OpenRaiser/Intern-Atlas huggingface dataset:
A Hybrid Quantum-AI Framework for Protein Structure Prediction on NISQ Devices
Venue: arXiv cs.ET 2025
Year: 2025

Variational quantum algorithms provide a direct, physics-based approach to protein structure prediction, but their accuracy is limited by the coarse resolution of the energy landscapes generated on current noisy devices. We propose a hybrid framework that combines quantum computation with deep learning, formulating structure prediction as a problem of energy fusion. Candidate conformations are obtained through the Variational Quantum Eigensolver (VQE) executed on IBM's 127-qubit superconducting processor, which defines a global yet low-resolution quantum energy surface. To refine these basins, secondary structure probabilities and dihedral angle distributions predicted by the NSP3 neural network are incorporated as statistical potentials. These additional terms sharpen the valleys of the quantum landscape, resulting in a fused energy function that enhances effective resolution and better distinguishes native-like structures. Evaluation on 375 conformations from 75 protein fragments shows consistent improvements over AlphaFold3, ColabFold, and quantum-only predictions, achieving a mean RMSD of 4.9 Å with statistical significance (p < 0.001). The findings demonstrate that energy fusion offers a systematic method for combining data-driven models with quantum algorithms, improving the practical applicability of near-term quantum computing to molecular and structural biology.
Breaking Precision Time: OS Vulnerability Exploits Against IEEE 1588
Venue: arXiv cs.CR 2025
Year: 2025

The Precision Time Protocol (PTP), standardized as IEEE 1588, provides sub-microsecond synchronization across distributed systems and underpins critical infrastructure in telecommunications, finance, power systems, and industrial automation. While prior work has extensively analyzed PTP's vulnerability to network-based attacks, prompting the development of cryptographic protections and anomaly detectors, these defenses presume an uncompromised host. In this paper, we identify and exploit a critical blind spot in current threat models: kernel-level adversaries operating from within the host running the PTP stack. We present the first systematic study of kernel-rooted attacks on PTP, demonstrating how privileged attackers can manipulate system time by corrupting key interfaces without altering PTP network traffic. We implement three attack primitives, constant offset, progressive skew, and random jitter, using in-kernel payloads, and evaluate their impact on the widely used ptp4l and phc2sys daemons. Our experiments reveal that these attacks can silently destabilize clock synchronization, bypassing existing PTP security extensions. These findings highlight the urgent need to reconsider host-level trust assumptions and integrate kernel integrity into the design of secure time synchronization systems.
A Survey on Agentic Security: Applications, Threats and Defenses
Venue: arXiv cs.CL 2025
Year: 2025

In this work we present the first holistic survey of the agentic security landscape, structuring the field around three fundamental pillars: Applications, Threats, and Defenses. We provide a comprehensive taxonomy of over 160 papers, explaining how agents are used in downstream cybersecurity applications, inherent threats to agentic systems, and countermeasures designed to protect them. A detailed cross-cutting analysis shows emerging trends in agent architecture while revealing critical research gaps in model and modality coverage. A complete and continuously updated list of all surveyed papers is publicly available at https://github.com/kagnlp/Awesome-Agentic-Security.
Attention-Enhanced Reinforcement Learning for Dynamic Portfolio Optimization
Venue: arXiv cs.CE 2025
Year: 2025

We develop a deep reinforcement learning framework for dynamic portfolio optimization that combines a Dirichlet policy with cross-sectional attention mechanisms. The Dirichlet formulation ensures that portfolio weights are always feasible, handles tradability constraints naturally, and provides a stable way to explore the allocation space. The model integrates per-asset temporal encoders with a global attention layer, allowing it to capture sector relationships, factor spillovers, and other cross asset dependencies. The reward function includes transaction costs and portfolio variance penalties, linking the learning objective to traditional mean variance trade offs. The results show that attention based Dirichlet policies outperform equal-weight and standard reinforcement learning benchmarks in terms of terminal wealth and Sharpe ratio, while maintaining realistic turnover and drawdown levels. Overall, the study shows that combining principled action design with attention-based representations improves both the stability and interpretability of reinforcement learning for portfolio management.
Addressing Visual Impairments with Model-Driven Engineering: A Systematic Literature Review
Venue: arXiv cs.SE 2025
Year: 2025

