OpenRaiser/Intern-Atlas huggingface dataset:
CryoSAMU: Enhancing 3D Cryo-EM Density Maps of Protein Structures at Intermediate Resolution with Structure-Aware Multimodal U-Nets
Venue: arXiv cs.CV 2025
Year: 2025

Enhancing cryogenic electron microscopy (cryo-EM) 3D density maps at intermediate resolution (4-8 Å) is crucial in protein structure determination. Recent advances in deep learning have led to the development of automated approaches for enhancing experimental cryo-EM density maps. Yet, these methods are not optimized for intermediate-resolution maps and rely on map density features alone. To address this, we propose CryoSAMU, a novel method designed to enhance 3D cryo-EM density maps of protein structures using structure-aware multimodal U-Nets and trained on curated intermediate-resolution density maps. We comprehensively evaluate CryoSAMU across various metrics and demonstrate its competitive performance compared to state-of-the-art methods. Notably, CryoSAMU achieves significantly faster processing speed, showing promise for future practical applications. Our code is available at https://github.com/chenwei-zhang/CryoSAMU.
Context-Aware Weakly Supervised Image Manipulation Localization with SAM Refinement
Venue: arXiv cs.CV 2025
Year: 2025

Malicious image manipulation poses societal risks, increasing the importance of effective image manipulation detection methods. Recent approaches in image manipulation detection have largely been driven by fully supervised approaches, which require labor-intensive pixel-level annotations. Thus, it is essential to explore weakly supervised image manipulation localization methods that only require image-level binary labels for training. However, existing weakly supervised image manipulation methods overlook the importance of edge information for accurate localization, leading to suboptimal localization performance. To address this, we propose a Context-Aware Boundary Localization (CABL) module to aggregate boundary features and learn context-inconsistency for localizing manipulated areas. Furthermore, by leveraging Class Activation Mapping (CAM) and Segment Anything Model (SAM), we introduce the CAM-Guided SAM Refinement (CGSR) module to generate more accurate manipulation localization maps. By integrating two modules, we present a novel weakly supervised framework based on a dual-branch Transformer-CNN architecture. Our method achieves outstanding localization performance across multiple datasets.
Finding Near-Optimal Maximum Set of Disjoint $k$-Cliques in Real-World Social Networks
Venue: arXiv cs.SI 2025
Year: 2025

A $k$-clique is a dense graph, consisting of $k$ fully-connected nodes, that finds numerous applications, such as community detection and network analysis. In this paper, we study a new problem, that finds a maximum set of disjoint $k$-cliques in a given large real-world graph with a user-defined fixed number $k$, which can contribute to a good performance of teaming collaborative events in online games. However, this problem is NP-hard when $k \geq 3$, making it difficult to solve. To address that, we propose an efficient lightweight method that avoids significant overheads and achieves a $k$-approximation to the optimal, which is equipped with several optimization techniques, including the ordering method, degree estimation in the clique graph, and a lightweight implementation. Besides, to handle dynamic graphs that are widely seen in real-world social networks, we devise an efficient indexing method with careful swapping operations, leading to the efficient maintenance of a near-optimal result with frequent updates in the graph. In various experiments on several large graphs, our proposed approaches significantly outperform the competitors by up to 2 orders of magnitude in running time and 13.3\% in the number of computed disjoint $k$-cliques, which demonstrates the superiority of the proposed approaches in terms of efficiency and effectiveness.
Enabling Heterogeneous Adversarial Transferability via Feature Permutation Attacks
Venue: arXiv cs.CV 2025
Year: 2025

