OpenRaiser/Intern-Atlas huggingface dataset:
ABConformer: Physics-inspired Sliding Attention for Antibody-Antigen Interface Prediction
Venue: arXiv cs.LG 2025
Year: 2025

Accurate prediction of antibody-antigen (Ab-Ag) interfaces is critical for vaccine design, immunodiagnostics, and therapeutic antibody development. However, achieving reliable predictions from sequences alone remains a challenge. In this paper, we present ABCONFORMER, a model based on the Conformer backbone that captures both local and global features of a biosequence. To accurately capture Ab-Ag interactions, we introduced the physics-inspired sliding attention, enabling residue-level contact recovery without relying on three-dimensional structural data. ABConformer can accurately predict paratopes and epitopes given the antibody and antigen sequence, and predict pan-epitopes on the antigen without antibody information. In comparison experiments, ABCONFORMER achieves state-of-the-art performance on a recent SARS-CoV-2 Ab-Ag dataset, and surpasses widely used sequence-based methods for antibody-agnostic epitope prediction. Ablation studies further quantify the contribution of each component, demonstrating that, compared to conventional cross-attention, sliding attention significantly enhances the precision of epitope prediction. To facilitate reproducibility, we will release the code under an open-source license upon acceptance.
A Neural ODE Approach to Aircraft Flight Dynamics Modelling
Venue: arXiv cs.LG 2025
Year: 2025

Accurate aircraft trajectory prediction is critical for air traffic management, airline operations, and environmental assessment. This paper introduces NODE-FDM, a Neural Ordinary Differential Equations-based Flight Dynamics Model trained on Quick Access Recorder (QAR) data. By combining analytical kinematic relations with data-driven components, NODE-FDM achieves a more accurate reproduction of recorded trajectories than state-of-the-art models such as a BADA-based trajectory generation methodology (BADA4 performance model combined with trajectory control routines), particularly in the descent phase of the flight. The analysis demonstrates marked improvements across altitude, speed, and mass dynamics. Despite current limitations, including limited physical constraints and the limited availability of QAR data, the results demonstrate the potential of physics-informed neural ordinary differential equations as a high-fidelity, data-driven approach to aircraft performance modelling. Future work will extend the framework to incorporate a full modelling of the lateral dynamics of the aircraft.
MELCOT: A Hybrid Learning Architecture with Marginal Preservation for Matrix-Valued Regression
Venue: arXiv cs.LG 2025
Year: 2025

Regression is essential across many domains but remains challenging in high-dimensional settings, where existing methods often lose spatial structure or demand heavy storage. In this work, we address the problem of matrix-valued regression, where each sample is naturally represented as a matrix. We propose MELCOT, a hybrid model that integrates a classical machine learning-based Marginal Estimation (ME) block with a deep learning-based Learnable-Cost Optimal Transport (LCOT) block. The ME block estimates data marginals to preserve spatial information, while the LCOT block learns complex global features. This design enables MELCOT to inherit the strengths of both classical and deep learning methods. Extensive experiments across diverse datasets and domains demonstrate that MELCOT consistently outperforms all baselines while remaining highly efficient.
C-Evolve: Consensus-based Evolution for Prompt Groups
Venue: arXiv cs.CL 2025
Year: 2025

Prompt evolution algorithms offer a powerful paradigm for enhancing AI systems based on closed-source models, while few work explores whether aggregating results from multiple prompts to reach a consensus can further advance the system capability boundary. In this paper, we introduce Consensus-Evolve (C-Evolve), an evolutionary algorithm that discovers a group of prompts whose aggregated outputs after majority voting achieve optimal performance. More specifically, C-Evolve employs an island-based evolutionary algorithm to maintain population diversity, and prompts from distinct islands are selected to form groups to aggregate their outputs. The key difference from single individual evolution is a voting score, which evaluates each individual prompt's contribution within groups. We take this as the fitness score for evolution instead of individual performance. Consequently, C-Evolve is more likely to produce and maintain prompts with higher potential to form a high-performing group and eliminate low-performing ones, gradually improving the group performance after reaching consensus. Our method achieves state-of-the-art performance across a wide range of tasks, including both open-ended tasks like HotpotQA and closed-ended tasks like MATH. On Qwen3-8B, C-Evolve achieves 70.67% on HotpotQA and 43.88% on IFBench, which are 4.95% and 2.73% higher than GEPA, respectively. For GPT-4.1-mini, the accuracy on IFBench is further improved to 47.96% and reaches 95.33% in the MATH benchmark. These results demonstrate the C-Evolve's competitive performance.
DiffTex: Differentiable Texturing for Architectural Proxy Models
Venue: arXiv cs.GR 2025
Year: 2025

