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.

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.

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.

arXiv:2511.02842v1 Announce Type: cross Abstract: Many organisations pursue digital transformation to enhance operational efficiency, reduce manual efforts, and optimise processes by automation and digital tools. To achieve this, a comprehensive understanding of their unique needs is required. However, traditional methods, such as expert interviews, while effective, face several challenges, including scheduling conflicts, resource constraints, inconsistency, etc. To tackle these issues, we investigate the use of a Large Language Model (LLM)-powered chatbot to acquire organisations' digital transformation needs. Specifically, the chatbot integrates workflow-based instruction with LLM's planning and reasoning capabilities, enabling it to function as a virtual expert and conduct interviews. We detail the chatbot's features and its implementation. Our preliminary evaluation indicates that the chatbot performs as designed, effectively following predefined workflows and supporting user interactions with areas for improvement. We conclude by discussing the implications of employing chatbots to elicit user information, emphasizing their potential and limitations.

arXiv:2511.02864v1 Announce Type: cross Abstract: AlphaEvolve is a generic evolutionary coding agent that combines the generative capabilities of LLMs with automated evaluation in an iterative evolutionary framework that proposes, tests, and refines algorithmic solutions to challenging scientific and practical problems. In this paper we showcase AlphaEvolve as a tool for autonomously discovering novel mathematical constructions and advancing our understanding of long-standing open problems. To demonstrate its breadth, we considered a list of 67 problems spanning mathematical analysis, combinatorics, geometry, and number theory. The system rediscovered the best known solutions in most of the cases and discovered improved solutions in several. In some instances, AlphaEvolve is also able to generalize results for a finite number of input values into a formula valid for all input values. Furthermore, we are able to combine this methodology with Deep Think and AlphaProof in a broader framework where the additional proof-assistants and reasoning systems provide automated proof generation and further mathematical insights. These results demonstrate that large language model-guided evolutionary search can autonomously discover mathematical constructions that complement human intuition, at times matching or even improving the best known results, highlighting the potential for significant new ways of interaction between mathematicians and AI systems. We present AlphaEvolve as a powerful new tool for mathematical discovery, capable of exploring vast search spaces to solve complex optimization problems at scale, often with significantly reduced requirements on preparation and computation time.

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.

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.

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.

arXiv:2511.03354v1 Announce Type: cross Abstract: Generative artificial intelligence (GenAI) has become a transformative approach in bioinformatics that often enables advancements in genomics, proteomics, transcriptomics, structural biology, and drug discovery. To systematically identify and evaluate these growing developments, this review proposed six research questions (RQs), according to the preferred reporting items for systematic reviews and meta-analysis methods. The objective is to evaluate impactful GenAI strategies in methodological advancement, predictive performance, and specialization, and to identify promising approaches for advanced modeling, data-intensive discovery, and integrative biological analysis. RQ1 highlights diverse applications across multiple bioinformatics subfields (sequence analysis, molecular design, and integrative data modeling), which demonstrate superior performance over traditional methods through pattern recognition and output generation. RQ2 reveals that adapted specialized model architectures outperformed general-purpose models, an advantage attributed to targeted pretraining and context-aware strategies. RQ3 identifies significant benefits in the bioinformatics domains, focusing on molecular analysis and data integration, which improves accuracy and reduces errors in complex analysis. RQ4 indicates improvements in structural modeling, functional prediction, and synthetic data generation, validated by established benchmarks. RQ5 suggests the main constraints, such as the lack of scalability and biases in data that impact generalizability, and proposes future directions focused on robust evaluation and biologically grounded modeling. RQ6 examines that molecular datasets (such as UniProtKB and ProteinNet12), cellular datasets (such as CELLxGENE and GTEx) and textual resources (such as PubMedQA and OMIM) broadly support the training and generalization of GenAI models.

arXiv:2412.08179v2 Announce Type: replace-cross Abstract: Financial analysis relies heavily on the interpretation of earnings reports to assess company performance and guide decision-making. Traditional methods for generating such analyses demand significant financial expertise and are often time-consuming. With the rapid advancement of Large Language Models (LLMs), domain-specific adaptations have emerged for financial tasks such as sentiment analysis and entity recognition. This paper introduces RAG-IT (Retrieval-Augmented Instruction Tuning), a novel framework designed to automate the generation of earnings report analyses through an LLM fine-tuned specifically for the financial domain. Our approach integrates retrieval augmentation with instruction-based fine-tuning to enhance factual accuracy, contextual relevance, and domain adaptability. We construct a comprehensive financial instruction dataset derived from extensive financial documents and earnings reports to guide the LLM's adaptation to specialized financial reasoning. Experimental results demonstrate that RAG-IT outperforms general-purpose open-source models and achieves performance comparable to commercial systems like GPT-3.5 on financial report generation tasks. This research highlights the potential of retrieval-augmented instruction tuning to streamline and elevate financial analysis automation, advancing the broader field of intelligent financial reporting.

