arXiv subjects

Nuno Moniz

Publications and source records attributed to Nuno Moniz.

At least 19 recordsLinked to original sources

arXiv2026

Getting Better at Working With You: Compiling User Corrections into Runtime Enforcement for Coding Agents

Interactive LLM agents are becoming part of daily work, but they do not reliably become easier to work with over time: a correction remembered in one session may still be violated in the next. We study this gap between preference access and preference compliance. In tasks derived from anonymized real-user friction cases, Mem0 memory still leaves 57.5% of applicable preference checks violated. We introduce Test-time Rule Acquisition and Compiled Enforcement (TRACE), a drop-in skill-layer pipeline for coding-agent runtimes that mines user corrections, rewrites them as atomic rules, and compiles them into runtime checks that must pass before an agent completes future tasks. Unlike runtime checks written ahead of time by developers, TRACE skills come from the user's own chat corrections. We evaluate TRACE with simulated user-in-the-loop experiments on ClawArena coding-agent tasks and MemoryArena-derived memory-intensive tasks. On ClawArena, TRACE reduces held-out preference violation from 100.0% to 37.6% on in-distribution tasks and from 100.0% to 2.0% on out-of-distribution tasks. On MemoryArena-derived tasks, TRACE reduces in-distribution violation from 100.0% to 60.5% while matching or exceeding the strongest memory baseline on task pass. These results suggest that compiling corrections into runtime enforcement can address a repeated-friction failure mode that memory alone does not reliably solve, reducing the need for users to restate the same correction across future sessions. Experiment code is available at https://github.com/YujunZhou/TRACE_exp, and the deployable skill is available at https://github.com/YujunZhou/tellonce.

cs.LG↗

arXiv2026

Evaluation Cards: An Interpretive Layer for AI Evaluation Reporting

AI evaluation results are produced at scale but reported inconsistently across leaderboards, model cards, benchmark papers, and company blogs. The cost is interpretive: readers cannot reliably compare results across sources, identify what a report omits, or trace an aggregate claim to its underlying evidence. Recent efforts address isolated components but leave three gaps: they cover only narrow slices of the evaluation lifecycle and do not compose into a single interpretable record; they specify static representations that do not differentiate the questions different stakeholders bring to the same evidence; and they remain proposals on paper, lacking the extraction infrastructure required for adoption at scale. We present \EvalCards{}, an operational reporting layer that composes benchmark metadata, evaluation run data, and model metadata into a unified record. We (1) derive a reporting schema from a structured review of 52 papers and 10 stakeholder interviews, (2) implement four interpretive signals (reproducibility, documentation completeness, provenance and risk, and score comparability), rendered through reader modes calibrated to research and non-research audiences, and (3) deploy a monitoring tool that applies \EvalCards{} across 5,816 models, 635 benchmarks, and 101,843 results, surfacing systematic gaps in current reporting practice.

cs.AI↗

arXiv2026

Genotype-Conditioned Molecular Generation via Evidence-Grounded Multi-Objective Latent Perturbation in Diffusion Models

Developing effective anticancer therapeutics remains challenging due to tumor heterogeneity and the absence of well-defined molecular targets across cancer subtypes. Generative models conditioned on cancer genotypes offer a promising avenue for personalized drug discovery, yet existing approaches lack explicit optimization for simultaneous sensitivity, synthesizability, and mechanistic binding plausibility. We present a latent-space optimization approach for a pretrained genotype-to-drug diffusion model, introducing a learnable perturbation over the molecular latent space optimized via gradient ascent to maximize a composite reward combining predicted drug sensitivity (AUC), drug-likeness (QED), and synthetic accessibility (SAS). Critically, biological realism is enforced by grounding both reward design and evaluation in experimentally-derived cancer cell line data and validated pharmacologic signals, anchoring candidate generation in real-world clinical evidence. Mechanistic consistency plausibility is further assessed by a multi-agent LLM pipeline grounded in the diffusion model's attention mechanism. Experiments across 15 cancer cell lines from three held-out evaluation sets demonstrate consistent and noticeable improvements over competing baselines in sensitivity, drug-likeness, synthesizability, and chemical validity.