Software applications often pose barriers for users with accessibility needs, e.g., visual impairments. Model-driven engineering (MDE), with its systematic nature of code derivation, offers systematic methods to integrate accessibility concerns into software development while reducing manual effort. This paper presents a systematic literature review on how MDE addresses accessibility for vision impairments. From 447 initially identified papers, 30 primary studies met the inclusion criteria. About two-thirds reference the Web Content Accessibility Guidelines (WCAG), yet their project-specific adaptions and end-user validations hinder wider adoption in MDE. The analyzed studies model user interface structures, interaction and navigation, user capabilities, requirements, and context information. However, only few specify concrete modeling techniques on how to incorporate accessibility needs or demonstrate fully functional systems. Insufficient details on MDE methods, i.e., transformation rules or code templates, hinder the reuse, generalizability, and reproducibility. Furthermore, limited involvement of affected users and limited developer expertise in accessibility contribute to weak empirical validation. Overall, the findings indicate that current MDE research insufficiently supports vision-related accessibility. Our paper concludes with a research agenda outlining how support for vision impairments can be more effectively embedded in MDE processes.
ATLO-ML: Adaptive Time-Length Optimizer for Machine Learning -- Insights from Air Quality Forecasting
Venue: arXiv cs.LG 2025
Year: 2025

Accurate time-series predictions in machine learning are heavily influenced by the selection of appropriate input time length and sampling rate. This paper introduces ATLO-ML, an adaptive time-length optimization system that automatically determines the optimal input time length and sampling rate based on user-defined output time length. The system provides a flexible approach to time-series data pre-processing, dynamically adjusting these parameters to enhance predictive performance. ATLO-ML is validated using air quality datasets, including both GAMS-dataset and proprietary data collected from a data center, both in time series format. Results demonstrate that utilizing the optimized time length and sampling rate significantly improves the accuracy of machine learning models compared to fixed time lengths. ATLO-ML shows potential for generalization across various time-sensitive applications, offering a robust solution for optimizing temporal input parameters in machine learning workflows.
Limited-Angle Tomography Reconstruction via Projector Guided 3D Diffusion
Venue: arXiv cs.CV 2025
Year: 2025

Limited-angle electron tomography aims to reconstruct 3D shapes from 2D projections of Transmission Electron Microscopy (TEM) within a restricted range and number of tilting angles, but it suffers from the missing-wedge problem that causes severe reconstruction artifacts. Deep learning approaches have shown promising results in alleviating these artifacts, yet they typically require large high-quality training datasets with known 3D ground truth which are difficult to obtain in electron microscopy. To address these challenges, we propose TEMDiff, a novel 3D diffusion-based iterative reconstruction framework. Our method is trained on readily available volumetric FIB-SEM data using a simulator that maps them to TEM tilt series, enabling the model to learn realistic structural priors without requiring clean TEM ground truth. By operating directly on 3D volumes, TEMDiff implicitly enforces consistency across slices without the need for additional regularization. On simulated electron tomography datasets with limited angular coverage, TEMDiff outperforms state-of-the-art methods in reconstruction quality. We further demonstrate that a trained TEMDiff model generalizes well to real-world TEM tilts obtained under different conditions and can recover accurate structures from tilt ranges as narrow as 8 degrees, with 2-degree increments, without any retraining or fine-tuning.
Cluster Paths: Navigating Interpretability in Neural Networks
Venue: arXiv cs.CV 2025
Year: 2025

