OpenRaiser/Intern-Atlas huggingface dataset:
Horizontal and Vertical Federated Causal Structure Learning via Higher-order Cumulants
Venue: arXiv cs.LG 2025
Year: 2025

Federated causal discovery aims to uncover the causal relationships between entities while protecting data privacy, which has significant importance and numerous applications in real-world scenarios. Existing federated causal structure learning methods primarily focus on horizontal federated settings. However, in practical situations, different clients may not necessarily contain data on the same variables. In a single client, the incomplete set of variables can easily lead to spurious causal relationships, thereby affecting the information transmitted to other clients. To address this issue, we comprehensively consider causal structure learning methods under both horizontal and vertical federated settings. We provide the identification theories and methods for learning causal structure in the horizontal and vertical federal setting via higher-order cumulants. Specifically, we first aggregate higher-order cumulant information from all participating clients to construct global cumulant estimates. These global estimates are then used for recursive source identification, ultimately yielding a global causal strength matrix. Our approach not only enables the reconstruction of causal graphs but also facilitates the estimation of causal strength coefficients. Our algorithm demonstrates superior performance in experiments conducted on both synthetic data and real-world data.
Developing and Maintaining an Open-Source Repository of AI Evaluations: Challenges and Insights
Venue: arXiv cs.CL 2025
Year: 2025

AI evaluations have become critical tools for assessing large language model capabilities and safety. This paper presents practical insights from eight months of maintaining $inspect\_evals$, an open-source repository of 70+ community-contributed AI evaluations. We identify key challenges in implementing and maintaining AI evaluations and develop solutions including: (1) a structured cohort management framework for scaling community contributions, (2) statistical methodologies for optimal resampling and cross-model comparison with uncertainty quantification, and (3) systematic quality control processes for reproducibility. Our analysis reveals that AI evaluation requires specialized infrastructure, statistical rigor, and community coordination beyond traditional software development practices.
SCoRE: Streamlined Corpus-based Relation Extraction using Multi-Label Contrastive Learning and Bayesian kNN
Venue: arXiv cs.CL 2025
Year: 2025

The growing demand for efficient knowledge graph (KG) enrichment leveraging external corpora has intensified interest in relation extraction (RE), particularly under low-supervision settings. To address the need for adaptable and noise-resilient RE solutions that integrate seamlessly with pre-trained large language models (PLMs), we introduce SCoRE, a modular and cost-effective sentence-level RE system. SCoRE enables easy PLM switching, requires no finetuning, and adapts smoothly to diverse corpora and KGs. By combining supervised contrastive learning with a Bayesian k-Nearest Neighbors (kNN) classifier for multi-label classification, it delivers robust performance despite the noisy annotations of distantly supervised corpora. To improve RE evaluation, we propose two novel metrics: Correlation Structure Distance (CSD), measuring the alignment between learned relational patterns and KG structures, and Precision at R (P@R), assessing utility as a recommender system. We also release Wiki20d, a benchmark dataset replicating real-world RE conditions where only KG-derived annotations are available. Experiments on five benchmarks show that SCoRE matches or surpasses state-of-the-art methods while significantly reducing energy consumption. Further analyses reveal that increasing model complexity, as seen in prior work, degrades performance, highlighting the advantages of SCoRE's minimal design. Combining efficiency, modularity, and scalability, SCoRE stands as an optimal choice for real-world RE applications.
VisualTrap: A Stealthy Backdoor Attack on GUI Agents via Visual Grounding Manipulation
Venue: arXiv cs.CL 2025
Year: 2025

