OpenRaiser/Intern-Atlas huggingface dataset:
Identity resolution of software metadata using Large Language Models
Venue: arXiv cs.SE 2025
Year: 2025

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.
CLIP-AE: CLIP-assisted Cross-view Audio-Visual Enhancement for Unsupervised Temporal Action Localization
Venue: arXiv cs.CV 2025
Year: 2025

Temporal Action Localization (TAL) has garnered significant attention in information retrieval. Existing supervised or weakly supervised methods heavily rely on labeled temporal boundaries and action categories, which are labor-intensive and time-consuming. Consequently, unsupervised temporal action localization (UTAL) has gained popularity. However, current methods face two main challenges: 1) Classification pre-trained features overly focus on highly discriminative regions; 2) Solely relying on visual modality information makes it difficult to determine contextual boundaries. To address these issues, we propose a CLIP-assisted cross-view audiovisual enhanced UTAL method. Specifically, we introduce visual language pre-training (VLP) and classification pre-training-based collaborative enhancement to avoid excessive focus on highly discriminative regions; we also incorporate audio perception to provide richer contextual boundary information. Finally, we introduce a self-supervised cross-view learning paradigm to achieve multi-view perceptual enhancement without additional annotations. Extensive experiments on two public datasets demonstrate our model's superiority over several state-of-the-art competitors.
Normalizing Flows are Capable Models for RL
Venue: arXiv cs.LG 2025
Year: 2025

Modern reinforcement learning (RL) algorithms have found success by using powerful probabilistic models, such as transformers, energy-based models, and diffusion/flow-based models. To this end, RL researchers often choose to pay the price of accommodating these models into their algorithms -- diffusion models are expressive, but are computationally intensive due to their reliance on solving differential equations, while autoregressive transformer models are scalable but typically require learning discrete representations. Normalizing flows (NFs), by contrast, seem to provide an appealing alternative, as they enable likelihoods and sampling without solving differential equations or autoregressive architectures. However, their potential in RL has received limited attention, partly due to the prevailing belief that normalizing flows lack sufficient expressivity. We show that this is not the case. Building on recent work in NFs, we propose a single NF architecture which integrates seamlessly into RL algorithms, serving as a policy, Q-function, and occupancy measure. Our approach leads to much simpler algorithms, and achieves higher performance in imitation learning, offline, goal conditioned RL and unsupervised RL.
Comparative assessment of fairness definitions and bias mitigation strategies in machine learning-based diagnosis of Alzheimer's disease from MR images
Venue: arXiv cs.LG 2025
Year: 2025

The present study performs a comprehensive fairness analysis of machine learning (ML) models for the diagnosis of Mild Cognitive Impairment (MCI) and Alzheimer's disease (AD) from MRI-derived neuroimaging features. Biases associated with age, race, and gender in a multi-cohort dataset, as well as the influence of proxy features encoding these sensitive attributes, are investigated. The reliability of various fairness definitions and metrics in the identification of such biases is also assessed. Based on the most appropriate fairness measures, a comparative analysis of widely used pre-processing, in-processing, and post-processing bias mitigation strategies is performed. Moreover, a novel composite measure is introduced to quantify the trade-off between fairness and performance by considering the F1-score and the equalized odds ratio, making it appropriate for medical diagnostic applications. The obtained results reveal the existence of biases related to age and race, while no significant gender bias is observed. The deployed mitigation strategies yield varying improvements in terms of fairness across the different sensitive attributes and studied subproblems. For race and gender, Reject Option Classification improves equalized odds by 46% and 57%, respectively, and achieves harmonic mean scores of 0.75 and 0.80 in the MCI versus AD subproblem, whereas for age, in the same subproblem, adversarial debiasing yields the highest equalized odds improvement of 40% with a harmonic mean score of 0.69. Insights are provided into how variations in AD neuropathology and risk factors, associated with demographic characteristics, influence model fairness.
Synchronizing Process Model and Event Abstraction for Grounded Process Intelligence (Extended Version)
Venue: arXiv cs.AI 2025
Year: 2025

Model abstraction (MA) and event abstraction (EA) are means to reduce complexity of (discovered) models and event data. Imagine a process intelligence project that aims to analyze a model discovered from event data which is further abstracted, possibly multiple times, to reach optimality goals, e.g., reducing model size. So far, after discovering the model, there is no technique that enables the synchronized abstraction of the underlying event log. This results in loosing the grounding in the real-world behavior contained in the log and, in turn, restricts analysis insights. Hence, in this work, we provide the formal basis for synchronized model and event abstraction, i.e., we prove that abstracting a process model by MA and discovering a process model from an abstracted event log yields an equivalent process model. We prove the feasibility of our approach based on behavioral profile abstraction as non-order preserving MA technique, resulting in a novel EA technique.
Comparing the Moore-Penrose Pseudoinverse and Gradient Descent for Solving Linear Regression Problems: A Performance Analysis
Venue: arXiv cs.LG 2025
Year: 2025

