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Evaluating Control Protocols for Untrusted AI Agents

arXiv:2511.02997v1 Announce Type: new Abstract: As AI systems become more capable and widely deployed as agents, ensuring their safe operation becomes critical. AI control offers one approach to mitigating the risk from untrusted AI agents by monitoring their actions and intervening or auditing when necessary. Evaluating the safety of these protocols requires understanding both their effectiveness against current attacks and their robustness to adaptive adversaries. In this work, we systematically evaluate a range of control protocols in SHADE-Arena, a dataset of diverse agentic environments. First, we evaluate blue team protocols, including deferral to trusted models, resampling, and deferring on critical actions, against a default attack policy. We find that resampling for incrimination and deferring on critical actions perform best, increasing safety from 50% to 96%. We then iterate on red team strategies against these protocols and find that attack policies with additional affordances, such as knowledge of when resampling occurs or the ability to simulate monitors, can substantially improve attack success rates against our resampling strategy, decreasing safety to 17%. However, deferring on critical actions is highly robust to even our strongest red team strategies, demonstrating the importance of denying attack policies access to protocol internals.
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No-Human in the Loop: Agentic Evaluation at Scale for Recommendation

arXiv:2511.03051v1 Announce Type: new Abstract: Evaluating large language models (LLMs) as judges is increasingly critical for building scalable and trustworthy evaluation pipelines. We present ScalingEval, a large-scale benchmarking study that systematically compares 36 LLMs, including GPT, Gemini, Claude, and Llama, across multiple product categories using a consensus-driven evaluation protocol. Our multi-agent framework aggregates pattern audits and issue codes into ground-truth labels via scalable majority voting, enabling reproducible comparison of LLM evaluators without human annotation. Applied to large-scale complementary-item recommendation, the benchmark reports four key findings: (i) Anthropic Claude 3.5 Sonnet achieves the highest decision confidence; (ii) Gemini 1.5 Pro offers the best overall performance across categories; (iii) GPT-4o provides the most favorable latency-accuracy-cost tradeoff; and (iv) GPT-OSS 20B leads among open-source models. Category-level analysis shows strong consensus in structured domains (Electronics, Sports) but persistent disagreement in lifestyle categories (Clothing, Food). These results establish ScalingEval as a reproducible benchmark and evaluation protocol for LLMs as judges, with actionable guidance on scaling, reliability, and model family tradeoffs.
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Explaining Decisions in ML Models: a Parameterized Complexity Analysis (Part I)

arXiv:2511.03545v1 Announce Type: new Abstract: This paper presents a comprehensive theoretical investigation into the parameterized complexity of explanation problems in various machine learning (ML) models. Contrary to the prevalent black-box perception, our study focuses on models with transparent internal mechanisms. We address two principal types of explanation problems: abductive and contrastive, both in their local and global variants. Our analysis encompasses diverse ML models, including Decision Trees, Decision Sets, Decision Lists, Boolean Circuits, and ensembles thereof, each offering unique explanatory challenges. This research fills a significant gap in explainable AI (XAI) by providing a foundational understanding of the complexities of generating explanations for these models. This work provides insights vital for further research in the domain of XAI, contributing to the broader discourse on the necessity of transparency and accountability in AI systems.
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FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equation

arXiv:2511.03113v1 Announce Type: cross Abstract: Computational antibody design holds immense promise for therapeutic discovery, yet existing generative models are fundamentally limited by two core challenges: (i) a lack of dynamical consistency, which yields physically implausible structures, and (ii) poor generalization due to data scarcity and structural bias. We introduce FP-AbDiff, the first antibody generator to enforce Fokker-Planck Equation (FPE) physics along the entire generative trajectory. Our method minimizes a novel FPE residual loss over the mixed manifold of CDR geometries (R^3 x SO(3)), compelling locally-learned denoising scores to assemble into a globally coherent probability flow. This physics-informed regularizer is synergistically integrated with deep biological priors within a state-of-the-art SE(3)-equivariant diffusion framework. Rigorous evaluation on the RAbD benchmark confirms that FP-AbDiff establishes a new state-of-the-art. In de novo CDR-H3 design, it achieves a mean Root Mean Square Deviation of 0.99 {\AA} when superposing on the variable region, a 25% improvement over the previous state-of-the-art model, AbX, and the highest reported Contact Amino Acid Recovery of 39.91%. This superiority is underscored in the more challenging six-CDR co-design task, where our model delivers consistently superior geometric precision, cutting the average full-chain Root Mean Square Deviation by ~15%, and crucially, achieves the highest full-chain Amino Acid Recovery on the functionally dominant CDR-H3 loop (45.67%). By aligning generative dynamics with physical laws, FP-AbDiff enhances robustness and generalizability, establishing a principled approach for physically faithful and functionally viable antibody design.
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LGM: Enhancing Large Language Models with Conceptual Meta-Relations and Iterative Retrieval

