arXiv:2510.26887v1 Announce Type: new Abstract: We present Denario, an AI multi-agent system designed to serve as a scientific research assistant. Denario can perform many different tasks, such as generating ideas, checking the literature, developing research plans, writing and executing code, making plots, and drafting and reviewing a scientific paper. The system has a modular architecture, allowing it to handle specific tasks, such as generating an idea, or carrying out end-to-end scientific analysis using Cmbagent as a deep-research backend. In this work, we describe in detail Denario and its modules, and illustrate its capabilities by presenting multiple AI-generated papers generated by it in many different scientific disciplines such as astrophysics, biology, biophysics, biomedical informatics, chemistry, material science, mathematical physics, medicine, neuroscience and planetary science. Denario also excels at combining ideas from different disciplines, and we illustrate this by showing a paper that applies methods from quantum physics and machine learning to astrophysical data. We report the evaluations performed on these papers by domain experts, who provided both numerical scores and review-like feedback. We then highlight the strengths, weaknesses, and limitations of the current system. Finally, we discuss the ethical implications of AI-driven research and reflect on how such technology relates to the philosophy of science. We publicly release the code at https://github.com/AstroPilot-AI/Denario. A Denario demo can also be run directly on the web at https://huggingface.co/spaces/astropilot-ai/Denario, and the full app will be deployed on the cloud.

arXiv:2510.27009v1 Announce Type: new Abstract: Language models are traditionally designed around causal masking. In domains with spatial or relational structure, causal masking is often viewed as inappropriate, and sequential linearizations are instead used. Yet the question of whether it is viable to accept the information loss introduced by causal masking on nonsequential data has received little direct study, in part because few domains offer both spatial and sequential representations of the same dataset. In this work, we investigate this issue in the domain of chess, which naturally supports both representations. We train language models with bidirectional and causal self-attention mechanisms on both spatial (board-based) and sequential (move-based) data. Our results show that models trained on spatial board states - \textit{even with causal masking} - consistently achieve stronger playing strength than models trained on sequential data. While our experiments are conducted on chess, our results are methodological and may have broader implications: applying causal masking to spatial data is a viable procedure for training unimodal LLMs on spatial data, and in some domains is even preferable to sequentialization.

arXiv:2510.27051v1 Announce Type: new Abstract: Enterprise AI agents must continuously adapt to maintain accuracy, reduce latency, and remain aligned with user needs. We present a practical implementation of a data flywheel in NVInfo AI, NVIDIA's Mixture-of-Experts (MoE) Knowledge Assistant serving over 30,000 employees. By operationalizing a MAPE-driven data flywheel, we built a closed-loop system that systematically addresses failures in retrieval-augmented generation (RAG) pipelines and enables continuous learning. Over a 3-month post-deployment period, we monitored feedback and collected 495 negative samples. Analysis revealed two major failure modes: routing errors (5.25\%) and query rephrasal errors (3.2\%). Using NVIDIA NeMo microservices, we implemented targeted improvements through fine-tuning. For routing, we replaced a Llama 3.1 70B model with a fine-tuned 8B variant, achieving 96\% accuracy, a 10x reduction in model size, and 70\% latency improvement. For query rephrasal, fine-tuning yielded a 3.7\% gain in accuracy and a 40\% latency reduction. Our approach demonstrates how human-in-the-loop (HITL) feedback, when structured within a data flywheel, transforms enterprise AI agents into self-improving systems. Key learnings include approaches to ensure agent robustness despite limited user feedback, navigating privacy constraints, and executing staged rollouts in production. This work offers a repeatable blueprint for building robust, adaptive enterprise AI agents capable of learning from real-world usage at scale.