This paper investigates the comparative performance of two fundamental approaches to solving linear regression problems: the closed-form Moore-Penrose pseudoinverse and the iterative gradient descent method. Linear regression is a cornerstone of predictive modeling, and the choice of solver can significantly impact efficiency and accuracy. I review and discuss the theoretical underpinnings of both methods, analyze their computational complexity, and evaluate their empirical behavior on synthetic datasets with controlled characteristics, as well as on established real-world datasets. My results delineate the conditions under which each method excels in terms of computational time, numerical stability, and predictive accuracy. This work aims to provide practical guidance for researchers and practitioners in machine learning when selecting between direct, exact solutions and iterative, approximate solutions for linear regression tasks.
A Unified Framework for Mapping and Synthesis of Approximate R-Blocks CGRAs
Venue: arXiv cs.AR 2025
Year: 2025

The ever-increasing complexity and operational diversity of modern Neural Networks (NNs) have caused the need for low-power and, at the same time, high-performance edge devices for AI applications. Coarse Grained Reconfigurable Architectures (CGRAs) form a promising design paradigm to address these challenges, delivering a close-to-ASIC performance while allowing for hardware programmability. In this paper, we introduce a novel end-to-end exploration and synthesis framework for approximate CGRA processors that enables transparent and optimized integration and mapping of state-of-the-art approximate multiplication components into CGRAs. Our methodology introduces a per-channel exploration strategy that maps specific output features onto approximate components based on accuracy degradation constraints. This enables the optimization of the system's energy consumption while retaining the accuracy above a certain threshold. At the circuit level, the integration of approximate components enables the creation of voltage islands that operate at reduced voltage levels, which is attributed to their inherently shorter critical paths. This key enabler allows us to effectively reduce the overall power consumption by an average of 30% across our analyzed architectures, compared to their baseline counterparts, while incurring only a minimal 2% area overhead. The proposed methodology was evaluated on a widely used NN model, MobileNetV2, on the ImageNet dataset, demonstrating that the generated architectures can deliver up to 440 GOPS/W with relatively small output error during inference, outperforming several State-of-the-Art CGRA architectures in terms of throughput and energy efficiency.
Adaptive Federated LoRA in Heterogeneous Wireless Networks with Independent Sampling
Venue: arXiv cs.LG 2025
Year: 2025

Federated LoRA has emerged as a promising technique for efficiently fine-tuning large language models (LLMs) on distributed devices by reducing the number of trainable parameters. However, existing approaches often inadequately overlook the theoretical and practical implications of system and data heterogeneity, thereby failing to optimize the overall training efficiency, particularly in terms of wall-clock time. In this paper, we propose an adaptive federated LoRA strategy with independent client sampling to minimize the convergence wall-clock time of federated fine-tuning under both computation and communication heterogeneity. We first derive a new convergence bound for federated LoRA with arbitrary and independent client sampling, notably without requiring the stringent bounded gradient assumption. Then, we introduce an adaptive bandwidth allocation scheme that accounts for heterogeneous client resources and system bandwidth constraints. Based on the derived theory, we formulate and solve a non-convex optimization problem to jointly determine the LoRA sketching ratios and sampling probabilities, aiming to minimize wall-clock convergence time. An efficient and low-complexity algorithm is developed to approximate the solution. Finally, extensive experiments demonstrate that our approach significantly reduces wall-clock training time compared to state-of-the-art methods across various models and datasets.
Jigsaw-R1: A Study of Rule-based Visual Reinforcement Learning with Jigsaw Puzzles
Venue: arXiv cs.CV 2025
Year: 2025

