OpenRaiser/Intern-Atlas huggingface dataset:
StarBASE-GP: Biologically-Guided Automated Machine Learning for Genotype-to-Phenotype Association Analysis
Venue: arXiv cs.NE 2025
Year: 2025

We present the Star-Based Automated Single-locus and Epistasis analysis tool - Genetic Programming (StarBASE-GP), an automated framework for discovering meaningful genetic variants associated with phenotypic variation in large-scale genomic datasets. StarBASE-GP uses a genetic programming-based multi-objective optimization strategy to evolve machine learning pipelines that simultaneously maximize explanatory power (r2) and minimize pipeline complexity. Biological domain knowledge is integrated at multiple stages, including the use of nine inheritance encoding strategies to model deviations from additivity, a custom linkage disequilibrium pruning node that minimizes redundancy among features, and a dynamic variant recommendation system that prioritizes informative candidates for pipeline inclusion. We evaluate StarBASE-GP on a cohort of Rattus norvegicus (brown rat) to identify variants associated with body mass index, benchmarking its performance against a random baseline and a biologically naive version of the tool. StarBASE-GP consistently evolves Pareto fronts with superior performance, yielding higher accuracy in identifying both ground truth and novel quantitative trait loci, highlighting relevant targets for future validation. By incorporating evolutionary search and relevant biological theory into a flexible automated machine learning framework, StarBASE-GP demonstrates robust potential for advancing variant discovery in complex traits.
MIAS-SAM: Medical Image Anomaly Segmentation without thresholding
Venue: arXiv cs.CV 2025
Year: 2025

This paper presents MIAS-SAM, a novel approach for the segmentation of anomalous regions in medical images. MIAS-SAM uses a patch-based memory bank to store relevant image features, which are extracted from normal data using the SAM encoder. At inference time, the embedding patches extracted from the SAM encoder are compared with those in the memory bank to obtain the anomaly map. Finally, MIAS-SAM computes the center of gravity of the anomaly map to prompt the SAM decoder, obtaining an accurate segmentation from the previously extracted features. Differently from prior works, MIAS-SAM does not require to define a threshold value to obtain the segmentation from the anomaly map. Experimental results conducted on three publicly available datasets, each with a different imaging modality (Brain MRI, Liver CT, and Retina OCT) show accurate anomaly segmentation capabilities measured using DICE score. The code is available at: https://github.com/warpcut/MIAS-SAM
Multivariate de Bruijn Graphs: A Symbolic Graph Framework for Time Series Forecasting
Venue: arXiv cs.LG 2025
Year: 2025

Time series forecasting remains a challenging task for foundation models due to temporal heterogeneity, high dimensionality, and the lack of inherent symbolic structure. In this work, we propose DRAGON (Discrete Representation and Augmented Graph encoding Over de BruijN Graphs), a novel encoder that introduces Multivariate de Bruijn Graphs (MdBGs) to bridge the gap between symbolic representations and neural modeling. DRAGON discretizes continuous input sequences and maps them onto a fixed graph structure, enabling dynamic context recovery via graph-based attention. Integrated as an auxiliary module within a dual-branch architecture, DRAGON augments conventional CNN-based encoders with symbolic, structure-aware representations. All code developed for this study is available at: https://github.com/KurbanIntelligenceLab/MultdBG-Time-Series-Library
Fast Trajectory-Independent Model-Based Reconstruction Algorithm for Multi-Dimensional Magnetic Particle Imaging
Venue: arXiv cs.CV 2025
Year: 2025

Magnetic Particle Imaging (MPI) is a promising tomographic technique for visualizing the spatio-temporal distribution of superparamagnetic nanoparticles, with applications ranging from cancer detection to real-time cardiovascular monitoring. Traditional MPI reconstruction relies on either time-consuming calibration (measured system matrix) or model-based simulation of the forward operator. Recent developments have shown the applicability of Chebyshev polynomials to multi-dimensional Lissajous Field-Free Point (FFP) scans. This method is bound to the particular choice of sinusoidal scanning trajectories. In this paper, we present the first reconstruction on real 2D MPI data with a trajectory-independent model-based MPI reconstruction algorithm. We further develop the zero-shot Plug-and-Play (PnP) algorithm of the authors -- with automatic noise level estimation -- to address the present deconvolution problem, leveraging a state-of-the-art denoiser trained on natural images without retraining on MPI-specific data. We evaluate our method on the publicly available 2D FFP MPI dataset ``MPIdata: Equilibrium Model with Anisotropy", featuring scans of six phantoms acquired using a Bruker preclinical scanner. Moreover, we show reconstruction performed on custom data on a 2D scanner with additional high-frequency excitation field and partial data. Our results demonstrate strong reconstruction capabilities across different scanning scenarios -- setting a precedent for general-purpose, flexible model-based MPI reconstruction.
Efficient Preimage Approximation for Neural Network Certification
Venue: arXiv cs.LG 2025
Year: 2025

