OpenRaiser/Intern-Atlas huggingface dataset:
OmegAMP: Targeted AMP Discovery through Biologically Informed Generation
Venue: arXiv cs.LG 2025
Year: 2025

Deep learning-based antimicrobial peptide (AMP) discovery faces critical challenges such as limited controllability, lack of representations that efficiently model antimicrobial properties, and low experimental hit rates. To address these challenges, we introduce OmegAMP, a framework designed for reliable AMP generation with increased controllability. Its diffusion-based generative model leverages a novel conditioning mechanism to achieve fine-grained control over desired physicochemical properties and to direct generation towards specific activity profiles, including species-specific effectiveness. This is further enhanced by a biologically informed encoding space that significantly improves overall generative performance. Complementing these generative capabilities, OmegAMP leverages a novel synthetic data augmentation strategy to train classifiers for AMP filtering, drastically reducing false positive rates and thereby increasing the likelihood of experimental success. Our in silico experiments demonstrate that OmegAMP delivers state-of-the-art performance across key stages of the AMP discovery pipeline, enabling us to achieve an unprecedented success rate in wet lab experiments. We tested 25 candidate peptides, 24 of them (96%) demonstrated antimicrobial activity, proving effective even against multi-drug resistant strains. Our findings underscore OmegAMP's potential to significantly advance computational frameworks in the fight against antimicrobial resistance.
Low-Resource Neural Machine Translation Using Recurrent Neural Networks and Transfer Learning: A Case Study on English-to-Igbo
Venue: arXiv cs.CL 2025
Year: 2025

In this study, we develop Neural Machine Translation (NMT) and Transformer-based transfer learning models for English-to-Igbo translation - a low-resource African language spoken by over 40 million people across Nigeria and West Africa. Our models are trained on a curated and benchmarked dataset compiled from Bible corpora, local news, Wikipedia articles, and Common Crawl, all verified by native language experts. We leverage Recurrent Neural Network (RNN) architectures, including Long Short-Term Memory (LSTM) and Gated Recurrent Units (GRU), enhanced with attention mechanisms to improve translation accuracy. To further enhance performance, we apply transfer learning using MarianNMT pre-trained models within the SimpleTransformers framework. Our RNN-based system achieves competitive results, closely matching existing English-Igbo benchmarks. With transfer learning, we observe a performance gain of +4.83 BLEU points, reaching an estimated translation accuracy of 70%. These findings highlight the effectiveness of combining RNNs with transfer learning to address the performance gap in low-resource language translation tasks.
Towards Generalized and Training-Free Text-Guided Semantic Manipulation
Venue: arXiv cs.CV 2025
Year: 2025

Text-guided semantic manipulation refers to semantically editing an image generated from a source prompt to match a target prompt, enabling the desired semantic changes (e.g., addition, removal, and style transfer) while preserving irrelevant contents. With the powerful generative capabilities of the diffusion model, the task has shown the potential to generate high-fidelity visual content. Nevertheless, existing methods either typically require time-consuming fine-tuning (inefficient), fail to accomplish multiple semantic manipulations (poorly extensible), and/or lack support for different modality tasks (limited generalizability). Upon further investigation, we find that the geometric properties of noises in the diffusion model are strongly correlated with the semantic changes. Motivated by this, we propose a novel $\textit{GTF}$ for text-guided semantic manipulation, which has the following attractive capabilities: 1) $\textbf{Generalized}$: our $\textit{GTF}$ supports multiple semantic manipulations (e.g., addition, removal, and style transfer) and can be seamlessly integrated into all diffusion-based methods (i.e., Plug-and-play) across different modalities (i.e., modality-agnostic); and 2) $\textbf{Training-free}$: $\textit{GTF}$ produces high-fidelity results via simply controlling the geometric relationship between noises without tuning or optimization. Our extensive experiments demonstrate the efficacy of our approach, highlighting its potential to advance the state-of-the-art in semantics manipulation.
Signal Recovery from Random Dot-Product Graphs Under Local Differential Privacy
Venue: arXiv cs.LG 2025
Year: 2025