Adversarial attacks in black-box settings are highly practical, with transfer-based attacks being the most effective at generating adversarial examples (AEs) that transfer from surrogate models to unseen target models. However, their performance significantly degrades when transferring across heterogeneous architectures -- such as CNNs, MLPs, and Vision Transformers (ViTs) -- due to fundamental architectural differences. To address this, we propose Feature Permutation Attack (FPA), a zero-FLOP, parameter-free method that enhances adversarial transferability across diverse architectures. FPA introduces a novel feature permutation (FP) operation, which rearranges pixel values in selected feature maps to simulate long-range dependencies, effectively making CNNs behave more like ViTs and MLPs. This enhances feature diversity and improves transferability both across heterogeneous architectures and within homogeneous CNNs. Extensive evaluations on 14 state-of-the-art architectures show that FPA achieves maximum absolute gains in attack success rates of 7.68% on CNNs, 14.57% on ViTs, and 14.48% on MLPs, outperforming existing black-box attacks. Additionally, FPA is highly generalizable and can seamlessly integrate with other transfer-based attacks to further boost their performance. Our findings establish FPA as a robust, efficient, and computationally lightweight strategy for enhancing adversarial transferability across heterogeneous architectures.
Including local feature interactions in deep non-negative matrix factorization networks improves performance
Venue: arXiv cs.LG 2025
Year: 2025

The brain uses positive signals as a means of signaling. Forward interactions in the early visual cortex are also positive, realized by excitatory synapses. Only local interactions also include inhibition. Non-negative matrix factorization (NMF) captures the biological constraint of positive long-range interactions and can be implemented with stochastic spikes. While NMF can serve as an abstract formalization of early neural processing in the visual system, the performance of deep convolutional networks with NMF modules does not match that of CNNs of similar size. However, when the local NMF modules are each followed by a module that mixes the NMF's positive activities, the performances on the benchmark data exceed that of vanilla deep convolutional networks of similar size. This setting can be considered a biologically more plausible emulation of the processing in cortical (hyper-)columns with the potential to improve the performance of deep networks.
Multi-dataset and Transfer Learning Using Gene Expression Knowledge Graphs
Venue: arXiv cs.LG 2025
Year: 2025

Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of disease pathology. Therefore, machine learning has been used to process gene expression data, with patient diagnosis emerging as one of the most popular applications. Although gene expression data can provide valuable insights, challenges arise because the number of patients in expression datasets is usually limited, and the data from different datasets with different gene expressions cannot be easily combined. This work proposes a novel methodology to address these challenges by integrating multiple gene expression datasets and domain-specific knowledge using knowledge graphs, a unique tool for biomedical data integration. Then, vector representations are produced using knowledge graph embedding techniques, which are used as inputs for a graph neural network and a multi-layer perceptron. We evaluate the efficacy of our methodology in three settings: single-dataset learning, multi-dataset learning, and transfer learning. The experimental results show that combining gene expression datasets and domain-specific knowledge improves patient diagnosis in all three settings.
Latent Beam Diffusion Models for Generating Visual Sequences
Venue: arXiv cs.CV 2025
Year: 2025

While diffusion models excel at generating high-quality images from text prompts, they struggle with visual consistency when generating image sequences. Existing methods generate each image independently, leading to disjointed narratives - a challenge further exacerbated in non-linear storytelling, where scenes must connect beyond adjacent images. We introduce a novel beam search strategy for latent space exploration, enabling conditional generation of full image sequences with beam search decoding. In contrast to earlier methods that rely on fixed latent priors, our method dynamically samples past latents to search for an optimal sequence of latent representations, ensuring coherent visual transitions. As the latent denoising space is explored, the beam search graph is pruned with a cross-attention mechanism that efficiently scores search paths, prioritizing alignment with both textual prompts and visual context. Human and automatic evaluations confirm that BeamDiffusion outperforms other baseline methods, producing full sequences with superior coherence, visual continuity, and textual alignment.
GrappaRE -- A Tool for Efficient Graph Recognition Based on Finite Automata and Regular Expressions
Venue: arXiv cs.FL 2025
Year: 2025

