OpenRaiser/Intern-Atlas huggingface dataset:
Helveg: Diagrams for Software Documentation
Venue: arXiv cs.SE 2025
Year: 2025

Software developers often have to gain an understanding of a codebase. Be it programmers getting onboarded onto a team project or, for example, developers striving to grasp an external open-source library. In either case, they frequently turn to the project's documentation. However, documentation in its traditional textual form is ill-suited for this kind of high-level exploratory analysis, since it is immutable from the readers' perspective and thus forces them to follow a predefined path. We have designed an approach bringing aspects of software architecture visualization to API reference documentation. It utilizes a highly interactive node-link diagram with expressive node glyphs and flexible filtering capabilities, providing a high-level overview of the codebase as well as details on demand. To test our design, we have implemented a prototype named Helveg, capable of automatically generating diagrams of C\# codebases. User testing of Helveg confirmed its potential, but it also revealed problems with the readability, intuitiveness, and user experience of our tool. Therefore, in this paper, which is an extended version of our VISSOFT paper with DOI 10.1109/VISSOFT64034.2024.00012, we address many of these problems through major changes to the glyph design, means of interaction, and user interface of the tool. To assess the improvements, this new version of Helveg was evaluated again with the same group of participants as the previous version.
Experimental Analysis and Evaluation of Cohesive Subgraph Discovery
Venue: arXiv cs.SI 2025
Year: 2025

Retrieving cohesive subgraphs in networks is a fundamental problem in social network analysis and graph data management. These subgraphs can be used for marketing strategies or recommendation systems. Despite the introduction of numerous models over the years, a systematic comparison of their performance, especially across varied network configurations, remains unexplored. In this study, we evaluated various cohesive subgraph models using task-based evaluations and conducted extensive experimental studies on both synthetic and real-world networks. Thus, we unveil the characteristics of cohesive subgraph models, highlighting their efficiency and applicability. Our findings not only provide a detailed evaluation of current models but also lay the groundwork for future research by shedding light on the balance between the interpretability and cohesion of the subgraphs. This research guides the selection of suitable models for specific analytical needs and applications, providing valuable insights.
Conditional Chemical Language Models are Versatile Tools in Drug Discovery
Venue: arXiv cs.LG 2025
Year: 2025

Generative chemical language models (CLMs) have demonstrated strong capabilities in molecular design, yet their impact in drug discovery remains limited by the absence of reliable reward signals and the lack of interpretability in their outputs. We present SAFE-T, a generalist chemical modeling framework that conditions on biological context -- such as protein targets or mechanisms of action -- to prioritize and design molecules without relying on structural information or engineered scoring functions. SAFE-T models the conditional likelihood of fragment-based molecular sequences given a biological prompt, enabling principled scoring of molecules across tasks such as virtual screening, drug-target interaction prediction, and activity cliff detection. Moreover, it supports goal-directed generation by sampling from this learned distribution, aligning molecular design with biological objectives. In comprehensive zero-shot evaluations across predictive (LIT-PCBA, DAVIS, KIBA, ACNet) and generative (DRUG, PMO) benchmarks, SAFE-T consistently achieves performance comparable to or better than existing approaches while being significantly faster. Fragment-level attribution further reveals that SAFE-T captures known structure-activity relationships, supporting interpretable and biologically grounded design. Together with its computational efficiency, these results demonstrate that conditional generative CLMs can unify scoring and generation to accelerate early-stage drug discovery.
TOP: Trajectory Optimization via Parallel Optimization towards Constant Time Complexity
Venue: arXiv cs.RO 2025
Year: 2025

Optimization has been widely used to generate smooth trajectories for motion planning. However, existing trajectory optimization methods show weakness when dealing with large-scale long trajectories. Recent advances in parallel computing have accelerated optimization in some fields, but how to efficiently solve trajectory optimization via parallelism remains an open question. In this paper, we propose a novel trajectory optimization framework based on the Consensus Alternating Direction Method of Multipliers (CADMM) algorithm, which decomposes the trajectory into multiple segments and solves the subproblems in parallel. The proposed framework reduces the time complexity to O(1) per iteration to the number of segments, compared to O(N) of the state-of-the-art (SOTA) approaches. Furthermore, we introduce a closed-form solution that integrates convex linear and quadratic constraints to speed up the optimization, and we also present numerical solutions for general inequality constraints. A series of simulations and experiments demonstrate that our approach outperforms the SOTA approach in terms of efficiency and smoothness. Especially for a large-scale trajectory, with one hundred segments, achieving over a tenfold speedup. To fully explore the potential of our algorithm on modern parallel computing architectures, we deploy our framework on a GPU and show high performance with thousands of segments.
Streamlined Airborne Software Development for Large UAVs: From Unified Data Collection to Automated Code Generation
Venue: arXiv cs.SE 2025
Year: 2025

