OpenRaiser/Intern-Atlas huggingface dataset:
Neural Operator based Reinforcement Learning for Control of first-order PDEs with Spatially-Varying State Delay
Venue: arXiv cs.AI 2025
Year: 2025

Control of distributed parameter systems affected by delays is a challenging task, particularly when the delays depend on spatial variables. The idea of integrating analytical control theory with learning-based control within a unified control scheme is becoming increasingly promising and advantageous. In this paper, we address the problem of controlling an unstable first-order hyperbolic PDE with spatially-varying delays by combining PDE backstepping control strategies and deep reinforcement learning (RL). To eliminate the assumption on the delay function required for the backstepping design, we propose a soft actor-critic (SAC) architecture incorporating a DeepONet to approximate the backstepping controller. The DeepONet extracts features from the backstepping controller and feeds them into the policy network. In simulations, our algorithm outperforms the baseline SAC without prior backstepping knowledge and the analytical controller.
Exploring Large Protein Language Models in Constrained Evaluation Scenarios within the FLIP Benchmark
Venue: arXiv cs.LG 2025
Year: 2025

In this study, we expand upon the FLIP benchmark-designed for evaluating protein fitness prediction models in small, specialized prediction tasks-by assessing the performance of state-of-the-art large protein language models, including ESM-2 and SaProt on the FLIP dataset. Unlike larger, more diverse benchmarks such as ProteinGym, which cover a broad spectrum of tasks, FLIP focuses on constrained settings where data availability is limited. This makes it an ideal framework to evaluate model performance in scenarios with scarce task-specific data. We investigate whether recent advances in protein language models lead to significant improvements in such settings. Our findings provide valuable insights into the performance of large-scale models in specialized protein prediction tasks.
Mining for Species, Locations, Habitats, and Ecosystems from Scientific Papers in Invasion Biology: A Large-Scale Exploratory Study with Large Language Models
Venue: arXiv cs.CL 2025
Year: 2025

This paper presents an exploratory study that harnesses the capabilities of large language models (LLMs) to mine key ecological entities from invasion biology literature. Specifically, we focus on extracting species names, their locations, associated habitats, and ecosystems, information that is critical for understanding species spread, predicting future invasions, and informing conservation efforts. Traditional text mining approaches often struggle with the complexity of ecological terminology and the subtle linguistic patterns found in these texts. By applying general-purpose LLMs without domain-specific fine-tuning, we uncover both the promise and limitations of using these models for ecological entity extraction. In doing so, this study lays the groundwork for more advanced, automated knowledge extraction tools that can aid researchers and practitioners in understanding and managing biological invasions.
Citation Recommendation based on Argumentative Zoning of User Queries
Venue: arXiv cs.IR 2025
Year: 2025

Citation recommendation aims to locate the important papers for scholars to cite. When writing the citing sentences, the authors usually hold different citing intents, which are referred to citation function in citation analysis. Since argumentative zoning is to identify the argumentative and rhetorical structure in scientific literature, we want to use this information to improve the citation recommendation task. In this paper, a multi-task learning model is built for citation recommendation and argumentative zoning classification. We also generated an annotated corpus of the data from PubMed Central based on a new argumentative zoning schema. The experimental results show that, by considering the argumentative information in the citing sentence, citation recommendation model will get better performance.
Model-Free RL Agents Demonstrate System 1-Like Intentionality
Venue: arXiv cs.AI 2025
Year: 2025

This paper argues that model-free reinforcement learning (RL) agents, while lacking explicit planning mechanisms, exhibit behaviours that can be analogised to System 1 ("thinking fast") processes in human cognition. Unlike model-based RL agents, which operate akin to System 2 ("thinking slow") reasoning by leveraging internal representations for planning, model-free agents react to environmental stimuli without anticipatory modelling. We propose a novel framework linking the dichotomy of System 1 and System 2 to the distinction between model-free and model-based RL. This framing challenges the prevailing assumption that intentionality and purposeful behaviour require planning, suggesting instead that intentionality can manifest in the structured, reactive behaviours of model-free agents. By drawing on interdisciplinary insights from cognitive psychology, legal theory, and experimental jurisprudence, we explore the implications of this perspective for attributing responsibility and ensuring AI safety. These insights advocate for a broader, contextually informed interpretation of intentionality in RL systems, with implications for their ethical deployment and regulation.
Simulation of microstructures and machine learning
Venue: arXiv cs.CV 2025
Year: 2025