A recent paper by Drewes, Hoffmann, and Minas (GCM 2023 proceedings) has shown that certain graph languages can be defined and efficiently recognized by finite automata when strings over typed symbols are interpreted as graphs. This approach has been implemented in the tool GrappaRE, which is described in this paper. GrappaRE allows for the convenient specification of graph languages through regular expressions, converts each of them into a minimized deterministic finite automaton, and checks whether it can recognize graphs without the need for backtracking. Measurements confirm that recognition runs in linear time.
Analyzing Modern NVIDIA GPU cores
Venue: arXiv cs.AR 2025
Year: 2025

GPUs are the most popular platform for accelerating HPC workloads, such as artificial intelligence and science simulations. However, most microarchitectural research in academia relies on GPU core pipeline designs based on architectures that are more than 15 years old. This paper reverse engineers modern NVIDIA GPU cores, unveiling many key aspects of its design and explaining how GPUs leverage hardware-compiler techniques where the compiler guides hardware during execution. In particular, it reveals how the issue logic works including the policy of the issue scheduler, the structure of the register file and its associated cache, and multiple features of the memory pipeline. Moreover, it analyses how a simple instruction prefetcher based on a stream buffer fits well with modern NVIDIA GPUs and is likely to be used. Furthermore, we investigate the impact of the register file cache and the number of register file read ports on both simulation accuracy and performance. By modeling all these new discovered microarchitectural details, we achieve 18.24% lower mean absolute percentage error (MAPE) in execution cycles than previous state-of-the-art simulators, resulting in an average of 13.98% MAPE with respect to real hardware (NVIDIA RTX A6000). Also, we demonstrate that this new model stands for other NVIDIA architectures, such as Turing. Finally, we show that the software-based dependence management mechanism included in modern NVIDIA GPUs outperforms a hardware mechanism based on scoreboards in terms of performance and area.
Towards Efficient and General-Purpose Few-Shot Misclassification Detection for Vision-Language Models
Venue: arXiv cs.CV 2025
Year: 2025

Reliable prediction by classifiers is crucial for their deployment in high security and dynamically changing situations. However, modern neural networks often exhibit overconfidence for misclassified predictions, highlighting the need for confidence estimation to detect errors. Despite the achievements obtained by existing methods on small-scale datasets, they all require training from scratch and there are no efficient and effective misclassification detection (MisD) methods, hindering practical application towards large-scale and ever-changing datasets. In this paper, we pave the way to exploit vision language model (VLM) leveraging text information to establish an efficient and general-purpose misclassification detection framework. By harnessing the power of VLM, we construct FSMisD, a Few-Shot prompt learning framework for MisD to refrain from training from scratch and therefore improve tuning efficiency. To enhance misclassification detection ability, we use adaptive pseudo sample generation and a novel negative loss to mitigate the issue of overconfidence by pushing category prompts away from pseudo features. We conduct comprehensive experiments with prompt learning methods and validate the generalization ability across various datasets with domain shift. Significant and consistent improvement demonstrates the effectiveness, efficiency and generalizability of our approach.
FireRedTTS-1S: An Upgraded Streamable Foundation Text-to-Speech System
Venue: arXiv cs.SD 2025
Year: 2025

