OpenRaiser/Intern-Atlas huggingface dataset:
Learning Genomic Structure from $k$-mers
Venue: arXiv cs.LG 2025
Year: 2025

Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data using contrastive learning, in which an encoder model is trained to produce embeddings that cluster together sequences from the same genomic region. The sequential nature of genomic regions is preserved in the form of trajectories through this embedding space. Trained solely to reflect the structure of the genome, the resulting model provides a general representation of $k$-mer sequences, suitable for a range of downstream tasks involving read data. We apply our framework to learn the structure of the $E.\ coli$ genome, and demonstrate its use in simulated ancient DNA (aDNA) read mapping and identification of structural variations. Furthermore, we illustrate the potential of using this type of model for metagenomic species identification. We show how incorporating a domain-specific noise model can enhance embedding robustness, and how a supervised contrastive learning setting can be adopted when a linear reference genome is available, by introducing a distance thresholding parameter $Γ$. The model can also be trained fully self-supervised on read data, enabling analysis without the need to construct a full genome assembly using specialized algorithms. Small prediction heads based on a pre-trained embedding are shown to perform on par with BWA-aln, the current gold standard approach for aDNA mapping, in terms of accuracy and runtime for short genomes. Given the method's favorable scaling properties with respect to total genome size, inference using our approach is highly promising for metagenomic applications and for mapping to genomes comparable in size to the human genome.
D-LIO: 6DoF Direct LiDAR-Inertial Odometry based on Simultaneous Truncated Distance Field Mapping
Venue: arXiv cs.RO 2025
Year: 2025

This paper presents a new approach for 6DoF Direct LiDAR-Inertial Odometry (D-LIO) based on the simultaneous mapping of truncated distance fields on CPU. Such continuous representation (in the vicinity of the points) enables working with raw 3D LiDAR data online, avoiding the need of LiDAR feature selection and tracking, simplifying the odometry pipeline and easily generalizing to many scenarios. The method is based on the proposed Fast Truncated Distance Field (Fast-TDF) method as a convenient tool to represent the environment. Such representation enables i) solving the LiDAR point-cloud registration as a nonlinear optimization process without the need of selecting/tracking LiDAR features in the input data, ii) simultaneously producing an accurate truncated distance field map of the environment, and iii) updating such map at constant time independently of its size. The approach is tested using open datasets, aerial and ground. It is also benchmarked against other state-of-the-art odometry approaches, demonstrating the same or better level of accuracy with the added value of an online-generated TDF representation of the environment, that can be used for other robotics tasks as planning or collision avoidance. The source code is publicly available at https://anonymous.4open.science/r/D-LIO
Can a domain-specific language improve program structure comprehension of data pipelines? A mixed-methods study
Venue: arXiv cs.PL 2025
Year: 2025

In many application domains, domain-specific languages can allow domain experts to contribute to collaborative projects more correctly and efficiently. To do so, they must be able to understand program structure from reading existing source code. With high-quality data becoming an increasingly important resource, the creation of data pipelines is an important application domain for domain-specific languages. We execute a mixed-method study consisting of a controlled experiment and a follow-up descriptive survey among the participants to understand the effects of a domain-specific language on bottom-up program understanding and generate hypotheses for future research. During the experiment, participants need the same time to solve program structure comprehension tasks, but are significantly more correct when using the domain-specific language. In the descriptive survey, participants describe reasons related to the programming language itself, such as a better pipeline overview, more enforced code structure, and a closer alignment to the mental model of a data pipeline. In addition, human factors such as less required programming experience and the ability to reuse experience from other data engineering tools are discussed. Based on these results, domain-specific languages are a promising tool for creating data pipelines that can increase correct understanding of program structure and lower barriers to entry for domain experts. Open questions exist to make more informed implementation decisions for domain-specific languages for data pipelines in the future.
IFEval-Audio: Benchmarking Instruction-Following Capability in Audio-based Large Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) have demonstrated strong instruction-following capabilities in text-based tasks. However, this ability often deteriorates in multimodal models after alignment with non-text modalities such as images or audio. While several recent efforts have investigated instruction-following performance in text and vision-language models, instruction-following in audio-based large language models remains largely unexplored. To bridge this gap, we introduce IFEval-Audio, a novel evaluation dataset designed to assess the ability to follow instructions in an audio LLM. IFEval-Audio contains 280 audio-instruction-answer triples across six diverse dimensions: Content, Capitalization, Symbol, List Structure, Length, and Format. Each example pairs an audio input with a text instruction, requiring the model to generate an output that follows a specified structure. We benchmark state-of-the-art audio LLMs on their ability to follow audio-involved instructions. The dataset is released publicly to support future research in this emerging area.
Hypergraph Tversky-Aware Domain Incremental Learning for Brain Tumor Segmentation with Missing Modalities
Venue: arXiv cs.CV 2025
Year: 2025

