OpenRaiser/Intern-Atlas huggingface dataset:
Can TabPFN Compete with GNNs for Node Classification via Graph Tabularization?
Venue: arXiv cs.LG 2025
Year: 2025

Foundation models pretrained on large data have demonstrated remarkable zero-shot generalization capabilities across domains. Building on the success of TabPFN for tabular data and its recent extension to time series, we investigate whether graph node classification can be effectively reformulated as a tabular learning problem. We introduce TabPFN-GN, which transforms graph data into tabular features by extracting node attributes, structural properties, positional encodings, and optionally smoothed neighborhood features. This enables TabPFN to perform direct node classification without any graph-specific training or language model dependencies. Our experiments on 12 benchmark datasets reveal that TabPFN-GN achieves competitive performance with GNNs on homophilous graphs and consistently outperforms them on heterophilous graphs. These results demonstrate that principled feature engineering can bridge the gap between tabular and graph domains, providing a practical alternative to task-specific GNN training and LLM-dependent graph foundation models.
Multicalibration for LLM-based Code Generation
Venue: arXiv cs.SE 2025
Year: 2025

As AI-based code generation becomes widespread, researchers are investigating the calibration of code LLMs - ensuring their confidence scores faithfully represent the true likelihood of code correctness. To do so, we investigate multicalibration, which can capture additional factors about a coding problem, such as complexity, code length, or programming language used. We study four multicalibration approaches on three function synthesis benchmarks, using latest-generation code LLMs (Qwen3 Coder, GPT-OSS, DeepSeek-R1-Distill). Our results demonstrate that multicalibration can yield distinct improvements over both uncalibrated token likelihoods (+1.03 in skill score) and baseline calibrations (+0.37 in skill score). We study the influence of the aforementioned factors in ablations, and make our dataset (consisting of code generations, likelihoods, and correctness labels) available for future research on code LLM calibration.
Tri-Bench: Stress-Testing VLM Reliability on Spatial Reasoning under Camera Tilt and Object Interference
Venue: arXiv cs.CV 2025
Year: 2025

Verifiable geometric reasoning is a critical component for trustworthy and controllable agentic AI. Despite impressive capabilities, Vision-Language Models (VLMs) often fail under realistic scene changes. We present Tri-Bench, a compact benchmark of planar triangle problems that isolates relative geometric reasoning while stressing two deployment-critical factors: camera pose (planar vs. tilted) and scene context via object interference (10 everyday objects). To test verifiability and control, we evaluate four recent VLMs using a single, fixed prompt whose guardrail explicitly describes a surrounding square border, enabling correct answers via homography. We evaluate six simple tasks over binary and continuous targets, and observe that the overall accuracy with respect to 3D ground truth is modest, ~69% on average (best ~75%, worst ~64%). The same responses align even more closely with 2D projections in the image plane, where mean accuracy is ~72%. All four VLMs consistently fail, with accuracy falling to ~0%, on recognizing minority shape classes (equilateral, isosceles, right-angled triangles). Additionally, overall VLM accuracy degrades by ~4.1% under camera tilt. This demonstrates that models fail to correctly utilize the explicit frame-of-reference hint provided in the prompt and default to 2D image plane cues. Finally, we find that object interference has no significant effect on VLM accuracy.
Siamese-Driven Optimization for Low-Resolution Image Latent Embedding in Image Captioning
Venue: arXiv cs.CV 2025
Year: 2025

Image captioning is essential in many fields including assisting visually impaired individuals, improving content management systems, and enhancing human-computer interaction. However, a recent challenge in this domain is dealing with low-resolution image (LRI). While performance can be improved by using larger models like transformers for encoding, these models are typically heavyweight, demanding significant computational resources and memory, leading to challenges in retraining. To address this, the proposed SOLI (Siamese-Driven Optimization for Low-Resolution Image Latent Embedding in Image Captioning) approach presents a solution specifically designed for lightweight, low-resolution images captioning. It employs a Siamese network architecture to optimize latent embeddings, enhancing the efficiency and accuracy of the image-to-text translation process. By focusing on a dual-pathway neural network structure, SOLI minimizes computational overhead without sacrificing performance, making it an ideal choice for training on resource-constrained scenarios.
When Tables Leak: Attacking String Memorization in LLM-Based Tabular Data Generation
Venue: arXiv cs.LG 2025
Year: 2025

