OpenRaiser/Intern-Atlas huggingface dataset:
How People Manage Knowledge in their "Second Brains"- A Case Study with Industry Researchers Using Obsidian
Venue: arXiv cs.HC 2025
Year: 2025

People face overwhelming information during work activities, necessitating effective organization and management strategies. Even in personal lives, individuals must keep, annotate, organize, and retrieve knowledge from daily routines. The collection of records for future reference is known as a personal knowledge base. Note-taking applications are valuable tools for building and maintaining these bases, often called a ''second brain''. This paper presents a case study on how people build and explore personal knowledge bases for various purposes. We selected the note-taking tool Obsidian and researchers from a Brazilian lab for an in-depth investigation. Our investigation reveals interesting findings about how researchers build and explore their personal knowledge bases. A key finding is that participants' knowledge retrieval strategy influences how they build and maintain their content. We suggest potential features for an AI system to support this process.
STAF: Leveraging LLMs for Automated Attack Tree-Based Security Test Generation
Venue: arXiv cs.CR 2025
Year: 2025

In modern automotive development, security testing is critical for safeguarding systems against increasingly advanced threats. Attack trees are widely used to systematically represent potential attack vectors, but generating comprehensive test cases from these trees remains a labor-intensive, error-prone task that has seen limited automation in the context of testing vehicular systems. This paper introduces STAF (Security Test Automation Framework), a novel approach to automating security test case generation. Leveraging Large Language Models (LLMs) and a four-step self-corrective Retrieval-Augmented Generation (RAG) framework, STAF automates the generation of executable security test cases from attack trees, providing an end-to-end solution that encompasses the entire attack surface. We particularly show the elements and processes needed to provide an LLM to actually produce sensible and executable automotive security test suites, along with the integration with an automated testing framework. We further compare our tailored approach with general purpose (vanilla) LLMs and the performance of different LLMs (namely GPT-4.1 and DeepSeek) using our approach. We also demonstrate the method of our operation step-by-step in a concrete case study. Our results show significant improvements in efficiency, accuracy, scalability, and easy integration in any workflow, marking a substantial advancement in automating automotive security testing methodologies. Using TARAs as an input for verfication tests, we create synergies by connecting two vital elements of a secure automotive development process.
Staying on the Manifold: Geometry-Aware Noise Injection
Venue: arXiv cs.LG 2025
Year: 2025

It has been shown that perturbing the input during training implicitly regularises the gradient of the learnt function, leading to smoother models and enhancing generalisation. However, previous research mostly considered the addition of ambient noise in the input space, without considering the underlying structure of the data. In this work, we propose several strategies of adding geometry-aware input noise that accounts for the lower dimensional manifold the input space inhabits. We start by projecting ambient Gaussian noise onto the tangent space of the manifold. In a second step, the noise sample is mapped on the manifold via the associated geodesic curve. We also consider Brownian motion noise, which moves in random steps along the manifold. We show that geometry-aware noise leads to improved generalisation and robustness to hyperparameter selection on highly curved manifolds, while performing at least as well as training without noise on simpler manifolds. Our proposed framework extends to data manifolds approximated by generative models and we observe similar trends on the MNIST digits dataset.
A HyperGraphMamba-Based Multichannel Adaptive Model for ncRNA Classification
Venue: arXiv cs.LG 2025
Year: 2025

