OpenRaiser/Intern-Atlas huggingface dataset:
MAGO-SP: Detection and Correction of Water-Fat Swaps in Magnitude-Only VIBE MRI
Venue: arXiv cs.CV 2025
Year: 2025

Volume Interpolated Breath-Hold Examination (VIBE) MRI generates images suitable for water and fat signal composition estimation. While the two-point VIBE provides water-fat-separated images, the six-point VIBE allows estimation of the effective transversal relaxation rate R2* and the proton density fat fraction (PDFF), which are imaging markers for health and disease. Ambiguity during signal reconstruction can lead to water-fat swaps. This shortcoming challenges the application of VIBE-MRI for automated PDFF analyses of large-scale clinical data and of population studies. This study develops an automated pipeline to detect and correct water-fat swaps in non-contrast-enhanced VIBE images. Our three-step pipeline begins with training a segmentation network to classify volumes as "fat-like" or "water-like," using synthetic water-fat swaps generated by merging fat and water volumes with Perlin noise. Next, a denoising diffusion image-to-image network predicts water volumes as signal priors for correction. Finally, we integrate this prior into a physics-constrained model to recover accurate water and fat signals. Our approach achieves a < 1% error rate in water-fat swap detection for a 6-point VIBE. Notably, swaps disproportionately affect individuals in the Underweight and Class 3 Obesity BMI categories. Our correction algorithm ensures accurate solution selection in chemical phase MRIs, enabling reliable PDFF estimation. This forms a solid technical foundation for automated large-scale population imaging analysis.
Disentangled Latent Spaces for Reduced Order Models using Deterministic Autoencoders
Venue: arXiv cs.LG 2025
Year: 2025

Data-driven reduced-order models based on autoencoders generally lack interpretability compared to classical methods such as the proper orthogonal decomposition. More interpretability can be gained by disentangling the latent variables and analyzing the resulting modes. For this purpose, probabilistic $β$-variational autoencoders ($β$-VAEs) are frequently used in computational fluid dynamics and other simulation sciences. Using a benchmark periodic flow dataset, we show that competitive results can be achieved using non-probabilistic autoencoder approaches that either promote orthogonality or penalize correlation between latent variables. Compared to probabilistic autoencoders, these approaches offer more robustness with respect to the choice of hyperparameters entering the loss function. We further demonstrate the ability of a non-probabilistic approach to identify a reduced number of active latent variables by introducing a correlation penalty, a function also known from the use of $β$-VAE. The investigated probabilistic and non-probabilistic autoencoder models are finally used for the dimensionality reduction of aircraft ditching loads, which serves as an industrial application in this work.
From Knowledge Generation to Knowledge Verification: Examining the BioMedical Generative Capabilities of ChatGPT
Venue: arXiv cs.AI 2025
Year: 2025

The generative capabilities of LLM models offer opportunities for accelerating tasks but raise concerns about the authenticity of the knowledge they produce. To address these concerns, we present a computational approach that evaluates the factual accuracy of biomedical knowledge generated by an LLM. Our approach consists of two processes: generating disease-centric associations and verifying these associations using the semantic framework of biomedical ontologies. Using ChatGPT as the selected LLM, we designed prompt-engineering processes to establish linkages between diseases and related drugs, symptoms, and genes, and assessed consistency across multiple ChatGPT models (e.g., GPT-turbo, GPT-4, etc.). Experimental results demonstrate high accuracy in identifying disease terms (88%-97%), drug names (90%-91%), and genetic information (88%-98%). However, symptom term identification was notably lower (49%-61%), due to the informal and verbose nature of symptom descriptions, which hindered effective semantic matching with the formal language of specialized ontologies. Verification of associations reveals literature coverage rates of 89%-91% for disease-drug and disease-gene pairs, while symptom-related associations exhibit lower coverage (49%-62%).
FLIGHT: Facility Location Integrating Generalized, Holistic Theory of Welfare
Venue: arXiv cs.GT 2025
Year: 2025

