OpenRaiser/Intern-Atlas huggingface dataset:
Global-to-local image quality assessment in optical microscopy via fast and robust deep learning predictions
Venue: arXiv cs.CV 2025
Year: 2025

Optical microscopy is one of the most widely used techniques in research studies for life sciences and biomedicine. These applications require reliable experimental pipelines to extract valuable knowledge from the measured samples and must be supported by image quality assessment (IQA) to ensure correct processing and analysis of the image data. IQA methods are implemented with variable complexity. However, while most quality metrics have a straightforward implementation, they might be time consuming and computationally expensive when evaluating a large dataset. In addition, quality metrics are often designed for well-defined image features and may be unstable for images out of the ideal domain. To overcome these limitations, recent works have proposed deep learning-based IQA methods, which can provide superior performance, increased generalizability and fast prediction. Our method, named $\mathrmμ$DeepIQA, is inspired by previous studies and applies a deep convolutional neural network designed for IQA on natural images to optical microscopy measurements. We retrained the same architecture to predict individual quality metrics and global quality scores for optical microscopy data. The resulting models provide fast and stable predictions of image quality by generalizing quality estimation even outside the ideal range of standard methods. In addition, $\mathrmμ$DeepIQA provides patch-wise prediction of image quality and can be used to visualize spatially varying quality in a single image. Our study demonstrates that optical microscopy-based studies can benefit from the generalizability of deep learning models due to their stable performance in the presence of outliers, the ability to assess small image patches, and rapid predictions.
Video Game Level Design as a Multi-Agent Reinforcement Learning Problem
Venue: arXiv cs.AI 2025
Year: 2025

Procedural Content Generation via Reinforcement Learning (PCGRL) offers a method for training controllable level designer agents without the need for human datasets, using metrics that serve as proxies for level quality as rewards. Existing PCGRL research focuses on single generator agents, but are bottlenecked by the need to frequently recalculate heuristics of level quality and the agent's need to navigate around potentially large maps. By framing level generation as a multi-agent problem, we mitigate the efficiency bottleneck of single-agent PCGRL by reducing the number of reward calculations relative to the number of agent actions. We also find that multi-agent level generators are better able to generalize to out-of-distribution map shapes, which we argue is due to the generators' learning more local, modular design policies. We conclude that treating content generation as a distributed, multi-agent task is beneficial for generating functional artifacts at scale.
In-Field Mapping of Grape Yield and Quality with Illumination-Invariant Deep Learning
Venue: arXiv cs.CV 2025
Year: 2025

This paper presents an end-to-end, IoT-enabled robotic system for the non-destructive, real-time, and spatially-resolved mapping of grape yield and quality (Brix, Acidity) in vineyards. The system features a comprehensive analytical pipeline that integrates two key modules: a high-performance model for grape bunch detection and weight estimation, and a novel deep learning framework for quality assessment from hyperspectral (HSI) data. A critical barrier to in-field HSI is the ``domain shift" caused by variable illumination. To overcome this, our quality assessment is powered by the Light-Invariant Spectral Autoencoder (LISA), a domain-adversarial framework that learns illumination-invariant features from uncalibrated data. We validated the system's robustness on a purpose-built HSI dataset spanning three distinct illumination domains: controlled artificial lighting (lab), and variable natural sunlight captured in the morning and afternoon. Results show the complete pipeline achieves a recall (0.82) for bunch detection and a $R^2$ (0.76) for weight prediction, while the LISA module improves quality prediction generalization by over 20% compared to the baselines. By combining these robust modules, the system successfully generates high-resolution, georeferenced data of both grape yield and quality, providing actionable, data-driven insights for precision viticulture.
Less is More: Recursive Reasoning with Tiny Networks
Venue: arXiv cs.LG 2025
Year: 2025

Hierarchical Reasoning Model (HRM) is a novel approach using two small neural networks recursing at different frequencies. This biologically inspired method beats Large Language models (LLMs) on hard puzzle tasks such as Sudoku, Maze, and ARC-AGI while trained with small models (27M parameters) on small data (around 1000 examples). HRM holds great promise for solving hard problems with small networks, but it is not yet well understood and may be suboptimal. We propose Tiny Recursive Model (TRM), a much simpler recursive reasoning approach that achieves significantly higher generalization than HRM, while using a single tiny network with only 2 layers. With only 7M parameters, TRM obtains 45% test-accuracy on ARC-AGI-1 and 8% on ARC-AGI-2, higher than most LLMs (e.g., Deepseek R1, o3-mini, Gemini 2.5 Pro) with less than 0.01% of the parameters.
Flow-Matching Based Refiner for Molecular Conformer Generation
Venue: arXiv cs.LG 2025
Year: 2025

