OpenRaiser/Intern-Atlas huggingface dataset:
3D Shape Tokenization via Latent Flow Matching
Venue: arXiv cs.CV 2025
Year: 2025

We introduce a latent 3D representation that models 3D surfaces as probability density functions in 3D, i.e., p(x,y,z), with flow-matching. Our representation is specifically designed for consumption by machine learning models, offering continuity and compactness by construction while requiring only point clouds and minimal data preprocessing. Despite being a data-driven method, our use of flow matching in the 3D space enables interesting geometry properties, including the capabilities to perform zero-shot estimation of surface normal and deformation field. We evaluate with several machine learning tasks, including 3D-CLIP, unconditional generative models, single-image conditioned generative model, and intersection-point estimation. Across all experiments, our models achieve competitive performance to existing baselines, while requiring less preprocessing and auxiliary information from training data.
Can Input Attributions Explain Inductive Reasoning in In-Context Learning?
Venue: arXiv cs.CL 2025
Year: 2025

Interpreting the internal process of neural models has long been a challenge. This challenge remains relevant in the era of large language models (LLMs) and in-context learning (ICL); for example, ICL poses a new issue of interpreting which example in the few-shot examples contributed to identifying/solving the task. To this end, in this paper, we design synthetic diagnostic tasks of inductive reasoning, inspired by the generalization tests typically adopted in psycholinguistics. Here, most in-context examples are ambiguous w.r.t. their underlying rule, and one critical example disambiguates it. The question is whether conventional input attribution (IA) methods can track such a reasoning process, i.e., identify the influential example, in ICL. Our experiments provide several practical findings; for example, a certain simple IA method works the best, and the larger the model, the generally harder it is to interpret the ICL with gradient-based IA methods.
Theory of Mixture-of-Experts for Mobile Edge Computing
Venue: arXiv cs.LG 2025
Year: 2025

In mobile edge computing (MEC) networks, mobile users generate diverse machine learning tasks dynamically over time. These tasks are typically offloaded to the nearest available edge server, by considering communication and computational efficiency. However, its operation does not ensure that each server specializes in a specific type of tasks and leads to severe overfitting or catastrophic forgetting of previous tasks. To improve the continual learning (CL) performance of online tasks, we are the first to introduce mixture-of-experts (MoE) theory in MEC networks and save MEC operation from the increasing generalization error over time. Our MoE theory treats each MEC server as an expert and dynamically adapts to changes in server availability by considering data transfer and computation time. Unlike existing MoE models designed for offline tasks, ours is tailored for handling continuous streams of tasks in the MEC environment. We introduce an adaptive gating network in MEC to adaptively identify and route newly arrived tasks of unknown data distributions to available experts, enabling each expert to specialize in a specific type of tasks upon convergence. We derived the minimum number of experts required to match each task with a specialized, available expert. Our MoE approach consistently reduces the overall generalization error over time, unlike the traditional MEC approach. Interestingly, when the number of experts is sufficient to ensure convergence, adding more experts delays the convergence time and worsens the generalization error. Finally, we perform extensive experiments on real datasets in deep neural networks (DNNs) to verify our theoretical results.
User Modeling in Model-Driven Engineering: A Systematic Literature Review
Venue: arXiv cs.SE 2025
Year: 2025

In software applications, user models can be used to specify the profile of the typical users of the application, including personality traits, preferences, skills, etc. In theory, this would enable an adaptive application behavior that could lead to a better user experience. Nevertheless, user models do not seem to be part of standard modeling languages nor common in current model-driven engineering (MDE) approaches. In this paper, we conduct a systematic literature review to analyze existing proposals for user modeling in MDE and identify their limitations. The results showcase that there is a lack of a unified and complete user modeling perspective. Instead, we observe a lot of fragmented and partial proposals considering only simple user dimensions and with lack of proper tool support. This limits the implementation of richer user interfaces able to better support the user-specific needs. Therefore, we hope this analysis triggers a discussion on the importance of user models and their inclusion in MDE pipelines. Especially in a context where, thanks to the rise of AI techniques, personalization, based on a rich number of user dimensions, is becoming more and more of a possibility.
Motif Caller: Sequence Reconstruction for Motif-Based DNA Storage
Venue: arXiv cs.OH 2025
Year: 2025