The aerospace industry has experienced significant transformations over the last decade, driven by technological advancements and innovative solutions in goods and personal transportation. This evolution has spurred the emergence of numerous start-ups that now face challenges traditionally encountered by established aerospace companies. Among these challenges is the efficient processing of digital intra-device communication interfaces for onboard equipment - a critical component for ensuring seamless system integration and functionality. Addressing this challenge requires solutions that emphasize clear and consistent interface descriptions, automation of processes, and reduced labor-intensive efforts. This paper presents a novel process and toolchain designed to streamline the development of digital interfaces and onboard software, which our team has successfully applied in several completed projects. The proposed approach focuses on automation and flexibility while maintaining compliance with design assurance requirements.
Toolsuite for Implementing Multiagent Systems Based on Communication Protocols
Venue: arXiv cs.MA 2025
Year: 2025

Interaction-Oriented Programming (IOP) is an approach to building a multiagent system by modeling the interactions between its roles via a flexible interaction protocol and implementing agents to realize the interactions of the roles they play in the protocol. In recent years, we have developed an extensive suite of software that enables multiagent system developers to apply IOP. These include tools for efficiently verifying protocols for properties such as liveness and safety and middleware that simplifies the implementation of agents. This paper presents some of that software suite.
Convergence of Agnostic Federated Averaging
Venue: arXiv cs.LG 2025
Year: 2025

Federated learning (FL) enables decentralized model training without centralizing raw data. However, practical FL deployments often face a key realistic challenge: Clients participate intermittently in server aggregation and with unknown, possibly biased participation probabilities. Most existing convergence results either assume full-device participation, or rely on knowledge of (in fact uniform) client availability distributions -- assumptions that rarely hold in practice. In this work, we characterize the optimization problem that consistently adheres to the stochastic dynamics of the well-known \emph{agnostic Federated Averaging (FedAvg)} algorithm under random (and variably-sized) client availability, and rigorously establish its convergence for convex, possibly nonsmooth losses, achieving a standard rate of order $\mathcal{O}(1/\sqrt{T})$, where $T$ denotes the aggregation horizon. Our analysis provides the first convergence guarantees for agnostic FedAvg under general, non-uniform, stochastic client participation, without knowledge of the participation distribution. We also empirically demonstrate that agnostic FedAvg in fact outperforms common (and suboptimal) weighted aggregation FedAvg variants, even with server-side knowledge of participation weights.
Using AI to replicate human experimental results: a motion study
Venue: arXiv cs.CL 2025
Year: 2025

This paper explores the potential of large language models (LLMs) as reliable analytical tools in linguistic research, focusing on the emergence of affective meanings in temporal expressions involving manner-of-motion verbs. While LLMs like GPT-4 have shown promise across a range of tasks, their ability to replicate nuanced human judgements remains under scrutiny. We conducted four psycholinguistic studies (on emergent meanings, valence shifts, verb choice in emotional contexts, and sentence-emoji associations) first with human participants and then replicated the same tasks using an LLM. Results across all studies show a striking convergence between human and AI responses, with statistical analyses (e.g., Spearman's rho = .73-.96) indicating strong correlations in both rating patterns and categorical choices. While minor divergences were observed in some cases, these did not alter the overall interpretative outcomes. These findings offer compelling evidence that LLMs can augment traditional human-based experimentation, enabling broader-scale studies without compromising interpretative validity. This convergence not only strengthens the empirical foundation of prior human-based findings but also opens possibilities for hypothesis generation and data expansion through AI. Ultimately, our study supports the use of LLMs as credible and informative collaborators in linguistic inquiry.
FGSSNet: Feature-Guided Semantic Segmentation of Real World Floorplans
Venue: arXiv cs.CV 2025
Year: 2025

We introduce FGSSNet, a novel multi-headed feature-guided semantic segmentation (FGSS) architecture designed to improve the generalization ability of wall segmentation on floorplans. FGSSNet features a U-Net segmentation backbone with a multi-headed dedicated feature extractor used to extract domain-specific feature maps which are injected into the latent space of U-Net to guide the segmentation process. This dedicated feature extractor is trained as an encoder-decoder with selected wall patches, representative of the walls present in the input floorplan, to produce a compressed latent representation of wall patches while jointly trained to predict the wall width. In doing so, we expect that the feature extractor encodes texture and width features of wall patches that are useful to guide the wall segmentation process. Our experiments show increased performance by the use of such injected features in comparison to the vanilla U-Net, highlighting the validity of the proposed approach.
Instance-Optimized String Fingerprints
Venue: arXiv cs.DB 2025
Year: 2025

