OpenRaiser/Intern-Atlas huggingface dataset:
Diffusion Decoding for Peptide De Novo Sequencing
Venue: arXiv cs.LG 2025
Year: 2025

Peptide de novo sequencing is a method used to reconstruct amino acid sequences from tandem mass spectrometry data without relying on existing protein sequence databases. Traditional deep learning approaches, such as Casanovo, mainly utilize autoregressive decoders and predict amino acids sequentially. Subsequently, they encounter cascading errors and fail to leverage high-confidence regions effectively. To address these issues, this paper investigates using diffusion decoders adapted for the discrete data domain. These decoders provide a different approach, allowing sequence generation to start from any peptide segment, thereby enhancing prediction accuracy. We experiment with three different diffusion decoder designs, knapsack beam search, and various loss functions. We find knapsack beam search did not improve performance metrics and simply replacing the transformer decoder with a diffusion decoder lowered performance. Although peptide precision and recall were still 0, the best diffusion decoder design with the DINOISER loss function obtained a statistically significant improvement in amino acid recall by 0.373 compared to the baseline autoregressive decoder-based Casanovo model. These findings highlight the potential of diffusion decoders to not only enhance model sensitivity but also drive significant advancements in peptide de novo sequencing.
Terms and Conditions (Do Not) Apply: Understanding Exploitation Disparities in Design of Mobile-Based Financial Services
Venue: arXiv cs.HC 2025
Year: 2025

Mobile-based financial services have made it possible for the traditionally unbanked to access infrastructure that have been routinely unattainable. Researchers have explored how these systems have made for safer environments to send and receive money and have expanded financial opportunities such as increased borrowing. With this expansion, challenges such as detrimental interest rates, lack of access to policy documents, and inadequate user protective guardrails emerge, amplifying the risks due to technology-aided unethical financial practices that are aided by design patterns. Supported by user interviews, we detail user experiences of mobile-based financial transactions and explore the foundations and guidelines that undergird the financial service provisions: highlighting both affordances and harms enabled in the design of such systems. We discuss the findings by highlighting financial exploitation disparities, deliberating strategies for mitigation of risks and enabling recovery from harms caused by the technology use. We then recommend guidelines for empowering design approaches that support users' mechanisms of trust, their understanding of technological processes, and determination of risks.
Adaptive Policy Synchronization for Scalable Reinforcement Learning
Venue: arXiv cs.LG 2025
Year: 2025

Scaling reinforcement learning (RL) often requires running environments across many machines, but most frameworks tie simulation, training, and infrastructure into rigid systems. We introduce ClusterEnv, a lightweight interface for distributed environment execution that preserves the familiar Gymnasium API. ClusterEnv uses the DETACH pattern, which moves environment reset() and step() operations to remote workers while keeping learning centralized. To reduce policy staleness without heavy communication, we propose Adaptive Policy Synchronization (APS), where workers request updates only when divergence from the central learner grows too large. ClusterEnv supports both on- and off-policy methods, integrates into existing training code with minimal changes, and runs efficiently on clusters. Experiments on discrete control tasks show that APS maintains performance while cutting synchronization overhead. Source code is available at https://github.com/rodlaf/ClusterEnv.
Uncertainty Aware Mapping for Vision-Based Underwater Robots
Venue: arXiv cs.RO 2025
Year: 2025

Vision-based underwater robots can be useful in inspecting and exploring confined spaces where traditional sensors and preplanned paths cannot be followed. Sensor noise and situational change can cause significant uncertainty in environmental representation. Thus, this paper explores how to represent mapping inconsistency in vision-based sensing and incorporate depth estimation confidence into the mapping framework. The scene depth and the confidence are estimated using the RAFT-Stereo model and are integrated into a voxel-based mapping framework, Voxblox. Improvements in the existing Voxblox weight calculation and update mechanism are also proposed. Finally, a qualitative analysis of the proposed method is performed in a confined pool and in a pier in the Trondheim fjord. Experiments using an underwater robot demonstrated the change in uncertainty in the visualization.
Misalignment from Treating Means as Ends
Venue: arXiv cs.LG 2025
Year: 2025