Large Language Models (LLMs) have recently demonstrated remarkable performance in generating high-quality tabular synthetic data. In practice, two primary approaches have emerged for adapting LLMs to tabular data generation: (i) fine-tuning smaller models directly on tabular datasets, and (ii) prompting larger models with examples provided in context. In this work, we show that popular implementations from both regimes exhibit a tendency to compromise privacy by reproducing memorized patterns of numeric digits from their training data. To systematically analyze this risk, we introduce a simple No-box Membership Inference Attack (MIA) called LevAtt that assumes adversarial access to only the generated synthetic data and targets the string sequences of numeric digits in synthetic observations. Using this approach, our attack exposes substantial privacy leakage across a wide range of models and datasets, and in some cases, is even a perfect membership classifier on state-of-the-art models. Our findings highlight a unique privacy vulnerability of LLM-based synthetic data generation and the need for effective defenses. To this end, we propose two methods, including a novel sampling strategy that strategically perturbs digits during generation. Our evaluation demonstrates that this approach can defeat these attacks with minimal loss of fidelity and utility of the synthetic data.
Unsupervised Learning of Density Estimates with Topological Optimization
Venue: arXiv cs.LG 2025
Year: 2025

Kernel density estimation is a key component of a wide variety of algorithms in machine learning, Bayesian inference, stochastic dynamics and signal processing. However, the unsupervised density estimation technique requires tuning a crucial hyperparameter: the kernel bandwidth. The choice of bandwidth is critical as it controls the bias-variance trade-off by over- or under-smoothing the topological features. Topological data analysis provides methods to mathematically quantify topological characteristics, such as connected components, loops, voids et cetera, even in high dimensions where visualization of density estimates is impossible. In this paper, we propose an unsupervised learning approach using a topology-based loss function for the automated and unsupervised selection of the optimal bandwidth and benchmark it against classical techniques -- demonstrating its potential across different dimensions.
Open Polymer Challenge: Post-Competition Report
Venue: arXiv cs.LG 2025
Year: 2025

Machine learning (ML) offers a powerful path toward discovering sustainable polymer materials, but progress has been limited by the lack of large, high-quality, and openly accessible polymer datasets. The Open Polymer Challenge (OPC) addresses this gap by releasing the first community-developed benchmark for polymer informatics, featuring a dataset with 10K polymers and 5 properties: thermal conductivity, radius of gyration, density, fractional free volume, and glass transition temperature. The challenge centers on multi-task polymer property prediction, a core step in virtual screening pipelines for materials discovery. Participants developed models under realistic constraints that include small data, label imbalance, and heterogeneous simulation sources, using techniques such as feature-based augmentation, transfer learning, self-supervised pretraining, and targeted ensemble strategies. The competition also revealed important lessons about data preparation, distribution shifts, and cross-group simulation consistency, informing best practices for future large-scale polymer datasets. The resulting models, analysis, and released data create a new foundation for molecular AI in polymer science and are expected to accelerate the development of sustainable and energy-efficient materials. Along with the competition, we release the test dataset at https://www.kaggle.com/datasets/alexliu99/neurips-open-polymer-prediction-2025-test-data. We also release the data generation pipeline at https://github.com/sobinalosious/ADEPT, which simulates more than 25 properties, including thermal conductivity, radius of gyration, and density.
Same Content, Different Answers: Cross-Modal Inconsistency in MLLMs
Venue: arXiv cs.AI 2025
Year: 2025

We introduce two new benchmarks REST and REST+(Render-Equivalence Stress Tests) to enable systematic evaluation of cross-modal inconsistency in multimodal large language models (MLLMs). MLLMs are trained to represent vision and language in the same embedding space, yet they cannot perform the same tasks in both modalities. Our benchmarks contain samples with the same semantic information in three modalities (image, text, mixed) and we show that state-of-the-art MLLMs cannot consistently reason over these different modalities. We evaluate 15 MLLMs and find that the degree of modality inconsistency varies substantially, even when accounting for problems with text recognition (OCR). Neither rendering text as image nor rendering an image as text solves the inconsistency. Even if OCR is correct, we find that visual characteristics (text colour and resolution, but not font) and the number of vision tokens have an impact on model performance. Finally, we find that our consistency score correlates with the modality gap between text and images, highlighting a mechanistic interpretation of cross-modal inconsistent MLLMs.
From Script to Stage: Automating Experimental Design for Social Simulations with LLMs
Venue: arXiv cs.HC 2025
Year: 2025

