of AI supply chains, where upstream foundation model providers offer fine-tuning and inference services to downstream firms developing domain-specific applications. Downstream firms pay providers to use their computing infrastructure to fine-tune models with proprietary data, creating a co-creation dynamic that enhances model quality. Amid concerns that foundation model providers and downstr
     
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The Economics of AI Supply Chain Regulation

✇cs.AI, q-bio.NC updates on arXiv.org
By: Sihan Qian · Amit Mehra · Dengpan Liu
16 March 2026 at 12:00
arXiv:2603.12630v1 Announce Type: cross Abstract: The rise of foundation models has driven the emergence of AI supply chains, where upstream foundation model providers offer fine-tuning and inference services to downstream firms developing domain-specific applications. Downstream firms pay providers to use their computing infrastructure to fine-tune models with proprietary data, creating a co-creation dynamic that enhances model quality. Amid concerns that foundation model providers and downstream firms may capture excessive consumer surplus, along with increasing regulatory measures, this study employs a game-theoretic model involving a provider and two competing downstream firms to analyze how policy interventions affect consumer surplus in the AI supply chain. Our analysis shows that policies promoting price competition in downstream markets (i.e., pro-price-competitive policies) boost consumer surplus only when compute or data preprocessing costs are high, while compute subsidies are effective only when these costs are low, suggesting these policies complement each other. In contrast, policies promoting quality competition in downstream markets (i.e., pro-quality-competitive policies) always improve consumer surplus. We also find that under pro-price-competitive policies or compute subsidies, both the provider and downstream firms can achieve higher profits along with greater consumer surplus, creating a win-win-win outcome. However, pro-quality-competitive policies increase the provider's profits while reducing those of downstream firms. Finally, as compute costs decline, pro-price-competitive policies may lose their effectiveness, whereas compute subsidies may shift from ineffective to effective. These findings offer insights for policymakers seeking to foster AI supply chains that are economically efficient and socially beneficial.

Cheers: Decoupling Patch Details from Semantic Representations Enables Unified Multimodal Comprehension and Generation

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yichen Zhang · Da Peng · Zonghao Guo · Zijian Zhang · Xuesong Yang · Tong Sun · Shichu Sun · Yidan Zhang · Yanghao Li · Haiyan Zhao · Wang Xu · Qi Shi · Yangang Sun · Chi Chen · Shuo Wang · Yukun Yan · Xu Han · Qiang Ma · Wei Ke · Liang Wang · Zhiyuan Liu · Maosong Sun
16 March 2026 at 12:00
arXiv:2603.12793v1 Announce Type: cross Abstract: A recent cutting-edge topic in multimodal modeling is to unify visual comprehension and generation within a single model. However, the two tasks demand mismatched decoding regimes and visual representations, making it non-trivial to jointly optimize within a shared feature space. In this work, we present Cheers, a unified multimodal model that decouples patch-level details from semantic representations, thereby stabilizing semantics for multimodal understanding and improving fidelity for image generation via gated detail residuals. Cheers includes three key components: (i) a unified vision tokenizer that encodes and compresses image latent states into semantic tokens for efficient LLM conditioning, (ii) an LLM-based Transformer that unifies autoregressive decoding for text generation and diffusion decoding for image generation, and (iii) a cascaded flow matching head that decodes visual semantics first and then injects semantically gated detail residuals from the vision tokenizer to refine high-frequency content. Experiments on popular benchmarks demonstrate that Cheers matches or surpasses advanced UMMs in both visual understanding and generation. Cheers also achieves 4x token compression, enabling more efficient high-resolution image encoding and generation. Notably, Cheers outperforms the Tar-1.5B on the popular benchmarks GenEval and MMBench, while requiring only 20% of the training cost, indicating effective and efficient (i.e., 4x token compression) unified multimodal modeling. We will release all code and data for future research.

OffTopicEval: When Large Language Models Enter the Wrong Chat, Almost Always!