Non-coding RNAs (ncRNAs) play pivotal roles in gene expression regulation and the pathogenesis of various diseases. Accurate classification of ncRNAs is essential for functional annotation and disease diagnosis. To address existing limitations in feature extraction depth and multimodal fusion, we propose HGMamba-ncRNA, a HyperGraphMamba-based multichannel adaptive model, which integrates sequence, secondary structure, and optionally available expression features of ncRNAs to enhance classification performance. Specifically, the sequence of ncRNA is modeled using a parallel Multi-scale Convolution and LSTM architecture (MKC-L) to capture both local patterns and long-range dependencies of nucleotides. The structure modality employs a multi-scale graph transformer (MSGraphTransformer) to represent the multi-level topological characteristics of ncRNA secondary structures. The expression modality utilizes a Chebyshev Polynomial-based Kolmogorov-Arnold Network (CPKAN) to effectively model and interpret high-dimensional expression profiles. Finally, by incorporating virtual nodes to facilitate efficient and comprehensive multimodal interaction, HyperGraphMamba is proposed to adaptively align and integrate multichannel heterogeneous modality features. Experiments conducted on three public datasets demonstrate that HGMamba-ncRNA consistently outperforms state-of-the-art methods in terms of accuracy and other metrics. Extensive empirical studies further confirm the model's robustness, effectiveness, and strong transferability, offering a novel and reliable strategy for complex ncRNA functional classification. Code and datasets are available at https://anonymous.4open.science/r/HGMamba-ncRNA-94D0.
4D Driving Scene Generation With Stereo Forcing
Venue: arXiv cs.CV 2025
Year: 2025

Current generative models struggle to synthesize dynamic 4D driving scenes that simultaneously support temporal extrapolation and spatial novel view synthesis (NVS) without per-scene optimization. Bridging generation and novel view synthesis remains a major challenge. We present PhiGenesis, a unified framework for 4D scene generation that extends video generation techniques with geometric and temporal consistency. Given multi-view image sequences and camera parameters, PhiGenesis produces temporally continuous 4D Gaussian splatting representations along target 3D trajectories. In its first stage, PhiGenesis leverages a pre-trained video VAE with a novel range-view adapter to enable feed-forward 4D reconstruction from multi-view images. This architecture supports single-frame or video inputs and outputs complete 4D scenes including geometry, semantics, and motion. In the second stage, PhiGenesis introduces a geometric-guided video diffusion model, using rendered historical 4D scenes as priors to generate future views conditioned on trajectories. To address geometric exposure bias in novel views, we propose Stereo Forcing, a novel conditioning strategy that integrates geometric uncertainty during denoising. This method enhances temporal coherence by dynamically adjusting generative influence based on uncertainty-aware perturbations. Our experimental results demonstrate that our method achieves state-of-the-art performance in both appearance and geometric reconstruction, temporal generation and novel view synthesis (NVS) tasks, while simultaneously delivering competitive performance in downstream evaluations. Homepage is at \href{https://jiangxb98.github.io/PhiGensis}{PhiGensis}.
Confidentiality-Preserving Verifiable Business Processes through Zero-Knowledge Proofs
Venue: arXiv cs.SE 2025
Year: 2025

Ensuring the integrity of business processes without disclosing confidential business information is a major challenge in inter-organizational processes. This paper introduces a zero-knowledge proof (ZKP)-based approach for the verifiable execution of business processes while preserving confidentiality. We integrate ZK virtual machines (zkVMs) into business process management engines through a comprehensive system architecture and a prototypical implementation. Our approach supports chained verifiable computations through proof compositions. On the example of product carbon footprinting, we model sequential footprinting activities and demonstrate how organizations can prove and verify the integrity of verifiable processes without exposing sensitive information. We assess different ZKP proving variants within process models for their efficiency in proving and verifying, and discuss the practical integration of ZKPs throughout the Business Process Management (BPM) lifecycle. Our experiment-driven evaluation demonstrates the automation of process verification under given confidentiality constraints.
SIM-CoT: Supervised Implicit Chain-of-Thought
Venue: arXiv cs.CL 2025
Year: 2025

