OpenRaiser/Intern-Atlas huggingface dataset:
ThermoRL:Structure-Aware Reinforcement Learning for Protein Mutation Design to Enhance Thermostability
Venue: arXiv cs.CE 2025
Year: 2025

Designing mutations to optimize protein thermostability remains challenging due to the complex relationship between sequence variations, structural dynamics, and thermostability, often assessed by δδG (the change in free energy of unfolding). Existing methods rely on experimental random mutagenesis or prediction models tested with pre-defined datasets, using sequence-based heuristics and treating enzyme design as a one-step process without iterative refinement, which limits design space exploration and restricts discoveries beyond known variations. We present ThermoRL, a framework based on reinforcement learning (RL) that leverages graph neural networks (GNN) to design mutations with enhanced thermostability. It combines a pre-trained GNN-based encoder with a hierarchical Q-learning network and employs a surrogate model for reward feedback, guiding the RL agent on where (the position) and which (mutant amino acid) to apply for enhanced thermostability. Experimental results show that ThermoRL achieves higher or comparable rewards than baselines while maintaining computational efficiency. It filters out destabilizing mutations and identifies stabilizing mutations aligned with experimental data. Moreover, ThermoRL accurately detects key mutation sites in unseen proteins, highlighting its strong generalizability. This RL-guided approach powered by GNN embeddings offers a robust alternative to traditional protein mutation design.
CueBuddy: helping non-native English speakers navigate English-centric STEM education
Venue: arXiv cs.CL 2025
Year: 2025

Students across the world in STEM classes, especially in the Global South, fall behind their peers who are more fluent in English, despite being at par with them in terms of scientific prerequisites. While many of them are able to follow everyday English at ease, key terms in English stay challenging. In most cases, such students have had most of their course prerequisites in a lower resource language. Live speech translation to lower resource languages is a promising area of research, however, models for speech translation can be too expensive on a large scale and often struggle with technical content. In this paper, we describe CueBuddy, which aims to remediate these issues by providing real-time "lexical cues" through technical keyword spotting along real-time multilingual glossary lookup to help students stay up to speed with complex English jargon without disrupting their concentration on the lecture. We also describe the limitations and future extensions of our approach.
Ethical Considerations for Observational Research in Social VR
Venue: arXiv cs.HC 2025
Year: 2025

Social VR introduces new ethical challenges for observational research. The current paper presents a narrative literature review of ethical considerations in observational methods, with a focus on work in HCI. We examine how unobtrusive or selectively disclosed observation is implemented in public face-to-face and social VR settings. Our review extends ethical discussions from traditional public research into the context of social VR, highlighting tensions between observer visibility, data traceability, and participant autonomy. Drawing on insights distilled from prior literature, we propose five constructive guidelines for ethical observational research in public social VR environments. Our work offers key implications for future research, addressing anticipated improvements in platform design, the management of researcher presence, and the development of community-informed consent mechanisms.
Transferable and Undefendable Point Cloud Attacks via Medial Axis Transform
Venue: arXiv cs.CV 2025
Year: 2025

Studying adversarial attacks on point clouds is essential for evaluating and improving the robustness of 3D deep learning models. However, most existing attack methods are developed under ideal white-box settings and often suffer from limited transferability to unseen models and insufficient robustness against common defense mechanisms. In this paper, we propose MAT-Adv, a novel adversarial attack framework that enhances both transferability and undefendability by explicitly perturbing the medial axis transform (MAT) representations, in order to induce inherent adversarialness in the resulting point clouds. Specifically, we employ an autoencoder to project input point clouds into compact MAT representations that capture the intrinsic geometric structure of point clouds. By perturbing these intrinsic representations, MAT-Adv introduces structural-level adversarial characteristics that remain effective across diverse models and defense strategies. To mitigate overfitting and prevent perturbation collapse, we incorporate a dropout strategy into the optimization of MAT perturbations, further improving transferability and undefendability. Extensive experiments demonstrate that MAT-Adv significantly outperforms existing state-of-the-art methods in both transferability and undefendability. Codes will be made public upon paper acceptance.
Success in Humanoid Reinforcement Learning under Partial Observation
Venue: arXiv cs.AI 2025
Year: 2025

Reinforcement learning has been widely applied to robotic control, but effective policy learning under partial observability remains a major challenge, especially in high-dimensional tasks like humanoid locomotion. To date, no prior work has demonstrated stable training of humanoid policies with incomplete state information in the benchmark Gymnasium Humanoid-v4 environment. The objective in this environment is to walk forward as fast as possible without falling, with rewards provided for staying upright and moving forward, and penalties incurred for excessive actions and external contact forces. This research presents the first successful instance of learning under partial observability in this environment. The learned policy achieves performance comparable to state-of-the-art results with full state access, despite using only one-third to two-thirds of the original states. Moreover, the policy exhibits adaptability to robot properties, such as variations in body part masses. The key to this success is a novel history encoder that processes a fixed-length sequence of past observations in parallel. Integrated into a standard model-free algorithm, the encoder enables performance on par with fully observed baselines. We hypothesize that it reconstructs essential contextual information from recent observations, thereby enabling robust decision-making.
MMESGBench: Pioneering Multimodal Understanding and Complex Reasoning Benchmark for ESG Tasks
Venue: arXiv cs.MM 2025
Year: 2025

