OpenRaiser/Intern-Atlas huggingface dataset:
Completion of the DrugMatrix Toxicogenomics Database using 3-Dimensional Tensors
Venue: arXiv cs.LG 2025
Year: 2025

We explore applying a tensor completion approach to complete the DrugMatrix toxicogenomics dataset. Our hypothesis is that by preserving the 3-dimensional structure of the data, which comprises tissue, treatment, and transcriptomic measurements, and by leveraging a machine learning formulation, our approach will improve upon prior state-of-the-art results. Our results demonstrate that the new tensor-based method more accurately reflects the original data distribution and effectively captures organ-specific variability. The proposed tensor-based methodology achieved lower mean squared errors and mean absolute errors compared to both conventional Canonical Polyadic decomposition and 2-dimensional matrix factorization methods. In addition, our non-negative tensor completion implementation reveals relationships among tissues. Our findings not only complete the world's largest in-vivo toxicogenomics database with improved accuracy but also offer a promising methodology for future studies of drugs that may cross species barriers, for example, from rats to humans.
Preserving Privacy, Increasing Accessibility, and Reducing Cost: An On-Device Artificial Intelligence Model for Medical Transcription and Note Generation
Venue: arXiv cs.CL 2025
Year: 2025

Background: Clinical documentation represents a significant burden for healthcare providers, with physicians spending up to 2 hours daily on administrative tasks. Recent advances in large language models (LLMs) offer promising solutions, but privacy concerns and computational requirements limit their adoption in healthcare settings. Objective: To develop and evaluate a privacy-preserving, on-device medical transcription system using a fine-tuned Llama 3.2 1B model capable of generating structured medical notes from medical transcriptions while maintaining complete data sovereignty entirely in the browser. Methods: We fine-tuned a Llama 3.2 1B model using Parameter-Efficient Fine-Tuning (PEFT) with LoRA on 1,500 synthetic medical transcription-to-structured note pairs. The model was evaluated against the base Llama 3.2 1B on two datasets: 100 endocrinology transcripts and 140 modified ACI benchmark cases. Evaluation employed both statistical metrics (ROUGE, BERTScore, BLEURT) and LLM-as-judge assessments across multiple clinical quality dimensions. Results: The fine-tuned OnDevice model demonstrated substantial improvements over the base model. On the ACI benchmark, ROUGE-1 scores increased from 0.346 to 0.496, while BERTScore F1 improved from 0.832 to 0.866. Clinical quality assessments showed marked reduction in major hallucinations (from 85 to 35 cases) and enhanced factual correctness (2.81 to 3.54 on 5-point scale). Similar improvements were observed on the internal evaluation dataset, with composite scores increasing from 3.13 to 4.43 (+41.5%). Conclusions: Fine-tuning compact LLMs for medical transcription yields clinically meaningful improvements while enabling complete on-device browser deployment. This approach addresses key barriers to AI adoption in healthcare: privacy preservation, cost reduction, and accessibility for resource-constrained environments.
Intelligent Histology for Tumor Neurosurgery
Venue: arXiv cs.CV 2025
Year: 2025

The importance of rapid and accurate histologic analysis of surgical tissue in the operating room has been recognized for over a century. Our standard-of-care intraoperative pathology workflow is based on light microscopy and H\&E histology, which is slow, resource-intensive, and lacks real-time digital imaging capabilities. Here, we present an emerging and innovative method for intraoperative histologic analysis, called Intelligent Histology, that integrates artificial intelligence (AI) with stimulated Raman histology (SRH). SRH is a rapid, label-free, digital imaging method for real-time microscopic tumor tissue analysis. SRH generates high-resolution digital images of surgical specimens within seconds, enabling AI-driven tumor histologic analysis, molecular classification, and tumor infiltration detection. We review the scientific background, clinical translation, and future applications of intelligent histology in tumor neurosurgery. We focus on the major scientific and clinical studies that have demonstrated the transformative potential of intelligent histology across multiple neurosurgical specialties, including neurosurgical oncology, skull base, spine oncology, pediatric tumors, and periperal nerve tumors. Future directions include the development of AI foundation models through multi-institutional datasets, incorporating clinical and radiologic data for multimodal learning, and predicting patient outcomes. Intelligent histology represents a transformative intraoperative workflow that can reinvent real-time tumor analysis for 21st century neurosurgery.
Optimisation Is Not What You Need
Venue: arXiv cs.LG 2025
Year: 2025

