OpenRaiser/Intern-Atlas huggingface dataset:
Energy-Based Models for Predicting Mutational Effects on Proteins
Venue: arXiv cs.LG 2025
Year: 2025

Predicting changes in binding free energy ($ΔΔG$) is a vital task in protein engineering and protein-protein interaction (PPI) engineering for drug discovery. Previous works have observed a high correlation between $ΔΔG$ and entropy, using probabilities of biologically important objects such as side chain angles and residue identities to estimate $ΔΔG$. However, estimating the full conformational distribution of a protein complex is generally considered intractable. In this work, we propose a new approach to $ΔΔG$ prediction that avoids this issue by instead leveraging energy-based models for estimating the probability of a complex's conformation. Specifically, we novelly decompose $ΔΔG$ into a sequence-based component estimated by an inverse folding model and a structure-based component estimated by an energy model. This decomposition is made tractable by assuming equilibrium between the bound and unbound states, allowing us to simplify the estimation of degeneracies associated with each state. Unlike previous deep learning-based methods, our method incorporates an energy-based physical inductive bias by connecting the often-used sequence log-odds ratio-based approach to $ΔΔG$ prediction with a new $ΔΔE$ term grounded in statistical mechanics. We demonstrate superiority over existing state-of-the-art structure and sequence-based deep learning methods in $ΔΔG$ prediction and antibody optimization against SARS-CoV-2.
Geospatial Diffusion for Land Cover Imperviousness Change Forecasting
Venue: arXiv cs.LG 2025
Year: 2025

Land cover, both present and future, has a significant effect on several important Earth system processes. For example, impervious surfaces heat up and speed up surface water runoff and reduce groundwater infiltration, with concomitant effects on regional hydrology and flood risk. While regional Earth System models have increasing skill at forecasting hydrologic and atmospheric processes at high resolution in future climate scenarios, our ability to forecast land-use and land-cover change (LULC), a critical input to risk and consequences assessment for these scenarios, has lagged behind. In this paper, we propose a new paradigm exploiting Generative AI (GenAI) for land cover change forecasting by framing LULC forecasting as a data synthesis problem conditioned on historical and auxiliary data-sources. We discuss desirable properties of generative models that fundament our research premise, and demonstrate the feasibility of our methodology through experiments on imperviousness forecasting using historical data covering the entire conterminous United States. Specifically, we train a diffusion model for decadal forecasting of imperviousness and compare its performance to a baseline that assumes no change at all. Evaluation across 12 metropolitan areas for a year held-out during training indicate that for average resolutions $\geq 0.7\times0.7km^2$ our model yields MAE lower than such a baseline. This finding corroborates that such a generative model can capture spatiotemporal patterns from historical data that are significant for projecting future change. Finally, we discuss future research to incorporate auxiliary information on physical properties about the Earth, as well as supporting simulation of different scenarios by means of driver variables.
Advancing Autonomous Incident Response: Leveraging LLMs and Cyber Threat Intelligence
Venue: arXiv cs.CR 2025
Year: 2025

Effective incident response (IR) is critical for mitigating cyber threats, yet security teams are overwhelmed by alert fatigue, high false-positive rates, and the vast volume of unstructured Cyber Threat Intelligence (CTI) documents. While CTI holds immense potential for enriching security operations, its extensive and fragmented nature makes manual analysis time-consuming and resource-intensive. To bridge this gap, we introduce a novel Retrieval-Augmented Generation (RAG)-based framework that leverages Large Language Models (LLMs) to automate and enhance IR by integrating dynamically retrieved CTI. Our approach introduces a hybrid retrieval mechanism that combines NLP-based similarity searches within a CTI vector database with standardized queries to external CTI platforms, facilitating context-aware enrichment of security alerts. The augmented intelligence is then leveraged by an LLM-powered response generation module, which formulates precise, actionable, and contextually relevant incident mitigation strategies. We propose a dual evaluation paradigm, wherein automated assessment using an auxiliary LLM is systematically cross-validated by cybersecurity experts. Empirical validation on real-world and simulated alerts demonstrates that our approach enhances the accuracy, contextualization, and efficiency of IR, alleviating analyst workload and reducing response latency. This work underscores the potential of LLM-driven CTI fusion in advancing autonomous security operations and establishing a foundation for intelligent, adaptive cybersecurity frameworks.
HyperTea: A Hypergraph-based Temporal Enhancement and Alignment Network for Moving Infrared Small Target Detection
Venue: arXiv cs.CV 2025
Year: 2025