Machine learning offers attractive solutions to challenging image processing tasks. Tedious development and parametrization of algorithmic solutions can be replaced by training a convolutional neural network or a random forest with a high potential to generalize. However, machine learning methods rely on huge amounts of representative image data along with a ground truth, usually obtained by manual annotation. Thus, limited availability of training data is a critical bottleneck. We discuss two use cases: optical quality control in industrial production and segmenting crack structures in 3D images of concrete. For optical quality control, all defect types have to be trained but are typically not evenly represented in the training data. Additionally, manual annotation is costly and often inconsistent. It is nearly impossible in the second case: segmentation of crack systems in 3D images of concrete. Synthetic images, generated based on realizations of stochastic geometry models, offer an elegant way out. A wide variety of structure types can be generated. The within structure variation is naturally captured by the stochastic nature of the models and the ground truth is for free. Many new questions arise. In particular, which characteristics of the real image data have to be met to which degree of fidelity.
PyExamine A Comprehensive, UnOpinionated Smell Detection Tool for Python
Venue: arXiv cs.SE 2025
Year: 2025

The growth of Python adoption across diverse domains has led to increasingly complex codebases, presenting challenges in maintaining code quality. While numerous tools attempt to address these challenges, they often fall short in providing comprehensive analysis capabilities or fail to consider Python-specific contexts. PyExamine addresses these critical limitations through an approach to code smell detection that operates across multiple levels of analysis. PyExamine architecture enables detailed examination of code quality through three distinct but interconnected layers: architectural patterns, structural relationships, and code-level implementations. This approach allows for the detection and analysis of 49 distinct metrics, providing developers with an understanding of their codebase's health. The metrics span across all levels of code organization, from high-level architectural concerns to granular implementation details. Through evaluation on 7 diverse projects, PyExamine achieved detection accuracy rates: 91.4\% for code-level smells, 89.3\% for structural smells, and 80.6\% for architectural smells. These results were further validated through extensive user feedback and expert evaluations, confirming PyExamine's capability to identify potential issues across all levels of code organization with high recall accuracy. In additional to this, we have also used PyExamine to analysis the prevalence of different type of smells, across 183 diverse Python projects ranging from small utilities to large-scale enterprise applications. PyExamine's distinctive combination of comprehensive analysis, Python-specific detection, and high customizability makes it a valuable asset for both individual developers and large teams seeking to enhance their code quality practices.
Stream-Based Monitoring of Algorithmic Fairness
Venue: arXiv cs.LG 2025
Year: 2025

Automatic decision and prediction systems are increasingly deployed in applications where they significantly impact the livelihood of people, such as for predicting the creditworthiness of loan applicants or the recidivism risk of defendants. These applications have given rise to a new class of algorithmic-fairness specifications that require the systems to decide and predict without bias against social groups. Verifying these specifications statically is often out of reach for realistic systems, since the systems may, e.g., employ complex learning components, and reason over a large input space. In this paper, we therefore propose stream-based monitoring as a solution for verifying the algorithmic fairness of decision and prediction systems at runtime. Concretely, we present a principled way to formalize algorithmic fairness over temporal data streams in the specification language RTLola and demonstrate the efficacy of this approach on a number of benchmarks. Besides synthetic scenarios that particularly highlight its efficiency on streams with a scaling amount of data, we notably evaluate the monitor on real-world data from the recidivism prediction tool COMPAS.
Using Read Promotion and Mixed Isolation Levels for Performant Yet Serializable Execution of Transaction Programs
Venue: arXiv cs.DB 2025
Year: 2025

We propose a theory that can determine the lowest isolation level that can be allocated to each transaction program in an application in a mixed-isolation-level setting, to guarantee that all executions will be serializable and thus preserve all integrity constraints, even those that are not explicitly declared. This extends prior work applied to completely known transactions, to deal with the realistic situation where transactions are generated by running programs with parameters that are not known in advance. Using our theory, we propose an optimization method that allows for high throughput while ensuring that all executions are serializable. Our method is based on searching for application code modifications that are semantics-preserving while improving the isolation level allocation. We illustrate our approach to the SmallBank benchmark.
Improved Replicable Boosting with Majority-of-Majorities
Venue: arXiv cs.LG 2025
Year: 2025

We introduce a new replicable boosting algorithm which significantly improves the sample complexity compared to previous algorithms. The algorithm works by doing two layers of majority voting, using an improved version of the replicable boosting algorithm introduced by Impagliazzo et al. [2022] in the bottom layer.
Efficient Transformer for High Resolution Image Motion Deblurring
Venue: arXiv cs.CV 2025
Year: 2025

This paper presents a comprehensive study and improvement of the Restormer architecture for high-resolution image motion deblurring. We introduce architectural modifications that reduce model complexity by 18.4% while maintaining or improving performance through optimized attention mechanisms. Our enhanced training pipeline incorporates additional transformations including color jitter, Gaussian blur, and perspective transforms to improve model robustness as well as a new frequency loss term. Extensive experiments on the RealBlur-R, RealBlur-J, and Ultra-High-Definition Motion blurred (UHDM) datasets demonstrate the effectiveness of our approach. The improved architecture shows better convergence behavior and reduced training time while maintaining competitive performance across challenging scenarios. We also provide detailed ablation studies analyzing the impact of our modifications on model behavior and performance. Our results suggest that thoughtful architectural simplification combined with enhanced training strategies can yield more efficient yet equally capable models for motion deblurring tasks. Code and Data Available at: https://github.com/hamzafer/image-deblurring
Segmentation of cracks in 3d images of fiber reinforced concrete using deep learning
Venue: arXiv cs.LG 2025
Year: 2025