arXiv:2510.27176v1 Announce Type: new Abstract: Can an AI autonomously design mechanisms for computer systems on par with the creativity and reasoning of human experts? We present Glia, an AI architecture for networked systems design that uses large language models (LLMs) in a human-inspired, multi-agent workflow. Each agent specializes in reasoning, experimentation, and analysis, collaborating through an evaluation framework that grounds abstract reasoning in empirical feedback. Unlike prior ML-for-systems methods that optimize black-box policies, Glia generates interpretable designs and exposes its reasoning process. When applied to a distributed GPU cluster for LLM inference, it produces new algorithms for request routing, scheduling, and auto-scaling that perform at human-expert levels in significantly less time, while yielding novel insights into workload behavior. Our results suggest that by combining reasoning LLMs with structured experimentation, an AI can produce creative and understandable designs for complex systems problems.

arXiv:2510.27353v1 Announce Type: new Abstract: Recent studies have suggested that Large Language Models (LLMs) could provide interesting ideas contributing to mathematical discovery. This claim was motivated by reports that LLM-based genetic algorithms produced heuristics offering new insights into the online bin packing problem under uniform and Weibull distributions. In this work, we reassess this claim through a detailed analysis of the heuristics produced by LLMs, examining both their behavior and interpretability. Despite being human-readable, these heuristics remain largely opaque even to domain experts. Building on this analysis, we propose a new class of algorithms tailored to these specific bin packing instances. The derived algorithms are significantly simpler, more efficient, more interpretable, and more generalizable, suggesting that the considered instances are themselves relatively simple. We then discuss the limitations of the claim regarding LLMs' contribution to this problem, which appears to rest on the mistaken assumption that the instances had previously been studied. Our findings instead emphasize the need for rigorous validation and contextualization when assessing the scientific value of LLM-generated outputs.

arXiv:2510.27617v1 Announce Type: new Abstract: Automation of Register Transfer Level (RTL) design can help developers meet increasing computational demands. Large Language Models (LLMs) show promise for Hardware Description Language (HDL) generation, but face challenges due to limited parametric knowledge and domain-specific constraints. While prompt engineering and fine-tuning have limitations in knowledge coverage and training costs, multi-agent architectures offer a training-free paradigm to enhance reasoning through collaborative generation. However, current multi-agent approaches suffer from two critical deficiencies: susceptibility to noise propagation and constrained reasoning space exploration. We propose VeriMoA, a training-free mixture-of-agents (MoA) framework with two synergistic innovations. First, a quality-guided caching mechanism to maintain all intermediate HDL outputs and enables quality-based ranking and selection across the entire generation process, encouraging knowledge accumulation over layers of reasoning. Second, a multi-path generation strategy that leverages C++ and Python as intermediate representations, decomposing specification-to-HDL translation into two-stage processes that exploit LLM fluency in high-resource languages while promoting solution diversity. Comprehensive experiments on VerilogEval 2.0 and RTLLM 2.0 benchmarks demonstrate that VeriMoA achieves 15--30% improvements in Pass@1 across diverse LLM backbones, especially enabling smaller models to match larger models and fine-tuned alternatives without requiring costly training.

arXiv:2510.27671v1 Announce Type: new Abstract: Structure-based drug design (SBDD), which maps target proteins to candidate molecular ligands, is a fundamental task in drug discovery. Effectively aligning protein structural representations with molecular representations, and ensuring alignment between generated drugs and their pharmacological properties, remains a critical challenge. To address these challenges, we propose MolChord, which integrates two key techniques: (1) to align protein and molecule structures with their textual descriptions and sequential representations (e.g., FASTA for proteins and SMILES for molecules), we leverage NatureLM, an autoregressive model unifying text, small molecules, and proteins, as the molecule generator, alongside a diffusion-based structure encoder; and (2) to guide molecules toward desired properties, we curate a property-aware dataset by integrating preference data and refine the alignment process using Direct Preference Optimization (DPO). Experimental results on CrossDocked2020 demonstrate that our approach achieves state-of-the-art performance on key evaluation metrics, highlighting its potential as a practical tool for SBDD.

