OpenRaiser/Intern-Atlas huggingface dataset:
A Large-Scale Study of Model Integration in ML-Enabled Software Systems
Venue: arXiv cs.SE 2025
Year: 2025

The rise of machine learning (ML) and its integration into software systems has drastically changed development practices. While software engineering traditionally focused on manually created code artifacts with dedicated processes and architectures, ML-enabled systems require additional data-science methods and tools to create ML artifacts -- especially ML models and training data. However, integrating models into systems, and managing the many different artifacts involved, is far from trivial. ML-enabled systems can easily have multiple ML models that interact with each other and with traditional code in intricate ways. Unfortunately, while challenges and practices of building ML-enabled systems have been studied, little is known about the characteristics of real-world ML-enabled systems beyond isolated examples. Improving engineering processes and architectures for ML-enabled systems requires improving the empirical understanding of these systems. We present a large-scale study of 2,928 open-source ML-enabled software systems. We classified and analyzed them to determine system characteristics, model and code reuse practices, and architectural aspects of integrating ML models. Our findings show that these systems still mainly consist of traditional source code, and that ML model reuse through code duplication or pre-trained models is common. We also identified different ML integration patterns and related implementation practices. We hope that our results help improve practices for integrating ML models, bringing data science and software engineering closer together.
Mambular: A Sequential Model for Tabular Deep Learning
Venue: arXiv cs.LG 2025
Year: 2025

The analysis of tabular data has traditionally been dominated by gradient-boosted decision trees (GBDTs), known for their proficiency with mixed categorical and numerical features. However, recent deep learning innovations are challenging this dominance. This paper investigates the use of autoregressive state-space models for tabular data and compares their performance against established benchmark models. Additionally, we explore various adaptations of these models, including different pooling strategies, feature interaction mechanisms, and bi-directional processing techniques to understand their effectiveness for tabular data. Our findings indicate that interpreting features as a sequence and processing them and their interactions through structured state-space layers can lead to significant performance improvement. This research underscores the versatility of autoregressive models in tabular data analysis, positioning them as a promising alternative that could substantially enhance deep learning capabilities in this traditionally challenging area. The source code is available at https://github.com/basf/mamba-tabular.
Hound: Locating Cryptographic Primitives in Desynchronized Side-Channel Traces Using Deep-Learning
Venue: arXiv cs.CR 2025
Year: 2025

Side-channel attacks allow to extract sensitive information from cryptographic primitives by correlating the partially known computed data and the measured side-channel signal. Starting from the raw side-channel trace, the preprocessing of the side-channel trace to pinpoint the time at which each cryptographic primitive is executed, and, then, to re-align all the collected data to this specific time represent a critical step to setup a successful side-channel attack. The use of hiding techniques has been widely adopted as a low-cost solution to hinder the preprocessing of side-channel traces thus limiting side-channel attacks in real scenarios. This work introduces Hound, a novel deep learning-based pipeline to locate the execution of cryptographic primitives within the side-channel trace even in the presence of trace deformations introduced by the use of dynamic frequency scaling actuators. Hound has been validated through successful attacks on various cryptographic primitives executed on an FPGA-based system-on-chip incorporating a RISC-V CPU, while dynamic frequency scaling is active. Experimental results demonstrate the possibility of identifying the cryptographic primitives in DFS-deformed side-channel traces.
Massively Parallel Minimum Spanning Tree in General Metric Spaces
Venue: arXiv cs.DS 2025
Year: 2025