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.

arXiv:2508.03159v2 Announce Type: replace-cross Abstract: Drug toxicity remains a major challenge in pharmaceutical development. Recent machine learning models have improved in silico toxicity prediction, but their reliance on annotated data and lack of interpretability limit their applicability. This limits their ability to capture organ-specific toxicities driven by complex biological mechanisms. Large language models (LLMs) offer a promising alternative through step-by-step reasoning and integration of textual data, yet prior approaches lack biological context and transparent rationale. To address this issue, we propose CoTox, a novel framework that integrates LLM with chain-of-thought (CoT) reasoning for multi-toxicity prediction. CoTox combines chemical structure data, biological pathways, and gene ontology (GO) terms to generate interpretable toxicity predictions through step-by-step reasoning. Using GPT-4o, we show that CoTox outperforms both traditional machine learning and deep learning model. We further examine its performance across various LLMs to identify where CoTox is most effective. Additionally, we find that representing chemical structures with IUPAC names, which are easier for LLMs to understand than SMILES, enhances the model's reasoning ability and improves predictive performance. To demonstrate its practical utility in drug development, we simulate the treatment of relevant cell types with drug and incorporated the resulting biological context into the CoTox framework. This approach allow CoTox to generate toxicity predictions aligned with physiological responses, as shown in case study. This result highlights the potential of LLM-based frameworks to improve interpretability and support early-stage drug safety assessment. The code and prompt used in this work are available at https://github.com/dmis-lab/CoTox.

arXiv:2509.18293v2 Announce Type: replace-cross Abstract: Detecting hateful content is a challenging and important problem. Automated tools, like machine-learning models, can help, but they require continuous training to adapt to the ever-changing landscape of social media. In this work, we evaluate eight open-source LLMs' capability to detect antisemitic content, specifically leveraging in-context definition. We also study how LLMs understand and explain their decisions given a moderation policy as a guideline. First, we explore various prompting techniques and design a new CoT-like prompt, Guided-CoT, and find that injecting domain-specific thoughts increases performance and utility. Guided-CoT handles the in-context policy well, improving performance and utility by reducing refusals across all evaluated models, regardless of decoding configuration, model size, or reasoning capability. Notably, Llama 3.1 70B outperforms fine-tuned GPT-3.5. Additionally, we examine LLM errors and introduce metrics to quantify semantic divergence in model-generated rationales, revealing notable differences and paradoxical behaviors among LLMs. Our experiments highlight the differences observed across LLMs' utility, explainability, and reliability. Code and resources available at: https://github.com/idramalab/quantify-llm-explanations

Nature Biotechnology, Published online: 06 November 2025; doi:10.1038/s41587-025-02901-8

Big pharma shares its machine learning models with biotechs, but awaits definitive data on success of artificial intelligence-generated drugs.

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.

Generating drug-like molecules that specifically bind to target proteins remains a resource-intensive challenge. Many studies focus on designing effective networks to accurately extract relevant features from target proteins, which can be challenging. Additionally, most target-specific molecule generation methods based on diffusion models process the 3D information of molecules and proteins, necessitating the maintenance of equivariance at each step. This paper proposes TarMGDif, a novel target-specific molecular graph generation model based on a discrete denoising diffusion framework which could handle graph structure. TarMGDif incorporates a global features embedding network that captures ring features to generate chemically valid rings, while the time step of the diffusion model is also learned through this network. Besides, a novel node-to-edge attention module is proposed to capture dependencies between nodes and edges. Extensive experiments conducted on three datasets demonstrate the advanced performance of TarMGDif. Furthermore, through transfer learning, the model generates molecules specifically targeting the DRD2 protein, with the newly designed molecules exhibiting pharmacological properties similar to known inhibitors. These findings underscore the potential of TarMGDif in facilitating the efficient design of target-specific drug-like molecules.