The Artificial Intelligence field has focused on developing optimisation methods to solve multiple problems, specifically problems that we thought to be only solvable through cognition. The obtained results have been outstanding, being able to even surpass the Turing Test. However, we have found that these optimisation methods share some fundamental flaws that impede them to become a true artificial cognition. Specifically, the field have identified catastrophic forgetting as a fundamental problem to develop such cognition. This paper formally proves that this problem is inherent to optimisation methods, and as such it will always limit approaches that try to solve the Artificial General Intelligence problem as an optimisation problem. Additionally, it addresses the problem of overfitting and discuss about other smaller problems that optimisation methods pose. Finally, it empirically shows how world-modelling methods avoid suffering from either problem. As a conclusion, the field of Artificial Intelligence needs to look outside the machine learning field to find methods capable of developing an artificial cognition.
LATTE: Latent Trajectory Embedding for Diffusion-Generated Image Detection
Venue: arXiv cs.CV 2025
Year: 2025

The rapid advancement of diffusion-based image generators has made it increasingly difficult to distinguish generated from real images. This erodes trust in digital media, making it critical to develop generated image detectors that remain reliable across different generators. While recent approaches leverage diffusion denoising cues, they typically rely on single-step reconstruction errors and overlook the sequential nature of the denoising process. In this work, we propose LATTE - LATent Trajectory Embedding - a novel approach that models the evolution of latent embeddings across multiple denoising steps. Instead of treating each denoising step in isolation, LATTE captures the trajectory of these representations, revealing subtle and discriminative patterns that distinguish real from generated images. Experiments on several benchmarks, such as GenImage, Chameleon, and Diffusion Forensics, show that LATTE achieves superior performance, especially in challenging cross-generator and cross-dataset scenarios, highlighting the potential of latent trajectory modeling. The code is available on the following link: https://github.com/AnaMVasilcoiu/LATTE-Diffusion-Detector.
AI-Based Reconstruction from Inherited Personal Data: Analysis, Feasibility, and Prospects
Venue: arXiv cs.CY 2025
Year: 2025

This article explores the feasibility of creating an "electronic copy" of a deceased researcher by training artificial intelligence (AI) on the data stored in their personal computers. By analyzing typical data volumes on inherited researcher computers, including textual files such as articles, emails, and drafts, it is estimated that approximately one million words are available for AI training. This volume is sufficient for fine-tuning advanced pre-trained models like GPT-4 to replicate a researcher's writing style, domain expertise, and rhetorical voice with high fidelity. The study also discusses the potential enhancements from including non-textual data and file metadata to enrich the AI's representation of the researcher. Extensions of the concept include communication between living researchers and their electronic copies, collaboration among individual electronic copies, as well as the creation and interconnection of organizational electronic copies to optimize information access and strategic decision-making. Ethical considerations such as ownership and security of these electronic copies are highlighted as critical for responsible implementation. The findings suggest promising opportunities for AI-driven preservation and augmentation of intellectual legacy.
Large Language Models for Automating Clinical Data Standardization: HL7 FHIR Use Case
Venue: arXiv cs.CL 2025
Year: 2025

For years, semantic interoperability standards have sought to streamline the exchange of clinical data, yet their deployment remains time-consuming, resource-intensive, and technically challenging. To address this, we introduce a semi-automated approach that leverages large language models specifically GPT-4o and Llama 3.2 405b to convert structured clinical datasets into HL7 FHIR format while assessing accuracy, reliability, and security. Applying our method to the MIMIC-IV database, we combined embedding techniques, clustering algorithms, and semantic retrieval to craft prompts that guide the models in mapping each tabular field to its corresponding FHIR resource. In an initial benchmark, resource identification achieved a perfect F1-score, with GPT-4o outperforming Llama 3.2 thanks to the inclusion of FHIR resource schemas within the prompt. Under real-world conditions, accuracy dipped slightly to 94 %, but refinements to the prompting strategy restored robust mappings. Error analysis revealed occasional hallucinations of non-existent attributes and mismatches in granularity, which more detailed prompts can mitigate. Overall, our study demonstrates the feasibility of context-aware, LLM-driven transformation of clinical data into HL7 FHIR, laying the groundwork for semi-automated interoperability workflows. Future work will focus on fine-tuning models with specialized medical corpora, extending support to additional standards such as HL7 CDA and OMOP, and developing an interactive interface to enable expert validation and iterative refinement.
Mechanics Simulation with Implicit Neural Representations of Complex Geometries
Venue: arXiv cs.CE 2025
Year: 2025

Implicit Neural Representations (INRs), characterized by neural network-encoded signed distance fields, provide a powerful means to represent complex geometries continuously and efficiently. While successful in computer vision and generative modeling, integrating INRs into computational analysis workflows, such as finite element simulations, remains underdeveloped. In this work, we propose a computational framework that seamlessly combines INRs with the Shifted Boundary Method (SBM) for high-fidelity linear elasticity simulations without explicit geometry transformations. By directly querying the neural implicit geometry, we obtain the surrogate boundaries and distance vectors essential for SBM, effectively eliminating the meshing step. We demonstrate the efficacy and robustness of our approach through elasticity simulations on complex geometries (Stanford Bunny, Eiffel Tower, gyroids) sourced from triangle soups and point clouds. Our method showcases significant computational advantages and accuracy, underscoring its potential in biomedical, geophysical, and advanced manufacturing applications.
Neural Dynamic Modes: Computational Imaging of Dynamical Systems from Sparse Observations
Venue: arXiv cs.CV 2025
Year: 2025