We study the minimum spanning tree (MST) problem in the massively parallel computation (MPC) model. Our focus is particularly on the *strictly sublinear* regime of MPC where the space per machine is $O(n^δ)$. Here $n$ is the number of vertices and constant $δ\in (0, 1)$ can be made arbitrarily small. The MST problem admits a simple and folklore $O(\log n)$-round algorithm in the MPC model. When the weights can be arbitrary, this matches a conditional lower bound of $Ω(\log n)$ which follows from a well-known 1vs2-Cycle conjecture. As such, much of the literature focuses on breaking the logarithmic barrier in more structured variants of the problem, such as when the vertices correspond to points in low- [ANOY14, STOC'14] or high-dimensional Euclidean spaces [JMNZ, SODA'24]. In this work, we focus more generally on metric spaces. Namely, all pairwise weights are provided and guaranteed to satisfy the triangle inequality, but are otherwise unconstrained. We show that for any $\varepsilon > 0$, a $(1+\varepsilon)$-approximate MST can be found in $O(\log \frac{1}{\varepsilon} + \log \log n)$ rounds, which is the first $o(\log n)$-round algorithm for finding any constant approximation in this setting. Other than being applicable to more general weight functions, our algorithm also slightly improves the $O(\log \log n \cdot \log \log \log n)$ round-complexity of [JMNZ24, SODA'24] and significantly improves its approximation from a large constant to $1+\varepsilon$. On the lower bound side, we prove that under the 1vs2-Cycle conjecture, $Ω(\log \frac{1}{\varepsilon})$ rounds are needed for finding a $(1+\varepsilon)$-approximate MST in general metrics. It is worth noting that while many existing lower bounds in the MPC model under the 1vs2-Cycle conjecture only hold against "component stable" algorithms, our lower bound applies to *all* algorithms.
UniT: Data Efficient Tactile Representation with Generalization to Unseen Objects
Venue: arXiv cs.RO 2025
Year: 2025

UniT is an approach to tactile representation learning, using VQGAN to learn a compact latent space and serve as the tactile representation. It uses tactile images obtained from a single simple object to train the representation with generalizability. This tactile representation can be zero-shot transferred to various downstream tasks, including perception tasks and manipulation policy learning. Our benchmarkings on in-hand 3D pose and 6D pose estimation tasks and a tactile classification task show that UniT outperforms existing visual and tactile representation learning methods. Additionally, UniT's effectiveness in policy learning is demonstrated across three real-world tasks involving diverse manipulated objects and complex robot-object-environment interactions. Through extensive experimentation, UniT is shown to be a simple-to-train, plug-and-play, yet widely effective method for tactile representation learning. For more details, please refer to our open-source repository https://github.com/ZhengtongXu/UniT and the project website https://zhengtongxu.github.io/unit-website/.
CTISum: A New Benchmark Dataset For Cyber Threat Intelligence Summarization
Venue: arXiv cs.CL 2025
Year: 2025

Cyber Threat Intelligence (CTI) summarization involves generating concise and accurate highlights from web intelligence data, which is critical for providing decision-makers with actionable insights to swiftly detect and respond to cyber threats in the cybersecurity domain. Despite that, the development of efficient techniques for summarizing CTI reports, comprising facts, analytical insights, attack processes, and more, has been hindered by the lack of suitable datasets. To address this gap, we introduce CTISum, a new benchmark dataset designed for the CTI summarization task. Recognizing the significance of understanding attack processes, we also propose a novel fine-grained subtask: attack process summarization, which aims to help defenders assess risks, identify security gaps, and uncover vulnerabilities. Specifically, a multi-stage annotation pipeline is designed to collect and annotate CTI data from diverse web sources, alongside a comprehensive benchmarking of CTISum using both extractive, abstractive and LLMs-based summarization methods. Experimental results reveal that current state-of-the-art models face significant challenges when applied to CTISum, highlighting that automatic summarization of CTI reports remains an open research problem. The code and example dataset can be made publicly available at https://github.com/pengwei-iie/CTISum.
Fast-and-Frugal Text-Graph Transformers are Effective Link Predictors
Venue: arXiv cs.CL 2025
Year: 2025