The rise of large language models (LLMs) has opened new avenues for social science research. Multi-agent simulations powered by LLMs are increasingly becoming a vital approach for exploring complex social phenomena and testing theoretical hypotheses. However, traditional computational experiments often rely heavily on interdisciplinary expertise, involve complex operations, and present high barriers to entry. While LLM-driven agents show great potential for automating experimental design, their reliability and scientific rigor remain insufficient for widespread adoption. To address these challenges, this paper proposes an automated multi-agent experiment design framework based on script generation, inspired by the concept of the Decision Theater. The experimental design process is divided into three stages: (1) Script Generation - a Screenwriter Agent drafts candidate experimental scripts; (2) Script Finalization - a Director Agent evaluates and selects the final script; (3) Actor Generation - an Actor Factory creates actor agents capable of performing on the experimental "stage" according to the finalized script. Extensive experiment conducted across multiple social science experimental scenarios demonstrate that the generated actor agents can perform according to the designed scripts and reproduce outcomes consistent with real-world situations. This framework not only lowers the barriers to experimental design in social science but also provides a novel decision-support tool for policy-making and research. The project's source code is available at: https://anonymous.4open.science/r/FSTS-DE1E
Assessing the Human-Likeness of LLM-Driven Digital Twins in Simulating Health Care System Trust
Venue: arXiv cs.HC 2025
Year: 2025

Serving as an emerging and powerful tool, Large Language Model (LLM)-driven Human Digital Twins are showing great potential in healthcare system research. However, its actual simulation ability for complex human psychological traits, such as distrust in the healthcare system, remains unclear. This research gap particularly impacts health professionals' trust and usage of LLM-based Artificial Intelligence (AI) systems in assisting their routine work. In this study, based on the Twin-2K-500 dataset, we systematically evaluated the simulation results of the LLM-driven human digital twin using the Health Care System Distrust Scale (HCSDS) with an established human-subject sample, analyzing item-level distributions, summary statistics, and demographic subgroup patterns. Results showed that the simulated responses by the digital twin were significantly more centralized with lower variance and had fewer selections of extreme options (all p<0.001). While the digital twin broadly reproduces human results in major demographic patterns, such as age and gender, it exhibits relatively low sensitivity in capturing minor differences in education levels. The LLM-based digital twin simulation has the potential to simulate population trends, but it also presents challenges in making detailed, specific distinctions in subgroups of human beings. This study suggests that the current LLM-driven Digital Twins have limitations in modeling complex human attitudes, which require careful calibration and validation before applying them in inferential analyses or policy simulations in health systems engineering. Future studies are necessary to examine the emotional reasoning mechanism of LLMs before their use, particularly for studies that involve simulations sensitive to social topics, such as human-automation trust.
Psychlysis: Towards the Creation of a Questionnaire-based Machine Learning Tool to Analyze States of Mind
Venue: arXiv cs.HC 2025
Year: 2025

This paper describes the development of Psychlysis, a work-in-progress questionnaire-based machine learning application analyzing the user's current state of mind and suggesting ways to improve their mood using Machine Learning. The application utilizes the OCEAN model to understand the user's personality traits and make customized suggestions to enhance their well-being. The proposed application focus on improving the user's mood rather than just detecting their emotions. Preliminary results of the model are presented, showing the potential of the application in predicting the user's mood and providing personalized recommendations. The paper concludes by highlighting the potential benefits of such an application for various societal segments, including doctors, individuals, and mental health organizations, in improving emotional well-being and reducing the negative impact of mental health issues on daily life.
Beyond Technical Debt: How AI-Assisted Development Creates Comprehension Debt in Resource-Constrained Indie Teams
Venue: arXiv cs.HC 2025
Year: 2025

Junior indie game developers in distributed, part-time teams lack production frameworks suited to their specific context, as traditional methodologies are often inaccessible. This study introduces the CIGDI (Co-Intelligence Game Development Ideation) Framework, an alternative approach for integrating AI tools to address persistent challenges of technical debt, coordination, and burnout. The framework emerged from a three-month reflective practice and autoethnographic study of a three-person distributed team developing the 2D narrative game "The Worm's Memoirs". Based on analysis of development data (N=157 Jira tasks, N=333 GitHub commits, N=13+ Miro boards, N=8 reflection sessions), CIGDI is proposed as a seven-stage iterative process structured around human-in-the-loop decision points (Priority Criteria and Timeboxing). While AI support democratized knowledge access and reduced cognitive load, our analysis identified a significant challenge: "comprehension debt." We define this as a novel form of technical debt where AI helps teams build systems more sophisticated than their independent skill level can create or maintain. This paradox (possessing functional systems the team incompletely understands) creates fragility and AI dependency, distinct from traditional code quality debt. This work contributes a practical production framework for resource-constrained teams and identifies critical questions about whether AI assistance constitutes a learning ladder or a dependency trap for developer skill.
Noise-Robust Abstractive Compression in Retrieval-Augmented Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Abstractive compression utilizes smaller langauge models to condense query-relevant context, reducing computational costs in retrieval-augmented generation (RAG). However, retrieved documents often include information that is either irrelevant to answering the query or misleading due to factual incorrect content, despite having high relevance scores. This behavior indicates that abstractive compressors are more likely to omit important information essential for the correct answer, especially in long contexts where attention dispersion occurs. To address this issue, we categorize retrieved documents in a more fine-grained manner and propose Abstractive Compression Robust against Noise (ACoRN), which introduces two novel training steps. First, we use offline data augmentation on the training dataset to enhance compressor robustness against two distinct types of retrieval noise. Second, since the language model based compressor cannot fully utilize information from multiple retrieved documents and exhibits positional bias, we perform finetuning to generate summaries centered around key information that directly supports the correct answer. Our experiments demonstrate that T5-large, trained with ACoRN as a compressor, improves EM and F1 scores while preserving the answer string, which could serve as direct evidence. ACoRN excels on datasets with many accuracy reducing documents, making it highly useful in real-world scenarios.
CluCERT: Certifying LLM Robustness via Clustering-Guided Denoising Smoothing
Venue: arXiv cs.LG 2025
Year: 2025