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jingdi Lei · Varun Gumma · Rishabh Bhardwaj · Seok Min Lim · Chuan Li · Amir Zadeh · Soujanya Poria
16 March 2026 at 12:00
arXiv:2509.26495v3 Announce Type: replace Abstract: Large Language Model (LLM) safety is one of the most pressing challenges for enabling wide-scale deployment. While most studies and global discussions focus on generic harms, such as models assisting users in harming themselves or others, enterprises face a more fundamental concern: whether LLM-based agents are safe for their intended use case. To address this, we introduce operational safety, defined as an LLM's ability to appropriately accept or refuse user queries when tasked with a specific purpose. We further propose OffTopicEval, an evaluation suite and benchmark for measuring operational safety both in general and within specific agentic use cases. Our evaluations on six model families comprising 20 open-weight LLMs reveal that while performance varies across models, all of them remain highly operationally unsafe. Even the strongest models - Qwen-3 (235B) with 77.77% and Mistral (24B) with 79.96% - fall far short of reliable operational safety, while GPT models plateau in the 62-73% range, Phi achieves only mid-level scores (48-70%), and Gemma and Llama-3 collapse to 39.53% and 23.84%, respectively. While operational safety is a core model alignment issue, to suppress these failures, we propose prompt-based steering methods: query grounding (Q-ground) and system-prompt grounding (P-ground), which substantially improve OOD refusal. Q-ground provides consistent gains of up to 23%, while P-ground delivers even larger boosts, raising Llama-3.3 (70B) by 41% and Qwen-3 (30B) by 27%. These results highlight both the urgent need for operational safety interventions and the promise of prompt-based steering as a first step toward more reliable LLM-based agents.

SkillsBench: Benchmarking How Well Agent Skills Work Across Diverse Tasks

✇cs.AI, q-bio.NC updates on arXiv.org
By: Xiangyi Li · Wenbo Chen · Yimin Liu · Shenghan Zheng · Xiaokun Chen · Yifeng He · Yubo Li · Bingran You · Haotian Shen · Jiankai Sun · Shuyi Wang · Binxu Li · Qunhong Zeng · Di Wang · Xuandong Zhao · Yuanli Wang · Roey Ben Chaim · Zonglin Di · Yipeng Gao · Junwei He · Yizhuo He · Liqiang Jing · Luyang Kong · Xin Lan · Jiachen Li · Songlin Li · Yijiang Li · Yueqian Lin · Xinyi Liu · Xuanqing Liu · Haoran Lyu · Ze Ma · Bowei Wang · Runhui Wang · Tianyu Wang · Wengao Ye · Yue Zhang · Hanwen Xing · Yiqi Xue · Steven Dillmann · Han-chung Lee
16 March 2026 at 12:00
arXiv:2602.12670v3 Announce Type: replace Abstract: Agent Skills are structured packages of procedural knowledge that augment LLM agents at inference time. Despite rapid adoption, there is no standard way to measure whether they actually help. We present SkillsBench, a benchmark of 86 tasks across 11 domains paired with curated Skills and deterministic verifiers. Each task is evaluated under three conditions: no Skills, curated Skills, and self-generated Skills. We test 7 agent-model configurations over 7,308 trajectories. Curated Skills raise average pass rate by 16.2 percentage points(pp), but effects vary widely by domain (+4.5pp for Software Engineering to +51.9pp for Healthcare) and 16 of 84 tasks show negative deltas. Self-generated Skills provide no benefit on average, showing that models cannot reliably author the procedural knowledge they benefit from consuming. Focused Skills with 2--3 modules outperform comprehensive documentation, and smaller models with Skills can match larger models without them.