Reward functions, learned or manually specified, are rarely perfect. Instead of accurately expressing human goals, these reward functions are often distorted by human beliefs about how best to achieve those goals. Specifically, these reward functions often express a combination of the human's terminal goals -- those which are ends in themselves -- and the human's instrumental goals -- those which are means to an end. We formulate a simple example in which even slight conflation of instrumental and terminal goals results in severe misalignment: optimizing the misspecified reward function results in poor performance when measured by the true reward function. This example distills the essential properties of environments that make reinforcement learning highly sensitive to conflation of instrumental and terminal goals. We discuss how this issue can arise with a common approach to reward learning and how it can manifest in real environments.
Mario at EXIST 2025: A Simple Gateway to Effective Multilingual Sexism Detection
Venue: arXiv cs.CL 2025
Year: 2025

This paper presents our approach to EXIST 2025 Task 1, addressing text-based sexism detection in English and Spanish tweets through hierarchical Low-Rank Adaptation (LoRA) of Llama 3.1 8B. Our method introduces conditional adapter routing that explicitly models label dependencies across three hierarchically structured subtasks: binary sexism identification, source intention detection, and multilabel sexism categorization. Unlike conventional LoRA applications that target only attention layers, we apply adaptation to all linear transformations, enhancing the model's capacity to capture task-specific patterns. In contrast to complex data processing and ensemble approaches, we show that straightforward parameter-efficient fine-tuning achieves strong performance. We train separate LoRA adapters (rank=16, QLoRA 4-bit) for each subtask using unified multilingual training that leverages Llama 3.1's native bilingual capabilities. The method requires minimal preprocessing and uses standard supervised learning. Our multilingual training strategy eliminates the need for separate language-specific models, achieving 1.7-2.4\% F1 improvements through cross-lingual transfer. With only 1.67\% trainable parameters compared to full fine-tuning, our approach reduces training time by 75\% and model storage by 98\%, while achieving competitive performance across all subtasks (ICM-Hard: 0.6774 for binary classification, 0.4991 for intention detection, 0.6519 for multilabel categorization).
Semantically Informed Salient Regions Guided Radiology Report Generation
Venue: arXiv cs.CV 2025
Year: 2025

Recent advances in automated radiology report generation from chest X-rays using deep learning algorithms have the potential to significantly reduce the arduous workload of radiologists. However, due to the inherent massive data bias in radiology images, where abnormalities are typically subtle and sparsely distributed, existing methods often produce fluent yet medically inaccurate reports, limiting their applicability in clinical practice. To address this issue effectively, we propose a Semantically Informed Salient Regions-guided (SISRNet) report generation method. Specifically, our approach explicitly identifies salient regions with medically critical characteristics using fine-grained cross-modal semantics. Then, SISRNet systematically focuses on these high-information regions during both image modeling and report generation, effectively capturing subtle abnormal findings, mitigating the negative impact of data bias, and ultimately generating clinically accurate reports. Compared to its peers, SISRNet demonstrates superior performance on widely used IU-Xray and MIMIC-CXR datasets.
Relative Entropy Pathwise Policy Optimization
Venue: arXiv cs.LG 2025
Year: 2025

Score-function based methods for policy learning, such as REINFORCE and PPO, have delivered strong results in game-playing and robotics, yet their high variance often undermines training stability. Using pathwise policy gradients, i.e. computing a derivative by differentiating the objective function, alleviates the variance issues. However, they require an accurate action-conditioned value function, which is notoriously hard to learn without relying on replay buffers for reusing past off-policy data. We present an on-policy algorithm that trains Q-value models purely from on-policy trajectories, unlocking the possibility of using pathwise policy updates in the context of on-policy learning. We show how to combine stochastic policies for exploration with constrained updates for stable training, and evaluate important architectural components that stabilize value function learning. The result, Relative Entropy Pathwise Policy Optimization (REPPO), is an efficient on-policy algorithm that combines the stability of pathwise policy gradients with the simplicity and minimal memory footprint of standard on-policy learning. Compared to state-of-the-art on two standard GPU-parallelized benchmarks, REPPO provides strong empirical performance at superior sample efficiency, wall-clock time, memory footprint, and hyperparameter robustness.
Human-Guided Shade Artifact Suppression in CBCT-to-MDCT Translation via Schrödinger Bridge with Conditional Diffusion
Venue: arXiv cs.CV 2025
Year: 2025