The application of rule-based reinforcement learning (RL) to multimodal large language models (MLLMs) introduces unique challenges and potential deviations from findings in text-only domains, particularly for perception-heavy tasks. This paper provides a comprehensive study of rule-based visual RL, using jigsaw puzzles as a structured experimental framework. Jigsaw puzzles offer inherent ground truth, adjustable difficulty, and demand complex decision-making, making them ideal for this study. Our research reveals several key findings: \textit{Firstly,} we find that MLLMs, initially performing near to random guessing on the simplest jigsaw puzzles, achieve near-perfect accuracy and generalize to complex, unseen configurations through fine-tuning. \textit{Secondly,} training on jigsaw puzzles can induce generalization to other visual tasks, with effectiveness tied to specific task configurations. \textit{Thirdly,} MLLMs can learn and generalize with or without explicit reasoning, though open-source models often favor direct answering. Consequently, even when trained for step-by-step reasoning, they can ignore the thinking process in deriving the final answer. \textit{Fourthly,} we observe that complex reasoning patterns appear to be pre-existing rather than emergent, with their frequency increasing alongside training and task difficulty. \textit{Finally,} our results demonstrate that RL exhibits more effective generalization than Supervised Fine-Tuning (SFT), and an initial SFT cold start phase can hinder subsequent RL optimization. Although these observations are based on jigsaw puzzles and may vary across other visual tasks, this research contributes a valuable piece of jigsaw to the larger puzzle of collective understanding rule-based visual RL and its potential in multimodal learning. The code is available at: https://github.com/zifuwanggg/Jigsaw-R1
Color Image Set Recognition Based on Quaternionic Grassmannians
Venue: arXiv cs.CV 2025
Year: 2025

We propose a new method for recognizing color image sets using quaternionic Grassmannians, which use the power of quaternions to capture color information and represent each color image set as a point on the quaternionic Grassmannian. We provide a direct formula to calculate the shortest distance between two points on the quaternionic Grassmannian, and use this distance to build a new classification framework. Experiments on the ETH-80 benchmark dataset and and the Highway Traffic video dataset show that our method achieves good recognition results. We also discuss some limitations in stability and suggest ways the method can be improved in the future.
Global optimization of graph acquisition functions for neural architecture search
Venue: arXiv cs.LG 2025
Year: 2025

Graph Bayesian optimization (BO) has shown potential as a powerful and data-efficient tool for neural architecture search (NAS). Most existing graph BO works focus on developing graph surrogates models, i.e., metrics of networks and/or different kernels to quantify the similarity between networks. However, the acquisition optimization, as a discrete optimization task over graph structures, is not well studied due to the complexity of formulating the graph search space and acquisition functions. This paper presents explicit optimization formulations for graph input space including properties such as reachability and shortest paths, which are used later to formulate graph kernels and the acquisition function. We theoretically prove that the proposed encoding is an equivalent representation of the graph space and provide restrictions for the NAS domain with either node or edge labels. Numerical results over several NAS benchmarks show that our method efficiently finds the optimal architecture for most cases, highlighting its efficacy.
Keyed Chaotic Dynamics for Privacy-Preserving Neural Inference
Venue: arXiv cs.CR 2025
Year: 2025

Neural network inference typically operates on raw input data, increasing the risk of exposure during preprocessing and inference. Moreover, neural architectures lack efficient built-in mechanisms for directly authenticating input data. This work introduces a novel encryption method for ensuring the security of neural inference. By constructing key-conditioned chaotic graph dynamical systems, we enable the encryption and decryption of real-valued tensors within the neural architecture. The proposed dynamical systems are particularly suited to encryption due to their sensitivity to initial conditions and their capacity to produce complex, key-dependent nonlinear transformations from compact rules. This work establishes a paradigm for securing neural inference and opens new avenues for research on the application of graph dynamical systems in neural network security.
Bayesian Perspective on Memorization and Reconstruction
Venue: arXiv cs.CR 2025
Year: 2025

We introduce a new Bayesian perspective on the concept of data reconstruction, and leverage this viewpoint to propose a new security definition that, in certain settings, provably prevents reconstruction attacks. We use our paradigm to shed new light on one of the most notorious attacks in the privacy and memorization literature - fingerprinting code attacks (FPC). We argue that these attacks are really a form of membership inference attacks, rather than reconstruction attacks. Furthermore, we show that if the goal is solely to prevent reconstruction (but not membership inference), then in some cases the impossibility results derived from FPC no longer apply.
Learning Compositional Functions with Transformers from Easy-to-Hard Data
Venue: arXiv cs.LG 2025
Year: 2025

