OpenRaiser/Intern-Atlas huggingface dataset:
Does GenAI Rewrite How We Write? An Empirical Study on Two-Million Preprints
Venue: arXiv cs.CY 2025
Year: 2025

Preprint repositories become central infrastructures for scholarly communication. Their expansion transforms how research is circulated and evaluated before journal publication. Generative large language models (LLMs) introduce a further potential disruption by altering how manuscripts are written. While speculation abounds, systematic evidence of whether and how LLMs reshape scientific publishing remains limited. This paper addresses the gap through a large-scale analysis of more than 2.1 million preprints spanning 2016--2025 (115 months) across four major repositories (i.e., arXiv, bioRxiv, medRxiv, SocArXiv). We introduce a multi-level analytical framework that integrates interrupted time-series models, collaboration and productivity metrics, linguistic profiling, and topic modeling to assess changes in volume, authorship, style, and disciplinary orientation. Our findings reveal that LLMs have accelerated submission and revision cycles, modestly increased linguistic complexity, and disproportionately expanded AI-related topics, while computationally intensive fields benefit more than others. These results show that LLMs act less as universal disruptors than as selective catalysts, amplifying existing strengths and widening disciplinary divides. By documenting these dynamics, the paper provides the first empirical foundation for evaluating the influence of generative AI on academic publishing and highlights the need for governance frameworks that preserve trust, fairness, and accountability in an AI-enabled research ecosystem.
Shock-Aware Physics-Guided Fusion-DeepONet Operator for Rarefied Micro-Nozzle Flows
Venue: arXiv cs.LG 2025
Year: 2025

We present a comprehensive, physics aware deep learning framework for constructing fast and accurate surrogate models of rarefied, shock containing micro nozzle flows. The framework integrates three key components, a Fusion DeepONet operator learning architecture for capturing parameter dependencies, a physics-guided feature space that embeds a shock-aligned coordinate system, and a two-phase curriculum strategy emphasizing high-gradient regions. To demonstrate the generality and inductive bias of the proposed framework, we first validate it on the canonical viscous Burgers equation, which exhibits advective steepening and shock like gradients.
Assignment-Routing Optimization with Cutting-Plane Subtour Elimination: Solver and Benchmark Dataset
Venue: arXiv cs.DS 2025
Year: 2025

We study a joint routing-assignment optimization problem in which a set of items must be paired one-to-one with a set of placeholders while simultaneously determining a Hamiltonian cycle that visits every node exactly once. Both the assignment and routing decisions are optimized jointly to minimize the total travel cost. In this work, we propose a method to solve this problem using an exact MIP formulation with Gurobi, including cutting-plane subtour elimination. With analysis of the computational complexity and through extensive experiments, we analyze the computational limitations of this approach as the problem size grows and reveal the challenges associated with the need for more efficient algorithms for larger instances. The dataset, formulations, and experimental results provided here can serve as benchmarks for future studies in this research area. GitHub repository: https://github.com/QL-YUAN/Joint-Assignment-Routing-Optimization
Hey Pentti, We Did It!: A Fully Vector-Symbolic Lisp
Venue: arXiv cs.PL 2025
Year: 2025

Kanerva (2014) suggested that it would be possible to construct a complete Lisp out of a vector-symbolic architecture. We present the general form of a vector-symbolic representation of the five Lisp elementary functions, lambda expressions, and other auxiliary functions, found in the Lisp 1.5 specification McCarthy (1960), which is near minimal and sufficient for Turing-completeness. Our specific implementation uses holographic reduced representations Plate (1995), with a lookup table cleanup memory. Lisp, as all Turing-complete languages, is a Cartesian closed category, unusual in its proximity to the mathematical abstraction. We discuss the mathematics, the purpose, and the significance of demonstrating vector-symbolic architectures' Cartesian-closure, as well as the importance of explicitly including cleanup memories in the specification of the architecture.
TACLA: An LLM-Based Multi-Agent Tool for Transactional Analysis Training in Education
Venue: arXiv cs.MA 2025
Year: 2025