While modern deep neural networks achieve impressive performance in vision tasks, they remain opaque in their decision processes, risking unwarranted trust, undetected biases and unexpected failures. We propose cluster paths, a post-hoc interpretability method that clusters activations at selected layers and represents each input as its sequence of cluster IDs. To assess these cluster paths, we introduce four metrics: path complexity (cognitive load), weighted-path purity (class alignment), decision-alignment faithfulness (predictive fidelity), and path agreement (stability under perturbations). In a spurious-cue CIFAR-10 experiment, cluster paths identify color-based shortcuts and collapse when the cue is removed. On a five-class CelebA hair-color task, they achieve 90% faithfulness and maintain 96% agreement under Gaussian noise without sacrificing accuracy. Scaling to a Vision Transformer pretrained on ImageNet, we extend cluster paths to concept paths derived from prompting a large language model on minimal path divergences. Finally, we show that cluster paths can serve as an effective out-of-distribution (OOD) detector, reliably flagging anomalous samples before the model generates over-confident predictions. Cluster paths uncover visual concepts, such as color palettes, textures, or object contexts, at multiple network depths, demonstrating that cluster paths scale to large vision models while generating concise and human-readable explanations.
Beyond More Context: How Granularity and Order Drive Code Completion Quality
Venue: arXiv cs.SE 2025
Year: 2025

Context plays an important role in the quality of code completion, as Large Language Models (LLMs) require sufficient and relevant information to assist developers in code generation tasks. However, composing a relevant context for code completion poses challenges in large repositories: First, the limited context length of LLMs makes it impractical to include all repository files. Second, the quality of generated code is highly sensitive to noisy or irrelevant context. In this paper, we present our approach for the ASE 2025 Context Collection Challenge. The challenge entails outperforming JetBrains baselines by designing effective retrieval and context collection strategies. We develop and evaluate a series of experiments that involve retrieval strategies at both the file and chunk levels. We focus our initial experiments on examining the impact of context size and file ordering on LLM performance. Our results show that the amount and order of context can significantly influence the performance of the models. We introduce chunk-based retrieval using static analysis, achieving a 6% improvement over our best file-retrieval strategy and a 16% improvement over the no-context baseline for Python in the initial phase of the competition. Our results highlight the importance of retrieval granularity, ordering and hybrid strategies in developing effective context collection pipelines for real-world development scenarios.
Investigating Students' Preferences for AI Roles in Mathematical Modelling: Evidence from a Randomized Controlled Trial
Venue: arXiv cs.HC 2025
Year: 2025

Mathematical modelling (MM) is a key competency for solving complex real-world problems, yet many students struggle with abstraction, representation, and iterative reasoning. Artificial intelligence (AI) has been proposed as a support for higher-order thinking, but its role in MM education is still underexplored. This study examines the relationships among students' design thinking (DT), computational thinking (CT), and mathematical modelling self-efficacy (MMSE), and investigates their preferences for different AI roles during the modelling process. Using a randomized controlled trial, we identify significant connections among DT, CT, and MMSE, and reveal distinct patterns in students' preferred AI roles, including AI as a tutor (providing explanations and feedback), AI as a tool (assisting with calculations and representations), AI as a collaborator (suggesting strategies and co-creating models), and AI as a peer (offering encouragement and fostering reflection). Differences across learner profiles highlight how students' dispositions shape their expectations for AI. These findings advance understanding of AI-supported MM and provide design implications for adaptive, learner-centered systems.
POME: Post Optimization Model Edit via Muon-style Projection
Venue: arXiv cs.LG 2025
Year: 2025

