OpenRaiser/Intern-Atlas huggingface dataset:
Describe Anything in Medical Images
Venue: arXiv cs.CV 2025
Year: 2025

Localized image captioning has made significant progress with models like the Describe Anything Model (DAM), which can generate detailed region-specific descriptions without explicit region-text supervision. However, such capabilities have yet to be widely applied to specialized domains like medical imaging, where diagnostic interpretation relies on subtle regional findings rather than global understanding. To mitigate this gap, we propose MedDAM, the first comprehensive framework leveraging large vision-language models for region-specific captioning in medical images. MedDAM employs medical expert-designed prompts tailored to specific imaging modalities and establishes a robust evaluation benchmark comprising a customized assessment protocol, data pre-processing pipeline, and specialized QA template library. This benchmark evaluates both MedDAM and other adaptable large vision-language models, focusing on clinical factuality through attribute-level verification tasks, thereby circumventing the absence of ground-truth region-caption pairs in medical datasets. Extensive experiments on the VinDr-CXR, LIDC-IDRI, and SkinCon datasets demonstrate MedDAM's superiority over leading peers (including GPT-4o, Claude 3.7 Sonnet, LLaMA-3.2 Vision, Qwen2.5-VL, GPT-4Rol, and OMG-LLaVA) in the task, revealing the importance of region-level semantic alignment in medical image understanding and establishing MedDAM as a promising foundation for clinical vision-language integration.
RefRef: A Synthetic Dataset and Benchmark for Reconstructing Refractive and Reflective Objects
Venue: arXiv cs.CV 2025
Year: 2025

Modern 3D reconstruction and novel view synthesis approaches have demonstrated strong performance on scenes with opaque Lambertian objects. However, most assume straight light paths and therefore cannot properly handle refractive and reflective materials. Moreover, datasets specialized for these effects are limited, stymieing efforts to evaluate performance and develop suitable techniques. In this work, we introduce a synthetic RefRef dataset and benchmark for reconstructing scenes with refractive and reflective objects from posed images. Our dataset has 50 such objects of varying complexity, from single-material convex shapes to multi-material non-convex shapes, each placed in three different background types, resulting in 150 scenes. We also propose an oracle method that, given the object geometry and refractive indices, calculates accurate light paths for neural rendering, and an approach based on this that avoids these assumptions. We benchmark these against several state-of-the-art methods and show that all methods lag significantly behind the oracle, highlighting the challenges of the task and dataset.
AgentVigil: Generic Black-Box Red-teaming for Indirect Prompt Injection against LLM Agents
Venue: arXiv cs.CR 2025
Year: 2025

The strong planning and reasoning capabilities of Large Language Models (LLMs) have fostered the development of agent-based systems capable of leveraging external tools and interacting with increasingly complex environments. However, these powerful features also introduce a critical security risk: indirect prompt injection, a sophisticated attack vector that compromises the core of these agents, the LLM, by manipulating contextual information rather than direct user prompts. In this work, we propose a generic black-box fuzzing framework, AgentVigil, designed to automatically discover and exploit indirect prompt injection vulnerabilities across diverse LLM agents. Our approach starts by constructing a high-quality initial seed corpus, then employs a seed selection algorithm based on Monte Carlo Tree Search (MCTS) to iteratively refine inputs, thereby maximizing the likelihood of uncovering agent weaknesses. We evaluate AgentVigil on two public benchmarks, AgentDojo and VWA-adv, where it achieves 71% and 70% success rates against agents based on o3-mini and GPT-4o, respectively, nearly doubling the performance of baseline attacks. Moreover, AgentVigil exhibits strong transferability across unseen tasks and internal LLMs, as well as promising results against defenses. Beyond benchmark evaluations, we apply our attacks in real-world environments, successfully misleading agents to navigate to arbitrary URLs, including malicious sites.
Collecting Human Motion Data in Large and Occlusion-Prone Environments using Ultra-Wideband Localization
Venue: arXiv cs.RO 2025
Year: 2025

With robots increasingly integrating into human environments, understanding and predicting human motion is essential for safe and efficient interactions. Modern human motion and activity prediction approaches require high quality and quantity of data for training and evaluation, usually collected from motion capture systems, onboard or stationary sensors. Setting up these systems is challenging due to the intricate setup of hardware components, extensive calibration procedures, occlusions, and substantial costs. These constraints make deploying such systems in new and large environments difficult and limit their usability for in-the-wild measurements. In this paper we investigate the possibility to apply the novel Ultra-Wideband (UWB) localization technology as a scalable alternative for human motion capture in crowded and occlusion-prone environments. We include additional sensing modalities such as eye-tracking, onboard robot LiDAR and radar sensors, and record motion capture data as ground truth for evaluation and comparison. The environment imitates a museum setup, with up to four active participants navigating toward random goals in a natural way, and offers more than 130 minutes of multi-modal data. Our investigation provides a step toward scalable and accurate motion data collection beyond vision-based systems, laying a foundation for evaluating sensing modalities like UWB in larger and complex environments like warehouses, airports, or convention centers.
DawnPiper: A Memory-scablable Pipeline Parallel Training Framework
Venue: arXiv cs.DC 2025
Year: 2025