arXiv:2510.26969v1 Announce Type: cross Abstract: We introduce a methodology for the identification of notifiable events in the domain of healthcare. The methodology harnesses semantic frames to define fine-grained patterns and search them in unstructured data, namely, open-text fields in e-medical records. We apply the methodology to the problem of underreporting of gender-based violence (GBV) in e-medical records produced during patients' visits to primary care units. A total of eight patterns are defined and searched on a corpus of 21 million sentences in Brazilian Portuguese extracted from e-SUS APS. The results are manually evaluated by linguists and the precision of each pattern measured. Our findings reveal that the methodology effectively identifies reports of violence with a precision of 0.726, confirming its robustness. Designed as a transparent, efficient, low-carbon, and language-agnostic pipeline, the approach can be easily adapted to other health surveillance contexts, contributing to the broader, ethical, and explainable use of NLP in public health systems.

arXiv:2510.26995v1 Announce Type: cross Abstract: Large language models (LLMs) excel at numerical estimation but struggle to correctly quantify uncertainty. We study how well LLMs construct confidence intervals around their own answers and find that they are systematically overconfident. To evaluate this behavior, we introduce FermiEval, a benchmark of Fermi-style estimation questions with a rigorous scoring rule for confidence interval coverage and sharpness. Across several modern models, nominal 99\% intervals cover the true answer only 65\% of the time on average. With a conformal prediction based approach that adjusts the intervals, we obtain accurate 99\% observed coverage, and the Winkler interval score decreases by 54\%. We also propose direct log-probability elicitation and quantile adjustment methods, which further reduce overconfidence at high confidence levels. Finally, we develop a perception-tunnel theory explaining why LLMs exhibit overconfidence: when reasoning under uncertainty, they act as if sampling from a truncated region of their inferred distribution, neglecting its tails.

arXiv:2510.27055v1 Announce Type: cross Abstract: We present Contamination Detection via Context (CoDeC), a practical and accurate method to detect and quantify training data contamination in large language models. CoDeC distinguishes between data memorized during training and data outside the training distribution by measuring how in-context learning affects model performance. We find that in-context examples typically boost confidence for unseen datasets but may reduce it when the dataset was part of training, due to disrupted memorization patterns. Experiments show that CoDeC produces interpretable contamination scores that clearly separate seen and unseen datasets, and reveals strong evidence of memorization in open-weight models with undisclosed training corpora. The method is simple, automated, and both model- and dataset-agnostic, making it easy to integrate with benchmark evaluations.

arXiv:2510.27163v1 Announce Type: cross Abstract: Before deploying an AI system to replace an existing process, it must be compared with the incumbent to ensure improvement without added risk. Traditional evaluation relies on ground truth for both systems, but this is often unavailable due to delayed or unknowable outcomes, high costs, or incomplete data, especially for long-standing systems deemed safe by convention. The more practical solution is not to compute absolute risk but the difference between systems. We therefore propose a marginal risk assessment framework, that avoids dependence on ground truth or absolute risk. It emphasizes three kinds of relative evaluation methodology, including predictability, capability and interaction dominance. By shifting focus from absolute to relative evaluation, our approach equips software teams with actionable guidance: identifying where AI enhances outcomes, where it introduces new risks, and how to adopt such systems responsibly.

arXiv:2510.27196v1 Announce Type: cross Abstract: The proliferation of memes on social media necessitates the capabilities of multimodal Large Language Models (mLLMs) to effectively understand multimodal harmfulness. Existing evaluation approaches predominantly focus on mLLMs' detection accuracy for binary classification tasks, which often fail to reflect the in-depth interpretive nuance of harmfulness across diverse contexts. In this paper, we propose MemeArena, an agent-based arena-style evaluation framework that provides a context-aware and unbiased assessment for mLLMs' understanding of multimodal harmfulness. Specifically, MemeArena simulates diverse interpretive contexts to formulate evaluation tasks that elicit perspective-specific analyses from mLLMs. By integrating varied viewpoints and reaching consensus among evaluators, it enables fair and unbiased comparisons of mLLMs' abilities to interpret multimodal harmfulness. Extensive experiments demonstrate that our framework effectively reduces the evaluation biases of judge agents, with judgment results closely aligning with human preferences, offering valuable insights into reliable and comprehensive mLLM evaluations in multimodal harmfulness understanding. Our code and data are publicly available at https://github.com/Lbotirx/MemeArena.