Simulating nuanced human social dynamics with Large Language Models (LLMs) remains a significant challenge, particularly in achieving psychological depth and consistent persona behavior crucial for high-fidelity training tools. This paper introduces TACLA (Transactional Analysis Contextual LLM-based Agents), a novel Multi-Agent architecture designed to overcome these limitations. TACLA integrates core principles of Transactional Analysis (TA) by modeling agents as an orchestrated system of distinct Parent, Adult, and Child ego states, each with its own pattern memory. An Orchestrator Agent prioritizes ego state activation based on contextual triggers and an agent's life script, ensuring psychologically authentic responses. Validated in an educational scenario, TACLA demonstrates realistic ego state shifts in Student Agents, effectively modeling conflict de-escalation and escalation based on different teacher intervention strategies. Evaluation shows high conversational credibility and confirms TACLA's capacity to create dynamic, psychologically-grounded social simulations, advancing the development of effective AI tools for education and beyond.
Uncertainty-Aware Post-Hoc Calibration: Mitigating Confidently Incorrect Predictions Beyond Calibration Metrics
Venue: arXiv cs.LG 2025
Year: 2025

Despite extensive research on neural network calibration, existing methods typically apply global transformations that treat all predictions uniformly, overlooking the heterogeneous reliability of individual predictions. Furthermore, the relationship between improved calibration and effective uncertainty-aware decision-making remains largely unexplored. This paper presents a post-hoc calibration framework that leverages prediction reliability assessment to jointly enhance calibration quality and uncertainty-aware decision-making. The framework employs proximity-based conformal prediction to stratify calibration samples into putatively correct and putatively incorrect groups based on semantic similarity in feature space. A dual calibration strategy is then applied: standard isotonic regression calibrated confidence in putatively correct predictions, while underconfidence-regularized isotonic regression reduces confidence toward uniform distributions for putatively incorrect predictions, facilitating their identification for further investigations. A comprehensive evaluation is conducted using calibration metrics, uncertainty-aware performance measures, and empirical conformal coverage. Experiments on CIFAR-10 and CIFAR-100 with BiT and CoAtNet backbones show that the proposed method achieves lower confidently incorrect predictions, and competitive Expected Calibration Error compared with isotonic and focal-loss baselines. This work bridges calibration and uncertainty quantification through instance-level adaptivity, offering a practical post-hoc solution that requires no model retraining while improving both probability alignment and uncertainty-aware decision-making.
Believe It or Not: How Deeply do LLMs Believe Implanted Facts?
Venue: arXiv cs.CL 2025
Year: 2025

Knowledge editing techniques promise to implant new factual knowledge into large language models (LLMs). But do LLMs really believe these facts? We develop a framework to measure belief depth and use it to evaluate the success of knowledge editing techniques. We operationalize belief depth as the extent to which implanted knowledge 1) generalizes to related contexts (e.g. Fermi estimates several logical steps removed), 2) is robust to self-scrutiny and direct challenge, and 3) is represented similarly to genuine knowledge (as measured by linear probes). Our evaluations show that simple prompting and mechanistic editing techniques fail to implant knowledge deeply. In contrast, Synthetic Document Finetuning (SDF) - where models are trained on LLM-generated documents consistent with a fact - often succeeds at implanting beliefs that behave similarly to genuine knowledge. However, SDF's success is not universal, as implanted beliefs that contradict basic world knowledge are brittle and representationally distinct from genuine knowledge. Overall, our work introduces measurable criteria for belief depth and enables the rigorous evaluation necessary for deploying knowledge editing in real-world applications.
Studying the Effects of Robot Intervention on School Shooters in Virtual Reality
Venue: arXiv cs.RO 2025
Year: 2025

We advance the understanding of robotic intervention in high-risk scenarios by examining their potential to distract and impede a school shooter. To evaluate this concept, we conducted a virtual reality study with 150 university participants role-playing as a school shooter. Within the simulation, an autonomous robot predicted the shooter's movements and positioned itself strategically to interfere and distract. The strategy the robot used to approach the shooter was manipulated -- either moving directly in front of the shooter (aggressive) or maintaining distance (passive) -- and the distraction method, ranging from no additional cues (low), to siren and lights (medium), to siren, lights, and smoke to impair visibility (high). An aggressive, high-distraction robot reduced the number of victims by 46.6% relative to a no-robot control. This outcome underscores both the potential of robotic intervention to enhance safety and the pressing ethical questions surrounding their use in school environments.
RoboChallenge: Large-scale Real-robot Evaluation of Embodied Policies
Venue: arXiv cs.RO 2025
Year: 2025