Graphical User Interface (GUI) agents powered by Large Vision-Language Models (LVLMs) have emerged as a revolutionary approach to automating human-machine interactions, capable of autonomously operating personal devices (e.g., mobile phones) or applications within the device to perform complex real-world tasks in a human-like manner. However, their close integration with personal devices raises significant security concerns, with many threats, including backdoor attacks, remaining largely unexplored. This work reveals that the visual grounding of GUI agent-mapping textual plans to GUI elements-can introduce vulnerabilities, enabling new types of backdoor attacks. With backdoor attack targeting visual grounding, the agent's behavior can be compromised even when given correct task-solving plans. To validate this vulnerability, we propose VisualTrap, a method that can hijack the grounding by misleading the agent to locate textual plans to trigger locations instead of the intended targets. VisualTrap uses the common method of injecting poisoned data for attacks, and does so during the pre-training of visual grounding to ensure practical feasibility of attacking. Empirical results show that VisualTrap can effectively hijack visual grounding with as little as 5% poisoned data and highly stealthy visual triggers (invisible to the human eye); and the attack can be generalized to downstream tasks, even after clean fine-tuning. Moreover, the injected trigger can remain effective across different GUI environments, e.g., being trained on mobile/web and generalizing to desktop environments. These findings underscore the urgent need for further research on backdoor attack risks in GUI agents.
Designing Adaptive Algorithms Based on Reinforcement Learning for Dynamic Optimization of Sliding Window Size in Multi-Dimensional Data Streams
Venue: arXiv cs.LG 2025
Year: 2025

Multi-dimensional data streams, prevalent in applications like IoT, financial markets, and real-time analytics, pose significant challenges due to their high velocity, unbounded nature, and complex inter-dimensional dependencies. Sliding window techniques are critical for processing such streams, but fixed-size windows struggle to adapt to dynamic changes like concept drift or bursty patterns. This paper proposes a novel reinforcement learning (RL)-based approach to dynamically optimize sliding window sizes for multi-dimensional data streams. By formulating window size selection as an RL problem, we enable an agent to learn an adaptive policy based on stream characteristics, such as variance, correlations, and temporal trends. Our method, RL-Window, leverages a Dueling Deep Q-Network (DQN) with prioritized experience replay to handle non-stationarity and high-dimensionality. Evaluations on benchmark datasets (UCI HAR, PAMAP2, Yahoo! Finance Stream) demonstrate that RL-Window outperforms state-of-the-art methods like ADWIN and CNN-Adaptive in classification accuracy, drift robustness, and computational efficiency. Additional qualitative analyses, extended metrics (e.g., energy efficiency, latency), and a comprehensive dataset characterization further highlight its adaptability and stability, making it suitable for real-time applications.
MultiJustice: A Chinese Dataset for Multi-Party, Multi-Charge Legal Prediction
Venue: arXiv cs.CL 2025
Year: 2025

Legal judgment prediction offers a compelling method to aid legal practitioners and researchers. However, the research question remains relatively under-explored: Should multiple defendants and charges be treated separately in LJP? To address this, we introduce a new dataset namely multi-person multi-charge prediction (MPMCP), and seek the answer by evaluating the performance of several prevailing legal large language models (LLMs) on four practical legal judgment scenarios: (S1) single defendant with a single charge, (S2) single defendant with multiple charges, (S3) multiple defendants with a single charge, and (S4) multiple defendants with multiple charges. We evaluate the dataset across two LJP tasks, i.e., charge prediction and penalty term prediction. We have conducted extensive experiments and found that the scenario involving multiple defendants and multiple charges (S4) poses the greatest challenges, followed by S2, S3, and S1. The impact varies significantly depending on the model. For example, in S4 compared to S1, InternLM2 achieves approximately 4.5% lower F1-score and 2.8% higher LogD, while Lawformer demonstrates around 19.7% lower F1-score and 19.0% higher LogD. Our dataset and code are available at https://github.com/lololo-xiao/MultiJustice-MPMCP.
Segmentation Regularized Training for Multi-Domain Deep Learning Registration applied to MR-Guided Prostate Cancer Radiotherapy
Venue: arXiv cs.CV 2025
Year: 2025