Cracks in concrete structures are very common and are an integral part of this heterogeneous material. Characteristics of cracks induced by standardized tests yield valuable information about the tested concrete formulation and its mechanical properties. Observing cracks on the surface of the concrete structure leaves a wealth of structural information unused. Computed tomography enables looking into the sample without interfering or destroying the microstructure. The reconstructed tomographic images are 3d images, consisting of voxels whose gray values represent local X-ray absorption. In order to identify voxels belonging to the crack, so to segment the crack structure in the images, appropriate algorithms need to be developed. Convolutional neural networks are known to solve this type of task very well given enough and consistent training data. We adapted a 3d version of the well-known U-Net and trained it on semi-synthetic 3d images of real concrete samples equipped with simulated crack structures. Here, we explain the general approach. Moreover, we show how to teach the network to detect also real crack systems in 3d images of varying types of real concrete, in particular of fiber reinforced concrete.
Guaranteed prediction sets for functional surrogate models
Venue: arXiv cs.LG 2025
Year: 2025

We propose a method for obtaining statistically guaranteed prediction sets for functional machine learning methods: surrogate models which map between function spaces, motivated by the need to build reliable PDE emulators. The method constructs nested prediction sets on a low-dimensional representation (an SVD) of the surrogate model's error, and then maps these sets to the prediction space using set-propagation techniques. This results in prediction sets for functional surrogate models with conformal prediction coverage guarantees. We use zonotopes as basis of the set construction, which allow an exact linear propagation and are closed under Cartesian products, making them well-suited to this high-dimensional problem. The method is model agnostic and can thus be applied to complex Sci-ML models, including Neural Operators, but also in simpler settings. We also introduce a technique to capture the truncation error of the SVD, preserving the guarantees of the method.
CLoQ: Enhancing Fine-Tuning of Quantized LLMs via Calibrated LoRA Initialization
Venue: arXiv cs.LG 2025
Year: 2025

Fine-tuning large language models (LLMs) using low-rank adaptation (LoRA) has become a highly efficient approach for downstream tasks, particularly in scenarios with limited computational resources. However, applying LoRA techniques to quantized LLMs poses unique challenges due to the reduced representational precision of quantized weights. In this paper, we introduce CLoQ (Calibrated LoRA initialization for Quantized LLMs), a simplistic initialization strategy designed to overcome these challenges. Our approach focuses on minimizing the layer-wise discrepancy between the original LLM and its quantized counterpart with LoRA components during initialization. By leveraging a small calibration dataset, CLoQ quantizes a pre-trained LLM and determines the optimal LoRA components for each layer, ensuring a strong foundation for subsequent fine-tuning. A key contribution of this work is a novel theoretical result that enables the accurate and closed-form construction of these optimal LoRA components. We validate the efficacy of CLoQ across multiple tasks such as language generation, arithmetic reasoning, and commonsense reasoning, demonstrating that it consistently outperforms existing LoRA fine-tuning methods for quantized LLMs, especially at ultra low-bit widths.
Transformer Semantic Genetic Programming for Symbolic Regression
Venue: arXiv cs.NE 2025
Year: 2025

In standard genetic programming (stdGP), solutions are varied by modifying their syntax, with uncertain effects on their semantics. Geometric-semantic genetic programming (GSGP), a popular variant of GP, effectively searches the semantic solution space using variation operations based on linear combinations, although it results in significantly larger solutions. This paper presents Transformer Semantic Genetic Programming (TSGP), a novel and flexible semantic approach that uses a generative transformer model as search operator. The transformer is trained on synthetic test problems and learns semantic similarities between solutions. Once the model is trained, it can be used to create offspring solutions with high semantic similarity also for unseen and unknown problems. Experiments on several symbolic regression problems show that TSGP generates solutions with comparable or even significantly better prediction quality than stdGP, SLIM_GSGP, DSR, and DAE-GP. Like SLIM_GSGP, TSGP is able to create new solutions that are semantically similar without creating solutions of large size. An analysis of the search dynamic reveals that the solutions generated by TSGP are semantically more similar than the solutions generated by the benchmark approaches allowing a better exploration of the semantic solution space.
GuardReasoner: Towards Reasoning-based LLM Safeguards
Venue: arXiv cs.CR 2025
Year: 2025