Low-energy molecular conformers generation (MCG) is a foundational yet challenging problem in drug discovery. Denoising-based methods include diffusion and flow-matching methods that learn mappings from a simple base distribution to the molecular conformer distribution. However, these approaches often suffer from error accumulation during sampling, especially in the low SNR steps, which are hard to train. To address these challenges, we propose a flow-matching refiner for the MCG task. The proposed method initializes sampling from mixed-quality outputs produced by upstream denoising models and reschedules the noise scale to bypass the low-SNR phase, thereby improving sample quality. On the GEOM-QM9 and GEOM-Drugs benchmark datasets, the generator-refiner pipeline improves quality with fewer total denoising steps while preserving diversity.
Federated Self-Supervised Learning for Automatic Modulation Classification under Non-IID and Class-Imbalanced Data
Venue: arXiv cs.LG 2025
Year: 2025

Training automatic modulation classification (AMC) models on centrally aggregated data raises privacy concerns, incurs communication overhead, and often fails to confer robustness to channel shifts. Federated learning (FL) avoids central aggregation by training on distributed clients but remains sensitive to class imbalance, non-IID client distributions, and limited labeled samples. We propose FedSSL-AMC, which trains a causal, time-dilated CNN with triplet-loss self-supervision on unlabeled I/Q sequences across clients, followed by per-client SVMs on small labeled sets. We establish convergence of the federated representation learning procedure and a separability guarantee for the downstream classifier under feature noise. Experiments on synthetic and over-the-air datasets show consistent gains over supervised FL baselines under heterogeneous SNR, carrier-frequency offsets, and non-IID label partitions.
The Geometry of Truth: Layer-wise Semantic Dynamics for Hallucination Detection in Large Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Large Language Models (LLMs) often produce fluent yet factually incorrect statements-a phenomenon known as hallucination-posing serious risks in high-stakes domains. We present Layer-wise Semantic Dynamics (LSD), a geometric framework for hallucination detection that analyzes the evolution of hidden-state semantics across transformer layers. Unlike prior methods that rely on multiple sampling passes or external verification sources, LSD operates intrinsically within the model's representational space. Using margin-based contrastive learning, LSD aligns hidden activations with ground-truth embeddings derived from a factual encoder, revealing a distinct separation in semantic trajectories: factual responses preserve stable alignment, while hallucinations exhibit pronounced semantic drift across depth. Evaluated on the TruthfulQA and synthetic factual-hallucination datasets, LSD achieves an F1-score of 0.92, AUROC of 0.96, and clustering accuracy of 0.89, outperforming SelfCheckGPT and Semantic Entropy baselines while requiring only a single forward pass. This efficiency yields a 5-20x speedup over sampling-based methods without sacrificing precision or interpretability. LSD offers a scalable, model-agnostic mechanism for real-time hallucination monitoring and provides new insights into the geometry of factual consistency within large language models.
Why Software Signing (Still) Matters: Trust Boundaries in the Software Supply Chain
Venue: arXiv cs.SE 2025
Year: 2025

Software signing provides a formal mechanism for provenance by ensuring artifact integrity and verifying producer identity. It also imposes tooling and operational costs to implement in practice. In an era of centralized registries such as PyPI, npm, Maven Central, and Hugging Face, it is reasonable to ask whether hardening registry security controls obviates the need for end-to-end artifact signing. In this work, we posit that the core guarantees of signing, provenance, integrity, and accountability are not automatically carried across different software distribution boundaries. These boundaries include mirrors, corporate proxies, re-hosting, and air-gapped transfers, where registry security controls alone cannot provide sufficient assurance. We synthesize historical practice and present a trust model for modern distribution modes to identify when signing is necessary to extend trust beyond registry control. Treating signing as a baseline layer of defense strengthens software supply chain assurance even when registries are secure.
Trust in Transparency: How Explainable AI Shapes User Perceptions
Venue: arXiv cs.HC 2025
Year: 2025

This study explores the integration of contextual explanations into AI-powered loan decision systems to enhance trust and usability. While traditional AI systems rely heavily on algorithmic transparency and technical accuracy, they often fail to account for broader social and economic contexts. Through a qualitative study, I investigated user interactions with AI explanations and identified key gaps, in- cluding the inability of current systems to provide context. My findings underscore the limitations of purely technical transparency and the critical need for contex- tual explanations that bridge the gap between algorithmic outputs and real-world decision-making. By aligning explanations with user needs and broader societal factors, the system aims to foster trust, improve decision-making, and advance the design of human-centered AI systems
NERVIS: An Interactive System for Graph-Based Exploration and Editing of Named Entities
Venue: arXiv cs.HC 2025
Year: 2025

