OpenRaiser/Intern-Atlas huggingface dataset:
Graph Transformer with Disease Subgraph Positional Encoding for Improved Comorbidity Prediction
Venue: arXiv cs.LG 2025
Year: 2025

Comorbidity, the co-occurrence of multiple medical conditions in a single patient, profoundly impacts disease management and outcomes. Understanding these complex interconnections is crucial, especially in contexts where comorbidities exacerbate outcomes. Leveraging insights from the human interactome (HI) and advancements in graph-based methodologies, this study introduces Transformer with Subgraph Positional Encoding (TSPE) for disease comorbidity prediction. Inspired by Biologically Supervised Embedding (BSE), TSPE employs Transformer's attention mechanisms and Subgraph Positional Encoding (SPE) to capture interactions between nodes and disease associations. Our proposed SPE proves more effective than LPE, as used in Dwivedi et al.'s Graph Transformer, underscoring the importance of integrating clustering and disease-specific information for improved predictive accuracy. Evaluated on real clinical benchmark datasets (RR0 and RR1), TSPE demonstrates substantial performance enhancements over the state-of-the-art method, achieving up to 28.24% higher ROC AUC and 4.93% higher accuracy. This method shows promise for adaptation to other complex graph-based tasks and applications. The source code is available in the GitHub repository at: https://github.com/xihan-qin/TSPE-GraphTransformer.
A2Perf: Real-World Autonomous Agents Benchmark
Venue: arXiv cs.LG 2025
Year: 2025

Autonomous agents and systems cover a number of application areas, from robotics and digital assistants to combinatorial optimization, all sharing common, unresolved research challenges. It is not sufficient for agents to merely solve a given task; they must generalize to out-of-distribution tasks, perform reliably, and use hardware resources efficiently during training and inference, among other requirements. Several methods, such as reinforcement learning and imitation learning, are commonly used to tackle these problems, each with different trade-offs. However, there is a lack of benchmarking suites that define the environments, datasets, and metrics which can be used to provide a meaningful way for the community to compare progress on applying these methods to real-world problems. We introduce A2Perf--a benchmark with three environments that closely resemble real-world domains: computer chip floorplanning, web navigation, and quadruped locomotion. A2Perf provides metrics that track task performance, generalization, system resource efficiency, and reliability, which are all critical to real-world applications. Using A2Perf, we demonstrate that web navigation agents can achieve latencies comparable to human reaction times on consumer hardware, reveal reliability trade-offs between algorithms for quadruped locomotion, and quantify the energy costs of different learning approaches for computer chip-design. In addition, we propose a data cost metric to account for the cost incurred acquiring offline data for imitation learning and hybrid algorithms, which allows us to better compare these approaches. A2Perf also contains several standard baselines, enabling apples-to-apples comparisons across methods and facilitating progress in real-world autonomy. As an open-source benchmark, A2Perf is designed to remain accessible, up-to-date, and useful to the research community over the long term.
A Linear Theory of Multi-Winner Voting
Venue: arXiv cs.GT 2025
Year: 2025

We introduces a general linear framework that unifies the study of multi-winner voting rules and proportionality axioms, demonstrating that many prominent multi-winner voting rules-including Thiele methods, their sequential variants, and approval-based committee scoring rules-are linear. Similarly, key proportionality axioms such as Justified Representation (JR), Extended JR (EJR), and their strengthened variants (PJR+, EJR+), along with core stability, can fit within this linear structure as well. Leveraging PAC learning theory, we establish general and novel upper bounds on the sample complexity of learning linear mappings. Our approach yields near-optimal guarantees for diverse classes of rules, including Thiele methods and ordered weighted average rules, and can be applied to analyze the sample complexity of learning proportionality axioms such as approximate core stability. Furthermore, the linear structure allows us to leverage prior work to extend our analysis beyond worst-case scenarios to study the likelihood of various properties of linear rules and axioms. We introduce a broad class of distributions that extend Impartial Culture for approval preferences, and show that under these distributions, with high probability, any Thiele method is resolute, CORE is non-empty, and any Thiele method satisfies CORE, among other observations on the likelihood of commonly-studied properties in social choice. We believe that this linear theory offers a new perspective and powerful new tools for designing and analyzing multi-winner rules in modern social choice applications.
Making AI-Enhanced Videos: Analyzing Generative AI Use Cases in YouTube Content Creation
Venue: arXiv cs.HC 2025
Year: 2025