Testing on real machines is indispensable for robotic control algorithms. In the context of learning-based algorithms, especially VLA models, demand for large-scale evaluation, i.e. testing a large number of models on a large number of tasks, is becoming increasingly urgent. However, doing this right is highly non-trivial, especially when scalability and reproducibility is taken into account. In this report, we describe our methodology for constructing RoboChallenge, an online evaluation system to test robotic control algorithms, and our survey of recent state-of-the-art VLA models using our initial benchmark Table30.
Humanoid Goalkeeper: Learning from Position Conditioned Task-Motion Constraints
Venue: arXiv cs.RO 2025
Year: 2025

We present a reinforcement learning framework for autonomous goalkeeping with humanoid robots in real-world scenarios. While prior work has demonstrated similar capabilities on quadrupedal platforms, humanoid goalkeeping introduces two critical challenges: (1) generating natural, human-like whole-body motions, and (2) covering a wider guarding range with an equivalent response time. Unlike existing approaches that rely on separate teleoperation or fixed motion tracking for whole-body control, our method learns a single end-to-end RL policy, enabling fully autonomous, highly dynamic, and human-like robot-object interactions. To achieve this, we integrate multiple human motion priors conditioned on perceptual inputs into the RL training via an adversarial scheme. We demonstrate the effectiveness of our method through real-world experiments, where the humanoid robot successfully performs agile, autonomous, and naturalistic interceptions of fast-moving balls. In addition to goalkeeping, we demonstrate the generalization of our approach through tasks such as ball escaping and grabbing. Our work presents a practical and scalable solution for enabling highly dynamic interactions between robots and moving objects, advancing the field toward more adaptive and lifelike robotic behaviors.
SAVANT: Semantic Analysis with Vision-Augmented Anomaly deTection
Venue: arXiv cs.CV 2025
Year: 2025

Autonomous driving systems remain critically vulnerable to the long-tail of rare, out-of-distribution scenarios with semantic anomalies. While Vision Language Models (VLMs) offer promising reasoning capabilities, naive prompting approaches yield unreliable performance and depend on expensive proprietary models, limiting practical deployment. We introduce SAVANT (Semantic Analysis with Vision-Augmented Anomaly deTection), a structured reasoning framework that achieves high accuracy and recall in detecting anomalous driving scenarios from input images through layered scene analysis and a two-phase pipeline: structured scene description extraction followed by multi-modal evaluation. Our approach transforms VLM reasoning from ad-hoc prompting to systematic analysis across four semantic layers: Street, Infrastructure, Movable Objects, and Environment. SAVANT achieves 89.6% recall and 88.0% accuracy on real-world driving scenarios, significantly outperforming unstructured baselines. More importantly, we demonstrate that our structured framework enables a fine-tuned 7B parameter open-source model (Qwen2.5VL) to achieve 90.8% recall and 93.8% accuracy - surpassing all models evaluated while enabling local deployment at near-zero cost. By automatically labeling over 9,640 real-world images with high accuracy, SAVANT addresses the critical data scarcity problem in anomaly detection and provides a practical path toward reliable, accessible semantic monitoring for autonomous systems.
Batch Distillation Data for Developing Machine Learning Anomaly Detection Methods
Venue: arXiv cs.LG 2025
Year: 2025