cs.LG↗

arXiv2026

From Controlled to the Wild: Evaluation of Pentesting Agents for the Real-World

AI pentesting agents are increasingly credible as offensive security systems, but current benchmarks still provide limited guidance on which will perform best in real-world targets. Existing evaluation protocols assess and optimize for predefined goals such as capture-the-flag, remote code execution, exploit reproduction, or trajectory similarity, in simplified or narrow settings. These tools are valuable for measuring bounded capabilities, yet they do not adequately capture the complexity, open-ended exploration, and strategic decision-making required in realistic pentesting. In this paper, we present a practical evaluation protocol that shifts assessment from task completion to validated vulnerability discovery, allowing evaluation in sufficiently complex targets spanning multiple attack surfaces and vulnerability classes. The protocol combines structured ground-truth with LLM-based semantic matching to identify vulnerabilities, bipartite resolution to score findings under realistic ambiguity, continuous ground-truth maintenance, repeated and cumulative evaluation of stochastic agents, efficiency metrics, and reduced-suite selection for sustainable experimentation. This protocol extends the state of the art by enabling a more realistic, operationally informative comparison of AI pentesting agents. To enable reproducibility, we also release expert-annotated ground truth and code for the proposed evaluation protocol: https://github.com/ethiack/ethibench.

cs.AI↗

arXiv2026

Emergent Risks in Generative Multi-Agent Systems

Multi-agent systems composed of large generative models are rapidly moving from laboratory prototypes to real-world deployments, where they jointly plan, negotiate, and allocate shared resources to solve complex tasks. While such systems promise unprecedented scalability and autonomy, their collective interaction also gives rise to failure modes that cannot be reduced to individual agents. Understanding these emergent risks is therefore critical. Here, we present a pioneer study of such emergent multi-agent risk in workflows that involve competition over shared resources (e.g., computing resources or market share), sequential handoff collaboration (where downstream agents see only predecessor outputs), collective decision aggregation, and others. Across these settings, we observe that such group behaviors arise frequently across repeated trials and a wide range of interaction conditions, rather than as rare or pathological cases. In particular, phenomena such as collusion-like coordination and conformity emerge with non-trivial frequency under realistic resource constraints, communication protocols, and role assignments, mirroring well-known pathologies in human societies despite no explicit instruction. Moreover, these risks cannot be prevented by existing agent-level safeguards alone. These findings expose the dark side of intelligent multi-agent systems: a social intelligence risk where agent collectives, despite no instruction to do so, spontaneously reproduce familiar failure patterns from human societies.

cs.MA↗

arXiv2026

Alignment Risks from Capability-Seeking RL Training

While most AI alignment research focuses on preventing models from generating explicitly harmful content, a more subtle risk arises from capability-seeking RL training in vulnerable environments. We investigate whether language models, when trained with reinforcement learning (RL) in environments with implicit loopholes, can learn to exploit these flaws to maximize reward, even without being explicitly instructed to do so. To test this, we design a suite of four diverse "vulnerability games," each presenting a structural vulnerability related to context-conditional compliance, proxy metrics, reward tampering, and self-evaluation. Our experiments show that models often learn to exploit these vulnerabilities, discovering opportunistic strategies that increase reward while sometimes preserving or even improving standard task-performance metrics. More critically, we find that these exploitative strategies are not always narrow "tricks": they can transfer in structured but limited ways, propagate from a capable teacher model to other student models through SFT, and in several cases remain more persistent when learned through RL than when distilled through SFT. Our findings show that alignment risks from capability-seeking RL training can be difficult to detect with standard performance monitoring, suggesting that future AI safety work should extend beyond content moderation to auditing and securing training environments, reward mechanisms, and evaluation channels. Code is available at https://github.com/YujunZhou/Capability-seeking-RL-risk.

cs.LG↗

arXiv2025

From Verification Burden to Trusted Collaboration: Design Goals for LLM-Assisted Literature Reviews