Existing methods for multimodal MRI segmentation with missing modalities typically assume that all MRI modalities are available during training. However, in clinical practice, some modalities may be missing due to the sequential nature of MRI acquisition, leading to performance degradation. Furthermore, retraining models to accommodate newly available modalities can be inefficient and may cause overfitting, potentially compromising previously learned knowledge. To address these challenges, we propose Replay-based Hypergraph Domain Incremental Learning (ReHyDIL) for brain tumor segmentation with missing modalities. ReHyDIL leverages Domain Incremental Learning (DIL) to enable the segmentation model to learn from newly acquired MRI modalities without forgetting previously learned information. To enhance segmentation performance across diverse patient scenarios, we introduce the Cross-Patient Hypergraph Segmentation Network (CHSNet), which utilizes hypergraphs to capture high-order associations between patients. Additionally, we incorporate Tversky-Aware Contrastive (TAC) loss to effectively mitigate information imbalance both across and within different modalities. Extensive experiments on the BraTS2019 dataset demonstrate that ReHyDIL outperforms state-of-the-art methods, achieving an improvement of over 2% in the Dice Similarity Coefficient across various tumor regions. Our code is available at https://github.com/reeive/ReHyDIL.
Dynamic Reservoir Computing with Physical Neuromorphic Networks
Venue: arXiv cs.ET 2025
Year: 2025

Reservoir Computing (RC) with physical systems requires an understanding of the underlying structure and internal dynamics of the specific physical reservoir. In this study, physical nano-electronic networks with neuromorphic dynamics are investigated for their use as physical reservoirs in an RC framework. These neuromorphic networks operate as dynamic reservoirs, with node activities in general coupled to the edge dynamics through nonlinear nano-electronic circuit elements, and the reservoir outputs influenced by the underlying network connectivity structure. This study finds that networks with varying degrees of sparsity generate more useful nonlinear temporal outputs for dynamic RC compared to dense networks. Dynamic RC is also tested on an autonomous multivariate chaotic time series prediction task with networks of varying densities, which revealed the importance of network sparsity in maintaining network activity and overall dynamics, that in turn enabled the learning of the chaotic Lorenz63 system's attractor behavior.
GUI-explorer: Autonomous Exploration and Mining of Transition-aware Knowledge for GUI Agent
Venue: arXiv cs.AI 2025
Year: 2025

