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Harbor Adapters and Harbor-Index: Infrastructure and a Curated Meta-Dataset for Large-Scale Agentic Evaluation

✇cs.AI, q-bio.NC updates on arXiv.org
By: Lin Shi (Audrey) · Haowei Lin (Audrey) · Zixuan Zhu (Audrey) · Xiaoyue Zhou (Audrey) · Xiang Li (Audrey) · Xiangning Lin (Audrey) · Yaxuan Deng (Audrey) · Han Xu (Audrey) · Yuangang Li (Audrey) · Shanda Li (Audrey) · Zizhao Chen (Audrey) · Hanwen Xing (Audrey) · Harsh Raj (Audrey) · Bo Chen (Audrey) · Quan Shi (Audrey) · Steven Dillmann (Audrey) · Yipeng Gao (Audrey) · Puneesh Khanna (Audrey) · Ruofan Lu (Audrey) · Chao Beyond Zhou (Audrey) · Michael Yang (Audrey) · Robert Zhang (Audrey) · Siyuan Chai (Audrey) · Jiayu Chang (Audrey) · Yizhao Chen (Audrey) · Xiaokun Chen (Audrey) · Yiwei Dai (Audrey) · Wenting Yang (Audrey) · Hange Liu (Audrey) · Minghao Liu (Audrey) · Zihan Wang (Audrey) · Adnan El Assadi (Audrey) · Benedikt Stroebl (Audrey) · E. Kelly Buchanan (Audrey) · Han Meng (Audrey) · Junwei He (Audrey) · Longxuan Yu (Audrey) · Radin Shayanfar (Audrey) · Yukyung Lee (Audrey) · Zhikang Dong (Audrey) · Allen G Hart (Audrey) · Anjiang Wei (Audrey) · Anurag Kashyap (Audrey) · Arpandeep Khatua (Audrey) · Audrey Jixin Zheng (Audrey) · Chengrui Ma (Aud
arXiv:2609.04298v2 Announce Type: replace Abstract: Evaluating agents on the growing number of agentic benchmarks is challenging because they often require complex environments and agent integrations. We introduce Harbor Adapters, a unified evaluation infrastructure for agentic benchmarks. Our work makes three contributions. First, we develop benchmark adapters that port more than 80 benchmarks to evaluate arbitrary agents, and validate them through rigorous code review and parity experiments. Second, we conduct a large-scale evaluation of 8 models spanning capability tiers across 54 benchmarks; every model is run with Terminus-2 and with one of 3 native harnesses. This enables a broader analysis of agent capabilities and failure modes than was previously possible. Third, we introduce Harbor-Index, a curated set of 82 difficult, diverse, and high-quality tasks spanning 29 benchmarks, refined from the adapted suite through difficulty filtering, AI and human audit, and an audit-and-fix loop. Harbor-Index preserves the challenge and breadth of large-scale agentic evaluations while being affordable to run; no evaluated model-harness configuration exceeds 30% pass rate, and the strongest (GPT-5.5 with Codex) reaches 28.0%. We release the adapters, evaluation results, in-depth analysis, and Harbor-Index as open-source artifacts to support more reliable and comprehensive evaluation of language-model agents.
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E3AD: An Emotion-Aware Vision-Language-Action Model for Human-Centric End-to-End Autonomous Driving

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yihong Tang · Haicheng Liao · Tong Nie · Junlin He · Ao Qu · Kehua Chen · Wei Ma · Zhenning Li · Lijun Sun · Chengzhong Xu
arXiv:2512.04733v2 Announce Type: replace-cross Abstract: End-to-end autonomous driving (AD) systems increasingly adopt vision-language-action (VLA) models, yet they typically ignore the passenger's emotional state, which is central to comfort and AD acceptance. We introduce Open-Domain End-to-End (OD-E2E) autonomous driving, where an autonomous vehicle (AV) must interpret free-form natural-language commands, infer the emotion, and plan a physically feasible trajectory. We propose E3AD, an emotion-aware VLA framework that augments semantic understanding with two cognitively inspired components: a continuous Valenc-Arousal-Dominance (VAD) emotion model that captures tone and urgency from language, and a dual-pathway spatial reasoning module that fuses egocentric and allocentric views for human-like spatial cognition. A consistency-oriented training scheme, combining modality pretraining with preference-based alignment, further enforces coherence between emotional intent and driving actions. Across real-world datasets, E3AD improves visual grounding and waypoint planning and achieves state-of-the-art (SOTA) VAD correlation for emotion estimation. These evaluation results show that injecting emotion into VLA-style driving yields more human-aligned grounding, planning, and feedback.
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The Ideation Bottleneck: Decomposing the Quality Gap Between AI-Generated and Human Economics Research