Environmental, Social, and Governance (ESG) reports are essential for evaluating sustainability practices, ensuring regulatory compliance, and promoting financial transparency. However, these documents are often lengthy, structurally diverse, and multimodal, comprising dense text, structured tables, complex figures, and layout-dependent semantics. Existing AI systems often struggle to perform reliable document-level reasoning in such settings, and no dedicated benchmark currently exists in ESG domain. To fill the gap, we introduce \textbf{MMESGBench}, a first-of-its-kind benchmark dataset targeted to evaluate multimodal understanding and complex reasoning across structurally diverse and multi-source ESG documents. This dataset is constructed via a human-AI collaborative, multi-stage pipeline. First, a multimodal LLM generates candidate question-answer (QA) pairs by jointly interpreting rich textual, tabular, and visual information from layout-aware document pages. Second, an LLM verifies the semantic accuracy, completeness, and reasoning complexity of each QA pair. This automated process is followed by an expert-in-the-loop validation, where domain specialists validate and calibrate QA pairs to ensure quality, relevance, and diversity. MMESGBench comprises 933 validated QA pairs derived from 45 ESG documents, spanning across seven distinct document types and three major ESG source categories. Questions are categorized as single-page, cross-page, or unanswerable, with each accompanied by fine-grained multimodal evidence. Initial experiments validate that multimodal and retrieval-augmented models substantially outperform text-only baselines, particularly on visually grounded and cross-page tasks. MMESGBench is publicly available as an open-source dataset at https://github.com/Zhanglei1103/MMESGBench.
PDT: Point Distribution Transformation with Diffusion Models
Venue: arXiv cs.CV 2025
Year: 2025

Point-based representations have consistently played a vital role in geometric data structures. Most point cloud learning and processing methods typically leverage the unordered and unconstrained nature to represent the underlying geometry of 3D shapes. However, how to extract meaningful structural information from unstructured point cloud distributions and transform them into semantically meaningful point distributions remains an under-explored problem. We present PDT, a novel framework for point distribution transformation with diffusion models. Given a set of input points, PDT learns to transform the point set from its original geometric distribution into a target distribution that is semantically meaningful. Our method utilizes diffusion models with novel architecture and learning strategy, which effectively correlates the source and the target distribution through a denoising process. Through extensive experiments, we show that our method successfully transforms input point clouds into various forms of structured outputs - ranging from surface-aligned keypoints, and inner sparse joints to continuous feature lines. The results showcase our framework's ability to capture both geometric and semantic features, offering a powerful tool for various 3D geometry processing tasks where structured point distributions are desired. Code will be available at this link: https://github.com/shanemankiw/PDT.
Classifying Issues in Open-source GitHub Repositories
Venue: arXiv cs.SE 2025
Year: 2025

GitHub is the most widely used platform for software maintenance in the open-source community. Developers report issues on GitHub from time to time while facing difficulties. Having labels on those issues can help developers easily address those issues with prior knowledge of labels. However, most of the GitHub repositories do not maintain regular labeling for the issues. The goal of this work is to classify issues in the open-source community using ML \& DNN models. There are thousands of open-source repositories on GitHub. Some of the repositories label their issues properly whereas some of them do not. When issues are pre-labeled, the problem-solving process and the immediate assignment of corresponding personnel are facilitated for the team, thereby expediting the development process. In this work, we conducted an analysis of prominent GitHub open-source repositories. We classified the issues in some common labels which are: API, Documentation, Enhancement, Question, Easy, Help-wanted, Dependency, CI, Waiting for OP's response, Test, Bug, etc. Our study shows that DNN models outperf
A diffusion-based generative model for financial time series via geometric Brownian motion
Venue: arXiv cs.LG 2025
Year: 2025

We propose a novel diffusion-based generative framework for financial time series that incorporates geometric Brownian motion (GBM), the foundation of the Black--Scholes theory, into the forward noising process. Unlike standard score-based models that treat price trajectories as generic numerical sequences, our method injects noise proportionally to asset prices at each time step, reflecting the heteroskedasticity observed in financial time series. By accurately balancing the drift and diffusion terms, we show that the resulting log-price process reduces to a variance-exploding stochastic differential equation, aligning with the formulation in score-based generative models. The reverse-time generative process is trained via denoising score matching using a Transformer-based architecture adapted from the Conditional Score-based Diffusion Imputation (CSDI) framework. Empirical evaluations on historical stock data demonstrate that our model reproduces key stylized facts heavy-tailed return distributions, volatility clustering, and the leverage effect more realistically than conventional diffusion models.
A Formalization of Elementary Linear Algebra: Part I
Venue: arXiv cs.DM 2025
Year: 2025