GUI automation faces critical challenges in dynamic environments. MLLMs suffer from two key issues: misinterpreting UI components and outdated knowledge. Traditional fine-tuning methods are costly for app-specific knowledge updates. We propose GUI-explorer, a training-free GUI agent that incorporates two fundamental mechanisms: (1) Autonomous Exploration of Function-aware Trajectory. To comprehensively cover all application functionalities, we design a Function-aware Task Goal Generator that automatically constructs exploration goals by analyzing GUI structural information (e.g., screenshots and activity hierarchies). This enables systematic exploration to collect diverse trajectories. (2) Unsupervised Mining of Transition-aware Knowledge. To establish precise screen-operation logic, we develop a Transition-aware Knowledge Extractor that extracts effective screen-operation logic through unsupervised analysis the state transition of structured interaction triples (observation, action, outcome). This eliminates the need for human involvement in knowledge extraction. With a task success rate of 53.7% on SPA-Bench and 47.4% on AndroidWorld, GUI-explorer shows significant improvements over SOTA agents. It requires no parameter updates for new apps. GUI-explorer is open-sourced and publicly available at https://github.com/JiuTian-VL/GUI-explorer.
ATR-Bench: A Federated Learning Benchmark for Adaptation, Trust, and Reasoning
Venue: arXiv cs.LG 2025
Year: 2025

Federated Learning (FL) has emerged as a promising paradigm for collaborative model training while preserving data privacy across decentralized participants. As FL adoption grows, numerous techniques have been proposed to tackle its practical challenges. However, the lack of standardized evaluation across key dimensions hampers systematic progress and fair comparison of FL methods. In this work, we introduce ATR-Bench, a unified framework for analyzing federated learning through three foundational dimensions: Adaptation, Trust, and Reasoning. We provide an in-depth examination of the conceptual foundations, task formulations, and open research challenges associated with each theme. We have extensively benchmarked representative methods and datasets for adaptation to heterogeneous clients and trustworthiness in adversarial or unreliable environments. Due to the lack of reliable metrics and models for reasoning in FL, we only provide literature-driven insights for this dimension. ATR-Bench lays the groundwork for a systematic and holistic evaluation of federated learning with real-world relevance. We will make our complete codebase publicly accessible and a curated repository that continuously tracks new developments and research in the FL literature.
Nested Named Entity Recognition as Single-Pass Sequence Labeling
Venue: arXiv cs.CL 2025
Year: 2025

We cast nested named entity recognition (NNER) as a sequence labeling task by leveraging prior work that linearizes constituency structures, effectively reducing the complexity of this structured prediction problem to straightforward token classification. By combining these constituency linearizations with pretrained encoders, our method captures nested entities while performing exactly n tagging actions. Our approach achieves competitive performance compared to less efficient systems, and it can be trained using any off-the-shelf sequence labeling library.
Predicate-Conditional Conformalized Answer Sets for Knowledge Graph Embeddings
Venue: arXiv cs.AI 2025
Year: 2025

Uncertainty quantification in Knowledge Graph Embedding (KGE) methods is crucial for ensuring the reliability of downstream applications. A recent work applies conformal prediction to KGE methods, providing uncertainty estimates by generating a set of answers that is guaranteed to include the true answer with a predefined confidence level. However, existing methods provide probabilistic guarantees averaged over a reference set of queries and answers (marginal coverage guarantee). In high-stakes applications such as medical diagnosis, a stronger guarantee is often required: the predicted sets must provide consistent coverage per query (conditional coverage guarantee). We propose CondKGCP, a novel method that approximates predicate-conditional coverage guarantees while maintaining compact prediction sets. CondKGCP merges predicates with similar vector representations and augments calibration with rank information. We prove the theoretical guarantees and demonstrate empirical effectiveness of CondKGCP by comprehensive evaluations.
Identifying, Evaluating, and Mitigating Risks of AI Thought Partnerships
Venue: arXiv cs.AI 2025
Year: 2025