✇cs.AI, q-bio.NC updates on arXiv.org
By: Ning Li
arXiv:2604.03338v1 Announce Type: cross Abstract: Autonomous AI systems can now generate complete economics research papers, but they substantially underperform human-authored publications in head-to-head comparisons. This paper decomposes the quality gap into two independent components: research idea quality and execution quality. Using a two-model ensemble of fine-tuned language models trained on publication decisions (Gong, Li, and Zhou, 2026) to evaluate idea quality and a comprehensive six-dimension rubric assessed by Gemini 3.1 Flash Lite -- the same model family used as the APE tournament judge, ensuring methodological consistency -- to evaluate execution quality, we analyze 953 economics papers -- 912 AI-generated papers from the APE project and 41 human papers published in the American Economic Review and AEJ: Economic Policy. The idea quality gap is large (Cohen's d = 2.23, p
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Think Before You Drive: World Model-Inspired Multimodal Grounding for Autonomous Vehicles

✇cs.AI, q-bio.NC updates on arXiv.org
By: Haicheng Liao · Huanming Shen · Bonan Wang · Yongkang Li · Yihong Tang · Chengyue Wang · Dingyi Zhuang · Kehua Chen · Hai Yang · Chengzhong Xu · Zhenning Li
arXiv:2512.03454v3 Announce Type: replace-cross Abstract: Interpreting natural-language commands to localize target objects is critical for autonomous driving (AD). Existing visual grounding (VG) methods for autonomous vehicles (AVs) typically struggle with ambiguous, context-dependent instructions, as they lack reasoning over 3D spatial relations and anticipated scene evolution. Grounded in the principles of world models, we propose ThinkDeeper, a framework that reasons about future spatial states before making grounding decisions. At its core is a Spatial-Aware World Model (SA-WM) that learns to reason ahead by distilling the current scene into a command-aware latent state and rolling out a sequence of future latent states, providing forward-looking cues for disambiguation. Complementing this, a hypergraph-guided decoder then hierarchically fuses these states with the multimodal input, capturing higher-order spatial dependencies for robust localization. In addition, we present DrivePilot, a multi-source VG dataset in AD, featuring semantic annotations generated by a Retrieval-Augmented Generation (RAG) and Chain-of-Thought (CoT)-prompted LLM pipeline. Extensive evaluations on six benchmarks, ThinkDeeper ranks #1 on the Talk2Car leaderboard and surpasses state-of-the-art baselines on DrivePilot, MoCAD, and RefCOCO/+/g benchmarks. Notably, it shows strong robustness and efficiency in challenging scenes (long-text, multi-agent, ambiguity) and retains superior performance even when trained on 50% of the data.
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SIRT3 deacetylates STEAP4 to modulate cuproptosis sensitivity via mitochondrial metabolic reprogramming in HBV-related HCC

✇Omics in Hepatocellular
By: Ze-Bang Du · Xin-Mou Wu · Jia-Ming Lei · Yu-Xin Cai · Jie He · Bo Qian · Xin-Xin He · Wen-Hao Han · Yuan Lu · Xiao-Gang Xia · Han-Ying Zheng · Dong-Bei Guo · You-Liang Yao · Wen-Gang Li · Yu-Chun Lin · Zhong-Ning Lin

Cell Death Differ. 2026 Mar 16. doi: 10.1038/s41418-026-01713-w. Online ahead of print.