Recent advancements in Large Language Models (LLMs) have led to their widespread adoption in daily applications. Despite their impressive capabilities, they remain vulnerable to adversarial attacks, as even minor meaning-preserving changes such as synonym substitutions can lead to incorrect predictions. As a result, certifying the robustness of LLMs against such adversarial prompts is of vital importance. Existing approaches focused on word deletion or simple denoising strategies to achieve robustness certification. However, these methods face two critical limitations: (1) they yield loose robustness bounds due to the lack of semantic validation for perturbed outputs and (2) they suffer from high computational costs due to repeated sampling. To address these limitations, we propose CluCERT, a novel framework for certifying LLM robustness via clustering-guided denoising smoothing. Specifically, to achieve tighter certified bounds, we introduce a semantic clustering filter that reduces noisy samples and retains meaningful perturbations, supported by theoretical analysis. Furthermore, we enhance computational efficiency through two mechanisms: a refine module that extracts core semantics, and a fast synonym substitution strategy that accelerates the denoising process. Finally, we conduct extensive experiments on various downstream tasks and jailbreak defense scenarios. Experimental results demonstrate that our method outperforms existing certified approaches in both robustness bounds and computational efficiency.
Enhancing Automatic Speech Recognition Through Integrated Noise Detection Architecture
Venue: arXiv cs.SD 2025
Year: 2025

This research presents a novel approach to enhancing automatic speech recognition systems by integrating noise detection capabilities directly into the recognition architecture. Building upon the wav2vec2 framework, the proposed method incorporates a dedicated noise identification module that operates concurrently with speech transcription. Experimental validation using publicly available speech and environmental audio datasets demonstrates substantial improvements in transcription quality and noise discrimination. The enhanced system achieves superior performance in word error rate, character error rate, and noise detection accuracy compared to conventional architectures. Results indicate that joint optimization of transcription and noise classification objectives yields more reliable speech recognition in challenging acoustic conditions.
Graph Deep Learning for Intracranial Aneurysm Blood Flow Simulation and Risk Assessment
Venue: arXiv cs.LG 2025
Year: 2025

Intracranial aneurysms remain a major cause of neurological morbidity and mortality worldwide, where rupture risk is tightly coupled to local hemodynamics particularly wall shear stress and oscillatory shear index. Conventional computational fluid dynamics simulations provide accurate insights but are prohibitively slow and require specialized expertise. Clinical imaging alternatives such as 4D Flow MRI offer direct in-vivo measurements, yet their spatial resolution remains insufficient to capture the fine-scale shear patterns that drive endothelial remodeling and rupture risk while being extremely impractical and expensive. We present a graph neural network surrogate model that bridges this gap by reproducing full-field hemodynamics directly from vascular geometries in less than one minute per cardiac cycle. Trained on a comprehensive dataset of high-fidelity simulations of patient-specific aneurysms, our architecture combines graph transformers with autoregressive predictions to accurately simulate blood flow, wall shear stress, and oscillatory shear index. The model generalizes across unseen patient geometries and inflow conditions without mesh-specific calibration. Beyond accelerating simulation, our framework establishes the foundation for clinically interpretable hemodynamic prediction. By enabling near real-time inference integrated with existing imaging pipelines, it allows direct comparison with hospital phase-diagram assessments and extends them with physically grounded, high-resolution flow fields. This work transforms high-fidelity simulations from an expert-only research tool into a deployable, data-driven decision support system. Our full pipeline delivers high-resolution hemodynamic predictions within minutes of patient imaging, without requiring computational specialists, marking a step-change toward real-time, bedside aneurysm analysis.