arXiv:2511.07669v1 Announce Type: new Abstract: Current large language models (LLMs) excel in verifiable domains where outputs can be checked before action but prove less reliable for high-stakes strategic decisions with uncertain outcomes. This gap, driven by mutually reinforcing cognitive biases in both humans and artificial intelligence (AI) systems, threatens the defensibility of valuations and sustainability of investments in the sector. This report describes a framework emerging from systematic qualitative assessment across 7 frontier-grade LLMs and 3 market-facing venture vignettes under time pressure. Detailed prompting specifying decision partnership and explicitly instructing avoidance of sycophancy, confabulation, solution drift, and nihilism achieved initial partnership state but failed to maintain it under operational pressure. Sustaining protective partnership state required an emergent 7-stage calibration sequence, built upon a 4-stage initialization process, within a 5-layer protection architecture enabling bias self-monitoring, human-AI adversarial challenge, partnership state verification, performance degradation detection, and stakeholder protection. Three discoveries resulted: partnership state is achievable through ordered calibration but requires emergent maintenance protocols; reliability degrades when architectural drift and context exhaustion align; and dissolution discipline prevents costly pursuit of fundamentally wrong directions. Cross-model validation revealed systematic performance differences across LLM architectures. This approach demonstrates that human-AI teams can achieve cognitive partnership capable of preventing avoidable regret in high-stakes decisions, addressing return-on-investment expectations that depend on AI systems supporting consequential decision-making without introducing preventable cognitive traps when verification arrives too late.

arXiv:2509.22242v2 Announce Type: replace Abstract: Clinical dataset labels are rarely certain as annotators disagree and confidence is not uniform across cases. Typical aggregation procedures, such as majority voting, obscure this variability. In simple experiments on medical imaging benchmarks, accounting for the confidence in binary labels significantly impacts model rankings. We therefore argue that machine-learning evaluations should explicitly account for annotation uncertainty using probabilistic metrics that directly operate on distributions. These metrics can be applied independently of the annotations' generating process, whether modeled by simple counting, subjective confidence ratings, or probabilistic response models. They are also computationally lightweight, as closed-form expressions have linear-time implementations once examples are sorted by model score. We thus urge the community to release raw annotations for datasets and to adopt uncertainty-aware evaluation so that performance estimates may better reflect clinical data.

arXiv:2511.05385v1 Announce Type: cross Abstract: Retrieval-Augmented Generation (RAG) utilizes external knowledge to augment Large Language Models' (LLMs) reliability. For flexibility, agentic RAG employs autonomous, multi-round retrieval and reasoning to resolve queries. Although recent agentic RAG has improved via reinforcement learning, they often incur substantial token overhead from search and reasoning processes. This trade-off prioritizes accuracy over efficiency. To address this issue, this work proposes TeaRAG, a token-efficient agentic RAG framework capable of compressing both retrieval content and reasoning steps. 1) First, the retrieved content is compressed by augmenting chunk-based semantic retrieval with a graph retrieval using concise triplets. A knowledge association graph is then built from semantic similarity and co-occurrence. Finally, Personalized PageRank is leveraged to highlight key knowledge within this graph, reducing the number of tokens per retrieval. 2) Besides, to reduce reasoning steps, Iterative Process-aware Direct Preference Optimization (IP-DPO) is proposed. Specifically, our reward function evaluates the knowledge sufficiency by a knowledge matching mechanism, while penalizing excessive reasoning steps. This design can produce high-quality preference-pair datasets, supporting iterative DPO to improve reasoning conciseness. Across six datasets, TeaRAG improves the average Exact Match by 4% and 2% while reducing output tokens by 61% and 59% on Llama3-8B-Instruct and Qwen2.5-14B-Instruct, respectively. Code is available at https://github.com/Applied-Machine-Learning-Lab/TeaRAG.

arXiv:2412.05447v3 Announce Type: replace-cross Abstract: Retrieval-Augmented Generation (RAG) is one of the leading and most widely used techniques for enhancing LLM retrieval capabilities, but it still faces significant limitations in commercial use cases. RAG primarily relies on the query-chunk text-to-text similarity in the embedding space for retrieval and can fail to capture deeper semantic relationships across chunks, is highly sensitive to chunking strategies, and is prone to hallucinations. To address these challenges, we propose TOBUGraph, a graph-based retrieval framework that first constructs the knowledge graph from unstructured data dynamically and automatically. Using LLMs, TOBUGraph extracts structured knowledge and diverse relationships among data, going beyond RAG's text-to-text similarity. Retrieval is achieved through graph traversal, leveraging the extracted relationships and structures to enhance retrieval accuracy, eliminating the need for chunking configurations while reducing hallucination. We demonstrate TOBUGraph's effectiveness in TOBU, a real-world application in production for personal memory organization and retrieval. Our evaluation using real user data demonstrates that TOBUGraph outperforms multiple RAG implementations in both precision and recall, significantly improving user experience through improved retrieval accuracy.