The Facility Location Problem (FLP) is a well-studied optimization problem with applications in many real-world scenarios. Past literature has explored the solutions from different perspectives to tackle FLPs. These include investigating FLPs under objective functions such as utilitarian, egalitarian, Nash welfare, etc. Also, there is no treatment for asymmetric welfare functions around the facility. We propose a unified framework, FLIGHT, to accommodate a broad class of welfare notions. The framework undergoes rigorous theoretical analysis, and we prove some structural properties of the solution to FLP. Additionally, we provide approximation bounds, which provide insight into an interesting fact: as the number of agents arbitrarily increases, the choice of welfare notion is irrelevant. Furthermore, the paper also includes results around concentration bounds under certain distributional assumptions over the preferred locations of agents.
On the Influence of Context Size and Model Choice in Retrieval-Augmented Generation Systems
Venue: arXiv cs.CL 2025
Year: 2025

Retrieval-augmented generation (RAG) has emerged as an approach to augment large language models (LLMs) by reducing their reliance on static knowledge and improving answer factuality. RAG retrieves relevant context snippets and generates an answer based on them. Despite its increasing industrial adoption, systematic exploration of RAG components is lacking, particularly regarding the ideal size of provided context, and the choice of base LLM and retrieval method. To help guide development of robust RAG systems, we evaluate various context sizes, BM25 and semantic search as retrievers, and eight base LLMs. Moving away from the usual RAG evaluation with short answers, we explore the more challenging long-form question answering in two domains, where a good answer has to utilize the entire context. Our findings indicate that final QA performance improves steadily with up to 15 snippets but stagnates or declines beyond that. Finally, we show that different general-purpose LLMs excel in the biomedical domain than the encyclopedic one, and that open-domain evidence retrieval in large corpora is challenging.
Tracking and Assigning Jobs to a Markov Machine
Venue: arXiv cs.IT 2025
Year: 2025

We consider a time-slotted communication system with a machine, a cloud server, and a sampler. Job requests from the users are queued on the server to be completed by the machine. The machine has two states, namely, a busy state and a free state. The server can assign a job to the machine in a first-in-first-served manner. If the machine is free, it completes the job request from the server; otherwise, it drops the request. Upon dropping a job request, the server is penalized. When the machine is in the free state, the machine can get into the busy state with an internal job. When the server does not assign a job request to the machine, the state of the machine evolves as a symmetric Markov chain. If the machine successfully accepts the job request from the server, the state of the machine goes to the busy state and follows a different dynamics compared to the dynamics when the machine goes to the busy state due to an internal job. The sampler samples the state of the machine and sends it to the server via an error-free channel. Thus, the server can estimate the state of the machine, upon receiving an update from the source. If the machine is in the free state but the estimated state at the server is busy, the sampler pays a cost. We incorporate the concept of the age of incorrect information to model the cost of the sampler. We aim to find an optimal sampling policy such that the cost of the sampler plus the penalty on the machine gets minimized. We formulate this problem in a Markov decision process framework and find how an optimal policy changes with several associated parameters. We show that a threshold policy is optimal for this problem. We show a necessary and sufficient condition for a threshold policy to be optimal. Finally, we find the optimal threshold without bounding the state space.
Real-Time Device Reach Forecasting Using HLL and MinHash Data Sketches
Venue: arXiv cs.DB 2025
Year: 2025

Predicting the right number of TVs (Device Reach) in real-time based on a user-specified targeting attributes is imperative for running multi-million dollar ADs business. The traditional approach of SQL queries to join billions of records across multiple targeting dimensions is extremely slow. As a workaround, many applications will have an offline process to crunch these numbers and present the results after many hours. In our case, the solution was an offline process taking 24 hours to onboard a customer resulting in a potential loss of business. To solve this problem, we have built a new real-time prediction system using MinHash and HyperLogLog (HLL) data sketches to compute the device reach at runtime when a user makes a request. However, existing MinHash implementations do not solve the complex problem of multilevel aggregation and intersection. This work will show how we have solved this problem, in addition, we have improved MinHash algorithm to run 4 times faster using Single Instruction Multiple Data (SIMD) vectorized operations for high speed and accuracy with constant space to process billions of records. Finally, by experiments, we prove that the results are as accurate as traditional offline prediction system with an acceptable error rate of 5%.
Structurally Disentangled Feature Fields Distillation for 3D Understanding and Editing
Venue: arXiv cs.CV 2025
Year: 2025