We present a novel framework for CBCT-to-MDCT translation, grounded in the Schrodinger Bridge (SB) formulation, which integrates GAN-derived priors with human-guided conditional diffusion. Unlike conventional GANs or diffusion models, our approach explicitly enforces boundary consistency between CBCT inputs and pseudo targets, ensuring both anatomical fidelity and perceptual controllability. Binary human feedback is incorporated via classifier-free guidance (CFG), effectively steering the generative process toward clinically preferred outcomes. Through iterative refinement and tournament-based preference selection, the model internalizes human preferences without relying on a reward model. Subtraction image visualizations reveal that the proposed method selectively attenuates shade artifacts in key anatomical regions while preserving fine structural detail. Quantitative evaluations further demonstrate superior performance across RMSE, SSIM, LPIPS, and Dice metrics on clinical datasets -- outperforming prior GAN- and fine-tuning-based feedback methods -- while requiring only 10 sampling steps. These findings underscore the effectiveness and efficiency of our framework for real-time, preference-aligned medical image translation.
Rapid Mixing of Glauber Dynamics for Monotone Systems via Entropic Independence
Venue: arXiv cs.DM 2025
Year: 2025

We study the mixing time of Glauber dynamics on monotone systems. For monotone systems satisfying the entropic independence condition, we prove a new mixing time comparison result for Glauber dynamics. For concrete applications, we obtain $\tilde{O}(n)$ mixing time for the random cluster model induced by the ferromagnetic Ising model with consistently biased external fields, and $\tilde{O}(n^2)$ mixing time for the bipartite hardcore model under the one-sided uniqueness condition, where $n$ is the number of variables in corresponding models, improving the best known results in [Chen and Zhang, SODA'23] and [Chen, Liu, and Yin, FOCS'23], respectively. Our proof combines ideas from the stochastic dominance argument in the classical censoring inequality and the recently developed high-dimensional expanders. The key step in the proof is a novel comparison result between the Glauber dynamics and the field dynamics for monotone systems.
GATE: Graph Attention Neural Networks with Real-Time Edge Construction for Robust Indoor Localization using Mobile Embedded Devices
Venue: arXiv cs.LG 2025
Year: 2025

Accurate indoor localization is crucial for enabling spatial context in smart environments and navigation systems. Wi-Fi Received Signal Strength (RSS) fingerprinting is a widely used indoor localization approach due to its compatibility with mobile embedded devices. Deep Learning (DL) models improve accuracy in localization tasks by learning RSS variations across locations, but they assume fingerprint vectors exist in a Euclidean space, failing to incorporate spatial relationships and the non-uniform distribution of real-world RSS noise. This results in poor generalization across heterogeneous mobile devices, where variations in hardware and signal processing distort RSS readings. Graph Neural Networks (GNNs) can improve upon conventional DL models by encoding indoor locations as nodes and modeling their spatial and signal relationships as edges. However, GNNs struggle with non-Euclidean noise distributions and suffer from the GNN blind spot problem, leading to degraded accuracy in environments with dense access points (APs). To address these challenges, we propose GATE, a novel framework that constructs an adaptive graph representation of fingerprint vectors while preserving an indoor state-space topology, modeling the non-Euclidean structure of RSS noise to mitigate environmental noise and address device heterogeneity. GATE introduces 1) a novel Attention Hyperspace Vector (AHV) for enhanced message passing, 2) a novel Multi-Dimensional Hyperspace Vector (MDHV) to mitigate the GNN blind spot, and 3) an new Real-Time Edge Construction (RTEC) approach for dynamic graph adaptation. Extensive real-world evaluations across multiple indoor spaces with varying path lengths, AP densities, and heterogeneous devices demonstrate that GATE achieves 1.6x to 4.72x lower mean localization errors and 1.85x to 4.57x lower worst-case errors compared to state-of-the-art indoor localization frameworks.
Social Media Sentiments Analysis on the July Revolution in Bangladesh: A Hybrid Transformer Based Machine Learning Approach
Venue: arXiv cs.CL 2025
Year: 2025

The July Revolution in Bangladesh marked a significant student-led mass uprising, uniting people across the nation to demand justice, accountability, and systemic reform. Social media platforms played a pivotal role in amplifying public sentiment and shaping discourse during this historic mass uprising. In this study, we present a hybrid transformer-based sentiment analysis framework to decode public opinion expressed in social media comments during and after the revolution. We used a brand new dataset of 4,200 Bangla comments collected from social media. The framework employs advanced transformer-based feature extraction techniques, including BanglaBERT, mBERT, XLM-RoBERTa, and the proposed hybrid XMB-BERT, to capture nuanced patterns in textual data. Principle Component Analysis (PCA) were utilized for dimensionality reduction to enhance computational efficiency. We explored eleven traditional and advanced machine learning classifiers for identifying sentiments. The proposed hybrid XMB-BERT with the voting classifier achieved an exceptional accuracy of 83.7% and outperform other model classifier combinations. This study underscores the potential of machine learning techniques to analyze social sentiment in low-resource languages like Bangla.
Beyond Traditional Algorithms: Leveraging LLMs for Accurate Cross-Border Entity Identification
Venue: arXiv cs.CL 2025
Year: 2025

