Functional correctness is critical for ensuring the reliability and security of network protocol implementations. Functional bugs, instances where implementations diverge from behaviors specified in RFC documents, can lead to severe consequences, including faulty routing, authentication bypasses, and service disruptions. Detecting these bugs requires deep semantic analysis across specification documents and source code, a task beyond the capabilities of traditional static analysis tools. This paper introduces RFCAudit, an autonomous agent that leverages large language models (LLMs) to detect functional bugs by checking conformance between network protocol implementations and their RFC specifications. Inspired by the human auditing procedure, RFCAudit comprises two key components: an indexing agent and a detection agent. The former hierarchically summarizes protocol code semantics, generating semantic indexes that enable the detection agent to narrow down the scanning scope. The latter employs demand-driven retrieval to iteratively collect additional relevant data structures and functions, eventually identifying potential inconsistencies with the RFC specifications effectively. We evaluate RFCAudit across six real-world network protocol implementations. RFCAudit identifies 47 functional bugs with 81.9% precision, of which 20 bugs have been confirmed or fixed by developers.

Receiver Operating Characteristic (ROC) and Precision-Recall (PR) curves are fundamental tools for evaluating machine learning classifiers, offering detailed insights into the trade-offs between true positive rate vs. false positive rate (ROC) or precision vs. recall (PR). However, in Federated Learning (FL) scenarios, where data is distributed across multiple clients, computing these curves is challenging due to privacy and communication constraints. Specifically, the server cannot access raw prediction scores and class labels, which are used to compute the ROC and PR curves in a centralized setting. In this paper, we propose a novel method for approximating ROC and PR curves in a federated setting by estimating quantiles of the prediction score distribution under distributed differential privacy. We provide theoretical bounds on the Area Error (AE) between the true and estimated curves, demonstrating the trade-offs between approximation accuracy, privacy, and communication cost. Empirical results on real-world datasets demonstrate that our method achieves high approximation accuracy with minimal communication and strong privacy guarantees, making it practical for privacy-preserving model evaluation in federated systems.

Controllers for structured LM reasoning (e.g., Chain-of-Thought, self-consistency, and Tree-of-Thoughts) often entangle what to try next with how to execute it, exposing only coarse global knobs and yielding brittle, compute-inefficient, and hard-to-audit behavior. We introduce Natural Language Edge Labelling (NLEL), a labeller-tuner overlay that attaches a free-form natural-language directive to each search edge and translates it into a schema-bounded control vector for decoding, search (branch quotas, exploration $β$), generation bundle size, retrieval mixtures, and verification passes. A labeller $Λ$ emits labels from the parent state and a compact context; a tuner $Ψ$ maps $(P, L, C)\to Π$, with strict schema validation and trust-region projection around safe defaults. Downstream selection remains ToT-style with score $S=μ+βσ$ and depth-annealed $β$. We show NLEL strictly generalizes CoT/ToT, prove an anytime-monotonicity property for top-$k$ selection under label-conditioned bundles, and bound selector shortfall by control-vector distortion, providing decision-relevant justification for guards like trust regions and verification passes. We instantiate $Ψ$ as a prompt-only JSON Parameter Emitter and preregister an evaluation on GSM8K, MATH (subset), StrategyQA, and ARC-Challenge with compute-aware reporting (success@compute, tokens-per-success) and ablations over $Λ$, $Ψ$, trust-region radius, and control quantization; preregistered forecasts anticipate accuracy gains at comparable token budgets and improved success@compute under constraints. NLEL offers an interpretable, model-agnostic interface that separates intent from execution for controllable, auditable LM inference.