FCMBench: The First Large-scale Financial Credit Multimodal Benchmark for Real-world Applications

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yehui Yang · Dalu Yang · Fangxin Shang · Wenshuo Zhou · Jie Ren · Yifan Liu · Haojun Fei · Qing Yang · Yanwu Xu · Tao Chen
16 March 2026 at 12:00
arXiv:2601.00150v3 Announce Type: replace-cross Abstract: FCMBench is the first large-scale and privacy-compliant multimodal benchmark for real-world financial credit applications, covering tasks and robustness challenges from domain specific workflows and constraints. The current version of FCMBench covers 26 certificate types, with 5198 privacy-compliant images and 13806 paired VQA samples. It evaluates models on Perception and Reasoning tasks under real-world Robustness interferences, including 3 foundational perception tasks, 4 credit-specific reasoning tasks demanding decision-oriented visual evidence interpretation, and 10 real-world challenges for rigorous robustness stress testing. Moreover, FCMBench offers privacy-compliant realism with minimal leakage risk through in-house scenario-aware captures of manually synthesized templates, without any publicly released images. We conduct extensive evaluations of 28 state-of-the-art vision-language models spanning 14 AI companies and research institutes. Among them, Gemini 3 Pro achieves the best F1 score as a commercial model (65.16), Kimi-K2.5 achieves the best score as an open-source baseline (60.58). The mean and the std. of all tested models is 44.8 and 10.3 respectively, indicating that FCMBench is non-trivial and provides strong resolution for separating modern vision-language model capabilities. Robustness evaluations reveal that even top-performing models experience notable performance degradation under the designed challenges. We have open-sourced this benchmark to advance AI research in the credit domain and provide a domain-specific task for real-world AI applications.

MalURLBench: A Benchmark Evaluating Agents' Vulnerabilities When Processing Web URLs

✇cs.AI, q-bio.NC updates on arXiv.org
By: Dezhang Kong · Zhuxi Wu · Shiqi Liu · Zhicheng Tan · Kuichen Lu · Minghao Li · Qichen Liu · Shengyu Chu · Zhenhua Xu · Xuan Liu · Meng Han
16 March 2026 at 12:00
arXiv:2601.18113v3 Announce Type: replace-cross Abstract: LLM-based web agents have become increasingly popular for their utility in daily life and work. However, they exhibit critical vulnerabilities when processing malicious URLs: accepting a disguised malicious URL enables subsequent access to unsafe webpages, which can cause severe damage to service providers and users. Despite this risk, no benchmark currently targets this emerging threat. To address this gap, we propose MalURLBench, the first benchmark for evaluating LLMs' vulnerabilities to malicious URLs. MalURLBench contains 61,845 attack instances spanning 10 real-world scenarios and 7 categories of real malicious websites. Experiments with 12 popular LLMs reveal that existing models struggle to detect elaborately disguised malicious URLs. We further identify and analyze key factors that impact attack success rates and propose URLGuard, a lightweight defense module. We believe this work will provide a foundational resource for advancing the security of web agents. Our code is available at https://github.com/JiangYingEr/MalURLBench.

LatentChem: From Textual CoT to Latent Thinking in Chemical Reasoning

✇cs.AI, q-bio.NC updates on arXiv.org
By: Xinwu Ye · Yicheng Mao · Jia Zhang · Yimeng Liu · Li Hao · Fang Wu · Zhiwei Li · Yuxuan Liao · Zehong Wang · Yingcheng Wu · Zhiyuan Liu · Zhenfei Yin · Li Yuan · Philip Torr · Huan Sun · Xiangxiang Zeng · Mengdi Wang · Le Cong · Shenghua Gao · Xiangru Tang
16 March 2026 at 12:00
arXiv:2602.07075v4 Announce Type: replace-cross Abstract: Chemical large language models (LLMs) predominantly rely on explicit Chain-of-Thought (CoT) in natural language to perform complex reasoning. However, chemical reasoning is inherently continuous and structural, and forcing it into discrete linguistic tokens introduces a fundamental representation mismatch that constrains both efficiency and performance. We introduce LatentChem, a latent reasoning interface that decouples chemical computation from textual generation, enabling models to perform multi-step reasoning directly in continuous latent space while emitting language only for final outputs. Remarkably, we observe a consistent emergent behavior: when optimized solely for task success, models spontaneously internalize reasoning, progressively abandoning verbose textual derivations in favor of implicit latent computation. This shift is not merely stylistic but computationally advantageous. Across diverse chemical reasoning benchmarks, LatentChem achieves a 59.88\% non-tie win rate over strong CoT-based baselines on ChemCoTBench, while delivering a 10.84$\times$ average reduction in reasoning overhead. Our results provide empirical evidence that chemical reasoning is more naturally and effectively realized as continuous latent dynamics rather than discretized linguistic trajectories.