We consider the problem of recovering latent information from graphs under $\varepsilon$-edge local differential privacy where the presence of relationships/edges between two users/vertices remains confidential, even from the data curator. For the class of generalized random dot-product graphs, we show that a standard local differential privacy mechanism induces a specific geometric distortion in the latent positions. Leveraging this insight, we show that consistent recovery of the latent positions is achievable by appropriately adjusting the statistical inference procedure for the privatized graph. Furthermore, we prove that our procedure is nearly minimax-optimal under local edge differential privacy constraints. Lastly, we show that this framework allows for consistent recovery of geometric and topological information underlying the latent positions, as encoded in their persistence diagrams. Our results extend previous work from the private community detection literature to a substantially richer class of models and inferential tasks.
HeRB: Heterophily-Resolved Structure Balancer for Graph Neural Networks
Venue: arXiv cs.LG 2025
Year: 2025

Recent research has witnessed the remarkable progress of Graph Neural Networks (GNNs) in the realm of graph data representation. However, GNNs still encounter the challenge of structural imbalance. Prior solutions to this problem did not take graph heterophily into account, namely that connected nodes process distinct labels or features, thus resulting in a deficiency in effectiveness. Upon verifying the impact of heterophily on solving the structural imbalance problem, we propose to rectify the heterophily first and then transfer homophilic knowledge. To the end, we devise a method named HeRB (Heterophily-Resolved Structure Balancer) for GNNs. HeRB consists of two innovative components: 1) A heterophily-lessening augmentation module which serves to reduce inter-class edges and increase intra-class edges; 2) A homophilic knowledge transfer mechanism to convey homophilic information from head nodes to tail nodes. Experimental results demonstrate that HeRB achieves superior performance on two homophilic and six heterophilic benchmark datasets, and the ablation studies further validate the efficacy of two proposed components.
Building Sustainable and Trustworthy Indigenous Knowledge Preservation Ecosystem
Venue: arXiv cs.CY 2025
Year: 2025

This paper focuses on the essential global issue of protecting and transmitting indigenous knowledge. It reveals the challenges in this area and proposes a sustainable supply chain framework for indigenous knowledge. The paper reviews existing technological solutions and identifies technical challenges and gaps. It then introduces cutting-edge technologies to protect and disseminate indigenous knowledge more effectively. The paper also discusses how the proposed framework can address real-world challenges in protecting and transmitting indigenous knowledge, and explores future research applications of the proposed solutions. Finally, it addresses open issues and provides a detailed analysis, offering promising research directions for the protection and transmission of indigenous knowledge worldwide.
Advanced Segmentation of Diabetic Retinopathy Lesions Using DeepLabv3+
Venue: arXiv cs.CV 2025
Year: 2025

To improve the segmentation of diabetic retinopathy lesions (microaneurysms, hemorrhages, exudates, and soft exudates), we implemented a binary segmentation method specific to each type of lesion. As post-segmentation, we combined the individual model outputs into a single image to better analyze the lesion types. This approach facilitated parameter optimization and improved accuracy, effectively overcoming challenges related to dataset limitations and annotation complexity. Specific preprocessing steps included cropping and applying contrast-limited adaptive histogram equalization to the L channel of the LAB image. Additionally, we employed targeted data augmentation techniques to further refine the model's efficacy. Our methodology utilized the DeepLabv3+ model, achieving a segmentation accuracy of 99%. These findings highlight the efficacy of innovative strategies in advancing medical image analysis, particularly in the precise segmentation of diabetic retinopathy lesions. The IDRID dataset was utilized to validate and demonstrate the robustness of our approach.
Collaborative Multi-Agent Reinforcement Learning for Automated Feature Transformation with Graph-Driven Path Optimization
Venue: arXiv cs.LG 2025
Year: 2025