DNA data storage is rapidly emerging as a promising solution for long-term data archiving, largely due to its exceptional durability. However, the synthesis of DNA strands remains a significant bottleneck in terms of cost and speed. To address this, new methods have been developed that encode information by concatenating long data-carrying DNA sequences from pre-synthesized DNA subsequences - known as motifs - from a library. Reading back data from DNA storage relies on basecalling - the process of translating raw nanopore sequencing signals into DNA base sequences using machine learning models. These sequences are then decoded back into binary data. However, current basecalling approaches are not optimized for decoding motif-carrying DNA: they first predict individual bases from the raw signal and only afterward attempt to identify higher-level motifs. This two-step, motif-agnostic process is both imprecise and inefficient. In this paper we introduce Motif Caller, a machine learning model designed to directly detect entire motifs from raw nanopore signals, bypassing the need for intermediate basecalling. By targeting motifs directly, Motif Caller leverages richer signal features associated with each motif, resulting in significantly improved accuracy. This direct approach also enhances the efficiency of data retrieval in motif-based DNA storage systems.
Boolean Functions with Minimal Spectral Sensitivity
Venue: arXiv cs.CC 2025
Year: 2025

We show examples of total Boolean functions that depend on $n$ variables and have spectral sensitivity $Θ(\sqrt{\log n})$, which is asymptotically minimal. Our main new function combines the Hamming code with the Boolean address function and has $λ(f) = \sqrt{(1+o(1)) \log_2 n}$, which is optimal even up to a constant factor. By combining this function with itself in a specific way, we also obtain a family of functions with $\text{s}_0(f) = (c+o(1)) \log_2 n$ and $\text{s}_0(f) = (1-c+o(1)) \log_2 n$ for any $c \in [0,1]$. This is an optimal tradeoff for Boolean functions with low sensitivity, as the lower bound on sensitivity by Simon generalizes to \[\text{s}_0(f)+\text{s}_1(f)\geq\log_2 n - \log_2 \log_2 n + 2.\] As a corollary, this gives a new example of a function with minimal possible sensitivity (up to a constant factor), $\text{s}(f) = (\frac{1}{2}+o(1)) \log_2 n$.
Machine Learning-Based Estimation Of Wave Direction For Unmanned Surface Vehicles
Venue: arXiv cs.LG 2025
Year: 2025

Unmanned Surface Vehicles (USVs) have become critical tools for marine exploration, environmental monitoring, and autonomous navigation. Accurate estimation of wave direction is essential for improving USV navigation and ensuring operational safety, but traditional methods often suffer from high costs and limited spatial resolution. This paper proposes a machine learning-based approach leveraging LSTM (Long Short-Term Memory) networks to predict wave direction using sensor data collected from USVs. Experimental results show the capability of the LSTM model to learn temporal dependencies and provide accurate predictions, outperforming simpler baselines.
Challenges learning from imbalanced data using tree-based models: Prevalence estimates systematically depend on hyperparameters and can be upwardly biased
Venue: arXiv cs.LG 2025
Year: 2025

When using machine learning for imbalanced binary classification problems, it is common to subsample the majority class to create a (more) balanced training dataset. This biases the model's predictions because the model learns from data whose data generating process differs from new data. One way of accounting for this bias is analytically mapping the resulting predictions to new values based on the sampling rate for the majority class. We show that calibrating a random forest this way has negative consequences, including prevalence estimates that depend on both the number of predictors considered at each split in the random forest and the sampling rate used. We explain the former using known properties of random forests and analytical calibration. Through investigating the latter issue, we made a surprising discovery - contrary to the widespread belief that decision trees are biased towards the majority class, they actually can be biased towards the minority class.
A Classification Benchmark for Artificial Intelligence Detection of Laryngeal Cancer from Patient Voice
Venue: arXiv cs.SD 2025
Year: 2025