In practical application scenarios, moving infrared small target detection (MIRSTD) remains highly challenging due to the target's small size, weak intensity, and complex motion pattern. Existing methods typically only model low-order correlations between feature nodes and perform feature extraction and enhancement within a single temporal scale. Although hypergraphs have been widely used for high-order correlation learning, they have received limited attention in MIRSTD. To explore the potential of hypergraphs and enhance multi-timescale feature representation, we propose HyperTea, which integrates global and local temporal perspectives to effectively model high-order spatiotemporal correlations of features. HyperTea consists of three modules: the global temporal enhancement module (GTEM) realizes global temporal context enhancement through semantic aggregation and propagation; the local temporal enhancement module (LTEM) is designed to capture local motion patterns between adjacent frames and then enhance local temporal context; additionally, we further develop a temporal alignment module (TAM) to address potential cross-scale feature misalignment. To our best knowledge, HyperTea is the first work to integrate convolutional neural networks (CNNs), recurrent neural networks (RNNs), and hypergraph neural networks (HGNNs) for MIRSTD, significantly improving detection performance. Experiments on DAUB and IRDST demonstrate its state-of-the-art (SOTA) performance. Our source codes are available at https://github.com/Lurenjia-LRJ/HyperTea.
Continuous Bangla Sign Language Translation: Mitigating the Expense of Gloss Annotation with the Assistance of Graph
Venue: arXiv cs.CL 2025
Year: 2025

Millions of individuals worldwide are affected by deafness and hearing impairment. Sign language serves as a sophisticated means of communication for the deaf and hard of hearing. However, in societies that prioritize spoken languages, sign language often faces underestimation, leading to communication barriers and social exclusion. The Continuous Bangla Sign Language Translation project aims to address this gap by enhancing translation methods. While recent approaches leverage transformer architecture for state-of-the-art results, our method integrates graph-based methods with the transformer architecture. This fusion, combining transformer and STGCN-LSTM architectures, proves more effective in gloss-free translation. Our contributions include architectural fusion, exploring various fusion strategies, and achieving a new state-of-the-art performance on diverse sign language datasets, namely RWTH-PHOENIX-2014T, CSL-Daily, How2Sign, and BornilDB v1.0. Our approach demonstrates superior performance compared to current translation outcomes across all datasets, showcasing notable improvements of BLEU-4 scores of 4.01, 2.07, and 0.5, surpassing those of GASLT, GASLT and slt_how2sign in RWTH-PHOENIX-2014T, CSL-Daily, and How2Sign, respectively. Also, we introduce benchmarking on the BornilDB v1.0 dataset for the first time. Our method sets a benchmark for future research, emphasizing the importance of gloss-free translation to improve communication accessibility for the deaf and hard of hearing.
Chem3DLLM: 3D Multimodal Large Language Models for Chemistry
Venue: arXiv cs.CE 2025
Year: 2025

In the real world, a molecule is a 3D geometric structure. Compared to 1D SMILES sequences and 2D molecular graphs, 3D molecules represent the most informative molecular modality. Despite the rapid progress of autoregressive-based language models, they cannot handle the generation of 3D molecular conformation due to several challenges: 1) 3D molecular structures are incompatible with LLMs' discrete token space, 2) integrating heterogeneous inputs like proteins, ligands, and text remains difficult within a unified model, and 3) LLMs lack essential scientific priors, hindering the enforcement of physical and chemical constraints during generation. To tackle these issues, we present Chem3DLLM, a unified protein-conditioned multimodal large language model. Our approach designs a novel reversible text encoding for 3D molecular structures using run-length compression, achieving 3x size reduction while preserving complete structural information. This enables seamless integration of molecular geometry with protein pocket features in a single LLM architecture. We employ reinforcement learning with stability-based rewards to optimize chemical validity and incorporate a lightweight protein embedding projector for end-to-end training. Experimental results on structure-based drug design demonstrate state-of-the-art performance with a Vina score of -7.21, validating our unified multimodal approach for practical drug discovery applications.
APFL: Analytic Personalized Federated Learning via Dual-Stream Least Squares
Venue: arXiv cs.LG 2025
Year: 2025