Large Language Models (LLMs) are increasingly embedded in academic writing practices. Although numerous studies have explored how researchers employ these tools for scientific writing, their concrete implementation, limitations, and design challenges within the literature review process remain underexplored. In this paper, we report a user study with researchers across multiple disciplines to characterize current practices, benefits, and \textit{pain points} in using LLMs to investigate related work. We identified three recurring gaps: (i) lack of trust in outputs, (ii) persistent verification burden, and (iii) requiring multiple tools. This motivates our proposal of six design goals and a high-level framework that operationalizes them through improved related papers visualization, verification at every step, and human-feedback alignment with generation-guided explanations. Overall, by grounding our work in the practical, day-to-day needs of researchers, we designed a framework that addresses these limitations and models real-world LLM-assisted writing, advancing trust through verifiable actions and fostering practical collaboration between researchers and AI systems.

cs.HC↗

arXiv2025

SPECTRA: Spectral Domain-Aware Graph Generation for Imbalanced Molecular Property Regression

Molecular property regression struggles with cases in chemically relevant target ranges that are underrepresented in datasets. Standard average error minimization approaches underperform in these highly relevant cases, and oversampling approaches lead to meaningless molecular representations. In this paper, we propose SPECTRA, a spectral, domain-aware graph generation method designed to improve the prediction of underrepresented but relevant molecular property values. It combines a rarity-aware budgeting scheme to focus generation where data are scarce, target-neighbors graph alignment to establish structural correspondence, and interpolation of Laplacian spectra, node features, and targets. Coupled with spectral GNN using edge-aware Chebyshev convolutions, SPECTRA shows its effectiveness in property prediction benchmarks with competitive performance over leading state-of-the-art methods in relevant target ranges, while requiring ~4x less computational time.

cs.LG↗

arXiv2025

LLMs4All: A Review of Large Language Models Across Academic Disciplines

Cutting-edge Artificial Intelligence (AI) techniques keep reshaping our view of the world. For example, Large Language Models (LLMs) based applications such as ChatGPT have shown the capability of generating human-like conversation on extensive topics. Due to the impressive performance on a variety of language-related tasks (e.g., open-domain question answering, translation, and document summarization), one can envision the far-reaching impacts that can be brought by the LLMs with broader real-world applications (e.g., customer service, education and accessibility, and scientific discovery). Inspired by their success, this paper will offer an overview of state-of-the-art LLMs and their integration into a wide range of academic disciplines, including: (1) arts, letters, and law (e.g., history, philosophy, political science, arts and architecture, law), (2) economics and business (e.g., finance, economics, accounting, marketing), and (3) science and engineering (e.g., mathematics, physics and mechanical engineering, chemistry and chemical engineering, life sciences and bioengineering, earth sciences and civil engineering, computer science and electrical engineering). Integrating humanity and technology, in this paper, we will explore how LLMs are shaping research and practice in these fields, while also discussing key limitations, open challenges, and future directions in the era of generative AI. The review of how LLMs are engaged across disciplines-along with key observations and insights-can help researchers and practitioners interested in exploiting LLMs to advance their works in diverse real-world applications.

cs.CL↗

arXiv2025

Spectral Manifold Harmonization for Graph Imbalanced Regression

Graph-structured data is ubiquitous in scientific domains, where models often face imbalanced learning settings. In imbalanced regression, domain preferences focus on specific target value ranges that represent the most scientifically valuable cases; however, we observe a significant lack of research regarding this challenge. In this paper, we present Spectral Manifold Harmonization (SMH), a novel approach to address imbalanced regression challenges on graph-structured data by generating synthetic graph samples that preserve topological properties while focusing on the most relevant target distribution regions. Conventional methods fail in this context because they either ignore graph topology in case generation or do not target specific domain ranges, resulting in models biased toward average target values. Experimental results demonstrate the potential of SMH on chemistry and drug discovery benchmark datasets, showing consistent improvements in predictive performance for target domain ranges. Code is available at https://github.com/brendacnogueira/smh-graph-imbalance.git.