Cases of laryngeal cancer are predicted to rise significantly in the coming years. Current diagnostic pathways are inefficient, putting undue stress on both patients and the medical system. Artificial intelligence offers a promising solution by enabling non-invasive detection of laryngeal cancer from patient voice, which could help prioritise referrals more effectively. A major barrier in this field is the lack of reproducible methods. Our work addresses this challenge by introducing a benchmark suite comprising 36 models trained and evaluated on open-source datasets. These models classify patients with benign and malignant voice pathologies. All models are accessible in a public repository, providing a foundation for future research. We evaluate three algorithms and three audio feature sets, including both audio-only inputs and multimodal inputs incorporating demographic and symptom data. Our best model achieves a balanced accuracy of 83.7%, sensitivity of 84.0%, specificity of 83.3%, and AUROC of 91.8%.
FairREAD: Re-fusing Demographic Attributes after Disentanglement for Fair Medical Image Classification
Venue: arXiv cs.CV 2025
Year: 2025

Recent advancements in deep learning have shown transformative potential in medical imaging, yet concerns about fairness persist due to performance disparities across demographic subgroups. Existing methods aim to address these biases by mitigating sensitive attributes in image data; however, these attributes often carry clinically relevant information, and their removal can compromise model performance-a highly undesirable outcome. To address this challenge, we propose Fair Re-fusion After Disentanglement (FairREAD), a novel, simple, and efficient framework that mitigates unfairness by re-integrating sensitive demographic attributes into fair image representations. FairREAD employs orthogonality constraints and adversarial training to disentangle demographic information while using a controlled re-fusion mechanism to preserve clinically relevant details. Additionally, subgroup-specific threshold adjustments ensure equitable performance across demographic groups. Comprehensive evaluations on a large-scale clinical X-ray dataset demonstrate that FairREAD significantly reduces unfairness metrics while maintaining diagnostic accuracy, establishing a new benchmark for fairness and performance in medical image classification.
Collision-based Dynamics for Multi-Marginal Optimal Transport
Venue: arXiv cs.AI 2025
Year: 2025

Inspired by the Boltzmann kinetics, we propose a collision-based dynamics with a Monte Carlo solution algorithm that approximates the solution of the multi-marginal optimal transport problem via randomized pairwise swapping of sample indices. The computational complexity and memory usage of the proposed method scale linearly with the number of samples, making it highly attractive for high-dimensional settings. In several examples, we demonstrate the efficiency of the proposed method compared to the state-of-the-art methods.
Learning Disease Progression Models That Capture Health Disparities
Venue: arXiv cs.LG 2025
Year: 2025

Disease progression models are widely used to inform the diagnosis and treatment of many progressive diseases. However, a significant limitation of existing models is that they do not account for health disparities that can bias the observed data. To address this, we develop an interpretable Bayesian disease progression model that captures three key health disparities: certain patient populations may (1) start receiving care only when their disease is more severe, (2) experience faster disease progression even while receiving care, or (3) receive follow-up care less frequently conditional on disease severity. We show theoretically and empirically that failing to account for any of these disparities can result in biased estimates of severity (e.g., underestimating severity for disadvantaged groups). On a dataset of heart failure patients, we show that our model can identify groups that face each type of health disparity, and that accounting for these disparities while inferring disease severity meaningfully shifts which patients are considered high-risk.
Optimizing Parameters for Static Equilibrium of Discrete Elastic Rods with Active-Set Cholesky
Venue: arXiv cs.GR 2025
Year: 2025

We propose a parameter optimization method for achieving static equilibrium of discrete elastic rods. Our method simultaneously optimizes material stiffness and rest shape parameters under box constraints to exactly enforce zero net force while avoiding stability issues and violations of physical laws. For efficiency, we split our constrained optimization problem into primal and dual subproblems via the augmented Lagrangian method, while handling the dual subproblem via simple vector updates. To efficiently solve the box-constrained primal subproblem, we propose a new active-set Cholesky preconditioner. Our method surpasses prior work in generality, robustness, and speed.
One Size Does Not Fit All: Investigating Efficacy of Perplexity in Detecting LLM-Generated Code
Venue: arXiv cs.SE 2025
Year: 2025