Simplified proxy models are commonly used to represent architectural structures, reducing storage requirements and enabling real-time rendering. However, the geometric simplifications inherent in proxies result in a loss of fine color and geometric details, making it essential for textures to compensate for the loss. Preserving the rich texture information from the original dense architectural reconstructions remains a daunting task, particularly when working with unordered RGB photographs. We propose an automated method for generating realistic texture maps for architectural proxy models at the texel level from an unordered collection of registered photographs. Our approach establishes correspondences between texels on a UV map and pixels in the input images, with each texel's color computed as a weighted blend of associated pixel values. Using differentiable rendering, we optimize blending parameters to ensure photometric and perspective consistency, while maintaining seamless texture coherence. Experimental results demonstrate the effectiveness and robustness of our method across diverse architectural models and varying photographic conditions, enabling the creation of high-quality textures that preserve visual fidelity and structural detail.
DentVLM: A Multimodal Vision-Language Model for Comprehensive Dental Diagnosis and Enhanced Clinical Practice
Venue: arXiv cs.CV 2025
Year: 2025

Diagnosing and managing oral diseases necessitate advanced visual interpretation across diverse imaging modalities and integrated information synthesis. While current AI models excel at isolated tasks, they often fall short in addressing the complex, multimodal requirements of comprehensive clinical dental practice. Here we introduce DentVLM, a multimodal vision-language model engineered for expert-level oral disease diagnosis. DentVLM was developed using a comprehensive, large-scale, bilingual dataset of 110,447 images and 2.46 million visual question-answering (VQA) pairs. The model is capable of interpreting seven 2D oral imaging modalities across 36 diagnostic tasks, significantly outperforming leading proprietary and open-source models by 19.6% higher accuracy for oral diseases and 27.9% for malocclusions. In a clinical study involving 25 dentists, evaluating 1,946 patients and encompassing 3,105 QA pairs, DentVLM surpassed the diagnostic performance of 13 junior dentists on 21 of 36 tasks and exceeded that of 12 senior dentists on 12 of 36 tasks. When integrated into a collaborative workflow, DentVLM elevated junior dentists' performance to senior levels and reduced diagnostic time for all practitioners by 15-22%. Furthermore, DentVLM exhibited promising performance across three practical utility scenarios, including home-based dental health management, hospital-based intelligent diagnosis and multi-agent collaborative interaction. These findings establish DentVLM as a robust clinical decision support tool, poised to enhance primary dental care, mitigate provider-patient imbalances, and democratize access to specialized medical expertise within the field of dentistry.
A Predictive and Synergistic Two-Layer Scheduling Framework for LLM Serving
Venue: arXiv cs.DC 2025
Year: 2025