The growing reliance on artificial intelligence in safety- and security-critical applications demands effective neural network certification. A challenging real-world use case is "patch attacks", where adversarial patches or lighting conditions obscure parts of images, for example, traffic signs. A significant step towards certification against patch attacks was recently achieved using PREMAP, which uses under- and over-approximations of the preimage, the set of inputs that lead to a specified output, for the certification. While the PREMAP approach is versatile, it is currently limited to fully-connected neural networks of moderate dimensionality. In order to tackle broader real-world use cases, we present novel algorithmic extensions to PREMAP involving tighter bounds, adaptive Monte Carlo sampling, and improved branching heuristics. Firstly, we demonstrate that these efficiency improvements significantly outperform the original PREMAP and enable scaling to convolutional neural networks that were previously intractable. Secondly, we showcase the potential of preimage approximation methodology for analysing and certifying reliability and robustness on a range of use cases from computer vision and control.
PGLearn -- An Open-Source Learning Toolkit for Optimal Power Flow
Venue: arXiv cs.LG 2025
Year: 2025

Machine Learning (ML) techniques for Optimal Power Flow (OPF) problems have recently garnered significant attention, reflecting a broader trend of leveraging ML to approximate and/or accelerate the resolution of complex optimization problems. These developments are necessitated by the increased volatility and scale in energy production for modern and future grids. However, progress in ML for OPF is hindered by the lack of standardized datasets and evaluation metrics, from generating and solving OPF instances, to training and benchmarking machine learning models. To address this challenge, this paper introduces PGLearn, a comprehensive suite of standardized datasets and evaluation tools for ML and OPF. PGLearn provides datasets that are representative of real-life operating conditions, by explicitly capturing both global and local variability in the data generation, and by, for the first time, including time series data for several large-scale systems. In addition, it supports multiple OPF formulations, including AC, DC, and second-order cone formulations. Standardized datasets are made publicly available to democratize access to this field, reduce the burden of data generation, and enable the fair comparison of various methodologies. PGLearn also includes a robust toolkit for training, evaluating, and benchmarking machine learning models for OPF, with the goal of standardizing performance evaluation across the field. By promoting open, standardized datasets and evaluation metrics, PGLearn aims at democratizing and accelerating research and innovation in machine learning applications for optimal power flow problems. Datasets are available for download at https://www.huggingface.co/PGLearn.
What Has Been Lost with Synthetic Evaluation?
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) are increasingly used for data generation. However, creating evaluation benchmarks raises the bar for this emerging paradigm. Benchmarks must target specific phenomena, penalize exploiting shortcuts, and be challenging. Through two case studies, we investigate whether LLMs can meet these demands by generating reasoning over-text benchmarks and comparing them to those created through careful crowdsourcing. Specifically, we evaluate both the validity and difficulty of LLM-generated versions of two high-quality reading comprehension datasets: CondaQA, which evaluates reasoning about negation, and DROP, which targets reasoning about quantities. We find that prompting LLMs can produce variants of these datasets that are often valid according to the annotation guidelines, at a fraction of the cost of the original crowdsourcing effort. However, we show that they are less challenging for LLMs than their human-authored counterparts. This finding sheds light on what may have been lost by generating evaluation data with LLMs, and calls for critically reassessing the immediate use of this increasingly prevalent approach to benchmark creation.
The National Research Platform: Stretched, Multi-Tenant, Scientific Kubernetes Cluster
Venue: arXiv cs.DC 2025
Year: 2025

The National Research Platform (NRP) represents a distributed, multi-tenant Kubernetes-based cyberinfrastructure designed to facilitate collaborative scientific computing. Spanning over 75 locations in the U.S. and internationally, the NRP uniquely integrates varied computational resources, ranging from single nodes to extensive GPU and CPU clusters, to support diverse research workloads including advanced AI and machine learning tasks. It emphasizes flexibility through user-friendly interfaces such as JupyterHub and low level control of resources through direct Kubernetes interaction. Critical operational insights are discussed, including security enhancements using Kubernetes-integrated threat detection, extensive monitoring, and comprehensive accounting systems. This paper highlights the NRP's growing importance and scalability in addressing the increasing demands for distributed scientific computational resources.
Visualizing Cloud-native Applications with KubeDiagrams
Venue: arXiv cs.SE 2025
Year: 2025