arXiv:2510.27281v1 Announce Type: cross Abstract: Accurate prediction of Drug-Target Affinity (DTA) is crucial for reducing experimental costs and accelerating early screening in computational drug discovery. While sequence-based deep learning methods avoid reliance on costly 3D structures, they still overlook simultaneous modeling of global sequence semantic features and local topological structural features within drugs and proteins, and represent drugs as flat sequences without atomic-level, substructural-level, and molecular-level multi-scale features. We propose HiF-DTA, a hierarchical network that adopts a dual-pathway strategy to extract both global sequence semantic and local topological features from drug and protein sequences, and models drugs multi-scale to learn atomic, substructural, and molecular representations fused via a multi-scale bilinear attention module. Experiments on Davis, KIBA, and Metz datasets show HiF-DTA outperforms state-of-the-art baselines, with ablations confirming the importance of global-local extraction and multi-scale fusion.

arXiv:2510.27287v1 Announce Type: cross Abstract: Enterprise systems are crucial for enhancing productivity and decision-making among employees and customers. Integrating LLM based systems into enterprise systems enables intelligent automation, personalized experiences, and efficient information retrieval, driving operational efficiency and strategic growth. However, developing and evaluating such systems is challenging due to the inherent complexity of enterprise environments, where data is fragmented across multiple sources and governed by sophisticated access controls. We present EnterpriseBench, a comprehensive benchmark that simulates enterprise settings, featuring 500 diverse tasks across software engineering, HR, finance, and administrative domains. Our benchmark uniquely captures key enterprise characteristics including data source fragmentation, access control hierarchies, and cross-functional workflows. Additionally, we provide a novel data generation pipeline that creates internally consistent enterprise tasks from organizational metadata. Experiments with state-of-the-art LLM agents demonstrate that even the most capable models achieve only 41.8% task completion, highlighting significant opportunities for improvement in enterprise-focused AI systems.

arXiv:2510.27442v1 Announce Type: cross Abstract: Vision Transformers (ViTs) have demonstrated strong potential in medical imaging; however, their high computational demands and tendency to overfit on small datasets limit their applicability in real-world clinical scenarios. In this paper, we present CoMViT, a compact and generalizable Vision Transformer architecture optimized for resource-constrained medical image analysis. CoMViT integrates a convolutional tokenizer, diagonal masking, dynamic temperature scaling, and pooling-based sequence aggregation to improve performance and generalization. Through systematic architectural optimization, CoMViT achieves robust performance across twelve MedMNIST datasets while maintaining a lightweight design with only ~4.5M parameters. It matches or outperforms deeper CNN and ViT variants, offering up to 5-20x parameter reduction without sacrificing accuracy. Qualitative Grad-CAM analyses show that CoMViT consistently attends to clinically relevant regions despite its compact size. These results highlight the potential of principled ViT redesign for developing efficient and interpretable models in low-resource medical imaging settings.

arXiv:2510.27606v1 Announce Type: cross Abstract: Spatial understanding remains a weakness of Large Vision-Language Models (LVLMs). Existing supervised fine-tuning (SFT) and recent reinforcement learning with verifiable rewards (RLVR) pipelines depend on costly supervision, specialized tools, or constrained environments that limit scale. We introduce Spatial-SSRL, a self-supervised RL paradigm that derives verifiable signals directly from ordinary RGB or RGB-D images. Spatial-SSRL automatically formulates five pretext tasks that capture 2D and 3D spatial structure: shuffled patch reordering, flipped patch recognition, cropped patch inpainting, regional depth ordering, and relative 3D position prediction. These tasks provide ground-truth answers that are easy to verify and require no human or LVLM annotation. Training on our tasks substantially improves spatial reasoning while preserving general visual capabilities. On seven spatial understanding benchmarks in both image and video settings, Spatial-SSRL delivers average accuracy gains of 4.63% (3B) and 3.89% (7B) over the Qwen2.5-VL baselines. Our results show that simple, intrinsic supervision enables RLVR at scale and provides a practical route to stronger spatial intelligence in LVLMs.