Personalized Federated Learning (PFL) has presented a significant challenge to deliver personalized models to individual clients through collaborative training. Existing PFL methods are often vulnerable to non-IID data, which severely hinders collective generalization and then compromises the subsequent personalization efforts. In this paper, to address this non-IID issue in PFL, we propose an Analytic Personalized Federated Learning (APFL) approach via dual-stream least squares. In our APFL, we use a foundation model as a frozen backbone for feature extraction. Subsequent to the feature extractor, we develop dual-stream analytic models to achieve both collective generalization and individual personalization. Specifically, our APFL incorporates a shared primary stream for global generalization across all clients, and a dedicated refinement stream for local personalization of each individual client. The analytical solutions of our APFL enable its ideal property of heterogeneity invariance, theoretically meaning that each personalized model remains identical regardless of how heterogeneous the data are distributed across all other clients. Empirical results across various datasets also validate the superiority of our APFL over state-of-the-art baselines, with advantages of at least 1.10%-15.45% in accuracy.
Privacy-enhancing Sclera Segmentation Benchmarking Competition: SSBC 2025
Venue: arXiv cs.CV 2025
Year: 2025

This paper presents a summary of the 2025 Sclera Segmentation Benchmarking Competition (SSBC), which focused on the development of privacy-preserving sclera-segmentation models trained using synthetically generated ocular images. The goal of the competition was to evaluate how well models trained on synthetic data perform in comparison to those trained on real-world datasets. The competition featured two tracks: $(i)$ one relying solely on synthetic data for model development, and $(ii)$ one combining/mixing synthetic with (a limited amount of) real-world data. A total of nine research groups submitted diverse segmentation models, employing a variety of architectural designs, including transformer-based solutions, lightweight models, and segmentation networks guided by generative frameworks. Experiments were conducted across three evaluation datasets containing both synthetic and real-world images, collected under diverse conditions. Results show that models trained entirely on synthetic data can achieve competitive performance, particularly when dedicated training strategies are employed, as evidenced by the top performing models that achieved $F_1$ scores of over $0.8$ in the synthetic data track. Moreover, performance gains in the mixed track were often driven more by methodological choices rather than by the inclusion of real data, highlighting the promise of synthetic data for privacy-aware biometric development. The code and data for the competition is available at: https://github.com/dariant/SSBC_2025.
An Efficient Model-Driven Groupwise Approach for Atlas Construction
Venue: arXiv cs.CV 2025
Year: 2025

Atlas construction is fundamental to medical image analysis, offering a standardized spatial reference for tasks such as population-level anatomical modeling. While data-driven registration methods have recently shown promise in pairwise settings, their reliance on large training datasets, limited generalizability, and lack of true inference phases in groupwise contexts hinder their practical use. In contrast, model-driven methods offer training-free, theoretically grounded, and data-efficient alternatives, though they often face scalability and optimization challenges when applied to large 3D datasets. In this work, we introduce DARC (Diffeomorphic Atlas Registration via Coordinate descent), a novel model-driven groupwise registration framework for atlas construction. DARC supports a broad range of image dissimilarity metrics and efficiently handles arbitrary numbers of 3D images without incurring GPU memory issues. Through a coordinate descent strategy and a centrality-enforcing activation function, DARC produces unbiased, diffeomorphic atlases with high anatomical fidelity. Beyond atlas construction, we demonstrate two key applications: (1) One-shot segmentation, where labels annotated only on the atlas are propagated to subjects via inverse deformations, outperforming state-of-the-art few-shot methods; and (2) shape synthesis, where new anatomical variants are generated by warping the atlas mesh using synthesized diffeomorphic deformation fields. Overall, DARC offers a flexible, generalizable, and resource-efficient framework for atlas construction and applications.
From Diagnosis to Improvement: Probing Spatio-Physical Reasoning in Vision Language Models
Venue: arXiv cs.CV 2025
Year: 2025