Machine learning (ML) holds great potential to advance anomaly detection (AD) in chemical processes. However, the development of ML-based methods is hindered by the lack of openly available experimental data. To address this gap, we have set up a laboratory-scale batch distillation plant and operated it to generate an extensive experimental database, covering fault-free experiments and experiments in which anomalies were intentionally induced, for training advanced ML-based AD methods. In total, 119 experiments were conducted across a wide range of operating conditions and mixtures. Most experiments containing anomalies were paired with a corresponding fault-free one. The database that we provide here includes time-series data from numerous sensors and actuators, along with estimates of measurement uncertainty. In addition, unconventional data sources -- such as concentration profiles obtained via online benchtop NMR spectroscopy and video and audio recordings -- are provided. Extensive metadata and expert annotations of all experiments are included. The anomaly annotations are based on an ontology developed in this work. The data are organized in a structured database and made freely available via doi.org/10.5281/zenodo.17395544. This new database paves the way for the development of advanced ML-based AD methods. As it includes information on the causes of anomalies, it further enables the development of interpretable and explainable ML approaches, as well as methods for anomaly mitigation.
MEG-GPT: A transformer-based foundation model for magnetoencephalography data
Venue: arXiv cs.LG 2025
Year: 2025

Modelling the complex spatiotemporal patterns of large-scale brain dynamics is crucial for neuroscience, but traditional methods fail to capture the rich structure in modalities such as magnetoencephalography (MEG). Recent advances in deep learning have enabled significant progress in other domains, such as language and vision, by using foundation models at scale. Here, we introduce MEG-GPT, a transformer based foundation model that uses time-attention and next time-point prediction. To facilitate this, we also introduce a novel data-driven tokeniser for continuous MEG data, which preserves the high temporal resolution of continuous MEG signals without lossy transformations. We trained MEG-GPT on tokenised brain region time-courses extracted from a large-scale MEG dataset (N=612, eyes-closed rest, Cam-CAN data), and show that the learnt model can generate data with realistic spatio-spectral properties, including transient events and population variability. Critically, it performs well in downstream decoding tasks, improving downstream supervised prediction task, showing improved zero-shot generalisation across sessions (improving accuracy from 0.54 to 0.59) and subjects (improving accuracy from 0.41 to 0.49) compared to a baseline methods. Furthermore, we show the model can be efficiently fine-tuned on a smaller labelled dataset to boost performance in cross-subject decoding scenarios. This work establishes a powerful foundation model for electrophysiological data, paving the way for applications in computational neuroscience and neural decoding.
HyperDiffusionFields (HyDiF): Diffusion-Guided Hypernetworks for Learning Implicit Molecular Neural Fields
Venue: arXiv cs.LG 2025
Year: 2025

We introduce HyperDiffusionFields (HyDiF), a framework that models 3D molecular conformers as continuous fields rather than discrete atomic coordinates or graphs. At the core of our approach is the Molecular Directional Field (MDF), a vector field that maps any point in space to the direction of the nearest atom of a particular type. We represent MDFs using molecule-specific neural implicit fields, which we call Molecular Neural Fields (MNFs). To enable learning across molecules and facilitate generalization, we adopt an approach where a shared hypernetwork, conditioned on a molecule, generates the weights of the given molecule's MNF. To endow the model with generative capabilities, we train the hypernetwork as a denoising diffusion model, enabling sampling in the function space of molecular fields. Our design naturally extends to a masked diffusion mechanism to support structure-conditioned generation tasks, such as molecular inpainting, by selectively noising regions of the field. Beyond generation, the localized and continuous nature of MDFs enables spatially fine-grained feature extraction for molecular property prediction, something not easily achievable with graph or point cloud based methods. Furthermore, we demonstrate that our approach scales to larger biomolecules, illustrating a promising direction for field-based molecular modeling.
ANGEL: A Novel Gripper for Versatile and Light-touch Fruit Harvesting
Venue: arXiv cs.RO 2025
Year: 2025