LLM inference serving typically scales out with a two-tier architecture: a cluster router distributes requests to multiple inference engines, each of which then in turn performs its own internal scheduling. However, this commonly used paradigm suffers from critical, systemic inefficiency caused by the information gaps across two layers. At the cluster-layer, the router mainly relies on lagging, coarse-grained metrics, such as average latency and queue length to make decisions, resulting in "decision lag" that leads to suboptimal request routing. At the engine-layer, static heuristic scheduling policies cannot effectively handle the dynamic workloads, leading a poor balance between latency and throughput. Besides, these gaps may cause SLO violations and resource waste, especially in heterogeneous cloud environments. To bridge such gaps, we propose NexusSched, a cross-layer framework that shifts LLM serving system from reactive load balancing to predictive orchestration. The core of NexusSched lies in a structurally-informed online performance model that provides accurate, forward-looking per-step latency and capacity estimations. This model empowers two key components. At the engine-layer, LENS performs SLO-aware, adaptive scheduling, dynamically optimizing batching to meet SLOs under real-time loads. At the cluster-layer, PRISM uses predictive signals to perform state-driven routing, maximizing cluster-wide performance and SLO attainment. Performance evaluations show that NexusSched improves SLO attainment by 43% on average and achieves up to 3x throughput speedup in long-context and heterogeneous scenarios. Besides, we also deploy NexusSched on FlowGPT's clusters to demonstrate its advantages in production environment.
Noise-Domain Non-Orthogonal Multiple Access for Three Users
Venue: arXiv cs.IT 2025
Year: 2025

In this study, we propose a novel three-user noise-domain non-orthogonal multiple access (ND-NOMA) scheme by introducing the correlation as a new dimension besides mean and variance quantities used in two-user ND-NOMA. The new three-user ND-NOMA scheme includes both uplink and downlink scenarios, with detectors designed to decode the information embedded in mean, variance, and correlation. Our theoretical analysis and simulation results under Rician fading channels show that the proposed system is capable of achieving promising bit error rate (BER) performance while preserving the low power and low complexity advantages of ND-NOMA. This new ND-NOMA design enables simultaneous communication among three users using different dimensions, paving the way for scalable multi-user communication in noise-domain systems and in the Internet-of-things (IoT) environments.
PATCH: Learnable Tile-level Hybrid Sparsity for LLMs
Venue: arXiv cs.LG 2025
Year: 2025

Large language models (LLMs) deliver impressive performance but incur prohibitive memory and compute costs at deployment. Model pruning is an effective way to reduce these overheads, yet existing approaches face challenges: unstructured sparsity, where nonzeros can appear anywhere, preserves accuracy but yields irregular access patterns that prevent GPU acceleration, while semi-structured 2:4 sparsity is hardware-friendly but enforces a rigid 50% pattern that degrades model quality. To bridge this gap, we introduce PATCH, a hybrid sparsity framework that enables a continuous sparsity ratio between 0% and 50%. PATCH partitions weight matrices into tiles, assigning each tile to be either dense or 2:4 sparse via a learnable mask selection mechanism. This design provides fine-grained control over accuracy-acceleration tradeoffs and supports non-uniform sparsity across layers, leading to superior overall quality. Across models from 0.5B to 8B parameters, PATCH consistently narrows the gap to dense accuracy while delivering practical speedups. For instance, on LLaMA-2 7B with an A6000 GPU, PATCH achieves 1.18x-1.38x end-to-end speedup over dense baselines while improving accuracy by 0.37%-2.96% compared to the state-of-the-art 2:4 pruning method, MaskLLM.
Fundamental Limits of Distributed Computing for Linearly Separable Functions
Venue: arXiv cs.IT 2025
Year: 2025

This work addresses the problem of distributed computation of linearly separable functions, where a master node with access to $K$ datasets, employs $N$ servers to compute $L$ user-requested functions, each defined over the datasets. Servers are instructed to compute subfunctions of the datasets and must communicate computed outputs to the user, who reconstructs the requested outputs. The central challenge is to reduce the per-server computational load and the communication cost from servers to the user, while ensuring recovery for any possible set of $L$ demanded functions. We here establish the fundamental communication-computation tradeoffs for arbitrary $K$ and $L$, through novel task-assignment and communication strategies that, under the linear-encoding and no-subpacketization assumptions, are proven to be either exactly optimal or within a factor of three from the optimum. In contrast to prior approaches that relied on fixed assignments of tasks -- either disjoint or cyclic assignments -- our key innovation is a nullspace-based design that jointly governs task assignment and server transmissions, ensuring exact decodability for all demands, and attaining optimality over all assignment and delivery methods. To prove this optimality, we here uncover a duality between nullspaces and sparse matrix factorizations, enabling us to recast the distributed computing problem as an equivalent factorization task and derive a sharp information-theoretic converse bound. Building on this, we establish an additional converse that, for the first time, links the communication cost to the covering number from the theory of general covering designs.
Robust Orientation Estimation with TRIAD-aided Manifold EKF
Venue: arXiv cs.RO 2025
Year: 2025