Implicit Chain-of-Thought (CoT) methods offer a token-efficient alternative to explicit CoT reasoning in Large Language Models (LLMs), but a persistent performance gap has limited their adoption. We identify a core latent instability issue when scaling the computational budget of implicit CoT: as the number of reasoning tokens increases, training often becomes unstable and collapses. Our analysis shows that this instability arises from latent representations becoming homogeneous and losing semantic diversity, caused by insufficient step-level supervision in current implicit CoT methods. To address this, we propose SIM-CoT, a plug-and-play training module that introduces step-level supervision to stabilize and enrich the latent reasoning space. SIM-CoT employs an auxiliary decoder during training to align each implicit token with its corresponding explicit reasoning step, ensuring latent states capture distinct and meaningful information. The auxiliary decoder is removed at inference, preserving the efficiency of implicit CoT with no added overhead. It also provides interpretability by projecting each latent token onto an explicit reasoning vocabulary, enabling per-step visualization and diagnosis. SIM-CoT significantly improves both in-domain accuracy and out-of-domain stability of implicit CoT methods, boosting Coconut by +8.2\% on GPT-2 and CODI by +3.0\% on LLaMA-3.1 8B. It further surpasses the explicit CoT baseline on GPT-2 by 2.1\% with 2.3$\times$ greater token efficiency, while closing the performance gap on larger models like LLaMA-3.1 8B. Code: https://github.com/InternLM/SIM-CoT
Z-Scores: A Metric for Linguistically Assessing Disfluency Removal
Venue: arXiv cs.CL 2025
Year: 2025

Evaluating disfluency removal in speech requires more than aggregate token-level scores. Traditional word-based metrics such as precision, recall, and F1 (E-Scores) capture overall performance but cannot reveal why models succeed or fail. We introduce Z-Scores, a span-level linguistically-grounded evaluation metric that categorizes system behavior across distinct disfluency types (EDITED, INTJ, PRN). Our deterministic alignment module enables robust mapping between generated text and disfluent transcripts, allowing Z-Scores to expose systematic weaknesses that word-level metrics obscure. By providing category-specific diagnostics, Z-Scores enable researchers to identify model failure modes and design targeted interventions -- such as tailored prompts or data augmentation -- yielding measurable performance improvements. A case study with LLMs shows that Z-Scores uncover challenges with INTJ and PRN disfluencies hidden in aggregate F1, directly informing model refinement strategies.
Video models are zero-shot learners and reasoners
Venue: arXiv cs.LG 2025
Year: 2025

The remarkable zero-shot capabilities of Large Language Models (LLMs) have propelled natural language processing from task-specific models to unified, generalist foundation models. This transformation emerged from simple primitives: large, generative models trained on web-scale data. Curiously, the same primitives apply to today's generative video models. Could video models be on a trajectory towards general-purpose vision understanding, much like LLMs developed general-purpose language understanding? We demonstrate that Veo 3 can solve a broad variety of tasks it wasn't explicitly trained for: segmenting objects, detecting edges, editing images, understanding physical properties, recognizing object affordances, simulating tool use, and more. These abilities to perceive, model, and manipulate the visual world enable early forms of visual reasoning like maze and symmetry solving. Veo's emergent zero-shot capabilities indicate that video models are on a path to becoming unified, generalist vision foundation models.
EmbeddingGemma: Powerful and Lightweight Text Representations
Venue: arXiv cs.CL 2025
Year: 2025

We introduce EmbeddingGemma, a new lightweight, open text embedding model based on the Gemma 3 language model family. Our innovative training recipe strategically captures knowledge from larger models via encoder-decoder initialization and geometric embedding distillation. We improve model robustness and expressiveness with a spread-out regularizer, and ensure generalizability by merging checkpoints from varied, optimized mixtures. Evaluated on the Massive Text Embedding Benchmark (MTEB) across multilingual, English, and code domains, EmbeddingGemma (300M) achieves state-of-the-art results. Notably, it outperforms prior top models, both proprietary and open, with fewer than 500M parameters, and provides performance comparable to models double its size, offering an exceptional performance-to-cost ratio. Remarkably, this lead persists when quantizing model weights or truncating embedding outputs. This makes EmbeddingGemma particularly well-suited for low-latency and high-throughput use cases such as on-device applications. We provide ablation studies exploring our key design choices. We release EmbeddingGemma to the community to promote further research.
Philosophy-informed Machine Learning
Venue: arXiv cs.AI 2025
Year: 2025