arXiv:2511.03214v1 Announce Type: cross Abstract: Large language models (LLMs) exhibit strong semantic understanding, yet struggle when user instructions involve ambiguous or conceptually misaligned terms. We propose the Language Graph Model (LGM) to enhance conceptual clarity by extracting meta-relations-inheritance, alias, and composition-from natural language. The model further employs a reflection mechanism to validate these meta-relations. Leveraging a Concept Iterative Retrieval Algorithm, these relations and related descriptions are dynamically supplied to the LLM, improving its ability to interpret concepts and generate accurate responses. Unlike conventional Retrieval-Augmented Generation (RAG) approaches that rely on extended context windows, our method enables large language models to process texts of any length without the need for truncation. Experiments on standard benchmarks demonstrate that the LGM consistently outperforms existing RAG baselines.
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Hybrid Fact-Checking that Integrates Knowledge Graphs, Large Language Models, and Search-Based Retrieval Agents Improves Interpretable Claim Verification

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.
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REFA: Reference Free Alignment for multi-preference optimization

arXiv:2412.16378v4 Announce Type: replace-cross Abstract: To mitigate reward hacking from response verbosity, modern preference optimization methods are increasingly adopting length normalization (e.g., SimPO, ORPO, LN-DPO). While effective against this bias, we demonstrate that length normalization itself introduces a failure mode: the URSLA shortcut. Here models learn to satisfy the alignment objective by prematurely truncating low-quality responses rather than learning from their semantic content. To address this, we introduce REFA, a new alignment framework that proposes probabilistic control on a structural token that controls termination. Our core innovation is a new class of regularizers that operate directly on the probability of the End-of-Sequence (EOS) token, a previously unexploited control lever. This token-level intervention provides a principled solution to the URSLA shortcut, ensuring genuine quality improvements. Furthermore, it unlocks a versatile mechanism for managing the alignment-efficiency tradeoff, enabling practitioners to fine-tune models that adhere to specific token budgets. Empirically, REFA achieves a 60.29% win rate and a 52.17% length-controlled win rate on AlpacaEval2 with Llama-3-8B-Instruct, demonstrating the power of our token-level control paradigm.
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Harnessing multi-omics approaches to decipher tumor evolution and improve diagnosis and therapy in lung cancer

Biomark Res. 2025 Nov 5;13(1):140. doi: 10.1186/s40364-025-00859-y.

ABSTRACT

With the advancement of novel technologies such as whole-genome sequencing, single-cell sequencing, and spatial transcriptomics, single-omics analyses have already promoted the research of tumorigenesis as well as development and have partly elucidated the evolutionary processes of lung cancer. However, it is still difficult to distinguish these confounding features via single dimensional approaches due to the complexity, heterogeneity and cell-cell interactions with the immune microenvironment in lung cancer. Multi-omics approaches provide a holistic framework for constructing detailed tumor ecosystem landscapes, thereby facilitating the development of a more robust classification system for precision diagnosis and treatment, and aiding in the discovery of novel cancer biomarkers. In this review, we summarize the potential and applications of multi-omics approaches in characterizing intratumor heterogeneity and the tumor microenvironment throughout the course of lung cancer development. By further discussing the discovery and application of diagnostic and therapeutic biomarkers across precancerous lesions, early-stage lung cancer, tumor progression, metastasis, and therapy resistance, we outline the current challenges and future prospects of using multi-omics to identify reliable biomarkers. Moreover, we emphasize that integrative multi-omics models hold great promise for elucidating the complex interactions within the lung cancer ecosystem, thereby contributing to improved diagnostic accuracy, optimized therapeutic strategies, and better patient outcomes.

PMID:41194170 | PMC:PMC12590604 | DOI:10.1186/s40364-025-00859-y

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Improving dataset transparency in dermatologic Artificial Intelligence using a dataset nutrition label

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.
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Evaluating clinical AI summaries with large language models as judges

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
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