Recent work has demonstrated the ability to leverage or distill pre-trained 2D features obtained using large pre-trained 2D models into 3D features, enabling impressive 3D editing and understanding capabilities using only 2D supervision. Although impressive, models assume that 3D features are captured using a single feature field and often make a simplifying assumption that features are view-independent. In this work, we propose instead to capture 3D features using multiple disentangled feature fields that capture different structural components of 3D features involving view-dependent and view-independent components, which can be learned from 2D feature supervision only. Subsequently, each element can be controlled in isolation, enabling semantic and structural understanding and editing capabilities. For instance, using a user click, one can segment 3D features corresponding to a given object and then segment, edit, or remove their view-dependent (reflective) properties. We evaluate our approach on the task of 3D segmentation and demonstrate a set of novel understanding and editing tasks.
RendBEV: Semantic Novel View Synthesis for Self-Supervised Bird's Eye View Segmentation
Venue: arXiv cs.CV 2025
Year: 2025

Bird's Eye View (BEV) semantic maps have recently garnered a lot of attention as a useful representation of the environment to tackle assisted and autonomous driving tasks. However, most of the existing work focuses on the fully supervised setting, training networks on large annotated datasets. In this work, we present RendBEV, a new method for the self-supervised training of BEV semantic segmentation networks, leveraging differentiable volumetric rendering to receive supervision from semantic perspective views computed by a 2D semantic segmentation model. Our method enables zero-shot BEV semantic segmentation, and already delivers competitive results in this challenging setting. When used as pretraining to then fine-tune on labeled BEV ground-truth, our method significantly boosts performance in low-annotation regimes, and sets a new state of the art when fine-tuning on all available labels.
Middle-Layer Representation Alignment for Cross-Lingual Transfer in Fine-Tuned LLMs
Venue: arXiv cs.CL 2025
Year: 2025

While large language models demonstrate remarkable capabilities at task-specific applications through fine-tuning, extending these benefits across diverse languages is essential for broad accessibility. However, effective cross-lingual transfer is hindered by LLM performance gaps across languages and the scarcity of fine-tuning data in many languages. Through analysis of LLM internal representations from over 1,000+ language pairs, we discover that middle layers exhibit the strongest potential for cross-lingual alignment. Building on this finding, we propose a middle-layer alignment objective integrated into task-specific training. Our experiments on slot filling, machine translation, and structured text generation show consistent improvements in cross-lingual transfer, especially to lower-resource languages. The method is robust to the choice of alignment languages and generalizes to languages unseen during alignment. Furthermore, we show that separately trained alignment modules can be merged with existing task-specific modules, improving cross-lingual capabilities without full re-training. Our code is publicly available (https://github.com/dannigt/mid-align).
Benchmarking Multimodal RAG through a Chart-based Document Question-Answering Generation Framework
Venue: arXiv cs.AI 2025
Year: 2025