Feature transformation methods aim to find an optimal mathematical feature-feature crossing process that generates high-value features and improves the performance of downstream machine learning tasks. Existing frameworks, though designed to mitigate manual costs, often treat feature transformations as isolated operations, ignoring dynamic dependencies between transformation steps. To address the limitations, we propose TCTO, a collaborative multi-agent reinforcement learning framework that automates feature engineering through graph-driven path optimization. The framework's core innovation lies in an evolving interaction graph that models features as nodes and transformations as edges. Through graph pruning and backtracking, it dynamically eliminates low-impact edges, reduces redundant operations, and enhances exploration stability. This graph also provides full traceability to empower TCTO to reuse high-utility subgraphs from historical transformations. To demonstrate the efficacy and adaptability of our approach, we conduct comprehensive experiments and case studies, which show superior performance across a range of datasets.
Highly Accurate and Diverse Traffic Data: The DeepScenario Open 3D Dataset
Venue: arXiv cs.CV 2025
Year: 2025

Accurate 3D trajectory data is crucial for advancing autonomous driving. Yet, traditional datasets are usually captured by fixed sensors mounted on a car and are susceptible to occlusion. Additionally, such an approach can precisely reconstruct the dynamic environment in the close vicinity of the measurement vehicle only, while neglecting objects that are further away. In this paper, we introduce the DeepScenario Open 3D Dataset (DSC3D), a high-quality, occlusion-free dataset of 6 degrees of freedom bounding box trajectories acquired through a novel monocular camera drone tracking pipeline. Our dataset includes more than 175,000 trajectories of 14 types of traffic participants and significantly exceeds existing datasets in terms of diversity and scale, containing many unprecedented scenarios such as complex vehicle-pedestrian interaction on highly populated urban streets and comprehensive parking maneuvers from entry to exit. DSC3D dataset was captured in five various locations in Europe and the United States and include: a parking lot, a crowded inner-city, a steep urban intersection, a federal highway, and a suburban intersection. Our 3D trajectory dataset aims to enhance autonomous driving systems by providing detailed environmental 3D representations, which could lead to improved obstacle interactions and safety. We demonstrate its utility across multiple applications including motion prediction, motion planning, scenario mining, and generative reactive traffic agents. Our interactive online visualization platform and the complete dataset are publicly available at https://app.deepscenario.com, facilitating research in motion prediction, behavior modeling, and safety validation.
Edge-weighted Online Stochastic Matching Under Jaillet-Lu LP
Venue: arXiv cs.DS 2025
Year: 2025

The online stochastic matching problem was introduced by [FMMM09], together with the $(1-\frac1e)$-competitive Suggested Matching algorithm. In the most general edge-weighted setting, this ratio has not been improved for more than one decade, until recently [Yan24] beat the $1-\frac1e$ bound and [QFZW23] further improved it to $0.650$. Both works measure the online competitiveness against the offline LP relaxation introduced by Jaillet and Lu [JL14]. The same LP has also played an important role in other settings as it is a natural choice for two-choice online algorithms. In this paper, we prove an upper bound of $0.663$ and a lower bound of $0.662$ for edge-weighted online stochastic matching under Jaillet-Lu LP. We propose a simple hard instance and identify the optimal online algorithm for this specific instance which has a competitive ratio of $<0.663$. Despite the simplicity of the instance, we then show that a near-optimal algorithm for it, which has a competitive ratio of $>0.662$, can be generalized to work on all instances without any loss. As our algorithm is generalized from a real near-optimal algorithm instead of manually combining trivial strategies, it has two natural advantages compared with previous works: (1) its matching strategy varies from time to time; (2) it utilizes global information about offline vertices. On the other hand, the upper bound suggests that more powerful LPs and multiple-choice strategies are needed if we want to further improve the ratio by $>0.001$.
Assessing the Capability of Large Language Models for Domain-Specific Ontology Generation
Venue: arXiv cs.AI 2025
Year: 2025