Dynamical systems are ubiquitous within science and engineering, from turbulent flow across aircraft wings to structural variability of proteins. Although some systems are well understood and simulated, scientific imaging often confronts never-before-seen dynamics observed through indirect, noisy, and highly sparse measurements. We present NeuralDMD, a model-free framework that combines neural implicit representations with Dynamic Mode Decomposition (DMD) to reconstruct continuous spatio-temporal dynamics from such measurements. The expressiveness of neural representations enables capturing complex spatial structures, while the linear dynamical modes of DMD introduce an inductive bias that guides training and supports stable, low-dimensional representations and forecasting. We validate NeuralDMD on two real-world problems: reconstructing near-surface wind-speed fields over North America from sparse station observations, and recovering the evolution of plasma near the Galactic-center black hole, Sgr A*. In both cases, NeuralDMD outperforms established baselines, demonstrating its potential as a general tool for imaging dynamical systems across geoscience, astronomy, and beyond.
RLVER: Reinforcement Learning with Verifiable Emotion Rewards for Empathetic Agents
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) excel at logical and algorithmic reasoning, yet their emotional intelligence (EQ) still lags far behind their cognitive prowess. While reinforcement learning from verifiable rewards (RLVR) has advanced in other domains, its application to dialogue-especially for emotional intelligence-remains underexplored. In this work, we introduce RLVER, the first end-to-end reinforcement learning framework that leverages verifiable emotion rewards from simulated users to cultivate higher-order empathetic abilities in LLMs. Within this framework, self-consistent affective simulated users engage in dialogue rollouts and produce deterministic emotion scores during conversations, serving as reward signals to guide the LLM's learning. Fine-tuning publicly available Qwen2.5-7B-Instruct model with PPO boosts its Sentient-Benchmark score from 13.3 to 79.2 while largely preserving mathematical and coding competence. Extensive experiments reveal that: (i) RLVER consistently improves multiple dialogue capabilities; (ii) Thinking and non-thinking models show distinct trends--thinking models excel in empathy and insight, while non-thinking models favor action; (iii) GRPO often yields stable gains, while PPO can push certain capabilities to a higher ceiling; (iv) More challenging environments are not always better-moderate ones can yield stronger outcomes. Our results show that RLVER is a practical route toward emotionally intelligent and broadly capable language agents.
Neural-Network solver of ideal MHD equilibria
Venue: arXiv cs.LG 2025
Year: 2025

We present a novel approach to compute three-dimensional Magnetohydrodynamic equilibria by parametrizing Fourier modes with artificial neural networks and compare it to equilibria computed by conventional solvers. The full nonlinear global force residual across the volume in real space is then minimized with first order optimizers. Already,we observe competitive computational cost to arrive at the same minimum residuals computed by existing codes. With increased computational cost,lower minima of the residual are achieved by the neural networks,establishing a new lower bound for the force residual. We use minimally complex neural networks,and we expect significant improvements for solving not only single equilibria with neural networks,but also for computing neural network models valid over continuous distributions of equilibria.
How Overconfidence in Initial Choices and Underconfidence Under Criticism Modulate Change of Mind in Large Language Models
Venue: arXiv cs.LG 2025
Year: 2025

Large language models (LLMs) exhibit strikingly conflicting behaviors: they can appear steadfastly overconfident in their initial answers whilst at the same time being prone to excessive doubt when challenged. To investigate this apparent paradox, we developed a novel experimental paradigm, exploiting the unique ability to obtain confidence estimates from LLMs without creating memory of their initial judgments -- something impossible in human participants. We show that LLMs -- Gemma 3, GPT4o and o1-preview -- exhibit a pronounced choice-supportive bias that reinforces and boosts their estimate of confidence in their answer, resulting in a marked resistance to change their mind. We further demonstrate that LLMs markedly overweight inconsistent compared to consistent advice, in a fashion that deviates qualitatively from normative Bayesian updating. Finally, we demonstrate that these two mechanisms -- a drive to maintain consistency with prior commitments and hypersensitivity to contradictory feedback -- parsimoniously capture LLM behavior in a different domain. Together, these findings furnish a mechanistic account of LLM confidence that explains both their stubbornness and excessive sensitivity to criticism.
Investigating VLM Hallucination from a Cognitive Psychology Perspective: A First Step Toward Interpretation with Intriguing Observations
Venue: arXiv cs.CV 2025
Year: 2025