arXiv:2510.27629v1 Announce Type: cross Abstract: Open-weight bio-foundation models present a dual-use dilemma. While holding great promise for accelerating scientific research and drug development, they could also enable bad actors to develop more deadly bioweapons. To mitigate the risk posed by these models, current approaches focus on filtering biohazardous data during pre-training. However, the effectiveness of such an approach remains unclear, particularly against determined actors who might fine-tune these models for malicious use. To address this gap, we propose \eval, a framework to evaluate the robustness of procedures that are intended to reduce the dual-use capabilities of bio-foundation models. \eval assesses models' virus understanding through three lenses, including sequence modeling, mutational effects prediction, and virulence prediction. Our results show that current filtering practices may not be particularly effective: Excluded knowledge can be rapidly recovered in some cases via fine-tuning, and exhibits broader generalizability in sequence modeling. Furthermore, dual-use signals may already reside in the pretrained representations, and can be elicited via simple linear probing. These findings highlight the challenges of data filtering as a standalone procedure, underscoring the need for further research into robust safety and security strategies for open-weight bio-foundation models.

arXiv:2506.12667v2 Announce Type: replace Abstract: Current advances in AI and its applicability have highlighted the need to ensure its trustworthiness for legal, ethical, and even commercial reasons. Sub-symbolic machine learning algorithms, such as the LLMs, simulate reasoning but hallucinate and their decisions cannot be explained or audited (crucial aspects for trustworthiness). On the other hand, rule-based reasoners, such as Cyc, are able to provide the chain of reasoning steps but are complex and use a large number of reasoners. We propose a middle ground using s(CASP), a goal-directed constraint-based answer set programming reasoner that employs a small number of mechanisms to emulate reliable and explainable human-style commonsense reasoning. In this paper, we explain how s(CASP) supports the 16 desiderata for trustworthy AI introduced by Doug Lenat and Gary Marcus (2023), and two additional ones: inconsistency detection and the assumption of alternative worlds. To illustrate the feasibility and synergies of s(CASP), we present a range of diverse applications, including a conversational chatbot and a virtually embodied reasoner.

arXiv:2510.05743v2 Announce Type: replace Abstract: We review the historical development and current trends of artificially intelligent agents (agentic AI) in the social and behavioral sciences: from the first programmable computers, and social simulations soon thereafter, to today's experiments with large language models. This overview emphasizes the role of AI in the scientific process and the changes brought about, both through technological advancements and the broader evolution of science from around 1950 to the present. Some of the specific points we cover include: the challenges of presenting the first social simulation studies to a world unaware of computers, the rise of social systems science, intelligent game theoretic agents, the age of big data and the epistemic upheaval in its wake, and the current enthusiasm around applications of generative AI, and many other topics. A pervasive theme is how deeply entwined we are with the technologies we use to understand ourselves.

arXiv:2510.23045v3 Announce Type: replace Abstract: Artificial intelligence is undergoing a profound transition from a computational instrument to an autonomous originator of scientific knowledge. This emerging paradigm, the AI scientist, is architected to emulate the complete scientific workflow-from initial hypothesis generation to the final synthesis of publishable findings-thereby promising to fundamentally reshape the pace and scale of discovery. However, the rapid and unstructured proliferation of these systems has created a fragmented research landscape, obscuring overarching methodological principles and developmental trends. This survey provides a systematic and comprehensive synthesis of this domain by introducing a unified, six-stage methodological framework that deconstructs the end-to-end scientific process into: Literature Review, Idea Generation, Experimental Preparation, Experimental Execution, Scientific Writing, and Paper Generation. Through this analytical lens, we chart the field's evolution from early Foundational Modules (2022-2023) to integrated Closed-Loop Systems (2024), and finally to the current frontier of Scalability, Impact, and Human-AI Collaboration (2025-present). By rigorously synthesizing these developments, this survey not only clarifies the current state of autonomous science but also provides a critical roadmap for overcoming remaining challenges in robustness and governance, ultimately guiding the next generation of systems toward becoming trustworthy and indispensable partners in human scientific inquiry.