Precise medical image segmentation is important for automating diagnosis and treatment planning in healthcare. While images present the most significant information for segmenting organs using deep learning models, text reports also provide complementary details that can be leveraged to improve segmentation precision. Performance improvement depends on the proper utilization of text reports and the corresponding images. Most attention modules focus on single-modality computation of spatial, channel, or pixel-level attention. They are ineffective in cross-modal alignment, raising issues in multi-modal scenarios. This study addresses these gaps by presenting a text-assisted vision (TAV) model for medical image segmentation with a novel attention computation module named tri-guided attention module (TGAM). TGAM computes visual-visual, language-language, and language-visual attention, enabling the model to understand the important features and correlation between images and medical notes. This module helps the model identify the relevant features within images, text annotations, and text annotations to visual interactions. We incorporate an attention gate (AG) that modulates the influence of TGAM, ensuring it does not overflow the encoded features with irrelevant or redundant information, while maintaining their uniqueness. We evaluated the performance of TAV on two popular datasets containing images and corresponding text annotations. We find TAV to be a new state-of-the-art model, as it improves the performance by 2-7% compared to other models. Extensive experiments were performed to demonstrate the effectiveness of each component of the proposed model.

Automated ultrasound (US) image analysis is hindered by challenges stemming from low resolution, noise, and non-uniform grayscale distribution, which compromise image quality. While many existing studies address these issues using super-resolution (SR) techniques, they often focus exclusively on SR without considering downstream tasks or tailoring to the unique characteristics of US images. In this work, we propose ZSG-Net, a zero-shot super-resolution-guided network, designed to bridge the gap between US image quality enhancement and its benefits in segmentation and classification. First, we introduce a zero-shot self-supervised cycle generative adversarial network (ZSCycle-GAN), tailored to the unique characteristics of US images, to perform SR while preserving critical structural details. Unlike conventional SR methods that focus solely on image enhancement, ZSCycle-GAN is designed to optimize downstream tasks. Second, we adopt a zero-shot self-supervised learning strategy, eliminating the reliance on labeled data and addressing the scarcity of annotated medical imaging datasets. Third, we incorporate a random image degradation (RID) strategy to expand the degradation space for clinical US images, enabling robust learning of diverse quality variations. Extensive experiments on three US image datasets validate the effectiveness of the proposed model. Results demonstrate superior performance in segmentation and classification tasks compared to existing approaches, underscoring the potential of our method to improve US image analysis in clinical settings.

Alzheimer’s disease (AD) is an incurable neurodegenerative disorder characterized by progressive cognitive and functional decline. Consequently, early diagnosis and accurate prediction of disease progression are of paramount importance and inherently complex, necessitating the integration of multi-modal data. While existing methods are typically task-specific and lack generalization, we present ADFound, the first multi-modal foundation model for AD capable of simultaneously addressing diagnosis and prognosis tasks through a unified framework. ADFound leverages a substantial amount of unlabeled 3D multi-modal neuroimaging, including paired and unpaired data, to achieve its objectives. Specifically, ADFound is developed upon the Multi-modal Vim encoder by Vision Mamba block to capture long-range dependencies inherent in 3D multi-modal medical images. To efficiently pre-train ADFound on unlabeled paired and upaired multi-modal neuroimaging data, we proposed a novel self-supervised learning framework that integrates multi-modal masked autoencoder (MAE) and contrastive learning. The multi-modal MAE aims to learn local relations among modalities by reconstructing images with unmasked image patches. Additionally, we introduce a Dual Contrastive Learning for Multi-modal Data to enhance the discriminative capabilities of multi-modal representations from intra-modal and inter-modal perspectives. Our experiments demonstrate that ADFound outperforms state-of-the-art methods across a wide range of downstream tasks relevant to the diagnosis and prognosis of AD. Furthermore, the results indicate that our foundation model can be extended to more modalities, such as non-image data, showing its versatility.

Text classification is a critical task for understanding the knowledge behind text, especially in medical text. In this paper, we propose a medical graph diffusion model, named the MGD model, for the medical text classification task. To model more structural relationships within a document, our MGD model constructs a text heterogeneous graph to represent word-level, sentence-level, and word-sentence-level structural relationships. To overcome the limitation of only considering direct neighbors, a graph diffusion convolution is employed to reconstruct the text heterogeneous graph. Subsequently, a heterogeneous graph convolutional network and a multilayer perceptron are used to complete the medical text classification task. To evaluate the performance of our MGD model, various text classification benchmarks, including long text standard benchmarks, short text standard benchmarks, and medical text benchmarks, are used to comprehensively assess the effectiveness and robustness of our MGD model. Compared with other representative baselines, it achieved notable improvements in both Accuracy and F1 score evaluation metrics. Ablation experiment results further demonstrated that the construction of heterogeneous graphs and the use of diffusion graph convolutional networks significantly impact the performance of our MGD model.