In this work, we upgrade FireRedTTS to a new version, FireRedTTS-1S, a high-quality streaming foundation text-to-speech system. FireRedTTS-1S achieves streaming speech generation via two steps: text-to-semantic decoding and semantic-to-acoustic decoding. In text-to-semantic decoding, a semantic-aware speech tokenizer converts the speech signal into semantic tokens, which can be synthesized from the text via a language model in an auto-regressive manner. Meanwhile, the semantic-to-acoustic decoding module simultaneously translates generated semantic tokens into the speech signal in a streaming way. We implement two approaches to achieve this module: 1) a chunk-wise streamable flow-matching approach, and 2) a multi-stream language model-based approach. They both present high-quality and streamable speech generation but differ in real-time factor (RTF) and latency. Specifically, flow-matching decoding can generate speech by chunks, presenting a lower RTF of 0.1 but a higher latency of 300ms. Instead, the multi-stream language model generates speech by frames in an autoregressive manner, presenting a higher RTF of 0.3 but a low latency of 150ms. In experiments on zero-shot voice cloning, the objective results validate FireRedTTS-1S as a high-quality foundation model with comparable intelligibility and speaker similarity over industrial baseline systems. Furthermore, the subjective score of FireRedTTS-1S highlights its impressive synthesis performance, achieving comparable quality to the ground-truth recordings. These results validate FireRedTTS-1S as a high-quality streaming foundation TTS system.
StableToolBench-MirrorAPI: Modeling Tool Environments as Mirrors of 7,000+ Real-World APIs
Venue: arXiv cs.CL 2025
Year: 2025

The rapid advancement of large language models (LLMs) has spurred significant interest in tool learning, where LLMs are augmented with external tools to tackle complex tasks. However, existing tool environments face challenges in balancing stability, scalability, and realness, particularly for benchmarking purposes. To address this problem, we propose MirrorAPI, a novel framework that trains specialized LLMs to accurately simulate real API responses, effectively acting as "mirrors" to tool environments. Using a comprehensive dataset of request-response pairs from 7,000+ APIs, we employ supervised fine-tuning and chain-of-thought reasoning to enhance simulation fidelity. MirrorAPI achieves superior accuracy and stability compared to state-of-the-art methods, as demonstrated by its performance on the newly constructed MirrorAPI-Bench and its integration into StableToolBench.
TerraTorch: The Geospatial Foundation Models Toolkit
Venue: arXiv cs.CV 2025
Year: 2025

TerraTorch is a fine-tuning and benchmarking toolkit for Geospatial Foundation Models built on PyTorch Lightning and tailored for satellite, weather, and climate data. It integrates domain-specific data modules, pre-defined tasks, and a modular model factory that pairs any backbone with diverse decoder heads. These components allow researchers and practitioners to fine-tune supported models in a no-code fashion by simply editing a training configuration. By consolidating best practices for model development and incorporating the automated hyperparameter optimization extension Iterate, TerraTorch reduces the expertise and time required to fine-tune or benchmark models on new Earth Observation use cases. Furthermore, TerraTorch directly integrates with GEO-Bench, allowing for systematic and reproducible benchmarking of Geospatial Foundation Models. TerraTorch is open sourced under Apache 2.0, available at https://github.com/IBM/terratorch, and can be installed via pip install terratorch.
Low-resource Information Extraction with the European Clinical Case Corpus
Venue: arXiv cs.CL 2025
Year: 2025

We present E3C-3.0, a multilingual dataset in the medical domain, comprising clinical cases annotated with diseases and test-result relations. The dataset includes both native texts in five languages (English, French, Italian, Spanish and Basque) and texts translated and projected from the English source into five target languages (Greek, Italian, Polish, Slovak, and Slovenian). A semi-automatic approach has been implemented, including automatic annotation projection based on Large Language Models (LLMs) and human revision. We present several experiments showing that current state-of-the-art LLMs can benefit from being fine-tuned on the E3C-3.0 dataset. We also show that transfer learning in different languages is very effective, mitigating the scarcity of data. Finally, we compare performance both on native data and on projected data. We release the data at https://huggingface.co/collections/NLP-FBK/e3c-projected-676a7d6221608d60e4e9fd89 .
Synthetic Data Augmentation for Cross-domain Implicit Discourse Relation Recognition
Venue: arXiv cs.CL 2025
Year: 2025