We introduce Post-Optimization Model Edit (POME), a new algorithm that enhances the performance of fine-tuned large language models using only their pretrained and fine-tuned checkpoints, without requiring extra data or further optimization. The core idea is to apply a muon-style projection to $ΔW$, the difference between the fine-tuned and pretrained weights. This projection uses truncated singular value decomposition (SVD) to equalize the influence of dominant update directions and prune small singular values, which often represent noise. As a simple post-processing step, POME is completely decoupled from the training pipeline. It requires zero modifications and imposes no overhead, making it universally compatible with any optimizer or distributed framework. POME delivers consistent gains, boosting average performance by +2.5\% on GSM8K and +1.0\% on code generation. Its broad applicability -- from 7B foundation models to 72B RLHF-instructed models -- establishes it as a practical, zero-cost enhancement for any fine-tuning pipeline. Code is available at https://github.com/NUS-HPC-AI-Lab/POME.
Unsupervised Backdoor Detection and Mitigation for Spiking Neural Networks
Venue: arXiv cs.CR 2025
Year: 2025

Spiking Neural Networks (SNNs) have gained increasing attention for their superior energy efficiency compared to Artificial Neural Networks (ANNs). However, their security aspects, particularly under backdoor attacks, have received limited attention. Existing defense methods developed for ANNs perform poorly or can be easily bypassed in SNNs due to their event-driven and temporal dependencies. This paper identifies the key blockers that hinder traditional backdoor defenses in SNNs and proposes an unsupervised post-training detection framework, Temporal Membrane Potential Backdoor Detection (TMPBD), to overcome these challenges. TMPBD leverages the maximum margin statistics of temporal membrane potential (TMP) in the final spiking layer to detect target labels without any attack knowledge or data access. We further introduce a robust mitigation mechanism, Neural Dendrites Suppression Backdoor Mitigation (NDSBM), which clamps dendritic connections between early convolutional layers to suppress malicious neurons while preserving benign behaviors, guided by TMP extracted from a small, clean, unlabeled dataset. Extensive experiments on multiple neuromorphic benchmarks and state-of-the-art input-aware dynamic trigger attacks demonstrate that TMPBD achieves 100% detection accuracy, while NDSBM reduces the attack success rate from 100% to 8.44%, and to 2.81% when combined with detection, without degrading clean accuracy.
Three Forms of Stochastic Injection for Improved Distribution-to-Distribution Generative Modeling
Venue: arXiv cs.LG 2025
Year: 2025

Modeling transformations between arbitrary data distributions is a fundamental scientific challenge, arising in applications like drug discovery and evolutionary simulation. While flow matching offers a natural framework for this task, its use has thus far primarily focused on the noise-to-data setting, while its application in the general distribution-to-distribution setting is underexplored. We find that in the latter case, where the source is also a data distribution to be learned from limited samples, standard flow matching fails due to sparse supervision. To address this, we propose a simple and computationally efficient method that injects stochasticity into the training process by perturbing source samples and flow interpolants. On five diverse imaging tasks spanning biology, radiology, and astronomy, our method significantly improves generation quality, outperforming existing baselines by an average of 9 FID points. Our approach also reduces the transport cost between input and generated samples to better highlight the true effect of the transformation, making flow matching a more practical tool for simulating the diverse distribution transformations that arise in science.
Implicit-Knowledge Visual Question Answering with Structured Reasoning Traces
Venue: arXiv cs.CV 2025
Year: 2025

Knowledge-based Visual Question Answering (KVQA) requires models to ground entities in images and reason over factual knowledge. Recent work has introduced its implicit-knowledge variant, IK-KVQA, where a multimodal large language model (MLLM) is the sole knowledge source and answers are produced without external retrieval. Existing IK-KVQA approaches, however, are typically trained with answer-only supervision: reasoning remains implicit, justifications are often weak or inconsistent, and generalization after standard supervised fine-tuning (SFT) can be brittle. We propose MODELNAME, a framework that equips IK-KVQA with dual-path structured reasoning traces (symbolic relation paths over text and vision together with path-grounded natural-language explanations) to provide a stronger inductive bias than generic answer-only supervision. These traces act as modality-aware scaffolds that guide the model toward relevant entities and attributes, offering more structure than generic chain-of-thought supervision while not constraining reasoning to any single fixed path. Using a single open-source MLLM, MODELNAME constructs and selects traces to build an offline trace-enriched dataset and then performs structure-aware self-distillation; no external retrievers, verifiers, or curated knowledge bases are used, and inference is a single autoregressive pass. Across benchmarks, MODELNAME consistently improves both answer accuracy and the transparency of intermediate reasoning, achieving up to 11.3% higher answer accuracy on OK-VQA over the strongest baseline.
Aligning Large Language Models via Fully Self-Synthetic Data
Venue: arXiv cs.CL 2025
Year: 2025