We present an interactive visualization system for exploring named entities and their relationships across document collections. The system is designed around a graph-based representation that integrates three types of nodes: documents, entity mentions, and entities. Connections capture two key relationship types: (i) identical entities across contexts, and (ii) co-locations of mentions within documents. Multiple coordinated views enable users to examine entity occurrences, discover clusters of related mentions, and explore higher-level entity group relationships. To support flexible and iterative exploration, the interface offers fuzzy views with approximate connections, as well as tools for interactively editing the graph by adding or removing links, entities, and mentions, as well as editing entity terms. Additional interaction features include filtering, mini-map navigation, and export options to JSON or image formats for downstream analysis and reporting. This approach contributes to human-centered exploration of entity-rich text data by combining graph visualization, interactive refinement, and adaptable perspectives on relationships.
StructuralDecompose: A Modular Framework for Robust Time Series Decomposition in R
Venue: arXiv cs.LG 2025
Year: 2025

We present StructuralDecompose, an R package for modular and interpretable time series decomposition. Unlike existing approaches that treat decomposition as a monolithic process, StructuralDecompose separates the analysis into distinct components: changepoint detection, anomaly detection, smoothing, and decomposition. This design provides flexibility and robust- ness, allowing users to tailor methods to specific time series characteristics. We demonstrate the package on simulated and real-world datasets, benchmark its performance against state-of-the- art tools such as Rbeast and autostsm, and discuss its role in interpretable machine learning workflows.
Resource-Efficient Fine-Tuning of LLaMA-3.2-3B for Medical Chain-of-Thought Reasoning
Venue: arXiv cs.CL 2025
Year: 2025

Large Language Models (LLMs) such as GPT-4 and LLaMA have demonstrated remarkable reasoning abilities but require significant computational resources for fine-tuning. This paper presents a resource-efficient fine-tuning approach for LLaMA-3.2-3B to enhance medical chain-of-thought reasoning while operating under constrained GPU and memory settings. Using parameter-efficient tuning techniques such as LoRA and QLoRA, we adapt the base model on publicly available medical reasoning datasets. The model achieves improved reasoning coherence and factual accuracy while reducing memory usage by up to 60% compared to standard full fine-tuning. Experimental evaluation demonstrates that lightweight adaptations can retain strong reasoning capability in medical question-answering tasks. This work highlights practical strategies for deploying LLMs in low-resource research environments and provides insights into balancing efficiency and domain specialization for medical AI systems.
Imperceptible Jailbreaking against Large Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Jailbreaking attacks on the vision modality typically rely on imperceptible adversarial perturbations, whereas attacks on the textual modality are generally assumed to require visible modifications (e.g., non-semantic suffixes). In this paper, we introduce imperceptible jailbreaks that exploit a class of Unicode characters called variation selectors. By appending invisible variation selectors to malicious questions, the jailbreak prompts appear visually identical to original malicious questions on screen, while their tokenization is "secretly" altered. We propose a chain-of-search pipeline to generate such adversarial suffixes to induce harmful responses. Our experiments show that our imperceptible jailbreaks achieve high attack success rates against four aligned LLMs and generalize to prompt injection attacks, all without producing any visible modifications in the written prompt. Our code is available at https://github.com/sail-sg/imperceptible-jailbreaks.
Test-Time Scaling in Diffusion LLMs via Hidden Semi-Autoregressive Experts
Venue: arXiv cs.LG 2025
Year: 2025

Diffusion-based large language models (dLLMs) are trained flexibly to model extreme dependence in the data distribution; however, how to best utilize this information at inference time remains an open problem. In this work, we uncover an interesting property of these models: dLLMs trained on textual data implicitly learn a mixture of semi-autoregressive experts, where different generation orders reveal different specialized behaviors. We show that committing to any single, fixed inference time schedule, a common practice, collapses performance by failing to leverage this latent ensemble. To address this, we introduce HEX (Hidden semiautoregressive EXperts for test-time scaling), a training-free inference method that ensembles across heterogeneous block schedules. By doing a majority vote over diverse block-sized generation paths, HEX robustly avoids failure modes associated with any single fixed schedule. On reasoning benchmarks such as GSM8K, it boosts accuracy by up to 3.56X (from 24.72% to 88.10%), outperforming top-K margin inference and specialized fine-tuned methods like GRPO, without additional training. HEX even yields significant gains on MATH benchmark from 16.40% to 40.00%, scientific reasoning on ARC-C from 54.18% to 87.80%, and TruthfulQA from 28.36% to 57.46%. Our results establish a new paradigm for test-time scaling in diffusion-based LLMs (dLLMs), revealing that the sequence in which masking is performed plays a critical role in determining performance during inference.
Neuroplastic Modular Framework: Cross-Domain Image Classification of Garbage and Industrial Surfaces
Venue: arXiv cs.CV 2025
Year: 2025