The manifold extended Kalman filter (Manifold EKF) has found extensive application for attitude determination. Magnetometers employed as sensors for such attitude determination are easily prone to disturbances by their sensitivity to calibration and external magnetic fields. The TRIAD (Tri-Axial Attitude Determination) algorithm is well known as a sub-optimal attitude estimator. In this article, we incorporate this sub-optimal feature of the TRIAD in mitigating the influence of the magnetometer reading in the pitch and roll axis determination in the Manifold EKF algorithm. We substantiate our results with experiments.
Stochastic Embedding of Digraphs into DAGs
Venue: arXiv cs.DS 2025
Year: 2025

Given a weighted digraph $G=(V,E,w)$, a stochastic embedding into DAGs is a distribution $\mathcal{D}$ over pairs of DAGs $(D_1,D_2)$ such that for every $u,v$: (1) the reachability is preserved: $u\rightsquigarrow_G v$ (i.e., $v$ is reachable from $u$ in $G$) implies that $u\rightsquigarrow_{D_1} v$ or $u\rightsquigarrow_{D_2} v$ (but not both), and (2) distances are dominated: $d_G(u,v)\le\min\{d_{D_1}(u,v),d_{D_2}(u,v)\}$. The stochastic embedding $\mathcal{D}$ has expected distortion $t$ if for every $u,v\in V$, \[ \mathbb{E}_{(D_{1},D_{2})\sim\mathcal{D}}\left[d_{D_{1}}(u,v)\cdot\boldsymbol{1}[u\rightsquigarrow_{D_{1}}v]+d_{D_{2}}(u,v)\cdot\boldsymbol{1}[u\rightsquigarrow_{D_{2}}v]\right]\le t\cdot d_{G}(u,v)~. \] Finally, the sparsity of $\mathcal{D}$ is the maximum number of edges in any of the DAGs in its support. Given an $n$ vertex digraph with $m$ edges, we construct a stochastic embedding into DAGs with expected distortion $\tilde{O}(\log n)$ and $\tilde{O}(m)$ sparsity, improving a previous result by Assadi, Hoppenworth, and Wein [STOC 25], which achieved expected distortion $\tilde{O}(\log^3 n)$. Further, we can sample DAGs from this distribution in $\tilde{O}(m)$ time.
From Human Annotation to Automation: LLM-in-the-Loop Active Learning for Arabic Sentiment Analysis
Venue: arXiv cs.CL 2025
Year: 2025

Natural language processing (NLP), particularly sentiment analysis, plays a vital role in areas like marketing, customer service, and social media monitoring by providing insights into user opinions and emotions. However, progress in Arabic sentiment analysis remains limited due to the lack of large, high-quality labeled datasets. While active learning has proven effective in reducing annotation efforts in other languages, few studies have explored it in Arabic sentiment tasks. Likewise, the use of large language models (LLMs) for assisting annotation and comparing their performance to human labeling is still largely unexplored in the Arabic context. In this paper, we propose an active learning framework for Arabic sentiment analysis designed to reduce annotation costs while maintaining high performance. We evaluate multiple deep learning architectures: Specifically, long short-term memory (LSTM), gated recurrent units (GRU), and recurrent neural networks (RNN), across three benchmark datasets: Hunger Station, AJGT, and MASAC, encompassing both modern standard Arabic and dialectal variations. Additionally, two annotation strategies are compared: Human labeling and LLM-assisted labeling. Five LLMs are evaluated as annotators: GPT-4o, Claude 3 Sonnet, Gemini 2.5 Pro, DeepSeek Chat, and LLaMA 3 70B Instruct. For each dataset, the best-performing LLM was used: GPT-4o for Hunger Station, Claude 3 Sonnet for AJGT, and DeepSeek Chat for MASAC. Our results show that LLM-assisted active learning achieves competitive or superior performance compared to human labeling. For example, on the Hunger Station dataset, the LSTM model achieved 93% accuracy with only 450 labeled samples using GPT-4o-generated labels, while on the MASAC dataset, DeepSeek Chat reached 82% accuracy with 650 labeled samples, matching the accuracy obtained through human labeling.
Pancreas Part Segmentation under Federated Learning Paradigm
Venue: arXiv cs.CV 2025
Year: 2025