Large Language Models (LLMs) have shown significant potential for ontology engineering. However, it is still unclear to what extent they are applicable to the task of domain-specific ontology generation. In this study, we explore the application of LLMs for automated ontology generation and evaluate their performance across different domains. Specifically, we investigate the generalizability of two state-of-the-art LLMs, DeepSeek and o1-preview, both equipped with reasoning capabilities, by generating ontologies from a set of competency questions (CQs) and related user stories. Our experimental setup comprises six distinct domains carried out in existing ontology engineering projects and a total of 95 curated CQs designed to test the models' reasoning for ontology engineering. Our findings show that with both LLMs, the performance of the experiments is remarkably consistent across all domains, indicating that these methods are capable of generalizing ontology generation tasks irrespective of the domain. These results highlight the potential of LLM-based approaches in achieving scalable and domain-agnostic ontology construction and lay the groundwork for further research into enhancing automated reasoning and knowledge representation techniques.
Object Pose Estimation by Camera Arm Control Based on the Next Viewpoint Estimation
Venue: arXiv cs.RO 2025
Year: 2025

We have developed a new method to estimate a Next Viewpoint (NV) which is effective for pose estimation of simple-shaped products for product display robots in retail stores. Pose estimation methods using Neural Networks (NN) based on an RGBD camera are highly accurate, but their accuracy significantly decreases when the camera acquires few texture and shape features at a current view point. However, it is difficult for previous mathematical model-based methods to estimate effective NV which is because the simple shaped objects have few shape features. Therefore, we focus on the relationship between the pose estimation and NV estimation. When the pose estimation is more accurate, the NV estimation is more accurate. Therefore, we develop a new pose estimation NN that estimates NV simultaneously. Experimental results showed that our NV estimation realized a pose estimation success rate 77.3\%, which was 7.4pt higher than the mathematical model-based NV calculation did. Moreover, we verified that the robot using our method displayed 84.2\% of products.
Detection, Classification and Prevalence of Self-Admitted Aging Debt
Venue: arXiv cs.SE 2025
Year: 2025

Context: Previous research on software aging is limited with focus on dynamic runtime indicators like memory and performance, often neglecting evolutionary indicators like source code comments and narrowly examining legacy issues within the TD context. Objective: We introduce the concept of Aging Debt (AD), representing the increased maintenance efforts and costs needed to keep software updated. We study AD through Self-Admitted Aging Debt (SAAD) observed in source code comments left by software developers. Method: We employ a mixed-methods approach, combining qualitative and quantitative analyses to detect and measure AD in software. This includes framing SAAD patterns from the source code comments after analysing the source code context, then utilizing the SAAD patterns to detect SAAD comments. In the process, we develop a taxonomy for SAAD that reflects the temporal aging of software and its associated debt. Then we utilize the taxonomy to quantify the different types of AD prevalent in OSS repositories. Results: Our proposed taxonomy categorizes temporal software aging into Active and Dormant types. Our extensive analysis of over 9,000+ Open Source Software (OSS) repositories reveals that more than 21% repositories exhibit signs of SAAD as observed from our gold standard SAAD dataset. Notably, Dormant AD emerges as the predominant category, highlighting a critical but often overlooked aspect of software maintenance. Conclusion: As software volume grows annually, so do evolutionary aging and maintenance challenges; our proposed taxonomy can aid researchers in detailed software aging studies and help practitioners develop improved and proactive maintenance strategies.
Adaptive Orchestration of Modular Generative Information Access Systems
Venue: arXiv cs.IR 2025
Year: 2025