Generative AI (GenAI) tools enhance social media video creation by streamlining tasks such as scriptwriting, visual and audio generation, and editing. These tools enable the creation of new content, including text, images, audio, and video, with platforms like ChatGPT and MidJourney becoming increasingly popular among YouTube creators. Despite their growing adoption, knowledge of their specific use cases across the video production process remains limited. This study analyzes 274 YouTube how-to videos to explore GenAI's role in planning, production, editing, and uploading. The findings reveal that YouTubers use GenAI to identify topics, generate scripts, create prompts, and produce visual and audio materials. Additionally, GenAI supports editing tasks like upscaling visuals and reformatting content while also suggesting titles and subtitles. Based on these findings, we discuss future directions for incorporating GenAI to support various video creation tasks.
Causality-Based Reinforcement Learning Method for Multi-Stage Robotic Tasks
Venue: arXiv cs.RO 2025
Year: 2025

Deep reinforcement learning has made significant strides in various robotic tasks. However, employing deep reinforcement learning methods to tackle multi-stage tasks still a challenge. Reinforcement learning algorithms often encounter issues such as redundant exploration, getting stuck in dead ends, and progress reversal in multi-stage tasks. To address this, we propose a method that integrates causal relationships with reinforcement learning for multi-stage tasks. Our approach enables robots to automatically discover the causal relationships between their actions and the rewards of the tasks and constructs the action space using only causal actions, thereby reducing redundant exploration and progress reversal. By integrating correct causal relationships using the causal policy gradient method into the learning process, our approach can enhance the performance of reinforcement learning algorithms in multi-stage robotic tasks.
Dango: A Mixed-Initiative Data Wrangling System using Large Language Model
Venue: arXiv cs.HC 2025
Year: 2025

Data wrangling is a time-consuming and challenging task in a data science pipeline. While many tools have been proposed to automate or facilitate data wrangling, they often misinterpret user intent, especially in complex tasks. We propose Dango, a mixed-initiative multi-agent system for data wrangling. Compared to existing tools, Dango enhances user communication of intent by allowing users to demonstrate on multiple tables and use natural language prompts in a conversation interface, enabling users to clarify their intent by answering LLM-posed multiple-choice clarification questions, and providing multiple forms of feedback such as step-by-step natural language explanations and data provenance to help users evaluate the data wrangling scripts. We conducted a within-subjects user study with 38 participants and demonstrated that Dango's features can significantly improve intent clarification, accuracy, and efficiency in data wrangling. Furthermore, we demonstrated the generalizability of Dango by applying it to a broader set of data wrangling tasks.
Dimensionality reduction for homological stability and global structure preservation
Venue: arXiv cs.LG 2025
Year: 2025

We propose a new dimensionality reduction toolkit designed to address some of the challenges faced by traditional methods like UMAP and tSNE such as loss of global structure and computational efficiency. Built on the JAX framework, DiRe leverages modern hardware acceleration to provide an efficient, scalable, and interpretable solution for visualizing complex data structures, and for quantitative analysis of lower-dimensional embeddings. The toolkit shows considerable promise in preserving both local and global structures within the data as compared to state-of-the-art UMAP and tSNE implementations. This makes it suitable for a wide range of applications in machine learning, bio-informatics, and data science.
Towards Robust Universal Information Extraction: Benchmark, Evaluation, and Solution
Venue: arXiv cs.CL 2025
Year: 2025