We propose Fast-and-Frugal Text-Graph (FnF-TG) Transformers, a Transformer-based framework that unifies textual and structural information for inductive link prediction in text-attributed knowledge graphs. We demonstrate that, by effectively encoding ego-graphs (1-hop neighbourhoods), we can reduce the reliance on resource-intensive textual encoders. This makes the model both fast at training and inference time, as well as frugal in terms of cost. We perform a comprehensive evaluation on three popular datasets and show that FnF-TG can achieve superior performance compared to previous state-of-the-art methods. We also extend inductive learning to a fully inductive setting, where relations don't rely on transductive (fixed) representations, as in previous work, but are a function of their textual description. Additionally, we introduce new variants of existing datasets, specifically designed to test the performance of models on unseen relations at inference time, thus offering a new test-bench for fully inductive link prediction.
PIR: Photometric Inverse Rendering with Shading Cues Modeling and Surface Reflectance Regularization
Venue: arXiv cs.CV 2025
Year: 2025

This paper addresses the problem of inverse rendering from photometric images. Existing approaches for this problem suffer from the effects of self-shadows, inter-reflections, and lack of constraints on the surface reflectance, leading to inaccurate decomposition of reflectance and illumination due to the ill-posed nature of inverse rendering. In this work, we propose a new method for neural inverse rendering. Our method jointly optimizes the light source position to account for the self-shadows in images, and computes indirect illumination using a differentiable rendering layer and an importance sampling strategy. To enhance surface reflectance decomposition, we introduce a new regularization by distilling DINO features to foster accurate and consistent material decomposition. Extensive experiments on synthetic and real datasets demonstrate that our method outperforms the state-of-the-art methods in reflectance decomposition.
Learn2Decompose: Learning Problem Decomposition for Efficient Sequential Multi-object Manipulation Planning
Venue: arXiv cs.RO 2025
Year: 2025

We present an efficient task and motion replanning approach for sequential multi-object manipulation in dynamic environments. Conventional Task And Motion Planning (TAMP) solvers experience an exponential increase in planning time as the planning horizon and number of objects grow, limiting their applicability in real-world scenarios. To address this, we propose learning problem decompositions from demonstrations to accelerate TAMP solvers. Our approach consists of three key components: goal decomposition learning, computational distance learning, and object reduction. Goal decomposition identifies the necessary sequences of states that the system must pass through before reaching the final goal, treating them as subgoal sequences. Computational distance learning predicts the computational complexity between two states, enabling the system to identify the temporally closest subgoal from a disturbed state. Object reduction minimizes the set of active objects considered during replanning, further improving efficiency. We evaluate our approach on three benchmarks, demonstrating its effectiveness in improving replanning efficiency for sequential multi-object manipulation tasks in dynamic environments.
Re-TASK: Revisiting LLM Tasks from Capability, Skill, and Knowledge Perspectives
Venue: arXiv cs.CL 2025
Year: 2025

The Chain-of-Thought (CoT) paradigm has become a pivotal method for solving complex problems with large language models (LLMs). However, its application to domain-specific tasks remains challenging, as LLMs often fail to decompose tasks accurately or execute subtasks effectively. This paper introduces the Re-TASK framework, a novel theoretical model that revisits LLM tasks from capability, skill, and knowledge perspectives, drawing on the principles of Bloom's Taxonomy and Knowledge Space Theory. While CoT provides a workflow-centric perspective on tasks, Re-TASK introduces a Chain-of-Learning (CoL) paradigm that highlights task dependencies on specific capability items, further broken down into their constituent knowledge and skill components. To address CoT failures, we propose a Re-TASK prompting strategy, which strengthens task-relevant capabilities through targeted knowledge injection and skill adaptation. Experiments across diverse domains demonstrate the effectiveness of Re-TASK. In particular, we achieve improvements of 45.00% on Yi-1.5-9B and 24.50% on Llama3-Chinese-8B for legal tasks. These results highlight the potential of Re-TASK to significantly enhance LLM performance and its applicability in specialized domains. We release our code and data at https://github.com/Uylee/Re-TASK.
AuToMATo: An Out-Of-The-Box Persistence-Based Clustering Algorithm
Venue: arXiv cs.LG 2025
Year: 2025