ABSTRACT

Hepatitis B virus (HBV) infection remains a leading etiological driver of hepatocellular carcinoma (HCC). Cuproptosis is a recently defined copper-dependent form of regulated cell death that selectively eliminates mitochondria-dependent cells; whether HBV rewires this vulnerability remains unknown. Here we unveil a novel HBV X protein (HBx)-driven mechanism of cuproptosis evasion. Integrative analysis of clinical specimens, HBx-transgenic (HBx-Tg) mice, and multi-omics datasets revealed marked downregulation of STEAP4 (six-transmembrane epithelial antigen of prostate 4), a metalloreductase essential for cuproptosis sensitivity, in HBV-positive HCC. Mechanistically, HBx attenuates sirtuin 3 (SIRT3), impairing deacetylation of STEAP4 at lysine 404 and abolishing its mitochondrial targeting. Consequently, cells switch from the tricarboxylic acid (TCA) cycle respiration to glycolysis, reducing sensitivity to the copper ionophore elesclomol (ES). Restoring STEAP4 expression or pharmacological activation of SIRT3 with honokiol (HKL) re-instated mitochondrial STEAP4 localization and re-sensitized HBV-related HCC cells to cuproptosis; combination with ES produced synergistic tumor suppression in vitro and in orthotopic models. Collectively, our findings establish the SIRT3-STEAP4 axis as a novel regulator of cuproptosis resistance in HBV-related HCC. HBx-mediated repression of SIRT3 disrupts STEAP4 deacetylation and mitochondrial targeting, fostering metabolic reprogramming and evasion of copper-induced cell death. The results provide a pre-clinical rationale for copper-directed combination strategies in HBV-associated HCC.

PMID:41840161 | DOI:10.1038/s41418-026-01713-w

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VORL-EXPLORE: A Hybrid Learning Planning Approach to Multi-Robot Exploration in Dynamic Environments

✇cs.AI, q-bio.NC updates on arXiv.org
By: Ning Liu · Sen Shen · Zheng Li · Sheng Liu · Dongkun Han · Shangke Lyu · Thomas Braunl
arXiv:2603.07973v1 Announce Type: cross Abstract: Hierarchical multi-robot exploration commonly decouples frontier allocation from local navigation, which can make the system brittle in dense and dynamic environments. Because the allocator lacks direct awareness of execution difficulty, robots may cluster at bottlenecks, trigger oscillatory replanning, and generate redundant coverage. We propose VORL-EXPLORE, a hybrid learning and planning framework that addresses this limitation through execution fidelity, a shared estimate of local navigability that couples task allocation with motion execution. This fidelity signal is incorporated into a fidelity-coupled Voronoi objective with inter-robot repulsion to reduce contention before it emerges. It also drives a risk-aware adaptive arbitration mechanism between global A* guidance and a reactive reinforcement learning policy, balancing long-range efficiency with safe interaction in confined spaces. The framework further supports online self-supervised recalibration of the fidelity model using pseudo-labels derived from recent progress and safety outcomes, enabling adaptation to non-stationary obstacles without manual risk tuning. We evaluate this capability separately in a dedicated severe-traffic ablation. Extensive experiments in randomized grids and a Gazebo factory scenario show high success rates, shorter path length, lower overlap, and robust collision avoidance. The source code will be made publicly available upon acceptance.
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Reallocating Attention Across Layers to Reduce Multimodal Hallucination

✇cs.AI, q-bio.NC updates on arXiv.org
By: Haolang Lu · Bolun Chu · WeiYe Fu · Guoshun Nan · Junning Liu · Minghui Pan · Qiankun Li · Yi Yu · Hua Wang · Kun Wang
arXiv:2510.10285v3 Announce Type: replace Abstract: Multimodal large reasoning models (MLRMs) often suffer from hallucinations that stem not only from insufficient visual grounding but also from imbalanced allocation between perception and reasoning processes. Building upon recent interpretability findings suggesting a staged division of attention across layers, we analyze how this functional misalignment leads to two complementary failure modes: perceptual bias in shallow layers and reasoning drift in deeper layers. To alleviate these issues, we propose Functional Head Identification and Class-Conditioned Rescaling , a lightweight, training-free plugin that identifies perception- and reasoning-oriented heads and adaptively rebalances their layerwise contributions. Our method improves reasoning consistency and visual faithfulness without retraining or any architectural modification. Evaluations across three representative MLRMs and five multimodal reasoning benchmarks show an average 4.2% point gain, with less than 1% additional computation and only 9% baseline latency. Beyond empirical improvements, our study provides an interpretable perspective on regulating cross-layer functional dynamics to enhance the reliability of multimodal reasoning.
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Language in the Flow of Time: Time-Series-Paired Texts Weaved into a Unified Temporal Narrative