VideoTemp-o3: Harmonizing Temporal Grounding and Video Understanding in Agentic Thinking-with-Videos

✇cs.AI, q-bio.NC updates on arXiv.org
By: Wenqi Liu · Yunxiao Wang · Shijie Ma · Meng Liu · Qile Su · Tianke Zhang · Haonan Fan · Changyi Liu · Kaiyu Jiang · Jiankang Chen · Kaiyu Tang · Bin Wen · Fan Yang · Tingting Gao · Han Li · Yinwei Wei · Xuemeng Song
16 March 2026 at 12:00
arXiv:2602.07801v3 Announce Type: replace-cross Abstract: In long-video understanding, conventional uniform frame sampling often fails to capture key visual evidence, leading to degraded performance and increased hallucinations. To address this, recent agentic thinking-with-videos paradigms have emerged, adopting a localize-clip-answer pipeline in which the model actively identifies relevant video segments, performs dense sampling within those clips, and then produces answers. However, existing methods remain inefficient, suffer from weak localization, and adhere to rigid workflows. To solve these issues, we propose VideoTemp-o3, a unified agentic thinking-with-videos framework that jointly models video grounding and question answering. VideoTemp-o3 exhibits strong localization capability, supports on-demand clipping, and can refine inaccurate localizations. Specifically, in the supervised fine-tuning stage, we design a unified masking mechanism that encourages exploration while preventing noise. For reinforcement learning, we introduce dedicated rewards to mitigate reward hacking. Besides, from the data perspective, we develop an effective pipeline to construct high-quality long video grounded QA data, along with a corresponding benchmark for systematic evaluation across various video durations. Experimental results demonstrate that our method achieves remarkable performance on both long video understanding and grounding.

Automatic In-Domain Exemplar Construction and LLM-Based Refinement of Multi-LLM Expansions for Query Expansion

✇cs.AI, q-bio.NC updates on arXiv.org
By: Minghan Li · Ercong Nie · Siqi Zhao · Tongna Chen · Huiping Huang · Guodong Zhou
16 March 2026 at 12:00
arXiv:2602.08917v2 Announce Type: replace-cross Abstract: Query expansion with large language models is promising but often relies on hand-crafted prompts, manually chosen exemplars, or a single LLM, making it non-scalable and sensitive to domain shift. We present an automated, domain-adaptive QE framework that builds in-domain exemplar pools by harvesting pseudo-relevant passages using a BM25-MonoT5 pipeline. A training-free cluster-based strategy selects diverse demonstrations, yielding strong and stable in-context QE without supervision. To further exploit model complementarity, we introduce a two-LLM ensemble in which two heterogeneous LLMs independently generate expansions and a refinement LLM consolidates them into one coherent expansion. Across TREC DL20, DBPedia, and SciFact, the refined ensemble delivers consistent and statistically significant gains over BM25, Rocchio, zero-shot, and fixed few-shot baselines. The framework offers a reproducible testbed for exemplar selection and multi-LLM generation, and a practical, label-free solution for real-world QE.

SOX4 induces cisplatin resistance in cervical cancer cells by inhibiting aerobic glycolysis

✇Cell Death Discovery nature.com science feeds
By: Ruili Sun · Haofei Gong · Ran Zhao · Huiying Lv · Huijie Yang · Xiaofei Zhu · Xinlai Qian · Jian Li · Qiongzi Wang
14 March 2026 at 08:00

Cell Death Discovery, Published online: 14 March 2026; doi:10.1038/s41420-026-02954-x

SOX4 induces cisplatin resistance in cervical cancer cells by inhibiting aerobic glycolysis
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