Traditional reinforcement learning from human feedback (RLHF) for large language models (LLMs) relies on expensive human-annotated datasets, while Reinforcement Learning from AI Feedback (RLAIF) also incurs significant costs, requiring the collection of diverse prompts and corresponding responses, often necessitating external reward models or proprietary models like GPT-4 to annotate preference pairs. In this work, we introduce Self-Alignment Optimization (SAO), a fully self-synthetic framework for LLM alignment, where all training data, including prompts (i.e., user queries), responses, and preferences, are generated by the model itself. Specifically, SAO first instructs the LLM to engage in persona role-play and generate diverse prompts and responses, which are then self-evaluated for preference optimization. Extensive experiments demonstrate that SAO effectively enhances the model's chat capabilities on standard benchmarks like AlpacaEval~2.0, while maintaining strong performance on downstream objective tasks (e.g., question-answering, math reasoning). Our work provides a practical solution for self-improvement in aligning LLMs, and the code for reproducing our results is available at: https://github.com/SJY8460/SAO.
Heptapod: Language Modeling on Visual Signals
Venue: arXiv cs.CV 2025
Year: 2025

We introduce Heptapod, an image autoregressive model that adheres to the foundational principles of language modeling. Heptapod employs \textbf{causal attention}, \textbf{eliminates reliance on CFG}, and \textbf{eschews the trend of semantic tokenizers}. Our key innovation is \textit{next 2D distribution prediction}: a causal Transformer with reconstruction-focused visual tokenizer, learns to predict the distribution over the entire 2D spatial grid of images at each timestep. This learning objective unifies the sequential modeling of autoregressive framework with the holistic self-supervised learning of masked autoencoding, enabling the model to capture comprehensive image semantics via generative training. On the ImageNet generation benchmark, Heptapod achieves an FID of $2.70$, significantly outperforming previous causal autoregressive approaches. We hope our work inspires a principled rethinking of language modeling on visual signals and beyond.
TimeFormer: Transformer with Attention Modulation Empowered by Temporal Characteristics for Time Series Forecasting
Venue: arXiv cs.LG 2025
Year: 2025

Although Transformers excel in natural language processing, their extension to time series forecasting remains challenging due to insufficient consideration of the differences between textual and temporal modalities. In this paper, we develop a novel Transformer architecture designed for time series data, aiming to maximize its representational capacity. We identify two key but often overlooked characteristics of time series: (1) unidirectional influence from the past to the future, and (2) the phenomenon of decaying influence over time. These characteristics are introduced to enhance the attention mechanism of Transformers. We propose TimeFormer, whose core innovation is a self-attention mechanism with two modulation terms (MoSA), designed to capture these temporal priors of time series under the constraints of the Hawkes process and causal masking. Additionally, TimeFormer introduces a framework based on multi-scale and subsequence analysis to capture semantic dependencies at different temporal scales, enriching the temporal dependencies. Extensive experiments conducted on multiple real-world datasets show that TimeFormer significantly outperforms state-of-the-art methods, achieving up to a 7.45% reduction in MSE compared to the best baseline and setting new benchmarks on 94.04\% of evaluation metrics. Moreover, we demonstrate that the MoSA mechanism can be broadly applied to enhance the performance of other Transformer-based models.