Background: Accurate deformable image registration (DIR) is required for contour propagation and dose accumulation in MR-guided adaptive radiotherapy (MRgART). This study trained and evaluated a deep learning DIR method for domain invariant MR-MR registration. Methods: A progressively refined registration and segmentation (ProRSeg) method was trained with 262 pairs of 3T MR simulation scans from prostate cancer patients using weighted segmentation consistency loss. ProRSeg was tested on same- (58 pairs), cross- (72 1.5T MR Linac pairs), and mixed-domain (42 MRSim-MRL pairs) datasets for contour propagation accuracy of clinical target volume (CTV), bladder, and rectum. Dose accumulation was performed for 42 patients undergoing 5-fraction MRgART. Results: ProRSeg demonstrated generalization for bladder with similar Dice Similarity Coefficients across domains (0.88, 0.87, 0.86). For rectum and CTV, performance was domain-dependent with higher accuracy on cross-domain MRL dataset (DSCs 0.89) versus same-domain data. The model's strong cross-domain performance prompted us to study the feasibility of using it for dose accumulation. Dose accumulation showed 83.3% of patients met CTV coverage (D95 >= 40.0 Gy) and bladder sparing (D50 <= 20.0 Gy) constraints. All patients achieved minimum mean target dose (>40.4 Gy), but only 9.5% remained under upper limit (<42.0 Gy). Conclusions: ProRSeg showed reasonable multi-domain MR-MR registration performance for prostate cancer patients with preliminary feasibility for evaluating treatment compliance to clinical constraints.
A multi-modal dataset for insect biodiversity with imagery and DNA at the trap and individual level
Venue: arXiv cs.CV 2025
Year: 2025

Insects comprise millions of species, many experiencing severe population declines under environmental and habitat changes. High-throughput approaches are crucial for accelerating our understanding of insect diversity, with DNA barcoding and high-resolution imaging showing strong potential for automatic taxonomic classification. However, most image-based approaches rely on individual specimen data, unlike the unsorted bulk samples collected in large-scale ecological surveys. We present the Mixed Arthropod Sample Segmentation and Identification (MassID45) dataset for training automatic classifiers of bulk insect samples. It uniquely combines molecular and imaging data at both the unsorted sample level and the full set of individual specimens. Human annotators, supported by an AI-assisted tool, performed two tasks on bulk images: creating segmentation masks around each individual arthropod and assigning taxonomic labels to over 17 000 specimens. Combining the taxonomic resolution of DNA barcodes with precise abundance estimates of bulk images holds great potential for rapid, large-scale characterization of insect communities. This dataset pushes the boundaries of tiny object detection and instance segmentation, fostering innovation in both ecological and machine learning research.
Cross-Modality Masked Learning for Survival Prediction in ICI Treated NSCLC Patients
Venue: arXiv cs.CV 2025
Year: 2025

Accurate prognosis of non-small cell lung cancer (NSCLC) patients undergoing immunotherapy is essential for personalized treatment planning, enabling informed patient decisions, and improving both treatment outcomes and quality of life. However, the lack of large, relevant datasets and effective multi-modal feature fusion strategies pose significant challenges in this domain. To address these challenges, we present a large-scale dataset and introduce a novel framework for multi-modal feature fusion aimed at enhancing the accuracy of survival prediction. The dataset comprises 3D CT images and corresponding clinical records from NSCLC patients treated with immune checkpoint inhibitors (ICI), along with progression-free survival (PFS) and overall survival (OS) data. We further propose a cross-modality masked learning approach for medical feature fusion, consisting of two distinct branches, each tailored to its respective modality: a Slice-Depth Transformer for extracting 3D features from CT images and a graph-based Transformer for learning node features and relationships among clinical variables in tabular data. The fusion process is guided by a masked modality learning strategy, wherein the model utilizes the intact modality to reconstruct missing components. This mechanism improves the integration of modality-specific features, fostering more effective inter-modality relationships and feature interactions. Our approach demonstrates superior performance in multi-modal integration for NSCLC survival prediction, surpassing existing methods and setting a new benchmark for prognostic models in this context.
Enhancing non-Rigid 3D Model Deformations Using Mesh-based Gaussian Splatting
Venue: arXiv cs.GR 2025
Year: 2025