Philosophy-informed machine learning (PhIML) directly infuses core ideas from analytic philosophy into ML model architectures, objectives, and evaluation protocols. Therefore, PhIML promises new capabilities through models that respect philosophical concepts and values by design. From this lens, this paper reviews conceptual foundations to demonstrate philosophical gains and alignment. In addition, we present case studies on how ML users/designers can adopt PhIML as an agnostic post-hoc tool or intrinsically build it into ML model architectures. Finally, this paper sheds light on open technical barriers alongside philosophical, practical, and governance challenges and outlines a research roadmap toward safe, philosophy-aware, and ethically responsible PhIML.
Assessing Classical Machine Learning and Transformer-based Approaches for Detecting AI-Generated Research Text
Venue: arXiv cs.CL 2025
Year: 2025

The rapid adoption of large language models (LLMs) such as ChatGPT has blurred the line between human and AI-generated texts, raising urgent questions about academic integrity, intellectual property, and the spread of misinformation. Thus, reliable AI-text detection is needed for fair assessment to safeguard human authenticity and cultivate trust in digital communication. In this study, we investigate how well current machine learning (ML) approaches can distinguish ChatGPT-3.5-generated texts from human-written texts employing a labeled data set of 250 pairs of abstracts from a wide range of research topics. We test and compare both classical (Logistic Regression armed with classical Bag-of-Words, POS, and TF-IDF features) and transformer-based (BERT augmented with N-grams, DistilBERT, BERT with a lightweight custom classifier, and LSTM-based N-gram models) ML detection techniques. As we aim to assess each model's performance in detecting AI-generated research texts, we also aim to test whether an ensemble of these models can outperform any single detector. Results show DistilBERT achieves the overall best performance, while Logistic Regression and BERT-Custom offer solid, balanced alternatives; LSTM- and BERT-N-gram approaches lag. The max voting ensemble of the three best models fails to surpass DistilBERT itself, highlighting the primacy of a single transformer-based representation over mere model diversity. By comprehensively assessing the strengths and weaknesses of these AI-text detection approaches, this work lays a foundation for more robust transformer frameworks with larger, richer datasets to keep pace with ever-improving generative AI models.
USB-Rec: An Effective Framework for Improving Conversational Recommendation Capability of Large Language Model
Venue: arXiv cs.CL 2025
Year: 2025

Recently, Large Language Models (LLMs) have been widely employed in Conversational Recommender Systems (CRSs). Unlike traditional language model approaches that focus on training, all existing LLMs-based approaches are mainly centered around how to leverage the summarization and analysis capabilities of LLMs while ignoring the issue of training. Therefore, in this work, we propose an integrated training-inference framework, User-Simulator-Based framework (USB-Rec), for improving the performance of LLMs in conversational recommendation at the model level. Firstly, we design a LLM-based Preference Optimization (PO) dataset construction strategy for RL training, which helps the LLMs understand the strategies and methods in conversational recommendation. Secondly, we propose a Self-Enhancement Strategy (SES) at the inference stage to further exploit the conversational recommendation potential obtained from RL training. Extensive experiments on various datasets demonstrate that our method consistently outperforms previous state-of-the-art methods.
R1-Fuzz: Specializing Language Models for Textual Fuzzing via Reinforcement Learning
Venue: arXiv cs.CR 2025
Year: 2025