Recent research found that cloud data warehouses are text-heavy. However, their capabilities for efficiently processing string columns remain limited, relying primarily on techniques like dictionary encoding and prefix-based partition pruning. In recent work, we introduced string fingerprints - a lightweight secondary index structure designed to approximate LIKE predicates, albeit with false positives. This approach is particularly compelling for columnar query engines, where fingerprints can help reduce both compute and I/O overhead. We show that string fingerprints can be optimized for specific workloads using mixed-integer optimization, and that they can generalize to unseen table predicates. On an IMDb column evaluated in DuckDB v1.3, this yields table-scan speedups of up to 1.36$\times$.
Non-exchangeable Conformal Prediction with Optimal Transport: Tackling Distribution Shifts with Unlabeled Data
Venue: arXiv cs.LG 2025
Year: 2025

Conformal prediction is a distribution-free uncertainty quantification method that has gained popularity in the machine learning community due to its finite-sample guarantees and ease of use. Its most common variant, dubbed split conformal prediction, is also computationally efficient as it boils down to collecting statistics of the model predictions on some calibration data not yet seen by the model. Nonetheless, these guarantees only hold if the calibration and test data are exchangeable, a condition that is difficult to verify and often violated in practice due to so-called distribution shifts. The literature is rife with methods to mitigate the loss in coverage in this non-exchangeable setting, but these methods require some prior information on the type of distribution shift to be expected at test time. In this work, we study this problem via a new perspective, through the lens of optimal transport, and show that it is possible to estimate the loss in coverage and mitigate arbitrary distribution shifts, offering a principled and broadly applicable solution.
CLA: Latent Alignment for Online Continual Self-Supervised Learning
Venue: arXiv cs.LG 2025
Year: 2025

Self-supervised learning (SSL) is able to build latent representations that generalize well to unseen data. However, only a few SSL techniques exist for the online CL setting, where data arrives in small minibatches, the model must comply with a fixed computational budget, and task boundaries are absent. We introduce Continual Latent Alignment (CLA), a novel SSL strategy for Online CL that aligns the representations learned by the current model with past representations to mitigate forgetting. We found that our CLA is able to speed up the convergence of the training process in the online scenario, outperforming state-of-the-art approaches under the same computational budget. Surprisingly, we also discovered that using CLA as a pretraining protocol in the early stages of pretraining leads to a better final performance when compared to a full i.i.d. pretraining.
CoralVQA: A Large-Scale Visual Question Answering Dataset for Coral Reef Image Understanding
Venue: arXiv cs.CV 2025
Year: 2025

Coral reefs are vital yet vulnerable ecosystems that require continuous monitoring to support conservation. While coral reef images provide essential information in coral monitoring, interpreting such images remains challenging due to the need for domain expertise. Visual Question Answering (VQA), powered by Large Vision-Language Models (LVLMs), has great potential in user-friendly interaction with coral reef images. However, applying VQA to coral imagery demands a dedicated dataset that addresses two key challenges: domain-specific annotations and multidimensional questions. In this work, we introduce CoralVQA, the first large-scale VQA dataset for coral reef analysis. It contains 12,805 real-world coral images from 67 coral genera collected from 3 oceans, along with 277,653 question-answer pairs that comprehensively assess ecological and health-related conditions. To construct this dataset, we develop a semi-automatic data construction pipeline in collaboration with marine biologists to ensure both scalability and professional-grade data quality. CoralVQA presents novel challenges and provides a comprehensive benchmark for studying vision-language reasoning in the context of coral reef images. By evaluating several state-of-the-art LVLMs, we reveal key limitations and opportunities. These insights form a foundation for future LVLM development, with a particular emphasis on supporting coral conservation efforts.
Some remarks on gradient dominance and LQR policy optimization
Venue: arXiv cs.LG 2025
Year: 2025

Solutions of optimization problems, including policy optimization in reinforcement learning, typically rely upon some variant of gradient descent. There has been much recent work in the machine learning, control, and optimization communities applying the Polyak-Łojasiewicz Inequality (PLI) to such problems in order to establish an exponential rate of convergence (a.k.a. ``linear convergence'' in the local-iteration language of numerical analysis) of loss functions to their minima under the gradient flow. Often, as is the case of policy iteration for the continuous-time LQR problem, this rate vanishes for large initial conditions, resulting in a mixed globally linear / locally exponential behavior. This is in sharp contrast with the discrete-time LQR problem, where there is global exponential convergence. That gap between CT and DT behaviors motivates the search for various generalized PLI-like conditions, and this talk will address that topic. Moreover, these generalizations are key to understanding the transient and asymptotic effects of errors in the estimation of the gradient, errors which might arise from adversarial attacks, wrong evaluation by an oracle, early stopping of a simulation, inaccurate and very approximate digital twins, stochastic computations (algorithm ``reproducibility''), or learning by sampling from limited data. We describe an ``input to state stability'' (ISS) analysis of this issue. The second part discusses convergence and PLI-like properties of ``linear feedforward neural networks'' in feedback control. Much of the work described here was done in collaboration with Arthur Castello B. de Oliveira, Leilei Cui, Zhong-Ping Jiang, and Milad Siami.
Radif Corpus: A Symbolic Dataset for Non-Metric Iranian Classical Music
Venue: arXiv cs.SD 2025
Year: 2025