Large language model-generated code (LLMgCode) has become increasingly common in software development. So far LLMgCode has more quality issues than human-authored code (HaCode). It is common for LLMgCode to mix with HaCode in a code change, while the change is signed by only human developers, without being carefully examined. Many automated methods have been proposed to detect LLMgCode from HaCode, in which the perplexity-based method (PERPLEXITY for short) is the state-of-the-art method. However, the efficacy evaluation of PERPLEXITY has focused on detection accuracy. Yet it is unclear whether PERPLEXITY is good enough in a wider range of realistic evaluation settings. To this end, we carry out a family of experiments to compare PERPLEXITY against feature- and pre-training-based methods from three perspectives: detection accuracy, detection speed, and generalization capability. The experimental results show that PERPLEXITY has the best generalization capability while having limited detection accuracy and detection speed. Based on that, we discuss the strengths and limitations of PERPLEXITY, e.g., PERPLEXITY is unsuitable for high-level programming languages. Finally, we provide recommendations to improve PERPLEXITY and apply it in practice. As the first large-scale investigation on detecting LLMgCode from HaCode, this article provides a wide range of findings for future improvement.
AIGCodeSet: A New Annotated Dataset for AI Generated Code Detection
Venue: arXiv cs.SE 2025
Year: 2025

While large language models provide significant convenience for software development, they can lead to ethical issues in job interviews and student assignments. Therefore, determining whether a piece of code is written by a human or generated by an artificial intelligence (AI) model is a critical issue. In this study, we present AIGCodeSet, which consists of 2.828 AI-generated and 4.755 human-written Python codes, created using CodeLlama 34B, Codestral 22B, and Gemini 1.5 Flash. In addition, we share the results of our experiments conducted with baseline detection methods. Our experiments show that a Bayesian classifier outperforms the other models.
Deep Learning for Spatio-Temporal Fusion in Land Surface Temperature Estimation: A Comprehensive Survey, Experimental Analysis, and Future Trends
Venue: arXiv cs.LG 2025
Year: 2025

Land Surface Temperature (LST) plays a key role in climate monitoring, urban heat assessment, and land-atmosphere interactions. However, current thermal infrared satellite sensors cannot simultaneously achieve high spatial and temporal resolution. Spatio-temporal fusion (STF) techniques address this limitation by combining complementary satellite data, one with high spatial but low temporal resolution, and another with high temporal but low spatial resolution. Existing STF techniques, from classical models to modern deep learning (DL) architectures, were primarily developed for surface reflectance (SR). Their application to thermal data remains limited and often overlooks LST-specific spatial and temporal variability. This study provides a focused review of DL-based STF methods for LST. We present a formal mathematical definition of the thermal fusion task, propose a refined taxonomy of relevant DL methods, and analyze the modifications required when adapting SR-oriented models to LST. To support reproducibility and benchmarking, we introduce a new dataset comprising 51 Terra MODIS-Landsat LST pairs from 2013 to 2024, and evaluate representative models to explore their behavior on thermal data. The analysis highlights performance gaps, architecture sensitivities, and open research challenges. The dataset and accompanying resources are publicly available at https://github.com/Sofianebouaziz1/STF-LST.
AlzheimerRAG: Multimodal Retrieval Augmented Generation for Clinical Use Cases using PubMed articles
Venue: arXiv cs.IR 2025
Year: 2025