Advancements in large language models (LLMs) have driven the emergence of complex new systems to provide access to information, that we will collectively refer to as modular generative information access (GenIA) systems. They integrate a broad and evolving range of specialized components, including LLMs, retrieval models, and a heterogeneous set of sources and tools. While modularity offers flexibility, it also raises critical challenges: How can we systematically characterize the space of possible modules and their interactions? How can we automate and optimize interactions among these heterogeneous components? And, how do we enable this modular system to dynamically adapt to varying user query requirements and evolving module capabilities? In this perspective paper, we argue that the architecture of future modular generative information access systems will not just assemble powerful components, but enable a self-organizing system through real-time adaptive orchestration -- where components' interactions are dynamically configured for each user input, maximizing information relevance while minimizing computational overhead. We give provisional answers to the questions raised above with a roadmap that depicts the key principles and methods for designing such an adaptive modular system. We identify pressing challenges, and propose avenues for addressing them in the years ahead. This perspective urges the IR community to rethink modular system designs for developing adaptive, self-optimizing, and future-ready architectures that evolve alongside their rapidly advancing underlying technologies.
Wolves in the Repository: A Software Engineering Analysis of the XZ Utils Supply Chain Attack
Venue: arXiv cs.SE 2025
Year: 2025

The digital economy runs on Open Source Software (OSS), with an estimated 90\% of modern applications containing open-source components. While this widespread adoption has revolutionized software development, it has also created critical security vulnerabilities, particularly in essential but under-resourced projects. This paper examines a sophisticated attack on the XZ Utils project (CVE-2024-3094), where attackers exploited not just code, but the entire open-source development process to inject a backdoor into a fundamental Linux compression library. Our analysis reveals a new breed of supply chain attack that manipulates software engineering practices themselves -- from community management to CI/CD configurations -- to establish legitimacy and maintain long-term control. Through a comprehensive examination of GitHub events and development artifacts, we reconstruct the attack timeline, analyze the evolution of attacker tactics. Our findings demonstrate how attackers leveraged seemingly beneficial contributions to project infrastructure and maintenance to bypass traditional security measures. This work extends beyond traditional security analysis by examining how software engineering practices themselves can be weaponized, offering insights for protecting the open-source ecosystem.
Towards Equitable Rail Service Allocation Through Fairness-Oriented Timetabling in Liberalized Markets
Venue: arXiv cs.NE 2025
Year: 2025

Over the last few decades, European rail transport has undergone major changes as part of the process of liberalization set out in European regulations. In this context of liberalization, railway undertakings compete with each other for the limited infrastructure capacity available to offer their rail services. The infrastructure manager is responsible for the equitable allocation of infrastructure between all companies in the market, which is essential to ensure the efficiency and sustainability of this competitive ecosystem. In this paper, a methodology based on Jain, Gini and Atkinson equity metrics is used to solve the rail service allocation problem in a liberalized railway market, analyzing the solutions obtained. The results show that the proposed methodology and the equity metrics used allow for equitable planning in different competitiveness scenarios. These results contrast with solutions where the objective of the infrastructure manager is to maximize its own profit, without regard for the equitable allocation of infrastructure. Therefore, the computational tests support the methodology and metrics used as a planning and decision support tool in a liberalized railway market.
Subcode Ensemble Decoding of Polar Codes
Venue: arXiv cs.IT 2025
Year: 2025

In the short block length regime, pre-transformed polar codes together with successive cancellation list (SCL) decoding possess excellent error correction capabilities. However, in practice, the list size is limited due to the suboptimal scaling of the required area in hardware implementations. Automorphism ensemble decoding (AED) can improve performance for a fixed list size by running multiple parallel SCL decodings on permuted received words, yielding a list of estimates from which the final estimate is selected. Yet, AED is limited to appropriately designed polar codes. Subcode ensemble decoding (ScED) was recently proposed for low-density parity-check codes and does not impose such design constraints. It uses multiple decodings in different subcodes, ensuring that the selected subcodes jointly cover the original code. We extend ScED to polar codes by expressing polar subcodes through suitable pre-transformations (PTs). To this end, we describe a framework classifying pre-transformations for pre-transformed polar codes based on their role in encoding and decoding. Within this framework, we propose a new type of PT enabling ScED for polar codes, analyze its properties, and discuss how to construct an efficient ensemble.