Multimodal Retrieval-Augmented Generation (MRAG) enhances reasoning capabilities by integrating external knowledge. However, existing benchmarks primarily focus on simple image-text interactions, overlooking complex visual formats like charts that are prevalent in real-world applications. In this work, we introduce a novel task, Chart-based MRAG, to address this limitation. To semi-automatically generate high-quality evaluation samples, we propose CHARt-based document question-answering GEneration (CHARGE), a framework that produces evaluation data through structured keypoint extraction, crossmodal verification, and keypoint-based generation. By combining CHARGE with expert validation, we construct Chart-MRAG Bench, a comprehensive benchmark for chart-based MRAG evaluation, featuring 4,738 question-answering pairs across 8 domains from real-world documents. Our evaluation reveals three critical limitations in current approaches: (1) unified multimodal embedding retrieval methods struggles in chart-based scenarios, (2) even with ground-truth retrieval, state-of-the-art MLLMs achieve only 58.19% Correctness and 73.87% Coverage scores, and (3) MLLMs demonstrate consistent text-over-visual modality bias during Chart-based MRAG reasoning. The CHARGE and Chart-MRAG Bench are released at https://github.com/Nomothings/CHARGE.git.
A Survey of Safety on Large Vision-Language Models: Attacks, Defenses and Evaluations
Venue: arXiv cs.CR 2025
Year: 2025

With the rapid advancement of Large Vision-Language Models (LVLMs), ensuring their safety has emerged as a crucial area of research. This survey provides a comprehensive analysis of LVLM safety, covering key aspects such as attacks, defenses, and evaluation methods. We introduce a unified framework that integrates these interrelated components, offering a holistic perspective on the vulnerabilities of LVLMs and the corresponding mitigation strategies. Through an analysis of the LVLM lifecycle, we introduce a classification framework that distinguishes between inference and training phases, with further subcategories to provide deeper insights. Furthermore, we highlight limitations in existing research and outline future directions aimed at strengthening the robustness of LVLMs. As part of our research, we conduct a set of safety evaluations on the latest LVLM, Deepseek Janus-Pro, and provide a theoretical analysis of the results. Our findings provide strategic recommendations for advancing LVLM safety and ensuring their secure and reliable deployment in high-stakes, real-world applications. This survey aims to serve as a cornerstone for future research, facilitating the development of models that not only push the boundaries of multimodal intelligence but also adhere to the highest standards of security and ethical integrity. Furthermore, to aid the growing research in this field, we have created a public repository to continuously compile and update the latest work on LVLM safety: https://github.com/XuankunRong/Awesome-LVLM-Safety .
Multi-Faceted Multimodal Monosemanticity
Venue: arXiv cs.CV 2025
Year: 2025

Humans experience the world through multiple modalities, such as, vision, language, and speech, making it natural to explore the commonality and distinctions among them. In this work, we take a data-driven approach to address this question by analyzing interpretable, monosemantic features extracted from deep multimodal models. Specifically, we investigate CLIP, a prominent visual-language representation model trained on massive image-text pairs. Building on prior research in single-modal interpretability, we develop a set of multi-modal interpretability tools and measures designed to disentangle and analyze features learned from CLIP. Specifically, we introduce the Modality Dominance Score (MDS) to attribute each CLIP feature to a specific modality. We then map CLIP features into a more interpretable space, enabling us to categorize them into three distinct classes: vision features (single-modal), language features (single-modal), and visual-language features (cross-modal). Interestingly, this data-driven categorization closely aligns with human intuitive understandings of different modalities. We further show that this modality decomposition can benefit multiple downstream tasks, including reducing bias in gender detection, generating cross-modal adversarial examples, and enabling modal-specific feature control in text-to-image generation. These results indicate that large-scale multimodal models, when equipped with task-agnostic interpretability tools, can offer valuable insights into the relationships between different data modalities.
NOTA: Multimodal Music Notation Understanding for Visual Large Language Model
Venue: arXiv cs.CV 2025
Year: 2025