Implicit discourse relation recognition (IDRR) -- the task of identifying the implicit coherence relation between two text spans -- requires deep semantic understanding. Recent studies have shown that zero- or few-shot approaches significantly lag behind supervised models, but LLMs may be useful for synthetic data augmentation, where LLMs generate a second argument following a specified coherence relation. We applied this approach in a cross-domain setting, generating discourse continuations using unlabelled target-domain data to adapt a base model which was trained on source-domain labelled data. Evaluations conducted on a large-scale test set revealed that different variations of the approach did not result in any significant improvements. We conclude that LLMs often fail to generate useful samples for IDRR, and emphasize the importance of considering both statistical significance and comparability when evaluating IDRR models.
RED2Hunt: an Actionable Framework for Cleaning Operational Databases with Surrogate Keys
Venue: arXiv cs.DB 2025
Year: 2025

Surrogate keys are now extensively utilized by database designers to implement keys in SQL tables. They are straightforward, easy to understand, and enable efficient access, despite lacking any real-world semantic meaning. In this context, complex redundancy issues might emerge and often go unnoticed as long as they do not affect the operational applications built on top of the databases. These issues become evident when organizations seek to leverage data science, posing significant challenges to the implementation of analytical projects. This paper, grounded in real-world applications, defines the concept of artificial unicity and proposes RED2Hunt (RElational Databases REDundancy Hunting), a human-in-the-loop framework for identifying hidden redundancy and, if problems occur, cleaning relational databases implemented with surrogate keys. We first define the central and intricate notion of artificial unicity and then the RED2Hunt framework to address it. We rely on simple abstractions easy to visualize based on the so-called redundancy profile associated to some relations and the notion of attribute stability. Quite interestingly, those profiles can be computed very efficiently in quasi-linear time. We have devised different metrics to guide the domain expert and an actionable framework to generate new redundancy-free databases. The proposed framework was implemented on top of PostgreSQL. From the publicly available IMDB database, we have generated synthetic databases, implementing different redundancy scenarios, on which we tested RED2Hunt to study its scalability. RED2Hunt has also been tested on operational databases implemented with surrogate keys. Lessons learned from these real-life applications are discussed.
Diffusion Counterfactuals for Image Regressors
Venue: arXiv cs.LG 2025
Year: 2025

Counterfactual explanations have been successfully applied to create human interpretable explanations for various black-box models. They are handy for tasks in the image domain, where the quality of the explanations benefits from recent advances in generative models. Although counterfactual explanations have been widely applied to classification models, their application to regression tasks remains underexplored. We present two methods to create counterfactual explanations for image regression tasks using diffusion-based generative models to address challenges in sparsity and quality: 1) one based on a Denoising Diffusion Probabilistic Model that operates directly in pixel-space and 2) another based on a Diffusion Autoencoder operating in latent space. Both produce realistic, semantic, and smooth counterfactuals on CelebA-HQ and a synthetic data set, providing easily interpretable insights into the decision-making process of the regression model and reveal spurious correlations. We find that for regression counterfactuals, changes in features depend on the region of the predicted value. Large semantic changes are needed for significant changes in predicted values, making it harder to find sparse counterfactuals than with classifiers. Moreover, pixel space counterfactuals are more sparse while latent space counterfactuals are of higher quality and allow bigger semantic changes.
$β$-GNN: A Robust Ensemble Approach Against Graph Structure Perturbation
Venue: arXiv cs.LG 2025
Year: 2025

Graph Neural Networks (GNNs) are playing an increasingly important role in the efficient operation and security of computing systems, with applications in workload scheduling, anomaly detection, and resource management. However, their vulnerability to network perturbations poses a significant challenge. We propose $β$-GNN, a model enhancing GNN robustness without sacrificing clean data performance. $β$-GNN uses a weighted ensemble, combining any GNN with a multi-layer perceptron. A learned dynamic weight, $β$, modulates the GNN's contribution. This $β$ not only weights GNN influence but also indicates data perturbation levels, enabling proactive mitigation. Experimental results on diverse datasets show $β$-GNN's superior adversarial accuracy and attack severity quantification. Crucially, $β$-GNN avoids perturbation assumptions, preserving clean data structure and performance.