Pipeline parallelism is a crucial paradigm for large-scale model training. However, imbalances in memory footprint across stages can lead to significant GPU memory wastage, limiting the model sizes that pipeline parallelism can effectively support. In this paper, we introduce DawnPiper, a memory-scalable pipeline parallel training framework. Firstly, we develop a DL compilation-based profiling method that transforms the model into a fine-grained computation graph. This refinement gives us a finer granularity of model partitioning and memory optimization while facilitating automatic code generation. Based on observed memory usage characteristics, we derive a performance-optimal theorem for pipeline parallel partitioning that substantially reduces the partition search space. Secondly, we propose a binary pipeline partitioning algorithm and utilize a cost-model based memory optimization approach to efficiently identify nearly optimal pipeline parallel strategy. DawnPiper achieves up to a 4x and 11x increase in trainable maximum batch size compared to vPipe and PipeDream, respectively, and provides up to a 1.5x performance speedup compared to vPipe.
Symbol-based entity marker highlighting for enhanced text mining in materials science with generative AI
Venue: arXiv cs.CL 2025
Year: 2025

The construction of experimental datasets is essential for expanding the scope of data-driven scientific discovery. Recent advances in natural language processing (NLP) have facilitated automatic extraction of structured data from unstructured scientific literature. While existing approaches-multi-step and direct methods-offer valuable capabilities, they also come with limitations when applied independently. Here, we propose a novel hybrid text-mining framework that integrates the advantages of both methods to convert unstructured scientific text into structured data. Our approach first transforms raw text into entity-recognized text, and subsequently into structured form. Furthermore, beyond the overall data structuring framework, we also enhance entity recognition performance by introducing an entity marker-a simple yet effective technique that uses symbolic annotations to highlight target entities. Specifically, our entity marker-based hybrid approach not only consistently outperforms previous entity recognition approaches across three benchmark datasets (MatScholar, SOFC, and SOFC slot NER) but also improve the quality of final structured data-yielding up to a 58% improvement in entity-level F1 score and up to 83% improvement in relation-level F1 score compared to direct approach.
Independence Under Incomplete Information
Venue: arXiv cs.DB 2025
Year: 2025

We initiate an investigation how the fundamental concept of independence can be represented effectively in the presence of incomplete information in relational databases. The concepts of possible and certain independence are proposed, and first results regarding the axiomatisability and computational complexity of implication problems associated with these concepts are established. In addition, several results for the data and the combined complexity of model checking are presented. The findings help reduce computational overheads associated with the processing of updates and answering of queries.
Generative Discovery of Partial Differential Equations by Learning from Math Handbooks
Venue: arXiv cs.LG 2025
Year: 2025

Data driven discovery of partial differential equations (PDEs) is a promising approach for uncovering the underlying laws governing complex systems. However, purely data driven techniques face the dilemma of balancing search space with optimization efficiency. This study introduces a knowledge guided approach that incorporates existing PDEs documented in a mathematical handbook to facilitate the discovery process. These PDEs are encoded as sentence like structures composed of operators and basic terms, and used to train a generative model, called EqGPT, which enables the generation of free form PDEs. A loop of generation evaluation optimization is constructed to autonomously identify the most suitable PDE. Experimental results demonstrate that this framework can recover a variety of PDE forms with high accuracy and computational efficiency, particularly in cases involving complex temporal derivatives or intricate spatial terms, which are often beyond the reach of conventional methods. The approach also exhibits generalizability to irregular spatial domains and higher dimensional settings. Notably, it succeeds in discovering a previously unreported PDE governing strongly nonlinear surface gravity waves propagating toward breaking, based on real world experimental data, highlighting its applicability to practical scenarios and its potential to support scientific discovery.
A 3D pocket-aware and evolutionary conserved interaction guided diffusion model for molecular optimization
Venue: arXiv cs.LG 2025
Year: 2025

Generating molecules that bind to specific protein targets via diffusion models has shown good promise for structure-based drug design and molecule optimization. Especially, the diffusion models with binding interaction guidance enables molecule generation with high affinity through forming favorable interaction within protein pocket. However, the generated molecules may not form interactions with the highly conserved residues, which are important for protein functions and bioactivities of the ligands. Herein, we developed a new 3D target-aware diffusion model DiffDecip, which explicitly incorporates the protein-ligand binding interactions and evolutionary conservation information of protein residues into both diffusion and sampling process, for molecule optimization through scaffold decoration. The model performance revealed that DiffDecip outperforms baseline model DiffDec on molecule optimization towards higher affinity through forming more non-covalent interactions with highly conserved residues in the protein pocket.
Combining Abstract Argumentation and Machine Learning for Efficiently Analyzing Low-Level Process Event Streams
Venue: arXiv cs.AI 2025
Year: 2025