Modern distributed applications increasingly rely on cloud-native platforms to abstract the complexity of deployment and scalability. As the de facto orchestration standard, Kubernetes enables this abstraction, but its declarative configuration model makes the architectural understanding difficult. Developers, operators, and architects struggle to form accurate mental models from raw manifests, Helm charts, or cluster state descriptions. We introduce KubeDiagrams, an open-source tool that transforms Kubernetes manifests into architecture diagrams. By grounding our design in a user-centered study of real-world visualization practices, we identify the specific challenges Kubernetes users face and map these to concrete design requirements. KubeDiagrams integrates seamlessly with standard Kubernetes artifacts, preserves semantic fidelity to core concepts, and supports extensibility and automation. We detail the tool's architecture, visual encoding strategies, and extensibility mechanisms. Three case studies illustrate how KubeDiagrams enhances system comprehension and supports architectural reasoning in distributed cloud-native systems. KubeDiagrams addresses concrete pain points in Kubernetes-based DevOps practices and is valued for its automation, clarity, and low-friction integration into real-world tooling environments.
When Models Reason in Your Language: Controlling Thinking Language Comes at the Cost of Accuracy
Venue: arXiv cs.CL 2025
Year: 2025

Recent Large Reasoning Models (LRMs) with thinking traces have shown strong performance on English reasoning tasks. However, their ability to think in other languages is less studied. This capability is as important as answer accuracy for real world applications because users may find the reasoning trace useful for oversight only when it is expressed in their own language. We comprehensively evaluate two leading families of LRMs on our XReasoning benchmark and find that even the most advanced models often revert to English or produce fragmented reasoning in other languages, revealing a substantial gap in multilingual reasoning. Prompt based interventions that force models to reason in the users language improve readability and oversight but reduce answer accuracy, exposing an important trade off. We further show that targeted post training on just 100 examples mitigates this mismatch, though some accuracy loss remains. Our results highlight the limited multilingual reasoning capabilities of current LRMs and outline directions for future work. Code and data are available at https://github.com/Betswish/mCoT-XReasoning.
HiLDe: Intentional Code Generation via Human-in-the-Loop Decoding
Venue: arXiv cs.HC 2025
Year: 2025

While AI programming tools hold the promise of increasing programmers' capabilities and productivity to a remarkable degree, they often exclude users from essential decision-making processes, causing many to effectively "turn off their brains" and over-rely on solutions provided by these systems. These behaviors can have severe consequences in critical domains, like software security. We propose Human-in-the-loop Decoding, a novel interaction technique that allows users to observe and directly influence LLM decisions during code generation, in order to align the model's output with their personal requirements. We implement this technique in HiLDe, a code completion assistant that highlights critical decisions made by the LLM and provides local alternatives for the user to explore. In a within-subjects study (N=18) on security-related tasks, we found that HiLDe led participants to generate significantly fewer vulnerabilities and better align code generation with their goals compared to a traditional code completion assistant.
Conversational Alignment with Artificial Intelligence in Context
Venue: arXiv cs.CY 2025
Year: 2025

The development of sophisticated artificial intelligence (AI) conversational agents based on large language models raises important questions about the relationship between human norms, values, and practices and AI design and performance. This article explores what it means for AI agents to be conversationally aligned to human communicative norms and practices for handling context and common ground and proposes a new framework for evaluating developers' design choices. We begin by drawing on the philosophical and linguistic literature on conversational pragmatics to motivate a set of desiderata, which we call the CONTEXT-ALIGN framework, for conversational alignment with human communicative practices. We then suggest that current large language model (LLM) architectures, constraints, and affordances may impose fundamental limitations on achieving full conversational alignment.
LLM-based HSE Compliance Assessment: Benchmark, Performance, and Advancements
Venue: arXiv cs.CL 2025
Year: 2025

Health, Safety, and Environment (HSE) compliance assessment demands dynamic real-time decision-making under complicated regulations and complex human-machine-environment interactions. While large language models (LLMs) hold significant potential for decision intelligence and contextual dialogue, their capacity for domain-specific knowledge in HSE and structured legal reasoning remains underexplored. We introduce HSE-Bench, the first benchmark dataset designed to evaluate the HSE compliance assessment capabilities of LLM. HSE-Bench comprises over 1,000 manually curated questions drawn from regulations, court cases, safety exams, and fieldwork videos, and integrates a reasoning flow based on Issue spotting, rule Recall, rule Application, and rule Conclusion (IRAC) to assess the holistic reasoning pipeline. We conduct extensive evaluations on different prompting strategies and more than 10 LLMs, including foundation models, reasoning models and multimodal vision models. The results show that, although current LLMs achieve good performance, their capabilities largely rely on semantic matching rather than principled reasoning grounded in the underlying HSE compliance context. Moreover, their native reasoning trace lacks the systematic legal reasoning required for rigorous HSE compliance assessment. To alleviate these, we propose a new prompting technique, Reasoning of Expert (RoE), which guides LLMs to simulate the reasoning process of different experts for compliance assessment and reach a more accurate unified decision. We hope our study highlights reasoning gaps in LLMs for HSE compliance and inspires further research on related tasks.
Seeing the Politics of Decentralized Social Media Protocols
Venue: arXiv cs.SI 2025
Year: 2025