In this paper, we aim to enhance the robustness of Universal Information Extraction (UIE) by introducing a new benchmark dataset, a comprehensive evaluation, and a feasible solution. Existing robust benchmark datasets have two key limitations: 1) They generate only a limited range of perturbations for a single Information Extraction (IE) task, which fails to evaluate the robustness of UIE models effectively; 2) They rely on small models or handcrafted rules to generate perturbations, often resulting in unnatural adversarial examples. Considering the powerful generation capabilities of Large Language Models (LLMs), we introduce a new benchmark dataset for Robust UIE, called RUIE-Bench, which utilizes LLMs to generate more diverse and realistic perturbations across different IE tasks. Based on this dataset, we comprehensively evaluate existing UIE models and reveal that both LLM-based models and other models suffer from significant performance drops. To improve robustness and reduce training costs, we propose a data-augmentation solution that dynamically selects hard samples for iterative training based on the model's inference loss. Experimental results show that training with only \textbf{15\%} of the data leads to an average \textbf{7.5\%} relative performance improvement across three IE tasks.
GenColor: Generative Color-Concept Association in Visual Design
Venue: arXiv cs.HC 2025
Year: 2025

Existing approaches for color-concept association typically rely on query-based image referencing, and color extraction from image references. However, these approaches are effective only for common concepts, and are vulnerable to unstable image referencing and varying image conditions. Our formative study with designers underscores the need for primary-accent color compositions and context-dependent colors (e.g., 'clear' vs. 'polluted' sky) in design. In response, we introduce a generative approach for mining semantically resonant colors leveraging images generated by text-to-image models. Our insight is that contemporary text-to-image models can resemble visual patterns from large-scale real-world data. The framework comprises three stages: concept instancing produces generative samples using diffusion models, text-guided image segmentation identifies concept-relevant regions within the image, and color association extracts primarily accompanied by accent colors. Quantitative comparisons with expert designs validate our approach's effectiveness, and we demonstrate the applicability through cases in various design scenarios and a gallery.
From Coverage to Prestige: A Comprehensive Assessment of Large-Scale Scientometric Data
Venue: arXiv cs.DL 2025
Year: 2025

As research in the Scientometric deepens, the impact of data quality on research outcomes has garnered increasing attention. This study, based on Web of Science (WoS) and Crossref datasets, systematically evaluates the differences between data sources and the effects of data merging through matching, comparison, and integration. Two core metrics were employed: Reference Coverage Rate (RCR) and Article Scientific Prestige (ASP), which respectively measure citation completeness (quantity) and academic influence (quality). The results indicate that the WoS dataset outperforms Crossref in its coverage of high-impact literature and ASP scores, while the Crossref dataset provides complementary value through its broader coverage of literature. Data merging significantly improves the completeness of the citation network, with particularly pronounced benefits in smaller disciplinary clusters such as Education and Arts. However, data merging also introduces some low-quality citations, resulting in a polarization of overall data quality. Moreover, the impact of data merging varies across disciplines; high-impact clusters such as Science, Biology, and Medicine benefit the most, whereas clusters like Social Sciences and Arts are more vulnerable to negative effects. This study highlights the critical role of data sources in Scientometric research and provides a framework for assessing and improving data quality.
Leap: Inductive Link Prediction via Learnable TopologyAugmentation
Venue: arXiv cs.LG 2025
Year: 2025

Link prediction is a crucial task in many downstream applications of graph machine learning. To this end, Graph Neural Network (GNN) is a widely used technique for link prediction, mainly in transductive settings, where the goal is to predict missing links between existing nodes. However, many real-life applications require an inductive setting that accommodates for new nodes, coming into an existing graph. Thus, recently inductive link prediction has attracted considerable attention, and a multi-layer perceptron (MLP) is the popular choice of most studies to learn node representations. However, these approaches have limited expressivity and do not fully capture the graph's structural signal. Therefore, in this work we propose LEAP, an inductive link prediction method based on LEArnable toPology augmentation. Unlike previous methods, LEAP models the inductive bias from both the structure and node features, and hence is more expressive. To the best of our knowledge, this is the first attempt to provide structural contexts for new nodes via learnable augmentation in inductive settings. Extensive experiments on seven real-world homogeneous and heterogeneous graphs demonstrates that LEAP significantly surpasses SOTA methods. The improvements are up to 22\% and 17\% in terms of AUC and average precision, respectively. The code and datasets are available on GitHub (https://github.com/AhmedESamy/LEAP/)
Navigating Intelligence: A Survey of Google OR-Tools and Machine Learning for Global Path Planning in Autonomous Vehicles
Venue: arXiv cs.RO 2025
Year: 2025