We present AuToMATo, a novel clustering algorithm based on persistent homology. While AuToMATo is not parameter-free per se, we provide default choices for its parameters that make it into an out-of-the-box clustering algorithm that performs well across the board. AuToMATo combines the existing ToMATo clustering algorithm with a bootstrapping procedure in order to separate significant peaks of an estimated density function from non-significant ones. We perform a thorough comparison of AuToMATo (with its parameters fixed to their defaults) against many other state-of-the-art clustering algorithms. We find not only that AuToMATo compares favorably against parameter-free clustering algorithms, but in many instances also significantly outperforms even the best selection of parameters for other algorithms. AuToMATo is motivated by applications in topological data analysis, in particular the Mapper algorithm, where it is desirable to work with a clustering algorithm that does not need tuning of its parameters. Indeed, we provide evidence that AuToMATo performs well when used with Mapper. Finally, we provide an open-source implementation of AuToMATo in Python that is fully compatible with the standard scikit-learn architecture.
Blessing of Dimensionality for Approximating Sobolev Classes on Manifolds
Venue: arXiv cs.LG 2025
Year: 2025

The manifold hypothesis says that natural high-dimensional data lie on or around a low-dimensional manifold. The recent success of statistical and learning-based methods in very high dimensions empirically supports this hypothesis, suggesting that typical worst-case analysis does not provide practical guarantees. A natural step for analysis is thus to assume the manifold hypothesis and derive bounds that are independent of any ambient dimensions that the data may be embedded in. Theoretical implications in this direction have recently been explored in terms of generalization of ReLU networks and convergence of Langevin methods. In this work, we consider optimal uniform approximations with functions of finite statistical complexity. While upper bounds on uniform approximation exist in the literature using ReLU neural networks, we consider the opposite: lower bounds to quantify the fundamental difficulty of approximation on manifolds. In particular, we demonstrate that the statistical complexity required to approximate a class of bounded Sobolev functions on a compact manifold is bounded from below, and moreover that this bound is dependent only on the intrinsic properties of the manifold, such as curvature, volume, and injectivity radius.
VERCATION: Precise Vulnerable Open-source Software Version Identification based on Static Analysis and LLM
Venue: arXiv cs.SE 2025
Year: 2025

Open-source software (OSS) has experienced a surge in popularity, attributed to its collaborative development model and cost-effective nature. However, the adoption of specific software versions in development projects may introduce security risks when these versions bring along vulnerabilities. Current methods of identifying vulnerable versions typically analyze and extract the code features involved in vulnerability patches using static analysis with pre-defined rules. They then use code clone detection to identify the vulnerable versions. These methods are hindered by imprecision due to (1) the exclusion of vulnerability-irrelevant code in the analysis and (2) the inadequacy of code clone detection. This paper presents VERCATION, an approach designed to identify vulnerable versions of OSS written in C/C++. VERCATION combines program slicing with a Large Language Model (LLM) to identify vulnerability-relevant code from vulnerability patches. It then backtracks historical commits to gather previous modifications of identified vulnerability-relevant code. We propose code clone detection based on expanded and normalized ASTs to compare the differences between pre-modification and post-modification code, thereby locating the vulnerability-introducing commit (vic) and enabling the identification of the vulnerable versions between the vulnerability-fixing commit and the vic. We curate a dataset linking 122 OSS vulnerabilities and 1,211 versions to evaluate VERCATION. On this dataset, our approach achieves an F1 score of 93.1%, outperforming current state-of-the-art methods. More importantly, VERCATION detected 202 incorrect vulnerable OSS versions in NVD reports.
M2L Translation Operators for Kernel Independent Fast Multipole Methods on Modern Architectures
Venue: arXiv cs.CE 2025
Year: 2025