Efficient and accurate classification of waste and industrial surface defects is essential for ensuring sustainable waste management and maintaining high standards in quality control. This paper introduces the Neuroplastic Modular Classifier, a novel hybrid architecture designed for robust and adaptive image classification in dynamic environments. The model combines a ResNet-50 backbone for localized feature extraction with a Vision Transformer (ViT) to capture global semantic context. Additionally, FAISS-based similarity retrieval is incorporated to provide a memory-like reference to previously encountered data, enriching the model's feature space. A key innovation of our architecture is the neuroplastic modular design composed of expandable, learnable blocks that dynamically grow during training when performance plateaus. Inspired by biological learning systems, this mechanism allows the model to adapt to data complexity over time, improving generalization. Beyond garbage classification, we validate the model on the Kolektor Surface Defect Dataset 2 (KolektorSDD2), which involves industrial defect detection on metal surfaces. Experimental results across domains show that the proposed architecture outperforms traditional static models in both accuracy and adaptability. The Neuroplastic Modular Classifier offers a scalable, high-performance solution for real-world image classification, with strong applicability in both environmental and industrial domains.
MICROTRIPS: MICRO-geography TRavel Intelligence and Pattern Synthesis
Venue: arXiv cs.LG 2025
Year: 2025

This study presents a novel small-area estimation framework to enhance urban transportation planning through detailed characterization of travel behavior. Our approach improves on the four-step travel model by employing publicly available microdata files and machine learning methods to predict travel behavior for a representative, synthetic population at small geographic areas. This approach enables high-resolution estimation of trip generation, trip distribution, mode choice, and route assignment. Validation using ACS/PUMS work-commute datasets demonstrates that our framework achieves higher accuracy compared to conventional approaches. The resulting granular insights enable the tailoring of interventions to address localized situations and support a range of policy applications and targeted interventions, including the optimal placement of micro-fulfillment centers, effective curb-space management, and the design of more inclusive transportation solutions particularly for vulnerable communities.
From Noisy Traces to Stable Gradients: Bias-Variance Optimized Preference Optimization for Aligning Large Reasoning Models
Venue: arXiv cs.LG 2025
Year: 2025

Large reasoning models (LRMs) generate intermediate reasoning traces before producing final answers, yielding strong gains on multi-step and mathematical tasks. Yet aligning LRMs with human preferences, a crucial prerequisite for model deployment, remains underexplored. The statistically correct objective for preference alignment requires marginalizing over reasoning traces, but this computation is intractable in practice. A common workaround optimizes a single sampled trajectory, which introduces substantial gradient variance from stochastic trace sampling. To address this challenge, we frame preference optimization for LRMs through the lens of the bias--variance trade-off and propose Bias--Variance Optimized Preference Optimization (BVPO), a simple, drop-in method that mixes two gradient estimators: a high-variance trace-based estimator and a low-variance empty-trace estimator obtained by disabling reasoning trace generation. Our theory shows that BVPO strictly reduces trace-induced variance for any nontrivial mixture, provides a closed-form choice of the mixing weight that minimizes mean-squared error relative to the true marginal gradient, and under standard smoothness and step-size conditions, tightens classical convergence bounds for stochastic gradient descent. Empirically, BVPO improves alignment over the best baseline by up to 7.8 points on AlpacaEval~2 and 6.8 points on Arena-Hard. Despite being trained only on general conversational data, BVPO also boosts reasoning performance for base models by up to 4.0 points on the average of six math reasoning benchmarks. These results identify variance from trace sampling as a key bottleneck and demonstrate that directly optimizing the bias--variance trade-off yields more stable training and stronger overall performance.
Collaborative and Proactive Management of Task-Oriented Conversations
Venue: arXiv cs.CL 2025
Year: 2025

Task oriented dialogue systems (TOD) complete particular tasks based on user preferences across natural language interactions. Considering the impressive performance of large language models (LLMs) in natural language processing (NLP) tasks, most of the latest TODs are centered on LLMs. While proactive planning is crucial for task completion, many existing TODs overlook effective goal-aware planning. This paper creates a model for managing task-oriented conversations, conceptualized centered on the information state approach to dialogue management. The created model incorporated constructive intermediate information in planning. Initially, predefined slots and text part informational components are created to model user preferences. Investigating intermediate information, critical circumstances are identified. Informational components corresponding to these circumstances are created. Possible configurations for these informational components lead to limited information states. Then, dialogue moves, which indicate movement between these information states and the procedures that must be performed in the movements, are created. Eventually, the update strategy is constructed. The created model is implemented leveraging in-context learning of LLMs. In this model, database queries are created centered on indicated predefined slots and the order of retrieved entities is indicated centered on text part. This mechanism enables passing the whole corresponding entities to the preferences in the order of congruency. Evaluations exploiting the complete test conversations of MultiWOZ, with no more than a domain in a conversation, illustrate maximal inform and success, and improvement compared with previous methods.