We present the first federated learning (FL) approach for pancreas part(head, body and tail) segmentation in MRI, addressing a critical clinical challenge as a significant innovation. Pancreatic diseases exhibit marked regional heterogeneity cancers predominantly occur in the head region while chronic pancreatitis causes tissue loss in the tail, making accurate segmentation of the organ into head, body, and tail regions essential for precise diagnosis and treatment planning. This segmentation task remains exceptionally challenging in MRI due to variable morphology, poor soft-tissue contrast, and anatomical variations across patients. Our novel contribution tackles two fundamental challenges: first, the technical complexity of pancreas part delineation in MRI, and second the data scarcity problem that has hindered prior approaches. We introduce a privacy-preserving FL framework that enables collaborative model training across seven medical institutions without direct data sharing, leveraging a diverse dataset of 711 T1W and 726 T2W MRI scans. Our key innovations include: (1) a systematic evaluation of three state-of-the-art segmentation architectures (U-Net, Attention U-Net,Swin UNETR) paired with two FL algorithms (FedAvg, FedProx), revealing Attention U-Net with FedAvg as optimal for pancreatic heterogeneity, which was never been done before; (2) a novel anatomically-informed loss function prioritizing region-specific texture contrasts in MRI. Comprehensive evaluation demonstrates that our approach achieves clinically viable performance despite training on distributed, heterogeneous datasets.
Benchmarking LLM-Assisted Blue Teaming via Standardized Threat Hunting
Venue: arXiv cs.CR 2025
Year: 2025

As cyber threats continue to grow in scale and sophistication, blue team defenders increasingly require advanced tools to proactively detect and mitigate risks. Large Language Models (LLMs) offer promising capabilities for enhancing threat analysis. However, their effectiveness in real-world blue team threat-hunting scenarios remains insufficiently explored. This paper presents CyberTeam, a benchmark designed to guide LLMs in blue teaming practice. CyberTeam constructs a standardized workflow in two stages. First, it models realistic threat-hunting workflows by capturing the dependencies among analytical tasks from threat attribution to incident response. Next, each task is addressed through a set of operational modules tailored to its specific analytical requirements. This transforms threat hunting into a structured sequence of reasoning steps, with each step grounded in a discrete operation and ordered according to task-specific dependencies. Guided by this framework, LLMs are directed to perform threat-hunting tasks through modularized steps. Overall, CyberTeam integrates 30 tasks and 9 operational modules to guide LLMs through standardized threat analysis. We evaluate both leading LLMs and state-of-the-art cybersecurity agents, comparing CyberTeam against open-ended reasoning strategies. Our results highlight the improvements enabled by standardized design, while also revealing the limitations of open-ended reasoning in real-world threat hunting.
ML-Asset Management: Curation, Discovery, and Utilization
Venue: arXiv cs.DB 2025
Year: 2025

Machine learning (ML) assets, such as models, datasets, and metadata, are central to modern ML workflows. Despite their explosive growth in practice, these assets are often underutilized due to fragmented documentation, siloed storage, inconsistent licensing, and lack of unified discovery mechanisms, making ML-asset management an urgent challenge. This tutorial offers a comprehensive overview of ML-asset management activities across its lifecycle, including curation, discovery, and utilization. We provide a categorization of ML assets, and major management issues, survey state-of-the-art techniques, and identify emerging opportunities at each stage. We further highlight system-level challenges related to scalability, lineage, and unified indexing. Through live demonstrations of systems, this tutorial equips both researchers and practitioners with actionable insights and practical tools for advancing ML-asset management in real-world and domain-specific settings.