We propose a novel framework that enhances non-rigid 3D model deformations by bridging mesh representations with 3D Gaussian splatting. While traditional Gaussian splatting delivers fast, real-time radiance-field rendering, its post-editing capabilities and support for large-scale, non-rigid deformations remain limited. Our method addresses these challenges by embedding Gaussian kernels directly onto explicit mesh surfaces. This allows the mesh's inherent topological and geometric priors to guide intuitive editing operations -- such as moving, scaling, and rotating individual 3D components -- and enables complex deformations like bending and stretching. This work paves the way for more flexible 3D content-creation workflows in applications spanning virtual reality, character animation, and interactive design.
On Construction of Approximate Real Mutually Unbiased Bases for an infinite class of dimensions $d \not\equiv 0 \bmod 4$
Venue: arXiv cs.DM 2025
Year: 2025

It is known that real Mutually Unbiased Bases (MUBs) do not exist for any dimension $d > 2$ which is not divisible by 4. Thus, the next combinatorial question is how one can construct Approximate Real MUBs (ARMUBs) in this direction with encouraging parameters. In this paper, for the first time, we show that it is possible to construct $> \lceil \sqrt{d} \rceil$ many ARMUBs for certain odd dimensions $d$ of the form $d = (4n-t)s$, $t = 1, 2, 3$, where $n$ is a natural number and $s$ is an odd prime power. Our method exploits any available $4n \times 4n$ real Hadamard matrix $H_{4n}$ (conjectured to be true) and uses this to construct an orthogonal matrix ${Y}_{4n-t}$ of size $(4n - t) \times (4n - t)$, such that the absolute value of each entry varies a little from $\frac{1}{\sqrt{4n-t}}$. In our construction, the absolute value of the inner product between any pair of basis vectors from two different ARMUBs will be $\leq \frac{1}{\sqrt{d}}(1 + O(d^{-\frac{1}{4}})) < 2$, for proper choices of parameters, the class of dimensions $d$ being infinitely large.
ZKTorch: Compiling ML Inference to Zero-Knowledge Proofs via Parallel Proof Accumulation
Venue: arXiv cs.CR 2025
Year: 2025

As AI models become ubiquitous in our daily lives, there has been an increasing demand for transparency in ML services. However, the model owner does not want to reveal the weights, as they are considered trade secrets. To solve this problem, researchers have turned to zero-knowledge proofs of ML model inference. These proofs convince the user that the ML model output is correct, without revealing the weights of the model to the user. Past work on these provers can be placed into two categories. The first method compiles the ML model into a low-level circuit, and proves the circuit using a ZK-SNARK. The second method uses custom cryptographic protocols designed only for a specific class of models. Unfortunately, the first method is highly inefficient, making it impractical for the large models used today, and the second method does not generalize well, making it difficult to update in the rapidly changing field of machine learning. To solve this, we propose ZKTorch, an open source end-to-end proving system that compiles ML models into base cryptographic operations called basic blocks, each proved using specialized protocols. ZKTorch is built on top of a novel parallel extension to the Mira accumulation scheme, enabling succinct proofs with minimal accumulation overhead. These contributions allow ZKTorch to achieve at least a $3\times$ reduction in the proof size compared to specialized protocols and up to a $6\times$ speedup in proving time over a general-purpose ZKML framework.
Lightweight MSA Design Advances Protein Folding From Evolutionary Embeddings
Venue: arXiv cs.LG 2025
Year: 2025

Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA design framework that leverages evolutionary embeddings from pretrained protein language models to generate MSAs that better support downstream folding. PLAME couples these embeddings with a conservation--diversity loss that balances agreement on conserved positions with coverage of plausible sequence variation. Beyond generation, we develop (i) an MSA selection strategy to filter high-quality candidates and (ii) a sequence-quality metric that is complementary to depth-based measures and predictive of folding gains. On AlphaFold2 low-homology/orphan benchmarks, PLAME delivers state-of-the-art improvements in structure accuracy (e.g., lDDT/TM-score), with consistent gains when paired with AlphaFold3. Ablations isolate the benefits of the selection strategy, and case studies elucidate how MSA characteristics shape AlphaFold confidence and error modes. Finally, we show PLAME functions as a lightweight adapter, enabling ESMFold to approach AlphaFold2-level accuracy while retaining ESMFold-like inference speed. PLAME thus provides a practical path to high-quality folding for proteins lacking strong evolutionary neighbors.
Discrete Diffusion Models for Language Generation
Venue: arXiv cs.CL 2025
Year: 2025