Hardware trends favor algorithm designs that maximize data reuse per FLOP. We develop and benchmark high-performance Multipole-to-Local (M2L) translation operators for the kernel-independent Fast Multipole Method (kiFMM), a widely adopted FMM variant that supports a broad class of kernels and has been favored by recent implementations for its simple specification. Naively implemented, M2L is bandwidth-limited and therefore a key bottleneck in the FMM. State-of-the-art FFT-based M2L implementations, though elegant and with a fast setup time, suffer from low operational intensity and require architecture-specific optimizations. We demonstrate that a BLAS-based M2L, combined with randomized low-rank compression, achieves competitive performance with greater portability and a simpler implementation leveraging existing BLAS infrastructure, at the cost of higher setup times-especially for high-accuracy settings in double precision. Our Rust-based implementation enables seamless switching between strategies for fair benchmarking. Results on CPUs show that FFT-based M2L is favorable in low-accuracy settings or dynamic particle simulations, while BLAS-based M2L is favored for high-accuracy settings for static particle distributions, where its higher setup costs are amortized in many practical applications of the FMM.
Problem Solving Through Human-AI Preference-Based Cooperation
Venue: arXiv cs.AI 2025
Year: 2025

While there is a widespread belief that artificial general intelligence (AGI) -- or even superhuman AI -- is imminent, complex problems in expert domains are far from being solved. We argue that such problems require human-AI cooperation and that the current state of the art in generative AI is unable to play the role of a reliable partner due to a multitude of shortcomings, including difficulty to keep track of a complex solution artifact (e.g., a software program), limited support for versatile human preference expression and lack of adapting to human preference in an interactive setting. To address these challenges, we propose HAICo2, a novel human-AI co-construction framework. We take first steps towards a formalization of HAICo2 and discuss the difficult open research problems that it faces.
Protected Test-Time Adaptation via Online Entropy Matching: A Betting Approach
Venue: arXiv cs.LG 2025
Year: 2025

We present a novel approach for test-time adaptation via online self-training, consisting of two components. First, we introduce a statistical framework that detects distribution shifts in the classifier's entropy values obtained on a stream of unlabeled samples. Second, we devise an online adaptation mechanism that utilizes the evidence of distribution shifts captured by the detection tool to dynamically update the classifier's parameters. The resulting adaptation process drives the distribution of test entropy values obtained from the self-trained classifier to match those of the source domain, building invariance to distribution shifts. This approach departs from the conventional self-training method, which focuses on minimizing the classifier's entropy. Our approach combines concepts in betting martingales and online learning to form a detection tool capable of quickly reacting to distribution shifts. We then reveal a tight relation between our adaptation scheme and optimal transport, which forms the basis of our novel self-supervised loss. Experimental results demonstrate that our approach improves test-time accuracy under distribution shifts while maintaining accuracy and calibration in their absence, outperforming leading entropy minimization methods across various scenarios.
Dinkel: State-Aware and Granular Framework for Validating Graph Databases
Venue: arXiv cs.DB 2025
Year: 2025

Graph database management systems (GDBMSs) have been powering many data-driven applications. To ensure GDBMS reliability, several testing approaches have been proposed. However, they all suffer from two key limitations: (1) insufficient support for generating complex and valid queries to exercise deep GDBMS code, and (2) lack of general oracles to validate the execution correctness of arbitrary queries. In this paper, we propose a novel and practical approach Dinkel, to thoroughly test GDBMSs. Our approach consists of two core techniques. First, to generate complex and valid queries, we model two kinds of graph state, query context and graph schema, to describe the Cypher variables and the manipulated graph labels and properties. We generate queries clause-by-clause, and modify the graph states on the fly to ensure each clause references the correct state information. Second, to generally validate query results, we introduce two fine-grained query transformations: clause-level and expression-level transformations. These transformations can operate on arbitrary queries while preserving their semantics. Dinkel validates GDBMSs by checking whether the transformed query produces the same results as the original. We evaluated Dinkel on three well-known GDBMSs. In total, we found 127 bugs, among which 113 were confirmed, 84 were fixed, and 33 were logic bugs. Compared to existing approaches, Dinkel can cover over 70% more code and find substantially more bugs within a 48-hour testing campaign. We expect Dinkel's powerful bug detection to lay a practical foundation for GDBMS testing.