Nature Medicine, Published online: 10 November 2025; doi:10.1038/s41591-025-04065-z

Author Correction: Global burden of chikungunya virus infections and the potential benefit of vaccination campaigns

Nature Biotechnology, Published online: 07 November 2025; doi:10.1038/s41587-025-02941-0

Publisher Correction: Deep-learning-based virtual screening of antibacterial compounds

arXiv:2511.03217v1 Announce Type: cross Abstract: Large language models (LLMs) excel in generating fluent utterances but can lack reliable grounding in verified information. At the same time, knowledge-graph-based fact-checkers deliver precise and interpretable evidence, yet suffer from limited coverage or latency. By integrating LLMs with knowledge graphs and real-time search agents, we introduce a hybrid fact-checking approach that leverages the individual strengths of each component. Our system comprises three autonomous steps: 1) a Knowledge Graph (KG) Retrieval for rapid one - hop lookups in DBpedia, 2) an LM-based classification guided by a task-specific labeling prompt, producing outputs with internal rule-based logic, and 3) a Web Search Agent invoked only when KG coverage is insufficient. Our pipeline achieves an F1 score of 0.93 on the FEVER benchmark on the Supported/Refuted split without task- specific fine - tuning. To address Not enough information cases, we conduct a targeted reannotation study showing that our approach frequently uncovers valid evidence for claims originally labeled as Not Enough Information (NEI), as confirmed by both expert annotators and LLM reviewers. With this paper, we present a modular, opensource fact-checking pipeline with fallback strategies and generalization across datasets.

Nature Biotechnology, Published online: 06 November 2025; doi:10.1038/s41587-025-02895-3

Engineered DNA recombinases efficiently and specifically insert genetic cargos without the use of landing pads.

npj Digital Medicine, Published online: 05 November 2025; doi:10.1038/s41746-025-02125-9

Biased and poorly documented dermatology datasets pose risks to the development of safe and generalizable artificial intelligence (AI) tools. We created a Dataset Nutrition Label (DNL) for multiple dermatology datasets to support transparent and responsible data use. The DNL offers a structured, digestible summary of key attributes, including metadata, limitations, and risks, enabling data users to better assess suitability and proactively address potential sources of bias in datasets.

npj Digital Medicine, Published online: 05 November 2025; doi:10.1038/s41746-025-02005-2

Evaluating clinical AI summaries with large language models as judges

Smoking has severe health consequences, and secondhand smoke (SHS) exposure among children increases the risk of sudden infant death syndrome, chronic respiratory diseases, such as asthma, and lung cancer in adulthood. For many parents, pediatricians are the primary source of interaction with the healthcare system. Nevertheless, in pediatric settings, appropriate tobacco treatments are rarely, if ever, provided to parents who smoke. To best address tobacco use among parents, it is ideal to develop scalable solutions that are coordinated across health systems, community partners, and national services within pediatric settings. We describe our experience developing and implementing a parent tobacco treatment platform (PTTP) within a pediatric institution that leverages multiple international standards to support interoperability, with the overarching goal of providing a model for how such work can be approached. The clinical decision support (CDS) system includes clinician- and patient-facing components, connects parents to three different treatment options (nicotine replacement therapy, text-based counseling, and telephonic counseling), and incorporates three international standards (Fast Healthcare Interoperability Resources [FHIR], SMART on FHIR, and CDS Hooks). FHIR is used across all components. SMART on FHIR is limited to the clinician-facing tool, and CDS Hooks is used in the patient-facing portion. While healthcare interoperability standards supported a significant portion of the overall system, non-standard technologies and enhancements of existing standards were also required. Further, no connections with community partners could use existing interoperability standards. Over one year, the CDS was used in 194,946 visits, identified 7,847 parents who smoke, and connected 2,954 parents to 6,320 distinct treatment services, a significant improvement compared to prior efforts. Our project demonstrates that building CDS systems using international standards, such as SMART on FHIR, FHIR, and CDS Hooks, is possible, but challenges remain. Limits in the CDS Hooks standard to support common workflows and a lack of communication standards used by 3rd parties outside the healthcare system represent areas for future work. To support these requirements, additional EHR-specific records and communication mechanisms were required.