Monitoring and analyzing process traces is a critical task for modern companies and organizations. In scenarios where there is a gap between trace events and reference business activities, this entails an interpretation problem, amounting to translating each event of any ongoing trace into the corresponding step of the activity instance. Building on a recent approach that frames the interpretation problem as an acceptance problem within an Abstract Argumentation Framework (AAF), one can elegantly analyze plausible event interpretations (possibly in an aggregated form), as well as offer explanations for those that conflict with prior process knowledge. Since, in settings where event-to-activity mapping is highly uncertain (or simply under-specified) this reasoning-based approach may yield lowly-informative results and heavy computation, one can think of discovering a sequencetagging model, trained to suggest highly-probable candidate event interpretations in a context-aware way. However, training such a model optimally may require using a large amount of manually-annotated example traces. Considering the urgent need of developing Green AI solutions enabling environmental and societal sustainability (with reduced labor/computational costs and carbon footprint), we propose a data/computation-efficient neuro-symbolic approach to the problem, where the candidate interpretations returned by the example-driven sequence tagger is refined by the AAF-based reasoner. This allows us to also leverage prior knowledge to compensate for the scarcity of example data, as confirmed by experimental results; clearly, this property is particularly useful in settings where data annotation and model optimization costs are subject to stringent constraints.
Register and [CLS] tokens yield a decoupling of local and global features in large ViTs
Venue: arXiv cs.CV 2025
Year: 2025

Recent work has shown that the attention maps of the widely popular DINOv2 model exhibit artifacts, which hurt both model interpretability and performance on dense image tasks. These artifacts emerge due to the model repurposing patch tokens with redundant local information for the storage of global image information. To address this problem, additional register tokens have been incorporated in which the model can store such information instead. We carefully examine the influence of these register tokens on the relationship between global and local image features, showing that while register tokens yield cleaner attention maps, these maps do not accurately reflect the integration of local image information in large models. Instead, global information is dominated by information extracted from register tokens, leading to a disconnect between local and global features. Inspired by these findings, we show that the [CLS] token itself leads to a very similar phenomenon in models without explicit register tokens. Our work shows that care must be taken when interpreting attention maps of large ViTs. Further, by clearly attributing the faulty behavior to register and [CLS] tokens, we show a path towards more interpretable vision models.
LightNobel: Improving Sequence Length Limitation in Protein Structure Prediction Model via Adaptive Activation Quantization
Venue: arXiv cs.AR 2025
Year: 2025

Recent advances in Protein Structure Prediction Models (PPMs), such as AlphaFold2 and ESMFold, have revolutionized computational biology by achieving unprecedented accuracy in predicting three-dimensional protein folding structures. However, these models face significant scalability challenges, particularly when processing proteins with long amino acid sequences (e.g., sequence length > 1,000). The primary bottleneck that arises from the exponential growth in activation sizes is driven by the unique data structure in PPM, which introduces an additional dimension that leads to substantial memory and computational demands. These limitations have hindered the effective scaling of PPM for real-world applications, such as analyzing large proteins or complex multimers with critical biological and pharmaceutical relevance. In this paper, we present LightNobel, the first hardware-software co-designed accelerator developed to overcome scalability limitations on the sequence length in PPM. At the software level, we propose Token-wise Adaptive Activation Quantization (AAQ), which leverages unique token-wise characteristics, such as distogram patterns in PPM activations, to enable fine-grained quantization techniques without compromising accuracy. At the hardware level, LightNobel integrates the multi-precision reconfigurable matrix processing unit (RMPU) and versatile vector processing unit (VVPU) to enable the efficient execution of AAQ. Through these innovations, LightNobel achieves up to 8.44x, 8.41x speedup and 37.29x, 43.35x higher power efficiency over the latest NVIDIA A100 and H100 GPUs, respectively, while maintaining negligible accuracy loss. It also reduces the peak memory requirement up to 120.05x in PPM, enabling scalable processing for proteins with long sequences.
Exploring the Susceptibility to Fraud of Monetary Incentive Mechanisms for Strengthening FOSS Projects
Venue: arXiv cs.CR 2025
Year: 2025