This is the first installment of an exposition of an ACL2 formalization of elementary linear algebra, focusing on aspects of the subject that apply to matrices over an arbitrary commutative ring with identity, in anticipation of a future treatment of the characteristic polynomial of a matrix, which has entries in a polyniomial ring. The main contribution of this paper is a formal theory of the determinant, including its characterization as the unique alternating n-linear function of the rows of an non matrix, multiplicativity of the determinant, and the correctness of cofactor expansion.
MLLM-based Speech Recognition: When and How is Multimodality Beneficial?
Venue: arXiv cs.SD 2025
Year: 2025

Recent advances in multi-modal large language models (MLLMs) have opened new possibilities for unified modeling of speech, text, images, and other modalities. Building on our prior work, this paper examines the conditions and model architectures under which multiple input modalities can improve automatic speech recognition (ASR) accuracy in noisy environments. Through experiments on synthetic and real-world data, we find that (1) harnessing more modalities usually improves ASR accuracy, as each modality provides complementary information, but the improvement depends on the amount of auditory noise. (2) Synchronized modalities (e.g., lip movements) are more useful at high noise levels whereas unsynchronized modalities (e.g., image context) are most helpful at moderate noise levels. (3) Higher-quality visual representations consistently improve ASR accuracy, highlighting the importance of developing more powerful visual encoders. (4) Mamba exhibits similar trends regarding the benefits of multimodality as do Transformers. (5) The input order of modalities as well as their weights in the loss function can significantly impact accuracy. These findings both offer practical insights and help to deepen our understanding of multi-modal speech recognition under challenging conditions.
A New One-Shot Federated Learning Framework for Medical Imaging Classification with Feature-Guided Rectified Flow and Knowledge Distillation
Venue: arXiv cs.CV 2025
Year: 2025

In multi-center scenarios, One-Shot Federated Learning (OSFL) has attracted increasing attention due to its low communication overhead, requiring only a single round of transmission. However, existing generative model-based OSFL methods suffer from low training efficiency and potential privacy leakage in the healthcare domain. Additionally, achieving convergence within a single round of model aggregation is challenging under non-Independent and Identically Distributed (non-IID) data. To address these challenges, in this paper a modified OSFL framework is proposed, in which a new Feature-Guided Rectified Flow Model (FG-RF) and Dual-Layer Knowledge Distillation (DLKD) aggregation method are developed. FG-RF on the client side accelerates generative modeling in medical imaging scenarios while preserving privacy by synthesizing feature-level images rather than pixel-level images. To handle non-IID distributions, DLKD enables the global student model to simultaneously mimic the output logits and align the intermediate-layer features of client-side teacher models during aggregation. Experimental results on three non-IID medical imaging datasets show that our new framework and method outperform multi-round federated learning approaches, achieving up to 21.73% improvement, and exceeds the baseline FedISCA by an average of 21.75%. Furthermore, our experiments demonstrate that feature-level synthetic images significantly reduce privacy leakage risks compared to pixel-level synthetic images. The code is available at https://github.com/LMIAPC/one-shot-fl-medical.
Heterogeneous Risk Management Using a Multi-Agent Framework for Supply Chain Disruption Response
Venue: arXiv cs.MA 2025
Year: 2025

In the highly complex and stochastic global, supply chain environments, local enterprise agents seek distributed and dynamic strategies for agile responses to disruptions. Existing literature explores both centralized and distributed approaches, while most work neglects temporal dynamics and the heterogeneity of the risk management of individual agents. To address this gap, this letter presents a heterogeneous risk management mechanism to incorporate uncertainties and risk attitudes into agent communication and decision-making strategy. Hence, this approach empowers enterprises to handle disruptions in stochastic environments in a distributed way, and in particular in the context of multi-agent control and management. Through a simulated case study, we showcase the feasibility and effectiveness of the proposed approach under stochastic settings and how the decision of disruption responses changes when agents hold various risk attitudes.
Exploring molecular assembly as a biosignature using mass spectrometry and machine learning
Venue: arXiv cs.LG 2025
Year: 2025