cs.LG↗

arXiv2025

Context Attribution with Multi-Armed Bandit Optimization

Understanding which parts of the retrieved context contribute to a large language model's generated answer is essential for building interpretable and trustworthy retrieval-augmented generation. We propose a novel framework that formulates context attribution as a combinatorial multi-armed bandit problem. We utilize Linear Thompson Sampling to efficiently identify the most influential context segments while minimizing the number of model queries. Our reward function leverages token log-probabilities to measure how well a subset of segments supports the original response, making it applicable to both open-source and black-box API-based models. Unlike SHAP and other perturbation-based methods that sample subsets uniformly, our approach adaptively prioritizes informative subsets based on posterior estimates of segment relevance, reducing computational costs. Experiments on multiple QA benchmarks demonstrate that our method achieves up to 30\% reduction in model queries while matching or exceeding the attribution quality of existing approaches. Our code is publicly available at https://github.com/pd90506/camab.

cs.AI↗

arXiv2025

Intersectional Divergence: Measuring Fairness in Regression

Fairness in machine learning research is commonly framed in the context of classification tasks, leaving critical gaps in regression. In this paper, we propose a novel approach to measure intersectional fairness in regression tasks, going beyond the focus on single protected attributes from existing work to consider combinations of all protected attributes. Furthermore, we contend that it is insufficient to measure the average error of groups without regard for imbalanced domain preferences. Accordingly, we propose Intersectional Divergence (ID) as the first fairness measure for regression tasks that 1) describes fair model behavior across multiple protected attributes and 2) differentiates the impact of predictions in target ranges most relevant to users. We extend our proposal demonstrating how ID can be adapted into a loss function, IDLoss, that satisfies convergence guarantees and has piecewise smooth properties that enable practical optimization. Through an extensive experimental evaluation, we demonstrate how ID allows unique insights into model behavior and fairness, and how incorporating IDLoss into optimization can considerably improve single-attribute and intersectional model fairness while maintaining a competitive balance in predictive performance.

cs.LG↗

arXiv2024

NGQA: A Nutritional Graph Question Answering Benchmark for Personalized Health-aware Nutritional Reasoning

Diet plays a critical role in human health, yet tailoring dietary reasoning to individual health conditions remains a major challenge. Nutrition Question Answering (QA) has emerged as a popular method for addressing this problem. However, current research faces two critical limitations. On one hand, the absence of datasets involving user-specific medical information severely limits \textit{personalization}. This challenge is further compounded by the wide variability in individual health needs. On the other hand, while large language models (LLMs), a popular solution for this task, demonstrate strong reasoning abilities, they struggle with the domain-specific complexities of personalized healthy dietary reasoning, and existing benchmarks fail to capture these challenges. To address these gaps, we introduce the Nutritional Graph Question Answering (NGQA) benchmark, the first graph question answering dataset designed for personalized nutritional health reasoning. NGQA leverages data from the National Health and Nutrition Examination Survey (NHANES) and the Food and Nutrient Database for Dietary Studies (FNDDS) to evaluate whether a food is healthy for a specific user, supported by explanations of the key contributing nutrients. The benchmark incorporates three question complexity settings and evaluates reasoning across three downstream tasks. Extensive experiments with LLM backbones and baseline models demonstrate that the NGQA benchmark effectively challenges existing models. In sum, NGQA addresses a critical real-world problem while advancing GraphQA research with a novel domain-specific benchmark.

cs.CL↗

arXiv2024

Class-Aware Contrastive Optimization for Imbalanced Text Classification

The unique characteristics of text data make classification tasks a complex problem. Advances in unsupervised and semi-supervised learning and autoencoder architectures addressed several challenges. However, they still struggle with imbalanced text classification tasks, a common scenario in real-world applications, demonstrating a tendency to produce embeddings with unfavorable properties, such as class overlap. In this paper, we show that leveraging class-aware contrastive optimization combined with denoising autoencoders can successfully tackle imbalanced text classification tasks, achieving better performance than the current state-of-the-art. Concretely, our proposal combines reconstruction loss with contrastive class separation in the embedding space, allowing a better balance between the truthfulness of the generated embeddings and the model's ability to separate different classes. Compared with an extensive set of traditional and state-of-the-art competing methods, our proposal demonstrates a notable increase in performance across a wide variety of text datasets.