Free and open source software (FOSS) is ubiquitous on modern IT systems, accelerating the speed of software engineering over the past decades. With its increasing importance and historical reliance on uncompensated contributions, questions have been raised regarding the continuous maintenance of FOSS and its implications from a security perspective. In recent years, different funding programs have emerged to provide external incentives to reinforce community FOSS' sustainability. Past research primarily focused on analyses what type of projects have been funded and for what reasons. However, it has neither been considered whether there is a need for such external incentives, nor whether the incentive mechanisms, especially with the development of decentralized approaches, are susceptible to fraud. In this study, we explore the need for funding through a literature review and compare the susceptibility to fraud of centralized and decentralized incentive programs by performing case studies on the Sovereign Tech Fund (STF) and the tea project. We find non-commercial incentives to fill an important gap, ensuring longevity and sustainability of projects. Furthermore, we find the STF to be able to achieve a high resilience against fraud attempts, while tea is highly susceptible to fraud, as evidenced by revelation of an associated sybil attack on npm. Our results imply that special considerations must be taken into account when utilizing quantitative repository metrics regardless whether spoofing is expected.
Privacy-Preserving Credit Card Approval Using Homomorphic SVM: Toward Secure Inference in FinTech Applications
Venue: arXiv cs.CR 2025
Year: 2025

The growing use of machine learning in cloud environments raises critical concerns about data security and privacy, especially in finance. Fully Homomorphic Encryption (FHE) offers a solution by enabling computations on encrypted data, but its high computational cost limits practicality. In this paper, we propose PP-FinTech, a privacy-preserving scheme for financial applications that employs a CKKS-based encrypted soft-margin SVM, enhanced with a hybrid kernel for modeling non-linear patterns and an adaptive thresholding mechanism for robust encrypted classification. Experiments on the Credit Card Approval dataset demonstrate comparable performance to the plaintext models, highlighting PP-FinTech's ability to balance privacy, and efficiency in secure financial ML systems.
NeoQA: Evidence-based Question Answering with Generated News Events
Venue: arXiv cs.CL 2025
Year: 2025

Evaluating Retrieval-Augmented Generation (RAG) in large language models (LLMs) is challenging because benchmarks can quickly become stale. Questions initially requiring retrieval may become answerable from pretraining knowledge as newer models incorporate more recent information during pretraining, making it difficult to distinguish evidence-based reasoning from recall. We introduce NeoQA (News Events for Out-of-training Question Answering), a benchmark designed to address this issue. To construct NeoQA, we generated timelines and knowledge bases of fictional news events and entities along with news articles and Q\&A pairs to prevent LLMs from leveraging pretraining knowledge, ensuring that no prior evidence exists in their training data. We propose our dataset as a new platform for evaluating evidence-based question answering, as it requires LLMs to generate responses exclusively from retrieved evidence and only when sufficient evidence is available. NeoQA enables controlled evaluation across various evidence scenarios, including cases with missing or misleading details. Our findings indicate that LLMs struggle to distinguish subtle mismatches between questions and evidence, and suffer from short-cut reasoning when key information required to answer a question is missing from the evidence, underscoring key limitations in evidence-based reasoning.
Modeling Multi-Hop Semantic Paths for Recommendation in Heterogeneous Information Networks
Venue: arXiv cs.IR 2025
Year: 2025

This study focuses on the problem of path modeling in heterogeneous information networks and proposes a multi-hop path-aware recommendation framework. The method centers on multi-hop paths composed of various types of entities and relations. It models user preferences through three stages: path selection, semantic representation, and attention-based fusion. In the path selection stage, a path filtering mechanism is introduced to remove redundant and noisy information. In the representation learning stage, a sequential modeling structure is used to jointly encode entities and relations, preserving the semantic dependencies within paths. In the fusion stage, an attention mechanism assigns different weights to each path to generate a global user interest representation. Experiments conducted on real-world datasets such as Amazon-Book show that the proposed method significantly outperforms existing recommendation models across multiple evaluation metrics, including HR@10, Recall@10, and Precision@10. The results confirm the effectiveness of multi-hop paths in capturing high-order interaction semantics and demonstrate the expressive modeling capabilities of the framework in heterogeneous recommendation scenarios. This method provides both theoretical and practical value by integrating structural information modeling in heterogeneous networks with recommendation algorithm design. It offers a more expressive and flexible paradigm for learning user preferences in complex data environments.
Maths with Coq in L1, a pedagogical experiment
Venue: arXiv cs.LO 2025
Year: 2025

In France, the first year of study at university is usually abbreviated L1 (for premiere annee de Licence). At Sorbonne Paris Nord University, we have been teaching an 18 hour introductory course in formal proofs to L1 students for 3 years. These students are in a double major mathematics and computer science curriculum. The course is mandatory and consists only of hands-on sessions with the Coq proof assistant. We present some of the practical sessions worksheets, the methodology we used to write them and some of the pitfalls we encountered. Finally we discuss how this course evolved over the years and will see that there is room for improvement in many different technical and pedagogical aspects.