Diffusion models have emerged as a powerful class of generative models, achieving state-of-the-art results in continuous data domains such as image and video generation. Their core mechanism involves a forward diffusion process that gradually transforms structured data into a Gaussian-like distribution, followed by a learned reverse process to reconstruct the data. While successful in continuous modalities, applying this framework to discrete data-particularly natural language-remains challenging due to token dependency complexities and the lack of a defined generation order.This thesis investigates the feasibility and performance of discrete diffusion models for natural language generation. Specifically, we evaluate the Discrete Denoising Diffusion Probabilistic Model (D3PM) and compare it with traditional autoregressive (AR) language models. To assess generative performance, we use Bits Per Token (BPT), Negative Log-Likelihood (NLL), Perplexity (PPL), and Batch Processing Speed. Results show the best-performing D3PM model achieves a BPT of 5.72, with a mean of 8.05. The AR model outperforms in compression with a lower mean BPT of 4.59, but D3PM achieves higher processing speed, reaching up to 3.97 batches per sec., indicating potential for parallel generation.All evaluations were conducted under consistent conditions-generating 100,000 tokens per model with a fixed batch size of four-for fair comparison. This research presents a detailed analysis of diffusion-based vs. autoregressive models, highlighting trade-offs in generative quality and efficiency. Findings emphasize both the promise and limitations of diffusion models for discrete data, supporting future work in non-autoregressive language generation.
Comparative Analysis of CNN and Transformer Architectures with Heart Cycle Normalization for Automated Phonocardiogram Classification
Venue: arXiv cs.SD 2025
Year: 2025

The automated classification of phonocardiogram (PCG) recordings represents a substantial advancement in cardiovascular diagnostics. This paper presents a systematic comparison of four distinct models for heart murmur detection: two specialized convolutional neural networks (CNNs) and two zero-shot universal audio transformers (BEATs), evaluated using fixed-length and heart cycle normalization approaches. Utilizing the PhysioNet2022 dataset, a custom heart cycle normalization method tailored to individual cardiac rhythms is introduced. The findings indicate the following AUROC values: the CNN model with fixed-length windowing achieves 79.5%, the CNN model with heart cycle normalization scores 75.4%, the BEATs transformer with fixed-length windowing achieves 65.7%, and the BEATs transformer with heart cycle normalization results in 70.1%. The findings indicate that physiological signal constraints, especially those introduced by different normalization strategies, have a substantial impact on model performance. The research provides evidence-based guidelines for architecture selection in clinical settings, emphasizing the need for a balance between accuracy and computational efficiency. Although specialized CNNs demonstrate superior performance overall, the zero-shot transformer models may offer promising efficiency advantages during development, such as faster training and evaluation cycles, despite their lower classification accuracy. These findings highlight the potential of automated classification systems to enhance cardiac diagnostics and improve patient care.
CoPT: Unsupervised Domain Adaptive Segmentation using Domain-Agnostic Text Embeddings
Venue: arXiv cs.CV 2025
Year: 2025

Unsupervised domain adaptation (UDA) involves learning class semantics from labeled data within a source domain that generalize to an unseen target domain. UDA methods are particularly impactful for semantic segmentation, where annotations are more difficult to collect than in image classification. Despite recent advances in large-scale vision-language representation learning, UDA methods for segmentation have not taken advantage of the domain-agnostic properties of text. To address this, we present a novel Covariance-based Pixel-Text loss, CoPT, that uses domain-agnostic text embeddings to learn domain-invariant features in an image segmentation encoder. The text embeddings are generated through our LLM Domain Template process, where an LLM is used to generate source and target domain descriptions that are fed to a frozen CLIP model and combined. In experiments on four benchmarks we show that a model trained using CoPT achieves the new state of the art performance on UDA for segmentation. The code can be found at https://github.com/cfmata/CoPT.