cs.CL↗

arXiv2024

LabSafety Bench: Benchmarking LLMs on Safety Issues in Scientific Labs

Artificial Intelligence (AI) is revolutionizing scientific research, yet its growing integration into laboratory environments presents critical safety challenges. Large language models (LLMs) and vision language models (VLMs) now assist in experiment design and procedural guidance, yet their "illusion of understanding" may lead researchers to overtrust unsafe outputs. Here we show that current models remain far from meeting the reliability needed for safe laboratory operation. We introduce LabSafety Bench, a comprehensive benchmark that evaluates models on hazard identification, risk assessment, and consequence prediction across 765 multiple-choice questions and 404 realistic lab scenarios, encompassing 3,128 open-ended tasks. Evaluations on 19 advanced LLMs and VLMs show that no model evaluated on hazard identification surpasses 70% accuracy. While proprietary models perform well on structured assessments, they do not show a clear advantage in open-ended reasoning. These results underscore the urgent need for specialized safety evaluation frameworks before deploying AI systems in real laboratory settings.

cs.CL↗

arXiv2024

BenchmarkCards: Standardized Documentation for Large Language Model Benchmarks

Large language models (LLMs) are powerful tools capable of handling diverse tasks. Comparing and selecting appropriate LLMs for specific tasks requires systematic evaluation methods, as models exhibit varying capabilities across different domains. However, finding suitable benchmarks is difficult given the many available options. This complexity not only increases the risk of benchmark misuse and misinterpretation but also demands substantial effort from LLM users, seeking the most suitable benchmarks for their specific needs. To address these issues, we introduce \texttt{BenchmarkCards}, an intuitive and validated documentation framework that standardizes critical benchmark attributes such as objectives, methodologies, data sources, and limitations. Through user studies involving benchmark creators and users, we show that \texttt{BenchmarkCards} can simplify benchmark selection and enhance transparency, facilitating informed decision-making in evaluating LLMs. Data & Code: https://github.com/SokolAnn/BenchmarkCards

cs.CL↗

arXiv2024

Justice or Prejudice? Quantifying Biases in LLM-as-a-Judge

LLM-as-a-Judge has been widely utilized as an evaluation method in various benchmarks and served as supervised rewards in model training. However, despite their excellence in many domains, potential issues are under-explored, undermining their reliability and the scope of their utility. Therefore, we identify 12 key potential biases and propose a new automated bias quantification framework-CALM-which systematically quantifies and analyzes each type of bias in LLM-as-a-Judge by using automated and principle-guided modification. Our experiments cover multiple popular language models, and the results indicate that while advanced models have achieved commendable overall performance, significant biases persist in certain specific tasks. Empirical results suggest that there remains room for improvement in the reliability of LLM-as-a-Judge. Moreover, we also discuss the explicit and implicit influence of these biases and give some suggestions for the reliable application of LLM-as-a-Judge. Our work highlights the need for stakeholders to address these issues and remind users to exercise caution in LLM-as-a-Judge applications.

cs.CL↗

arXiv2024

Empowering Open Data Sharing for Social Good: A Privacy-Aware Approach

The Covid-19 pandemic has affected the world at multiple levels. Data sharing was pivotal for advancing research to understand the underlying causes and implement effective containment strategies. In response, many countries have promoted the availability of daily cases to support research initiatives, fostering collaboration between organisations and making such data available to the public through open data platforms. Despite the several advantages of data sharing, one of the major concerns before releasing health data is its impact on individuals' privacy. Such a sharing process should be based on state-of-the-art methods in Data Protection by Design and by Default. In this paper, we use a data set related to Covid-19 cases in the second largest hospital in Portugal to show how it is feasible to ensure data privacy while improving the quality and maintaining the utility of the data. Our goal is to demonstrate how knowledge exchange in multidisciplinary teams of healthcare practitioners, data privacy, and data science experts is crucial to co-developing strategies that ensure high utility of de-identified data.

cs.DB↗