Transformer-based language models have demonstrated impressive capabilities across a range of complex reasoning tasks. Prior theoretical work exploring the expressive power of transformers has shown that they can efficiently perform multi-step reasoning tasks involving parallelizable computations. However, the learnability of such constructions, particularly the conditions on the data distribution that enable efficient learning via gradient-based optimization, remains an open question. Towards answering this question, in this work we study the learnability of the $k$-fold composition task, which requires computing an interleaved composition of $k$ input permutations and $k$ hidden permutations, and can be expressed by a transformer with $O(\log k)$ layers. On the negative front, we prove a Statistical Query (SQ) lower bound showing that any SQ learner that makes only polynomially-many queries to an SQ oracle for the $k$-fold composition task distribution must have sample size exponential in $k$, thus establishing a statistical-computational gap. On the other hand, we show that this function class can be efficiently learned, with runtime and sample complexity polynomial in $k$, by gradient descent on an $O(\log k)$-depth transformer via two different curriculum learning strategies: one in which data consists of $k'$-fold composition functions with $k' \le k$ presented in increasing difficulty, and another in which all such data is presented simultaneously. Our work sheds light on the necessity and sufficiency of having both easy and hard examples in the data distribution for transformers to learn complex compositional tasks.
(U)NFV: Supervised and Unsupervised Neural Finite Volume Methods for Solving Hyperbolic PDEs
Venue: arXiv cs.LG 2025
Year: 2025

We introduce (U)NFV, a modular neural network architecture that generalizes classical finite volume (FV) methods for solving hyperbolic conservation laws. Hyperbolic partial differential equations (PDEs) are challenging to solve, particularly conservation laws whose physically relevant solutions contain shocks and discontinuities. FV methods are widely used for their mathematical properties: convergence to entropy solutions, flow conservation, or total variation diminishing, but often lack accuracy and flexibility in complex settings. Neural Finite Volume addresses these limitations by learning update rules over extended spatial and temporal stencils while preserving conservation structure. It supports both supervised training on solution data (NFV) and unsupervised training via weak-form residual loss (UNFV). Applied to first-order conservation laws, (U)NFV achieves up to 10x lower error than Godunov's method, outperforms ENO/WENO, and rivals discontinuous Galerkin solvers with far less complexity. On traffic modeling problems, both from PDEs and from experimental highway data, (U)NFV captures nonlinear wave dynamics with significantly higher fidelity and scalability than traditional FV approaches.
Distributed Federated Learning for Vehicular Network Security: Anomaly Detection Benefits and Multi-Domain Attack Threats
Venue: arXiv cs.NI 2025
Year: 2025

In connected and autonomous vehicles, machine learning for safety message classification has become critical for detecting malicious or anomalous behavior. However, conventional approaches that rely on centralized data collection or purely local training face limitations due to the large scale, high mobility, and heterogeneous data distributions inherent in inter-vehicle networks. To overcome these challenges, this paper explores Distributed Federated Learning (DFL), whereby vehicles collaboratively train deep learning models by exchanging model updates among one-hop neighbors and propagating models over multiple hops. Using the Vehicular Reference Misbehavior (VeReMi) Extension Dataset, we show that DFL can significantly improve classification accuracy across all vehicles compared to learning strictly with local data. Notably, vehicles with low individual accuracy see substantial accuracy gains through DFL, illustrating the benefit of knowledge sharing across the network. We further show that local training data size and time-varying network connectivity correlate strongly with the model's overall accuracy. We investigate DFL's resilience and vulnerabilities under attacks in multiple domains, namely wireless jamming and training data poisoning attacks. Our results reveal important insights into the vulnerabilities of DFL when confronted with multi-domain attacks, underlining the need for more robust strategies to secure DFL in vehicular networks.
DiffER: Categorical Diffusion for Chemical Retrosynthesis
Venue: arXiv cs.LG 2025
Year: 2025

Methods for automatic chemical retrosynthesis have found recent success through the application of models traditionally built for natural language processing, primarily through transformer neural networks. These models have demonstrated significant ability to translate between the SMILES encodings of chemical products and reactants, but are constrained as a result of their autoregressive nature. We propose DiffER, an alternative template-free method for retrosynthesis prediction in the form of categorical diffusion, which allows the entire output SMILES sequence to be predicted in unison. We construct an ensemble of diffusion models which achieves state-of-the-art performance for top-1 accuracy and competitive performance for top-3, top-5, and top-10 accuracy among template-free methods. We prove that DiffER is a strong baseline for a new class of template-free model, capable of learning a variety of synthetic techniques used in laboratory settings and outperforming a variety of other template-free methods on top-k accuracy metrics. By constructing an ensemble of categorical diffusion models with a novel length prediction component with variance, our method is able to approximately sample from the posterior distribution of reactants, producing results with strong metrics of confidence and likelihood. Furthermore, our analyses demonstrate that accurate prediction of the SMILES sequence length is key to further boosting the performance of categorical diffusion models.