Fruit harvesting remains predominantly a labor-intensive process, motivating the development of research for robotic grippers. Conventional rigid or vacuum-driven grippers require complex mechanical design or high energy consumption. Current enveloping-based fruit harvesting grippers lack adaptability to fruits of different sizes. This paper introduces a drawstring-inspired, cable-driven soft gripper for versatile and gentle fruit harvesting. The design employs 3D-printed Thermoplastic Polyurethane (TPU) pockets with integrated steel wires that constrict around the fruit when actuated, distributing pressure uniformly to minimize bruising and allow versatility to fruits of varying sizes. The lightweight structure, which requires few components, reduces mechanical complexity and cost compared to other grippers. Actuation is achieved through servo-driven cable control, while motor feedback provides autonomous grip adjustment with tunable grip strength. Experimental validation shows that, for tomatoes within the gripper's effective size range, harvesting was achieved with a 0% immediate damage rate and a bruising rate of less than 9% after five days, reinforcing the gripper's suitability for fruit harvesting.
BlueCodeAgent: A Blue Teaming Agent Enabled by Automated Red Teaming for CodeGen AI
Venue: arXiv cs.SE 2025
Year: 2025

As large language models (LLMs) are increasingly used for code generation, concerns over the security risks have grown substantially. Early research has primarily focused on red teaming, which aims to uncover and evaluate vulnerabilities and risks of CodeGen models. However, progress on the blue teaming side remains limited, as developing defense requires effective semantic understanding to differentiate the unsafe from the safe. To fill in this gap, we propose BlueCodeAgent, an end-to-end blue teaming agent enabled by automated red teaming. Our framework integrates both sides: red teaming generates diverse risky instances, while the blue teaming agent leverages these to detect previously seen and unseen risk scenarios through constitution and code analysis with agentic integration for multi-level defense. Our evaluation across three representative code-related tasks--bias instruction detection, malicious instruction detection, and vulnerable code detection--shows that BlueCodeAgent achieves significant gains over the base models and safety prompt-based defenses. In particular, for vulnerable code detection tasks, BlueCodeAgent integrates dynamic analysis to effectively reduce false positives, a challenging problem as base models tend to be over-conservative, misclassifying safe code as unsafe. Overall, BlueCodeAgent achieves an average 12.7\% F1 score improvement across four datasets in three tasks, attributed to its ability to summarize actionable constitutions that enhance context-aware risk detection. We demonstrate that the red teaming benefits the blue teaming by continuously identifying new vulnerabilities to enhance defense performance.
Learning from Generalization Patterns: An Evaluation-Driven Approach to Enhanced Data Augmentation for Fine-Tuning Small Language Models
Venue: arXiv cs.AI 2025
Year: 2025

Small Language Models (SLMs) offer compelling advantages in deployment cost and latency, but their accuracy often lags behind larger models, particularly for complex domain-specific tasks. While supervised fine-tuning can help bridge this performance gap, it requires substantial manual effort in data preparation and iterative optimization. We present PaDA-Agent (Pattern-guided Data Augmentation Agent), an evaluation-driven approach that streamlines the data augmentation process for SLMs through coordinated operations. Unlike state-of-the-art approaches that focus on model training errors only and generating error-correcting samples, PaDA-Agent discovers failure patterns from the validation data via evaluations and drafts targeted data augmentation strategies aiming to directly reduce the generalization gap. Our experimental results demonstrate significant improvements over state-of-the-art LLM-based data augmentation approaches for Llama 3.2 1B Instruct model fine-tuning.
Annotating the Chain-of-Thought: A Behavior-Labeled Dataset for AI Safety
Venue: arXiv cs.AI 2025
Year: 2025

Recent work has highlighted the importance of monitoring chain-of-thought reasoning for AI safety; however, current approaches that analyze textual reasoning steps can miss subtle harmful patterns and may be circumvented by models that hide unsafe reasoning. We present a sentence-level labeled dataset that enables activation-based monitoring of safety behaviors during LLM reasoning. Our dataset contains reasoning sequences with sentence-level annotations of safety behaviors such as expression of safety concerns or speculation on user intent, which we use to extract steering vectors for detecting and influencing these behaviors within model activations. The dataset fills a key gap in safety research: while existing datasets label reasoning holistically, effective application of steering vectors for safety monitoring could be improved by identifying precisely when specific behaviors occur within reasoning chains. We demonstrate the dataset's utility by extracting representations that both detect and steer safety behaviors in model activations, showcasing the potential of activation-level techniques for improving safety oversight on reasoning. Content Warning: This paper discusses AI safety in the context of harmful prompts and may contain references to potentially harmful content.