Molecular assembly offers a promising path to detect life beyond Earth, while minimizing assumptions based on terrestrial life. As mass spectrometers will be central to upcoming Solar System missions, predicting molecular assembly from their data without needing to elucidate unknown structures will be essential for unbiased life detection. An ideal agnostic biosignature must be interpretable and experimentally measurable. Here, we show that molecular assembly, a recently developed approach to measure objects that have been produced by evolution, satisfies both criteria. First, it is interpretable for life detection, as it reflects the assembly of molecules with their bonds as building blocks, in contrast to approaches that discount construction history. Second, it can be determined without structural elucidation, as it can be physically measured by mass spectrometry, a property that distinguishes it from other approaches that use structure-based information measures for molecular complexity. Whilst molecular assembly is directly measurable using mass spectrometry data, there are limits imposed by mission constraints. To address this, we developed a machine learning model that predicts molecular assembly with high accuracy, reducing error by three-fold compared to baseline models. Simulated data shows that even small instrumental inconsistencies can double model error, emphasizing the need for standardization. These results suggest that standardized mass spectrometry databases could enable accurate molecular assembly prediction, without structural elucidation, providing a proof-of-concept for future astrobiology missions.
PBiLoss: Popularity-Aware Regularization to Improve Fairness in Graph-Based Recommender Systems
Venue: arXiv cs.IR 2025
Year: 2025

Recommender systems, especially those based on graph neural networks (GNNs), have achieved remarkable success in capturing user-item interaction patterns. However, they remain susceptible to popularity bias--the tendency to over-recommend popular items--resulting in reduced content diversity and compromised fairness. In this paper, we propose PBiLoss, a novel regularization-based loss function designed to counteract popularity bias in graph-based recommender models explicitly. PBiLoss augments traditional training objectives by penalizing the model's inclination toward popular items, thereby encouraging the recommendation of less popular but potentially more personalized content. We introduce two sampling strategies: Popular Positive (PopPos) and Popular Negative (PopNeg), which respectively modulate the contribution of the positive and negative popular items during training. We further explore two methods to distinguish popular items: one based on a fixed popularity threshold and another without any threshold, making the approach flexible and adaptive. Our proposed method is model-agnostic and can be seamlessly integrated into state-of-the-art graph-based frameworks such as LightGCN and its variants. Comprehensive experiments across multiple real-world datasets demonstrate that PBiLoss significantly improves fairness, as demonstrated by reductions in the Popularity-Rank Correlation for Users (PRU) and Popularity-Rank Correlation for Items (PRI), while maintaining or even enhancing standard recommendation accuracy and ranking metrics. These results highlight the effectiveness of directly embedding fairness objectives into the optimization process, providing a practical and scalable solution for balancing accuracy and equitable content exposure in modern recommender systems.
Multi-Task Dense Prediction Fine-Tuning with Mixture of Fine-Grained Experts
Venue: arXiv cs.CV 2025
Year: 2025

Multi-task learning (MTL) for dense prediction has shown promising results but still faces challenges in balancing shared representations with task-specific specialization. In this paper, we introduce a novel Fine-Grained Mixture of Experts (FGMoE) architecture that explores MoE-based MTL models through a combination of three key innovations and fine-tuning. First, we propose intra-task experts that partition along intermediate hidden dimensions of MLPs, enabling finer decomposition of task information while maintaining parameter efficiency. Second, we introduce shared experts that consolidate common information across different contexts of the same task, reducing redundancy, and allowing routing experts to focus on unique aspects. Third, we design a global expert that facilitates adaptive knowledge transfer across tasks based on both input feature and task requirements, promoting beneficial information sharing while preventing harmful interference. In addition, we use the fine-tuning approach to improve parameter efficiency only by training the parameters of the decoder. Extensive experimental results show that the proposed FGMoE uses fewer parameters and significantly outperforms current MoE-based competitive MTL models on two dense prediction datasets (\textit{i.e.,} NYUD-v2, PASCAL-Context) in various metrics.
A Protocol to Address Ecological Redirection for Digital Practices in Organizations
Venue: arXiv cs.CY 2025
Year: 2025

The digitalization of societies raises questions about its sustainability and the socio-technical impacts it generates. Ecological redirection applied to organizations is a field of research aiming for achieving sustainability as a direction, rather than for technical means. Arbitration and renunciation to some digital usage and technologies are investigated. Ecological redirection is, however, not yet addressing concrete methodologies for its implementation in organizations. This paper therefore proposes a protocol to support stakeholders in the ecological redirection of their digital practices. This protocol is based on mapping attachments to digital tools through a multi-disciplinary survey. It then proposes increasing stakeholders' knowledge and skills to prepare a debate on the arbitration of renunciations, and finally, to operationalize the closure/transformation of targeted digital practices. This protocol will be tested in real conditions in different contexts. An empirical study is proposed to measure 1) the fluidity with which participants carry out the protocol, 2) the effectiveness of the protocol in terms of the redirection objective, 3) the socio-technical barriers to the redirection process. The paper concludes on the potential benefits for organizations to better understand both the barriers related to its ecological redirection and the transformative aim of such protocols. This will help them trigger large and radical policies towards a desirable and sustainable society.