Hallucination is a long-standing problem that has been actively investigated in Vision-Language Models (VLMs). Existing research commonly attributes hallucinations to technical limitations or sycophancy bias, where the latter means the models tend to generate incorrect answers to align with user expectations. However, these explanations primarily focus on technical or externally driven factors, and may have neglected the possibility that hallucination behaviours might mirror cognitive biases observed in human psychology. In this work, we introduce a psychological taxonomy, categorizing VLMs' cognitive biases that lead to hallucinations, including sycophancy, logical inconsistency, and a newly identified VLMs behaviour: appeal to authority. To systematically analyze these behaviours, we design AIpsych, a scalable benchmark that reveals psychological tendencies in model response patterns. Leveraging this benchmark, we investigate how variations in model architecture and parameter size influence model behaviour when responding to strategically manipulated questions. Our experiments reveal that as model size increases, VLMs exhibit stronger sycophantic tendencies but reduced authority bias, suggesting increasing competence but a potential erosion of response integrity. A human subject study further validates our hypotheses and highlights key behavioural differences between VLMs and human respondents. This work suggests a new perspective for understanding hallucination in VLMs and highlights the importance of integrating psychological principles into model evaluation.
Holographic Projection and Cyber Attack Surface: A Physical Analogy for Digital Security
Venue: arXiv cs.CR 2025
Year: 2025

This article presents an in-depth exploration of the analogy between the Holographic Principle in theoretical physics and cyber attack surfaces in digital security. Building on concepts such as black hole entropy and AdS/CFT duality, it highlights how complex infrastructures project their vulnerabilities onto their external interfaces. The paper draws a parallel between a black hole's event horizon, which encodes all internal information, and the attack surface, which reflects the internal architecture's security posture. Additionally, the article outlines how this conceptual framework can guide cybersecurity practices, emphasizing strategies such as attack surface reduction, continuous scanning with tools like OWASP ZAP and Greenbone OpenVAS, and the implementation of Zero Trust Architecture. This analogy not only provides a unique perspective on digital security but also underscores the critical importance of boundary-level defenses in protecting vast internal infrastructures.
HGCA: Hybrid GPU-CPU Attention for Long Context LLM Inference
Venue: arXiv cs.LG 2025
Year: 2025

Scaling inference for large language models (LLMs) is increasingly constrained by limited GPU memory, especially due to growing key-value (KV) caches required for long-context generation. While existing approaches offload KV caches to CPU memory or apply sparse attention to reduce GPU load, they often underutilize CPU compute resources and compromise accuracy. We present HGCA, a hybrid CPU-GPU attention mechanism that enables scalable, high-throughput LLM inference with near-full attention quality. HGCA performs dense attention on recently generated KV entries retained in GPU memory and parallel sparse attention on selected, salient KV entries in CPU memory. The attention outputs are efficiently merged using log-sum-exp fusion, minimizing PCIe transfer overhead. HGCA also introduces a finegrained, per-head sparsification strategy optimized for CPU execution, preserving contextual relevance while reducing computation. Our implementation seamlessly integrates into existing LLM frameworks without requiring model retraining. Experiments across diverse models and workloads show that HGCA achieves superior scalability, supports longer sequences and larger batch sizes, and outperforms existing sparse attention baselines in both performance and accuracy -- all on commodity GPU hardware.
The Impact of LLM-Assistants on Software Developer Productivity: A Systematic Literature Review
Venue: arXiv cs.SE 2025
Year: 2025

Large language model assistants (LLM-assistants) present new opportunities to transform software development. Developers are increasingly adopting these tools across tasks, including coding, testing, debugging, documentation, and design. Yet, despite growing interest, there is no synthesis of how LLM-assistants affect software developer productivity. In this paper, we present a systematic literature review of 37 peer-reviewed studies published between January 2014 and December 2024 that examine this impact. Our analysis reveals that LLM-assistants offer both considerable benefits and critical risks. Commonly reported gains include minimized code search, accelerated development, and the automation of trivial and repetitive tasks. However, studies also highlight concerns around cognitive offloading, reduced team collaboration, and inconsistent effects on code quality. While the majority of studies (92%) adopt a multi-dimensional perspective by examining at least two SPACE dimensions, reflecting increased awareness of the complexity of developer productivity, only 14% extend beyond three dimensions, indicating substantial room for more integrated evaluations. Satisfaction, Performance, and Efficiency are the most frequently investigated dimensions, whereas Communication and Activity remain underexplored. Most studies are exploratory (64%) and methodologically diverse, but lack longitudinal and team-based evaluations. This review surfaces key research gaps and provides recommendations for future research and practice. All artifacts associated with this study are publicly available at https://zenodo.org/records/15788502.