Non-metric music forms the core of the repertoire in Iranian classical music. Dastgahi music serves as the underlying theoretical system for both Iranian art music and certain folk traditions. At the heart of Iranian classical music lies the radif, a foundational repertoire that organizes melodic material central to performance and pedagogy. In this study, we introduce a digital corpus representing the complete non-metrical radif repertoire, covering all 13 existing components of this repertoire. We provide MIDI files (about 281 minutes in total) and data spreadsheets describing notes, note durations, intervals, and hierarchical structures for 228 pieces of music. We faithfully represent the tonality including quarter-tones, and the non-metric aspect. Furthermore, we provide supporting basic statistics, and measures of complexity and similarity over the corpus. Our corpus provides a platform for computational studies of Iranian classical music. Researchers might employ it in studying melodic patterns, investigating improvisational styles, or for other tasks in music information retrieval, music theory, and computational (ethno)musicology.
Logic layer Prompt Control Injection (LPCI): A Novel Security Vulnerability Class in Agentic Systems
Venue: arXiv cs.CR 2025
Year: 2025

The integration of large language models (LLMs) into enterprise systems has introduced a new class of covert security vulnerabilities, particularly within logic execution layers and persistent memory contexts. This paper introduces Logic-layer Prompt Control Injection (LPCI), a novel category of attacks that embeds encoded, delayed, and conditionally triggered payloads within memory, vector stores, or tool outputs. These payloads can bypass conventional input filters and trigger unauthorised behaviour across sessions.
RefSTAR: Blind Facial Image Restoration with Reference Selection, Transfer, and Reconstruction
Venue: arXiv cs.CV 2025
Year: 2025

Blind facial image restoration is highly challenging due to unknown complex degradations and the sensitivity of humans to faces. Although existing methods introduce auxiliary information from generative priors or high-quality reference images, they still struggle with identity preservation problems, mainly due to improper feature introduction on detailed textures. In this paper, we focus on effectively incorporating appropriate features from high-quality reference images, presenting a novel blind facial image restoration method that considers reference selection, transfer, and reconstruction (RefSTAR). In terms of selection, we construct a reference selection (RefSel) module. For training the RefSel module, we construct a RefSel-HQ dataset through a mask generation pipeline, which contains annotating masks for 10,000 ground truth-reference pairs. As for the transfer, due to the trivial solution in vanilla cross-attention operations, a feature fusion paradigm is designed to force the features from the reference to be integrated. Finally, we propose a reference image reconstruction mechanism that further ensures the presence of reference image features in the output image. The cycle consistency loss is also redesigned in conjunction with the mask. Extensive experiments on various backbone models demonstrate superior performance, showing better identity preservation ability and reference feature transfer quality. Source code, dataset, and pre-trained models are available at https://github.com/yinzhicun/RefSTAR.
SynthGuard: Redefining Synthetic Data Generation with a Scalable and Privacy-Preserving Workflow Framework
Venue: arXiv cs.CR 2025
Year: 2025

The growing reliance on data-driven applications in sectors such as healthcare, finance, and law enforcement underscores the need for secure, privacy-preserving, and scalable mechanisms for data generation and sharing. Synthetic data generation (SDG) has emerged as a promising approach but often relies on centralized or external processing, raising concerns about data sovereignty, domain ownership, and compliance with evolving regulatory standards. To overcome these issues, we introduce SynthGuard, a framework designed to ensure computational governance by enabling data owners to maintain control over SDG workflows. SynthGuard supports modular and privacy-preserving workflows, ensuring secure, auditable, and reproducible execution across diverse environments. In this paper, we demonstrate how SynthGuard addresses the complexities at the intersection of domain-specific needs and scalable SDG by aligning with requirements for data sovereignty and regulatory compliance. Developed iteratively with domain expert input, SynthGuard has been validated through real-world use cases, demonstrating its ability to balance security, privacy, and scalability while ensuring compliance. The evaluation confirms its effectiveness in implementing and executing SDG workflows and integrating privacy and utility assessments across various computational environments.