Artificial Intelligence (AI) systems have historically been used as tools that execute narrowly defined tasks. Yet recent advances in AI have unlocked possibilities for a new class of models that genuinely collaborate with humans in complex reasoning, from conceptualizing problems to brainstorming solutions. Such AI thought partners enable novel forms of collaboration and extended cognition, yet they also pose major risks-including and beyond risks of typical AI tools and agents. In this commentary, we systematically identify risks of AI thought partners through a novel framework that identifies risks at multiple levels of analysis, including Real-time, Individual, and Societal risks arising from collaborative cognition (RISc). We leverage this framework to propose concrete metrics for risk evaluation, and finally suggest specific mitigation strategies for developers and policymakers. As AI thought partners continue to proliferate, these strategies can help prevent major harms and ensure that humans actively benefit from productive thought partnerships.
RealEngine: Simulating Autonomous Driving in Realistic Context
Venue: arXiv cs.CV 2025
Year: 2025

Driving simulation plays a crucial role in developing reliable driving agents by providing controlled, evaluative environments. To enable meaningful assessments, a high-quality driving simulator must satisfy several key requirements: multi-modal sensing capabilities (e.g., camera and LiDAR) with realistic scene rendering to minimize observational discrepancies; closed-loop evaluation to support free-form trajectory behaviors; highly diverse traffic scenarios for thorough evaluation; multi-agent cooperation to capture interaction dynamics; and high computational efficiency to ensure affordability and scalability. However, existing simulators and benchmarks fail to comprehensively meet these fundamental criteria. To bridge this gap, this paper introduces RealEngine, a novel driving simulation framework that holistically integrates 3D scene reconstruction and novel view synthesis techniques to achieve realistic and flexible closed-loop simulation in the driving context. By leveraging real-world multi-modal sensor data, RealEngine reconstructs background scenes and foreground traffic participants separately, allowing for highly diverse and realistic traffic scenarios through flexible scene composition. This synergistic fusion of scene reconstruction and view synthesis enables photorealistic rendering across multiple sensor modalities, ensuring both perceptual fidelity and geometric accuracy. Building upon this environment, RealEngine supports three essential driving simulation categories: non-reactive simulation, safety testing, and multi-agent interaction, collectively forming a reliable and comprehensive benchmark for evaluating the real-world performance of driving agents.
Unsupervised Prompting for Graph Neural Networks
Venue: arXiv cs.LG 2025
Year: 2025

Prompt tuning methods for Graph Neural Networks (GNNs) have become popular to address the semantic gap between pre-training and fine-tuning steps. However, existing GNN prompting methods rely on labeled data and involve lightweight fine-tuning for downstream tasks. Meanwhile, in-context learning methods for Large Language Models (LLMs) have shown promising performance with no parameter updating and no or minimal labeled data. Inspired by these approaches, in this work, we first introduce a challenging problem setup to evaluate GNN prompting methods. This setup encourages a prompting function to enhance a pre-trained GNN's generalization to a target dataset under covariate shift without updating the GNN's parameters and with no labeled data. Next, we propose a fully unsupervised prompting method based on consistency regularization through pseudo-labeling. We use two regularization techniques to align the prompted graphs' distribution with the original data and reduce biased predictions. Through extensive experiments under our problem setting, we demonstrate that our unsupervised approach outperforms the state-of-the-art prompting methods that have access to labels.
Risk-Averse Reinforcement Learning with Itakura-Saito Loss
Venue: arXiv cs.LG 2025
Year: 2025

Risk-averse reinforcement learning finds application in various high-stakes fields. Unlike classical reinforcement learning, which aims to maximize expected returns, risk-averse agents choose policies that minimize risk, occasionally sacrificing expected value. These preferences can be framed through utility theory. We focus on the specific case of the exponential utility function, where one can derive the Bellman equations and employ various reinforcement learning algorithms with few modifications. To address this, we introduce to the broad machine learning community a numerically stable and mathematically sound loss function based on the Itakura-Saito divergence for learning state-value and action-value functions. We evaluate the Itakura-Saito loss function against established alternatives, both theoretically and empirically. In the experimental section, we explore multiple scenarios, some with known analytical solutions, and show that the considered loss function outperforms the alternatives.
Bigger Isn't Always Memorizing: Early Stopping Overparameterized Diffusion Models
Venue: arXiv cs.LG 2025
Year: 2025