We offer a new in-depth investigation of global path planning (GPP) for unmanned ground vehicles, an autonomous mining sampling robot named ROMIE. GPP is essential for ROMIE's optimal performance, which is translated into solving the traveling salesman problem, a complex graph theory challenge that is crucial for determining the most effective route to cover all sampling locations in a mining field. This problem is central to enhancing ROMIE's operational efficiency and competitiveness against human labor by optimizing cost and time. The primary aim of this research is to advance GPP by developing, evaluating, and improving a cost-efficient software and web application. We delve into an extensive comparison and analysis of Google operations research (OR)-Tools optimization algorithms. Our study is driven by the goal of applying and testing the limits of OR-Tools capabilities by integrating Reinforcement Learning techniques for the first time. This enables us to compare these methods with OR-Tools, assessing their computational effectiveness and real-world application efficiency. Our analysis seeks to provide insights into the effectiveness and practical application of each technique. Our findings indicate that Q-Learning stands out as the optimal strategy, demonstrating superior efficiency by deviating only 1.2% on average from the optimal solutions across our datasets.
Transformers for molecular property prediction: Domain adaptation efficiently improves performance
Venue: arXiv cs.LG 2025
Year: 2025

Over the past six years, molecular transformer models have become key tools in drug discovery. Most existing models are pre-trained on large, unlabeled datasets such as ZINC or ChEMBL. However, the extent to which large-scale pre-training improves molecular property prediction remains unclear. This study evaluates transformer models for this task while addressing their limitations. We explore how pre-training dataset size and chemically informed objectives impact performance. Our results show that increasing the dataset beyond approximately 400K to 800K molecules from large-scale unlabeled databases does not enhance performance across seven datasets covering five ADME endpoints: lipophilicity, permeability, solubility (two datasets), microsomal stability (two datasets), and plasma protein binding. In contrast, domain adaptation on a small, domain-specific dataset (less than or equal 4K molecules) using multi-task regression of physicochemical properties significantly boosts performance (P-value less than 0.001). A model pre-trained on 400K molecules and adapted with domain-specific data outperforms larger models such as MolFormer and performs comparably to MolBERT. Benchmarks against Random Forest (RF) baselines using descriptors and Morgan fingerprints show that chemically and physically informed features consistently yield better performance across model types. While RF remains a strong baseline, we identify concrete practices to enhance transformer performance. Aligning pre-training and adaptation with chemically meaningful tasks and domain-relevant data presents a promising direction for molecular property prediction. Our models are available on HuggingFace for easy use and adaptation.
A Novel Multi-Criteria Local Latin Hypercube Refinement System for Commutation Angle Improvement in IPMSMs
Venue: arXiv cs.CE 2025
Year: 2025

The commutation angle is defined as the angle between the fundamental of the motor phase current and the fundamental of the back-EMF. It can be utilised to provide a compensating effect in IPMSMs. This is due to the reluctance torque component being dependent on the commutation angle of the phase current even before entering the extended speed range. A real-time maximum torque per current and voltage strategy is demonstrated to find the trajectory and optimum commutation angles, gamma, where the level of accuracy depends on the application and available computational speed. A magnet volume reduction using a novel multi-criteria local Latin hypercube refinement (MLHR) sampling system is also presented to improve the optimisation process. The proposed new technique minimises the magnet mass to motor torque density whilst maintaining a similar phase current level. A mapping of gamma allows the determination of the optimum angles, as shown in this paper. The 3rd generation Toyota Prius IPMSM is considered as the reference motor, where the rotor configuration is altered to allow for an individual assessment.
Multi-Agent DRL for Queue-Aware Task Offloading in Hierarchical MEC-Enabled Air-Ground Networks
Venue: arXiv cs.LG 2025
Year: 2025