Spatio-physical reasoning, a foundation capability for understanding the real physics world, is a critical step towards building robust world models. While recent vision language models (VLMs) have shown remarkable progress in specialized domains like multimodal mathematics and pure spatial understanding, their capability for spatio-physical reasoning remains largely unexplored. This paper provides a comprehensive diagnostic analysis of mainstream VLMs, revealing that current models perform inadequately on this crucial task. Further detailed analysis shows that this underperformance is largely attributable to biases caused by human-like prior and a lack of deep reasoning. To address these challenges, we apply supervised fine-tuning followed by rule-based reinforcement learning to Qwen2.5-VL-7B, resulting in significant improvements in spatio-physical reasoning capabilities and surpassing leading proprietary models. Nevertheless, despite this success, the model's generalization to new physics scenarios remains limited -- underscoring the pressing need for new approaches in spatio-physical reasoning.
Cooperative Face Liveness Detection from Optical Flow
Venue: arXiv cs.CV 2025
Year: 2025

In this work, we proposed a novel cooperative video-based face liveness detection method based on a new user interaction scenario where participants are instructed to slowly move their frontal-oriented face closer to the camera. This controlled approaching face protocol, combined with optical flow analysis, represents the core innovation of our approach. By designing a system where users follow this specific movement pattern, we enable robust extraction of facial volume information through neural optical flow estimation, significantly improving discrimination between genuine faces and various presentation attacks (including printed photos, screen displays, masks, and video replays). Our method processes both the predicted optical flows and RGB frames through a neural classifier, effectively leveraging spatial-temporal features for more reliable liveness detection compared to passive methods.
The SET Perceptual Factors Framework: Towards Assured Perception for Autonomous Systems
Venue: arXiv cs.RO 2025
Year: 2025

Future autonomous systems promise significant societal benefits, yet their deployment raises concerns about safety and trustworthiness. A key concern is assuring the reliability of robot perception, as perception seeds safe decision-making. Failures in perception are often due to complex yet common environmental factors and can lead to accidents that erode public trust. To address this concern, we introduce the SET (Self, Environment, and Target) Perceptual Factors Framework. We designed the framework to systematically analyze how factors such as weather, occlusion, or sensor limitations negatively impact perception. To achieve this, the framework employs SET State Trees to categorize where such factors originate and SET Factor Trees to model how these sources and factors impact perceptual tasks like object detection or pose estimation. Next, we develop Perceptual Factor Models using both trees to quantify the uncertainty for a given task. Our framework aims to promote rigorous safety assurances and cultivate greater public understanding and trust in autonomous systems by offering a transparent and standardized method for identifying, modeling, and communicating perceptual risks.
Non-Stationary Restless Multi-Armed Bandits with Provable Guarantee
Venue: arXiv cs.LG 2025
Year: 2025

Online restless multi-armed bandits (RMABs) typically assume that each arm follows a stationary Markov Decision Process (MDP) with fixed state transitions and rewards. However, in real-world applications like healthcare and recommendation systems, these assumptions often break due to non-stationary dynamics, posing significant challenges for traditional RMAB algorithms. In this work, we specifically consider $N$-armd RMAB with non-stationary transition constrained by bounded variation budgets $B$. Our proposed \rmab\; algorithm integrates sliding window reinforcement learning (RL) with an upper confidence bound (UCB) mechanism to simultaneously learn transition dynamics and their variations. We further establish that \rmab\; achieves $\widetilde{\mathcal{O}}(N^2 B^{\frac{1}{4}} T^{\frac{3}{4}})$ regret bound by leveraging a relaxed definition of regret, providing a foundational theoretical framework for non-stationary RMAB problems for the first time.
Advances in Speech Separation: Techniques, Challenges, and Future Trends
Venue: arXiv cs.SD 2025
Year: 2025