Recent advancements in generative AI have fostered the development of highly adept Large Language Models (LLMs) that integrate diverse data types to empower decision-making. Among these, multimodal retrieval-augmented generation (RAG) applications are promising because they combine the strengths of information retrieval and generative models, enhancing their utility across various domains, including clinical use cases. This paper introduces AlzheimerRAG, a Multimodal RAG application for clinical use cases, primarily focusing on Alzheimer's Disease case studies from PubMed articles. This application incorporates cross-modal attention fusion techniques to integrate textual and visual data processing by efficiently indexing and accessing vast amounts of biomedical literature. Our experimental results, compared to benchmarks such as BioASQ and PubMedQA, have yielded improved performance in the retrieval and synthesis of domain-specific information. We also present a case study using our multimodal RAG in various Alzheimer's clinical scenarios. We infer that AlzheimerRAG can generate responses with accuracy non-inferior to humans and with low rates of hallucination.
Towards More Robust Retrieval-Augmented Generation: Evaluating RAG Under Adversarial Poisoning Attacks
Venue: arXiv cs.IR 2025
Year: 2025

Retrieval-Augmented Generation (RAG) systems have emerged as a promising solution to mitigate LLM hallucinations and enhance their performance in knowledge-intensive domains. However, these systems are vulnerable to adversarial poisoning attacks, where malicious passages injected into the retrieval corpus can mislead models into producing factually incorrect outputs. In this paper, we present a rigorously controlled empirical study of how RAG systems behave under such attacks and how their robustness can be improved. On the generation side, we introduce a structured taxonomy of context types-adversarial, untouched, and guiding-and systematically analyze their individual and combined effects on model outputs. On the retrieval side, we evaluate several retrievers to measure how easily they expose LLMs to adversarial contexts. Our findings also reveal that "skeptical prompting" can activate LLMs' internal reasoning, enabling partial self-defense against adversarial passages, though its effectiveness depends strongly on the model's reasoning capacity. Together, our experiments (code available at https://github.com/JinyanSu1/eval_PoisonRaG) and analysis provide actionable insights for designing safer and more resilient RAG systems, paving the way for more reliable real-world deployments.
Enhancing Conflict Resolution in Language Models via Abstract Argumentation
Venue: arXiv cs.AI 2025
Year: 2025

In recent years, large language models (LLMs) have made significant advancements in developing human-like and engaging dialogue systems. However, in tasks such as consensus-building and persuasion, LLMs often struggle to resolve conflicts arising from incomplete or inconsistent information, revealing their limitations in real-world applications. Given these limitations, abstract argumentation, a specialized logical framework designed to resolve conflicts and inconsistencies, becomes particularly relevant. In this paper, we aim to enhance the conflict-solving capabilities of LLMs by leveraging formal abstract argumentation, integrating language model learning with symbolic computation. To achieve this, we develop and curate a dataset comprising diverse abstract argumentation frameworks, accompanied by detailed explanations of the argument acceptability computation process. Subsequently, we fine-tune LLMs on this dataset, focusing on abstract conflict resolution tasks. As a comparative baseline, LLMs are also evaluated using a chain-of-thought approach, however, they fail to solve the conflict-based arguments effectively. Our experiments demonstrate that process explanations play a crucial role in learning. Models trained with explanations exhibit superior generalization accuracy compared to those trained solely on question-answer pairs. Furthermore, leveraging LLMs' self-explanation capabilities, our approach provides detailed illustrations that mitigate the lack of transparency typically associated with neural networks.
SubData: Bridging Heterogeneous Datasets to Enable Theory-Driven Evaluation of Political and Demographic Perspectives in LLMs
Venue: arXiv cs.CL 2025
Year: 2025

As increasingly capable large language models (LLMs) emerge, researchers have begun exploring their potential for subjective tasks. While recent work demonstrates that LLMs can be aligned with diverse human perspectives, evaluating this alignment on downstream tasks (e.g., hate speech detection) remains challenging due to the use of inconsistent datasets across studies. To address this issue, in this resource paper we propose a two-step framework: we (1) introduce SubData, an open-source Python library designed for standardizing heterogeneous datasets to evaluate LLMs perspective alignment; and (2) present a theory-driven approach leveraging this library to test how differently-aligned LLMs (e.g., aligned with different political viewpoints) classify content targeting specific demographics. SubData's flexible mapping and taxonomy enable customization for diverse research needs, distinguishing it from existing resources. We illustrate its usage with an example application and invite contributions to extend our initial release into a multi-construct benchmark suite for evaluating LLMs perspective alignment on natural language processing tasks.