Symbolic music is represented in two distinct forms: two-dimensional, visually intuitive score images, and one-dimensional, standardized text annotation sequences. While large language models have shown extraordinary potential in music, current research has primarily focused on unimodal symbol sequence text. Existing general-domain visual language models still lack the ability of music notation understanding. Recognizing this gap, we propose NOTA, the first large-scale comprehensive multimodal music notation dataset. It consists of 1,019,237 records, from 3 regions of the world, and contains 3 tasks. Based on the dataset, we trained NotaGPT, a music notation visual large language model. Specifically, we involve a pre-alignment training phase for cross-modal alignment between the musical notes depicted in music score images and their textual representation in ABC notation. Subsequent training phases focus on foundational music information extraction, followed by training on music notation analysis. Experimental results demonstrate that our NotaGPT-7B achieves significant improvement on music understanding, showcasing the effectiveness of NOTA and the training pipeline. Our datasets are open-sourced at https://huggingface.co/datasets/MYTH-Lab/NOTA-dataset.
A Comprehensive Survey on Concept Erasure in Text-to-Image Diffusion Models
Venue: arXiv cs.CV 2025
Year: 2025

Text-to-Image (T2I) models have made remarkable progress in generating high-quality, diverse visual content from natural language prompts. However, their ability to reproduce copyrighted styles, sensitive imagery, and harmful content raises significant ethical and legal concerns. Concept erasure offers a proactive alternative to external filtering by modifying T2I models to prevent the generation of undesired content. In this survey, we provide a structured overview of concept erasure, categorizing existing methods based on their optimization strategies and the architectural components they modify. We categorize concept erasure methods into fine-tuning for parameter updates, closed-form solutions for efficient edits, and inference-time interventions for content restriction without weight modification. Additionally, we explore adversarial attacks that bypass erasure techniques and discuss emerging defenses. To support further research, we consolidate key datasets, evaluation metrics, and benchmarks for assessing erasure effectiveness and model robustness. This survey serves as a comprehensive resource, offering insights into the evolving landscape of concept erasure, its challenges, and future directions.
Reading the unreadable: Creating a dataset of 19th century English newspapers using image-to-text language models
Venue: arXiv cs.CL 2025
Year: 2025

Oscar Wilde said, "The difference between literature and journalism is that journalism is unreadable, and literature is not read." Unfortunately, The digitally archived journalism of Oscar Wilde's 19th century often has no or poor quality Optical Character Recognition (OCR), reducing the accessibility of these archives and making them unreadable both figuratively and literally. This paper helps address the issue by performing OCR on "The Nineteenth Century Serials Edition" (NCSE), an 84k-page collection of 19th-century English newspapers and periodicals, using Pixtral 12B, a pre-trained image-to-text language model. The OCR capability of Pixtral was compared to 4 other OCR approaches, achieving a median character error rate of 1%, 5x lower than the next best model. The resulting NCSE v2.0 dataset features improved article identification, high-quality OCR, and text classified into four types and seventeen topics. The dataset contains 1.4 million entries, and 321 million words. Example use cases demonstrate analysis of topic similarity, readability, and event tracking. NCSE v2.0 is freely available to encourage historical and sociological research. As a result, 21st-century readers can now share Oscar Wilde's disappointment with 19th-century journalistic standards, reading the unreadable from the comfort of their own computers.
PathRAG: Pruning Graph-based Retrieval Augmented Generation with Relational Paths
Venue: arXiv cs.CL 2025
Year: 2025

Retrieval-augmented generation (RAG) improves the response quality of large language models (LLMs) by retrieving knowledge from external databases. Typical RAG approaches split the text database into chunks, organizing them in a flat structure for efficient searches. To better capture the inherent dependencies and structured relationships across the text database, researchers propose to organize textual information into an indexing graph, known asgraph-based RAG. However, we argue that the limitation of current graph-based RAG methods lies in the redundancy of the retrieved information, rather than its insufficiency. Moreover, previous methods use a flat structure to organize retrieved information within the prompts, leading to suboptimal performance. To overcome these limitations, we propose PathRAG, which retrieves key relational paths from the indexing graph, and converts these paths into textual form for prompting LLMs. Specifically, PathRAG effectively reduces redundant information with flow-based pruning, while guiding LLMs to generate more logical and coherent responses with path-based prompting. Experimental results show that PathRAG consistently outperforms state-of-the-art baselines across six datasets and five evaluation dimensions. The code is available at the following link: https://github.com/BUPT-GAMMA/PathRAG