Fuzzing is effective for vulnerability discovery but struggles with complex targets such as compilers, interpreters, and database engines, which accept textual input that must satisfy intricate syntactic and semantic constraints. Although language models (LMs) have attracted interest for this task due to their vast latent knowledge and reasoning potential, their practical adoption has been limited. The major challenges stem from insufficient exploration of deep program logic among real-world codebases, and the high cost of leveraging larger models. To overcome these challenges, we propose R1-Fuzz, the first framework that leverages reinforcement learning (RL) to specialize cost-efficient LMs and integrate them for complex textual fuzzing input generation. R1-Fuzz introduces two key designs: coverage-slicing-based question construction and a distance-based reward calculation. Through RL-based post-training of a model with our constructed dataset, R1-Fuzz designs a fuzzing workflow that tightly integrates LMs to reason deep program semantics during fuzzing. Evaluations on diverse real-world targets show that our design enables a small model, named R1-Fuzz-7B, to rival or even outperform much larger models in real-world fuzzing. Notably, R1-Fuzz achieves up to 75\% higher coverage than state-of-the-art fuzzers and discovers 29 previously unknown vulnerabilities, demonstrating its practicality.
State-of-the-Art in Software Security Visualization: A Systematic Review
Venue: arXiv cs.SE 2025
Year: 2025

Software security visualization is an interdisciplinary field that combines the technical complexity of cybersecurity, including threat intelligence and compliance monitoring, with visual analytics, transforming complex security data into easily digestible visual formats. As software systems get more complex and the threat landscape evolves, traditional text-based and numerical methods for analyzing and interpreting security concerns become increasingly ineffective. The purpose of this paper is to systematically review existing research and create a comprehensive taxonomy of software security visualization techniques through literature, categorizing these techniques into four types: graph-based, notation-based, matrix-based, and metaphor-based visualization. This systematic review explores over 60 recent key research papers in software security visualization, highlighting its key issues, recent advancements, and prospective future research directions. From the comprehensive analysis, the two main areas were distinctly highlighted as extensive software development visualization, focusing on advanced methods for depicting software architecture: operational security visualization and cybersecurity visualization. The findings highlight the necessity for innovative visualization techniques that adapt to the evolving security landscape, with practical implications for enhancing threat detection, improving security response strategies, and guiding future research.
The Secret Agenda: LLMs Strategically Lie and Our Current Safety Tools Are Blind
Venue: arXiv cs.CY 2025
Year: 2025

We investigate strategic deception in large language models using two complementary testbeds: Secret Agenda (across 38 models) and Insider Trading compliance (via SAE architectures). Secret Agenda reliably induced lying when deception advantaged goal achievement across all model families. Analysis revealed that autolabeled SAE features for "deception" rarely activated during strategic dishonesty, and feature steering experiments across 100+ deception-related features failed to prevent lying. Conversely, insider trading analysis using unlabeled SAE activations separated deceptive versus compliant responses through discriminative patterns in heatmaps and t-SNE visualizations. These findings suggest autolabel-driven interpretability approaches fail to detect or control behavioral deception, while aggregate unlabeled activations provide population-level structure for risk assessment. Results span Llama 8B/70B SAE implementations and GemmaScope under resource constraints, representing preliminary findings that motivate larger studies on feature discovery, labeling methodology, and causal interventions in realistic deception contexts.
Online-Optimized RAG for Tool Use and Function Calling
Venue: arXiv cs.SE 2025
Year: 2025

In many applications, retrieval-augmented generation (RAG) drives tool use and function calling by embedding the (user) queries and matching them to pre-specified tool/function descriptions. In this paper, we address an embedding misalignment issue that often arises in practical applications due to imperfect embedding models or noisy descriptions; such misalignment may lead to incorrect retrieval and task failure. We introduce Online-Optimized RAG, a deployment-time framework that continually adapts retrieval embeddings from live interactions using minimal feedback (e.g., task success). Online-Optimized RAG applies lightweight online gradient updates with negligible per-query latency and requires no changes to the underlying LLM. The method is plug-and-play: it supports both single- and multi-hop tool use, dynamic tool inventories, and $K$-retrieval with re-ranking. We provide a problem-dependent theoretical analysis that quantifies how the method's performance depends on the initialization quality of the embeddings and other related quantities. Across diverse tool-use and document-retrieval scenarios, our Online-Optimized RAG consistently improves tool selection accuracy and end-task success, thus providing a simple, practical path to robust, self-improving RAG systems.