Mobile edge computing (MEC)-enabled air-ground networks are a key component of 6G, employing aerial base stations (ABSs) such as unmanned aerial vehicles (UAVs) and high-altitude platform stations (HAPS) to provide dynamic services to ground IoT devices (IoTDs). These IoTDs support real-time applications (e.g., multimedia and Metaverse services) that demand high computational resources and strict quality of service (QoS) guarantees in terms of latency and task queue management. Given their limited energy and processing capabilities, IoTDs rely on UAVs and HAPS to offload tasks for distributed processing, forming a multi-tier MEC system. This paper tackles the overall energy minimization problem in MEC-enabled air-ground integrated networks (MAGIN) by jointly optimizing UAV trajectories, computing resource allocation, and queue-aware task offloading decisions. The optimization is challenging due to the nonconvex, nonlinear nature of this hierarchical system, which renders traditional methods ineffective. We reformulate the problem as a multi-agent Markov decision process (MDP) with continuous action spaces and heterogeneous agents, and propose a novel variant of multi-agent proximal policy optimization with a Beta distribution (MAPPO-BD) to solve it. Extensive simulations show that MAPPO-BD outperforms baseline schemes, achieving superior energy savings and efficient resource management in MAGIN while meeting queue delay and edge computing constraints.
Coordinated Trajectories for Non-stop Flying Carriers Holding a Cable-Suspended Load
Venue: arXiv cs.RO 2025
Year: 2025

Multirotor UAVs have been typically considered for aerial manipulation, but their scarce endurance prevents long-lasting manipulation tasks. This work demonstrates that the non-stop flights of three or more carriers are compatible with holding a constant pose of a cable-suspended load, thus potentially enabling aerial manipulation with energy-efficient non-stop carriers. It also presents an algorithm for generating the coordinated non-stop trajectories. The proposed method builds upon two pillars: (1)~the choice of $n$ special linearly independent directions of internal forces within the $3n-6$-dimensional nullspace of the grasp matrix of the load, chosen as the edges of a Hamiltonian cycle on the graph that connects the cable attachment points on the load. Adjacent pairs of directions are used to generate $n$ forces evolving on distinct 2D affine subspaces, despite the attachment points being generically in 3D; (2)~the construction of elliptical trajectories within these subspaces by mapping, through appropriate graph coloring, each edge of the Hamiltonian cycle to a periodic coordinate while ensuring that no adjacent coordinates exhibit simultaneous zero derivatives. Combined with conditions for load statics and attachment point positions, these choices ensure that each of the $n$ force trajectories projects onto the corresponding cable constraint sphere with non-zero tangential velocity, enabling perpetual motion of the carriers while the load is still. The theoretical findings are validated through simulations and laboratory experiments with non-stopping multirotor UAVs.
Logarithmic-Time Internal Pattern Matching Queries in Compressed and Dynamic Texts
Venue: arXiv cs.DS 2025
Year: 2025

Internal Pattern Matching (IPM) queries on a text $T$, given two fragments $X$ and $Y$ of $T$ such that $|Y|<2|X|$, ask to compute all exact occurrences of $X$ within $Y$. IPM queries have been introduced by Kociumaka, Radoszewski, Rytter, and Waleń [SODA'15 & SICOMP'24], who showed that they can be answered in $O(1)$ time using a data structure of size $O(n)$ and used this result to answer various queries about fragments of $T$. In this work, we study IPM queries on compressed and dynamic strings. Our result is an $O(\log n)$-time query algorithm applicable to any balanced recompression-based run-length straight-line program (RLSLP). In particular, one can use it on top of the RLSLP of Kociumaka, Navarro, and Prezza [IEEE TIT'23], whose size $O\big(δ\log \frac{n\log σ}{δ\log n}\big)$ is optimal (among all text representations) as a function of the text length $n$, the alphabet size $σ$, and the substring complexity $δ$. Our procedure does not rely on any preprocessing of the underlying RLSLP, which makes it readily applicable on top of the dynamic strings data structure of Gawrychowski, Karczmarz, Kociumaka, Łącki and Sankowski [SODA'18], which supports fully persistent updates in logarithmic time with high probability.