Diffusion probabilistic models have become a cornerstone of modern generative AI, yet the mechanisms underlying their generalization remain poorly understood. In fact, if these models were perfectly minimizing their training loss, they would just generate data belonging to their training set, i.e., memorize, as empirically found in the overparameterized regime. We revisit this view by showing that, in highly overparameterized diffusion models, generalization in natural data domains is progressively achieved during training before the onset of memorization. Our results, ranging from image to language diffusion models, systematically support the empirical law that memorization time is proportional to the dataset size. Generalization vs. memorization is then best understood as a competition between time scales. We show that this phenomenology is recovered in diffusion models learning a simple probabilistic context-free grammar with random rules, where generalization corresponds to the hierarchical acquisition of deeper grammar rules as training time grows, and the generalization cost of early stopping can be characterized. We summarize these results in a phase diagram. Overall, our results support that a principled early-stopping criterion - scaling with dataset size - can effectively optimize generalization while avoiding memorization, with direct implications for hyperparameter transfer and privacy-sensitive applications.
OpenSeg-R: Improving Open-Vocabulary Segmentation via Step-by-Step Visual Reasoning
Venue: arXiv cs.CV 2025
Year: 2025

Open-Vocabulary Segmentation (OVS) has drawn increasing attention for its capacity to generalize segmentation beyond predefined categories. However, existing methods typically predict segmentation masks with simple forward inference, lacking explicit reasoning and interpretability. This makes it challenging for OVS model to distinguish similar categories in open-world settings due to the lack of contextual understanding and discriminative visual cues. To address this limitation, we propose a step-by-step visual reasoning framework for open-vocabulary segmentation, named OpenSeg-R. The proposed OpenSeg-R leverages Large Multimodal Models (LMMs) to perform hierarchical visual reasoning before segmentation. Specifically, we generate both generic and image-specific reasoning for each image, forming structured triplets that explain the visual reason for objects in a coarse-to-fine manner. Based on these reasoning steps, we can compose detailed description prompts, and feed them to the segmentor to produce more accurate segmentation masks. To the best of our knowledge, OpenSeg-R is the first framework to introduce explicit step-by-step visual reasoning into OVS. Experimental results demonstrate that OpenSeg-R significantly outperforms state-of-the-art methods on open-vocabulary semantic segmentation across five benchmark datasets. Moreover, it achieves consistent gains across all metrics on open-vocabulary panoptic segmentation. Qualitative results further highlight the effectiveness of our reasoning-guided framework in improving both segmentation precision and interpretability. Our code is publicly available at https://github.com/Hanzy1996/OpenSeg-R.
Creatively Upscaling Images with Global-Regional Priors
Venue: arXiv cs.CV 2025
Year: 2025

Contemporary diffusion models show remarkable capability in text-to-image generation, while still being limited to restricted resolutions (e.g., 1,024 X 1,024). Recent advances enable tuning-free higher-resolution image generation by recycling pre-trained diffusion models and extending them via regional denoising or dilated sampling/convolutions. However, these models struggle to simultaneously preserve global semantic structure and produce creative regional details in higher-resolution images. To address this, we present C-Upscale, a new recipe of tuning-free image upscaling that pivots on global-regional priors derived from given global prompt and estimated regional prompts via Multimodal LLM. Technically, the low-frequency component of low-resolution image is recognized as global structure prior to encourage global semantic consistency in high-resolution generation. Next, we perform regional attention control to screen cross-attention between global prompt and each region during regional denoising, leading to regional attention prior that alleviates object repetition issue. The estimated regional prompts containing rich descriptive details further act as regional semantic prior to fuel the creativity of regional detail generation. Both quantitative and qualitative evaluations demonstrate that our C-Upscale manages to generate ultra-high-resolution images (e.g., 4,096 X 4,096 and 8,192 X 8,192) with higher visual fidelity and more creative regional details.