The field of speech separation, addressing the "cocktail party problem", has seen revolutionary advances with DNNs. Speech separation enhances clarity in complex acoustic environments and serves as crucial pre-processing for speech recognition and speaker recognition. However, current literature focuses narrowly on specific architectures or isolated approaches, creating fragmented understanding. This survey addresses this gap by providing systematic examination of DNN-based speech separation techniques. Our work differentiates itself through: (I) Comprehensive perspective: We systematically investigate learning paradigms, separation scenarios with known/unknown speakers, comparative analysis of supervised/self-supervised/unsupervised frameworks, and architectural components from encoders to estimation strategies. (II) Timeliness: Coverage of cutting-edge developments ensures access to current innovations and benchmarks. (III) Unique insights: Beyond summarization, we evaluate technological trajectories, identify emerging patterns, and highlight promising directions including domain-robust frameworks, efficient architectures, multimodal integration, and novel self-supervised paradigms. (IV) Fair evaluation: We provide quantitative evaluations on standard datasets, revealing true capabilities and limitations of different methods. This comprehensive survey serves as an accessible reference for experienced researchers and newcomers navigating speech separation's complex landscape.
Generalizable Federated Learning using Client Adaptive Focal Modulation
Venue: arXiv cs.CV 2025
Year: 2025

Federated learning (FL) has proven essential for privacy-preserving, collaborative training across distributed clients. Our prior work, TransFed, introduced a robust transformer-based FL framework that leverages a learn-to-adapt hypernetwork to generate personalized focal modulation layers per client, outperforming traditional methods in non-IID and cross-domain settings. In this extended version, we propose AdaptFED, where we deepen the investigation of focal modulation in generalizable FL by incorporating: (1) a refined adaptation strategy that integrates task-aware client embeddings to personalize modulation dynamics further, (2) enhanced theoretical bounds on adaptation performance, and (3) broader empirical validation across additional modalities, including time-series and multilingual data. We also introduce an efficient variant of TransFed that reduces server-client communication overhead via low-rank hypernetwork conditioning, enabling scalable deployment in resource-constrained environments. Extensive experiments on eight diverse datasets reaffirm the superiority of our method over state-of-the-art baselines, particularly in source-free and cross-task federated setups. Our findings not only extend the capabilities of focal modulation in FL but also pave the way for more adaptive, scalable, and generalizable transformer-based federated systems. The code is available at http://github.com/Tajamul21/TransFed
EVOSCAT: Exploring Software Change Dynamics in Large-Scale Historical Datasets
Venue: arXiv cs.SE 2025
Year: 2025

Long lived software projects encompass a large number of artifacts, which undergo many revisions throughout their history. Empirical software engineering researchers studying software evolution gather and collect datasets with millions of events, representing changes introduced to specific artifacts. In this paper, we propose EvoScat, a tool that attempts addressing temporal scalability through the usage of interactive density scatterplot to provide a global overview of large historical datasets mined from open source repositories in a single visualization. EvoScat intents to provide researchers with a mean to produce scalable visualizations that can help them explore and characterize evolution datasets, as well as comparing the histories of individual artifacts, both in terms of 1) observing how rapidly different artifacts age over multiple-year-long time spans 2) how often metrics associated with each artifacts tend towards an improvement or worsening. The paper shows how the tool can be tailored to specific analysis needs (pace of change comparison, clone detection, freshness assessment) thanks to its support for flexible configuration of history scaling and alignment along the time axis, artifacts sorting and interactive color mapping, enabling the analysis of millions of events obtained by mining the histories of tens of thousands of software artifacts. We include in this paper a gallery showcasing datasets gathering specific artifacts (OpenAPI descriptions, GitHub workflow definitions) across multiple repositories, as well as diving into the history of specific popular open source projects.