As LLMs increasingly impact safety-critical applications, ensuring their safety using guardrails remains a key challenge. This paper proposes GuardReasoner, a new safeguard for LLMs, by guiding the guard model to learn to reason. Concretely, we first create the GuardReasonerTrain dataset, which consists of 127K samples with 460K detailed reasoning steps. Then, we introduce reasoning SFT to unlock the reasoning capability of guard models. In addition, we present hard sample DPO to further strengthen their reasoning ability. In this manner, GuardReasoner achieves better performance, explainability, and generalizability. Extensive experiments and analyses on 13 benchmarks of 3 guardrail tasks demonstrate its superiority. Remarkably, GuardReasoner 8B surpasses GPT-4o+CoT by 5.74% and LLaMA Guard 3 8B by 20.84% F1 score on average. We release the training data, code, and models with different scales (1B, 3B, 8B) of GuardReasoner : https://github.com/yueliu1999/GuardReasoner/.
Design and Validation of Learning Aware HMI For Learning-Enabled Increasingly Autonomous Systems
Venue: arXiv cs.HC 2025
Year: 2025

With the rapid advancements in Artificial Intelligence (AI), autonomous agents are increasingly expected to manage complex situations where learning-enabled algorithms are vital. However, the integration of these advanced algorithms poses significant challenges, especially concerning safety and reliability. This research emphasizes the importance of incorporating human-machine collaboration into the systems engineering process to design learning-enabled increasingly autonomous systems (LEIAS). Our proposed LEIAS architecture emphasizes communication representation and pilot preference learning to boost operational safety. Leveraging the Soar cognitive architecture, the system merges symbolic decision logic with numeric decision preferences enhanced through reinforcement learning. A core aspect of this approach is transparency; the LEIAS provides pilots with a comprehensive, interpretable view of the system's state, encompassing detailed evaluations of sensor reliability, including GPS, IMU, and LIDAR data. This multi-sensor assessment is critical for diagnosing discrepancies and maintaining trust. Additionally, the system learns and adapts to pilot preferences, enabling responsive, context-driven decision-making. Autonomy is incrementally escalated based on necessity, ensuring pilots retain control in standard scenarios and receive assistance only when required. Simulation studies conducted in Microsoft's XPlane simulation environment to validate this architecture's efficacy, showcasing its performance in managing sensor anomalies and enhancing human-machine collaboration, ultimately advancing safety in complex operational environments.
Streaming DiLoCo with overlapping communication: Towards a Distributed Free Lunch
Venue: arXiv cs.CL 2025
Year: 2025

Training of large language models (LLMs) is typically distributed across a large number of accelerators to reduce training time. Since internal states and parameter gradients need to be exchanged at each and every single gradient step, all devices need to be co-located using low-latency high-bandwidth communication links to support the required high volume of exchanged bits. Recently, distributed algorithms like DiLoCo have relaxed such co-location constraint: accelerators can be grouped into ``workers'', where synchronizations between workers only occur infrequently. This in turn means that workers can afford being connected by lower bandwidth communication links without affecting learning quality. However, in these methods, communication across workers still requires the same peak bandwidth as before, as the synchronizations require all parameters to be exchanged across all workers. In this paper, we improve DiLoCo in three ways. First, we synchronize only subsets of parameters in sequence, rather than all at once, which greatly reduces peak bandwidth. Second, we allow workers to continue training while synchronizing, which decreases wall clock time. Third, we quantize the data exchanged by workers, which further reduces bandwidth across workers. By properly combining these modifications, we show experimentally that we can distribute training of billion-scale parameters and reach similar quality as before, but reducing required bandwidth by two orders of magnitude.
Illusions of Relevance: Arbitrary Content Injection Attacks Deceive Retrievers, Rerankers, and LLM Judges
Venue: arXiv cs.IR 2025
Year: 2025

This work considers a black-box threat model in which adversaries attempt to propagate arbitrary non-relevant content in search. We show that retrievers, rerankers, and LLM relevance judges are all highly vulnerable to attacks that enable arbitrary content to be promoted to the top of search results and to be assigned perfect relevance scores. We investigate how attackers may achieve this via content injection, injecting arbitrary sentences into relevant passages or query terms into arbitrary passages. Our study analyzes how factors such as model class and size, the balance between relevant and non-relevant content, injection location, toxicity and severity of injected content, and the role of LLM-generated content influence attack success, yielding novel, concerning, and often counterintuitive results. Our results reveal a weakness in embedding models, LLM-based scoring models, and generative LLMs, raising concerns about the general robustness, safety, and trustworthiness of language models regardless of the type of model or the role in which they are employed. We also emphasize the challenges of robust defenses against these attacks. Classifiers and more carefully prompted LLM judges often fail to recognize passages with content injection, especially when considering diverse text topics and styles. Our findings highlight the need for further research into arbitrary content injection attacks. We release our code for further study.