✇cs.AI, q-bio.NC updates on arXiv.org
By: Zihao Li · Xiao Lin · Zhining Liu · Jiaru Zou · Ziwei Wu · Lecheng Zheng · Dongqi Fu · Yada Zhu · Hendrik Hamann · Hanghang Tong · Jingrui He
arXiv:2502.08942v3 Announce Type: replace-cross Abstract: While many advances in time series models focus exclusively on numerical data, research on multimodal time series, particularly those involving contextual textual information, remains in its infancy. With recent progress in large language models and time series learning, we revisit the integration of paired texts with time series through the Platonic Representation Hypothesis, which posits that representations of different modalities converge to shared spaces. In this context, we identify that time-series-paired texts may naturally exhibit periodic properties that closely mirror those of the original time series. Building on this insight, we propose a novel framework, Texts as Time Series (TaTS), which considers the time-series-paired texts to be auxiliary variables of the time series. TaTS can be plugged into any existing numerical-only time series models and effectively enable them to handle time series data with paired texts. Through extensive experiments on both multimodal time series forecasting and imputation tasks across benchmark datasets with various existing time series models, we demonstrate that TaTS can enhance multimodal predictive performance without modifying model architectures. Our Code is available at https://github.com/iDEA-iSAIL-Lab-UIUC/TaTS.
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Flow Matching Meets Biology and Life Science: A Survey

✇cs.AI, q-bio.NC updates on arXiv.org
By: Zihao Li · Zhichen Zeng · Xiao Lin · Feihao Fang · Yanru Qu · Zhe Xu · Zhining Liu · Xuying Ning · Tianxin Wei · Ge Liu · Hanghang Tong · Jingrui He
arXiv:2507.17731v2 Announce Type: replace-cross Abstract: Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, catalysis discovery, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions. The corresponding curated resources are available at https://github.com/Violet24K/Awesome-Flow-Matching-Meets-Biology.
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SpatialBench: Benchmarking Multimodal Large Language Models for Spatial Cognition

✇cs.AI, q-bio.NC updates on arXiv.org
By: Peiran Xu · Sudong Wang · Yao Zhu · Jianing Li · Gege Qi · Yunjian Zhang
arXiv:2511.21471v2 Announce Type: replace Abstract: Spatial cognition is fundamental to real-world multimodal intelligence, allowing models to effectively interact with the physical environment. While multimodal large language models (MLLMs) have made significant strides, existing benchmarks often oversimplify spatial cognition, reducing it to a single-dimensional metric, which fails to capture the hierarchical structure and interdependence of spatial abilities. To address this gap, we propose a hierarchical spatial cognition framework that decomposes spatial intelligence into five progressively complex levels from basic observation to high-level planning. Building upon this taxonomy, we construct SpatialBench, a large-scale, fine-grained benchmark covering 15 tasks aligned with these cognitive levels. To provide a unified evaluation across heterogeneous tasks, we further introduce a high-level capability-oriented metric that reliably assesses a model's overall spatial reasoning ability. Extensive experiments over massive MLLMs reveal distinct performance stratification across cognitive levels: models exhibit strong perceptual grounding yet remain limited in symbolic reasoning, causal inference, and planning. Additional human tests demonstrate that humans perform selective, goal-directed abstraction, while MLLMs tend to over-attend to surface details without coherent spatial intent. Our work establishes the first systematic framework for measuring hierarchical spatial cognition in MLLMs, laying the foundation for future spatially intelligent systems.
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