Nature Medicine, Published online: 05 November 2025; doi:10.1038/s41591-025-03982-3

Pretrained using 335,645 whole-slide images, a foundation model is developed to provide representations for slide- and patient-level tasks. It is capable of performing clinical tasks and generating reports even in data-scarce scenarios, such as rare cancer diagnosis and survival prediction, without requiring further fine-tuning.

Nature, Published online: 05 November 2025; doi:10.1038/s41586-025-09716-2

The Fair Human-Centric Image Benchmark (FHIBE, pronounced ‘Feebee’)—an image dataset that implements best practices for consent, privacy, compensation, safety, diversity and utility—can be used responsibly as a fairness evaluation dataset for many human-centric computer vision applications.

arXiv:2510.09801v2 Announce Type: replace Abstract: LLM-powered agents are both a promising new technology and a source of complexity, where choices about models, tools, and prompting can affect their usefulness. While numerous benchmarks measure agent accuracy across domains, they mostly assume full automation, failing to represent the collaborative nature of real-world use cases. In this paper, we make two major steps towards the rigorous assessment of human-agent interactions. First, we propose PULSE, a framework for more efficient human-centric evaluation of agent designs, which comprises collecting user feedback, training an ML model to predict user satisfaction, and computing results by combining human satisfaction ratings with model-generated pseudo-labels. Second, we deploy the framework on a large-scale web platform built around the open-source software agent OpenHands, collecting in-the-wild usage data across over 15k users. We conduct case studies around how three agent design decisions -- choice of LLM backbone, planning strategy, and memory mechanisms -- impact developer satisfaction rates, yielding practical insights for software agent design. We also show how our framework can lead to more robust conclusions about agent design, reducing confidence intervals by 40% compared to a standard A/B test. Finally, we find substantial discrepancies between in-the-wild results and benchmark performance (e.g., the anti-correlation between results comparing claude-sonnet-4 and gpt-5), underscoring the limitations of benchmark-driven evaluation. Our findings provide guidance for evaluations of LLM agents with humans and identify opportunities for better agent designs.

arXiv:2511.00094v1 Announce Type: cross Abstract: Robotic systems have become integral to smart environments, enabling applications ranging from urban surveillance and automated agriculture to industrial automation. However, their effective operation in dynamic settings - such as smart cities and precision farming - is challenged by continuously evolving topographies and environmental conditions. Traditional control systems often struggle to adapt quickly, leading to inefficiencies or operational failures. To address this limitation, we propose a novel framework for autonomous and dynamic reconfiguration of robotic controllers using Digital Twin technology. Our approach leverages a virtual replica of the robot's operational environment to simulate and optimize movement trajectories in response to real-world changes. By recalculating paths and control parameters in the Digital Twin and deploying the updated code to the physical robot, our method ensures rapid and reliable adaptation without manual intervention. This work advances the integration of Digital Twins in robotics, offering a scalable solution for enhancing autonomy in smart, dynamic environments.

arXiv:2510.22814v2 Announce Type: replace Abstract: This article analyzes the existential risks artificial intelligence (AI) poses to humanity, tracing the trajectory from current AI to ultraintelligence. Drawing on Irving J. Good and Nick Bostrom's theoretical work, plus recent publications (AI 2027; If Anyone Builds It, Everyone Dies), it explores AGI and superintelligence. Considering machines' exponentially growing cognitive power and hypothetical IQs, it addresses the ethical and existential implications of an intelligence vastly exceeding humanity's, fundamentally alien. Human extinction may result not from malice, but from uncontrollable, indifferent cognitive superiority.

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:2510.26969v1 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:2410.22377v3 Announce Type: replace-cross Abstract: In recent years, spatio-temporal graph neural networks (GNNs) have attracted considerable interest in the field of time series analysis, due to their ability to capture, at once, dependencies among variables and across time points. The objective of this systematic literature review is hence to provide a comprehensive overview of the various modeling approaches and application domains of GNNs for time series classification and forecasting. A database search was conducted, and 366 papers were selected for a detailed examination of the current state-of-the-art in the field. This examination is intended to offer to the reader a comprehensive review of proposed models, links to related source code, available datasets, benchmark models, and fitting results. All this information is hoped to assist researchers in their studies. To the best of our knowledge, this is the first and broadest systematic literature review presenting a detailed comparison of results from current spatio-temporal GNN models applied to different domains. In its final part, this review discusses current limitations and challenges in the application of spatio-temporal GNNs, such as comparability, reproducibility, explainability, poor information capacity, and scalability. This paper is complemented by a GitHub repository at https://github.com/FlaGer99/SLR-Spatio-Temporal-GNN.git providing additional interactive tools to further explore the presented findings.