Calls to decentralize feed-based social media have been driven by concerns about the concentrated power of centralized platforms and their societal impact. In response, numerous decentralized social media protocols have emerged, each interpreting "decentralization" in different ways. We analyze four such protocols -- ActivityPub, AT Protocol, Nostr, and Farcaster -- to develop a novel conceptual framework for understanding how protocols operationalize decentralization. Drawing from protocol documentation, media coverage, and first-hand interviews with protocol developers and experts, we contextualize each protocol's approach within their respective socio-technical goals. Our framework highlights how control over key components is distributed differently across each protocol, shaping who holds power over what kinds of decisions. How components are arranged in relation to one another further impacts how component owners might offset each other's power in shaping social media. We argue that examining protocols as artifacts reveals how values shape infrastructure and power dynamics -- and that with a holistic framework as a guide, we can more effectively evaluate and design decentralized platforms aligned with the social and political futures we envision.
Agile Orchestration at Will: An Entire Smart Service-Based Security Architecture Towards 6G
Venue: arXiv cs.NI 2025
Year: 2025

The upcoming 6G will fundamentally reshape mobile networks beyond communications, unlocking a multitude of applications that were once considered unimaginable. Meanwhile, security and resilience are especially highlighted in the 6G design principles. However, safeguarding 6G networks will be quite challenging due to various known and unknown threats from highly heterogeneous networks and diversified security requirements of distinct use cases, calling for a comprehensive re-design of security architecture. This motivates us to propose ES3A (Entire Smart Service-based Security Architecture), a novel security architecture for 6G networks. Specifically, we first discuss six high-level principles of our ES3A that include hierarchy, flexibility, scalability, resilience, endogeny, and trust and privacy. With these goals in mind, we then introduce three guidelines from a deployment perspective, envisioning our ES3A that offers service-based security, end-to-end protection, and smart security automation for 6G networks. Our architecture consists of three layers and three domains. It relies on a two-stage orchestration mechanism to tailor smart security strategies for customized protection in high-dynamic 6G networks, thereby addressing the aforementioned challenges. Finally, we prototype the proposed ES3A on a real-world radio system based on Software-Defined Radio (SDR). Experiments show the effectiveness of our ES3A. We also provide a case to show the superiority of our architecture.
MermaidFlow: Redefining Agentic Workflow Generation via Safety-Constrained Evolutionary Programming
Venue: arXiv cs.LG 2025
Year: 2025

Despite the promise of autonomous agentic reasoning, existing workflow generation methods frequently produce fragile, unexecutable plans due to unconstrained LLM-driven construction. We introduce MermaidFlow, a framework that redefines the agentic search space through safety-constrained graph evolution. At its core, MermaidFlow represent workflows as a verifiable intermediate representation using Mermaid, a structured and human-interpretable graph language. We formulate domain-aware evolutionary operators, i.e., crossover, mutation, insertion, and deletion, to preserve semantic correctness while promoting structural diversity, enabling efficient exploration of a high-quality, statically verifiable workflow space. Without modifying task settings or evaluation protocols, MermaidFlow achieves consistent improvements in success rates and faster convergence to executable plans on the agent reasoning benchmark. The experimental results demonstrate that safety-constrained graph evolution offers a scalable, modular foundation for robust and interpretable agentic reasoning systems.
MOVi: Training-free Text-conditioned Multi-Object Video Generation
Venue: arXiv cs.CV 2025
Year: 2025

Recent advances in diffusion-based text-to-video (T2V) models have demonstrated remarkable progress, but these models still face challenges in generating videos with multiple objects. Most models struggle with accurately capturing complex object interactions, often treating some objects as static background elements and limiting their movement. In addition, they often fail to generate multiple distinct objects as specified in the prompt, resulting in incorrect generations or mixed features across objects. In this paper, we present a novel training-free approach for multi-object video generation that leverages the open world knowledge of diffusion models and large language models (LLMs). We use an LLM as the ``director'' of object trajectories, and apply the trajectories through noise re-initialization to achieve precise control of realistic movements. We further refine the generation process by manipulating the attention mechanism to better capture object-specific features and motion patterns, and prevent cross-object feature interference. Extensive experiments validate the effectiveness of our training free approach in significantly enhancing the multi-object generation capabilities of existing video diffusion models, resulting in 42% absolute improvement in motion dynamics and object generation accuracy, while also maintaining high fidelity and motion smoothness.