Purpose: The FedSurg challenge was designed to benchmark the state of the art in federated learning for surgical video classification. Its goal was to assess how well current methods generalize to unseen clinical centers and adapt through local fine-tuning while enabling collaborative model development without sharing patient data. Methods: Participants developed strategies to classify inflammation stages in appendicitis using a preliminary version of the multi-center Appendix300 video dataset. The challenge evaluated two tasks: generalization to an unseen center and center-specific adaptation after fine-tuning. Submitted approaches included foundation models with linear probing, metric learning with triplet loss, and various FL aggregation schemes (FedAvg, FedMedian, FedSAM). Performance was assessed using F1-score and Expected Cost, with ranking robustness evaluated via bootstrapping and statistical testing. Results: In the generalization task, performance across centers was limited. In the adaptation task, all teams improved after fine-tuning, though ranking stability was low. The ViViT-based submission achieved the strongest overall performance. The challenge highlighted limitations in generalization, sensitivity to class imbalance, and difficulties in hyperparameter tuning in decentralized training, while spatiotemporal modeling and context-aware preprocessing emerged as promising strategies. Conclusion: The FedSurg Challenge establishes the first benchmark for evaluating FL strategies in surgical video classification. Findings highlight the trade-off between local personalization and global robustness, and underscore the importance of architecture choice, preprocessing, and loss design. This benchmarking offers a reference point for future development of imbalance-aware, adaptive, and robust FL methods in clinical surgical AI.

Large language models are rapidly transforming social science research by enabling the automation of labor-intensive tasks like data annotation and text analysis. However, LLM outputs vary significantly depending on the implementation choices made by researchers (e.g., model selection or prompting strategy). Such variation can introduce systematic biases and random errors, which propagate to downstream analyses and cause Type I (false positive), Type II (false negative), Type S (wrong sign), or Type M (exaggerated effect) errors. We call this phenomenon where configuration choices lead to incorrect conclusions LLM hacking. We find that intentional LLM hacking is strikingly simple. By replicating 37 data annotation tasks from 21 published social science studies, we show that, with just a handful of prompt paraphrases, virtually anything can be presented as statistically significant. Beyond intentional manipulation, our analysis of 13 million labels from 18 different LLMs across 2361 realistic hypotheses shows that there is also a high risk of accidental LLM hacking, even when following standard research practices. We find incorrect conclusions in approximately 31% of hypotheses for state-of-the-art LLMs, and in half the hypotheses for smaller language models. While higher task performance and stronger general model capabilities reduce LLM hacking risk, even highly accurate models remain susceptible. The risk of LLM hacking decreases as effect sizes increase, indicating the need for more rigorous verification of LLM-based findings near significance thresholds. We analyze 21 mitigation techniques and find that human annotations provide crucial protection against false positives. Common regression estimator correction techniques can restore valid inference but trade off Type I vs. Type II errors. We publish a list of practical recommendations to prevent LLM hacking.

Stroke is one of the leading causes of death globally, making early and accurate diagnosis essential for improving patient outcomes, particularly in emergency settings where timely intervention is critical. CT scans are the key imaging modality because of their speed, accessibility, and cost-effectiveness. This study proposed an artificial intelligence framework for multiclass stroke classification (ischemic, hemorrhagic, and no stroke) using CT scan images from a dataset provided by the Republic of Turkey's Ministry of Health. The proposed method adopted MaxViT, a state-of-the-art Vision Transformer, as the primary deep learning model for image-based stroke classification, with additional transformer variants (vision transformer, transformer-in-transformer, and ConvNext). To enhance model generalization and address class imbalance, we applied data augmentation techniques, including synthetic image generation. The MaxViT model trained with augmentation achieved the best performance, reaching an accuracy and F1-score of 98.00%, outperforming all other evaluated models and the baseline methods. The primary goal of this study was to distinguish between stroke types with high accuracy while addressing crucial issues of transparency and trust in artificial intelligence models. To achieve this, Explainable Artificial Intelligence (XAI) was integrated into the framework, particularly Grad-CAM++. It provides visual explanations of the model's decisions by highlighting relevant stroke regions in the CT scans and establishing an accurate, interpretable, and clinically applicable solution for early stroke detection. This research contributed to the development of a trustworthy AI-assisted diagnostic tool for stroke, facilitating its integration into clinical practice and enhancing access to timely and optimal stroke diagnosis in emergency departments, thereby saving more lives.

We study the problem active sequential hypothesis testing, also known as pure exploration: given a new task, the learner adaptively collects data from the environment to efficiently determine an underlying correct hypothesis. A classical instance of this problem is the task of identifying the best arm in a multi-armed bandit problem (a.k.a. BAI, Best-Arm Identification), where actions index hypotheses. Another important case is generalized search, a problem of determining the correct label through a sequence of strategically selected queries that indirectly reveal information about the label. In this work, we introduce In-Context Pure Exploration (ICPE), which meta-trains Transformers to map observation histories to query actions and a predicted hypothesis, yielding a model that transfers in-context. At inference time, ICPE actively gathers evidence on new tasks and infers the true hypothesis without parameter updates. Across deterministic, stochastic, and structured benchmarks, including BAI and generalized search, ICPE is competitive with adaptive baselines while requiring no explicit modeling of information structure. Our results support Transformers as practical architectures for general sequential testing.

Software is an essential component of research. However, little attention has been paid to it compared with that paid to research data. Recently, there has been an increase in efforts to acknowledge and highlight the importance of software in research activities. Structured metadata from platforms like bio.tools, Bioconductor, and Galaxy ToolShed offers valuable insights into research software in the Life Sciences. Although originally intended to support discovery and integration, this metadata can be repurposed for large-scale analysis of software practices. However, its quality and completeness vary across platforms, reflecting diverse documentation practices. To gain a comprehensive view of software development and sustainability, consolidating this metadata is necessary, but requires robust mechanisms to address its heterogeneity and scale. This article presents an evaluation of instruction-tuned large language models for the task of software metadata identity resolution, a critical step in assembling a cohesive collection of research software. Such a collection is the reference component for the Software Observatory at OpenEBench, a platform that aggregates metadata to monitor the FAIRness of research software in the Life Sciences. We benchmarked multiple models against a human-annotated gold standard, examined their behavior on ambiguous cases, and introduced an agreement-based proxy for high-confidence automated decisions. The proxy achieved high precision and statistical robustness, while also highlighting the limitations of current models and the broader challenges of automating semantic judgment in FAIR-aligned software metadata across registries and repositories.

Neural networks trained on real-world data often exhibit biases while simultaneously being vulnerable to privacy attacks aimed at extracting sensitive information. Despite extensive research on each problem individually, their intersection remains poorly understood. In this work, we investigate the privacy impact of spurious correlation bias. We introduce \emph{spurious privacy leakage}, a phenomenon in which spurious groups are significantly more vulnerable to privacy attacks than non-spurious groups. We observe that privacy disparity between groups increases in tasks with simpler objectives (e.g. fewer classes) due to spurious features. Counterintuitively, we demonstrate that spurious robust methods, designed to reduce spurious bias, fail to mitigate privacy disparity. Our analysis reveals that this occurs because robust methods can reduce reliance on spurious features for prediction, but do not prevent their memorization during training. Finally, we systematically compare the privacy of different model architectures trained with spurious data, demonstrating that, contrary to previous work, architectural choice can affect privacy evaluation.

T cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes is a central component of adaptive immunity, with implications for vaccine design, cancer immunotherapy, and autoimmune disease. While recent advances in machine learning have improved prediction of TCR-pMHC binding, the most effective approaches are black-box transformer models that cannot provide a rationale for predictions. Post-hoc explanation methods can provide insight with respect to the input but do not explicitly model biochemical mechanisms (e.g. "Explain-by-design" models (i.e., with architectural components that can be examined directly after training) have been explored in other domains, but have not been used for TCR-pMHC binding. We propose explainable model layers (TCR-EML) that can be incorporated into protein-language model backbones for TCR-pMHC modeling. Our approach uses prototype layers for amino acid residue contacts drawn from known TCR-pMHC binding mechanisms, enabling high-quality explanations for predicted TCR-pMHC binding. Experiments of our proposed method on large-scale datasets demonstrate competitive predictive accuracy and generalization, and evaluation on the TCR-XAI benchmark demonstrates improved explainability compared with existing approaches. For the adaptive immune system, T cells are essential for detecting and responding to antigens from pathogens such as viruses, bacteria, and cancer cells (Joglekar & Li, 2021), as well as in autoimmune contexts.