The growing prevalence of cross-border financial activities in global markets has underscored the necessity of accurately identifying and classifying foreign entities. This practice is essential within the Spanish financial system for ensuring robust risk management, regulatory adherence, and the prevention of financial misconduct. This process involves a labor-intensive entity-matching task, where entities need to be validated against available reference sources. Challenges arise from linguistic variations, special characters, outdated names, and changes in legal forms, complicating traditional matching algorithms like Jaccard, cosine, and Levenshtein distances. These methods struggle with contextual nuances and semantic relationships, leading to mismatches. To address these limitations, we explore Large Language Models (LLMs) as a flexible alternative. LLMs leverage extensive training to interpret context, handle abbreviations, and adapt to legal transitions. We evaluate traditional methods, Hugging Face-based LLMs, and interface-based LLMs (e.g., Microsoft Copilot, Alibaba's Qwen 2.5) using a dataset of 65 Portuguese company cases. Results show traditional methods achieve accuracies over 92% but suffer high false positive rates (20-40%). Interface-based LLMs outperform, achieving accuracies above 93%, F1 scores exceeding 96%, and lower false positives (40-80%).
Generating Dynamic Graph Algorithms for Multiple Backends for a Graph DSL
Venue: arXiv cs.DC 2025
Year: 2025

With the rapid growth of unstructured and semistructured data, parallelizing graph algorithms has become essential for efficiency. However, due to the inherent irregularity in computation, memory access patterns, and communication, graph algorithms are notoriously difficult to parallelize. To address this challenge, several libraries, frameworks, and domain-specific languages (DSLs) have been proposed to ease the parallel programming burden for domain experts. Existing frameworks partially or fully abstract away parallelism intricacies, provide intuitive scheduling mnemonics, and employ program analysis to identify data races and generate synchronization code. Despite these advances, most frameworks are limited in their abstractions and runtime optimizations, especially when dealing with static graphs. In contrast, many real-world graphs are inherently dynamic, with evolving structures over time through insertions, deletions, and modifications of vertices, edges, and attributes. Generating efficient and correctly synchronized code for such dynamic graph algorithms remains a significant challenge. In this work, we introduce an abstraction scheme and runtime optimizations for the efficient processing of morph algorithms. Specifically, given an initial graph G and a set of updates $Δ$G involving edge insertions and deletions, we express the dynamic processing logic through a DSL and automatically generate parallel code targeting multicore, distributed, and many-core environments. We demonstrate the effectiveness of our approach by applying the DSL-generated code to ten large graphs with diverse characteristics and three widely used algorithms: Shortest Paths, PageRank, and Triangle Counting.
KptLLM++: Towards Generic Keypoint Comprehension with Large Language Model
Venue: arXiv cs.CV 2025
Year: 2025

The emergence of Multimodal Large Language Models (MLLMs) has revolutionized image understanding by bridging textual and visual modalities. However, these models often struggle with capturing fine-grained semantic information, such as the precise identification and analysis of object keypoints. Keypoints, as structure-aware, pixel-level, and compact representations of objects, particularly articulated ones, play a crucial role in applications such as fine-grained image analysis, object retrieval, and behavior recognition. In this paper, we propose KptLLM++, a novel multimodal large language model that specifically designed for generic keypoint comprehension through the integration of diverse input modalities guided by user-defined instructions. By unifying keypoint detection across varied contexts, KptLLM++ establishes itself as an advanced interface, fostering more effective human-AI collaboration. The model is built upon a novel identify-then-detect paradigm, which first interprets keypoint semantics and subsequently localizes their precise positions through a structured chain-of-thought reasoning mechanism. To push the boundaries of performance, we have scaled up the training dataset to over 500K samples, encompassing diverse objects, keypoint categories, image styles, and scenarios with complex occlusions. This extensive scaling enables KptLLM++ to unlock its potential, achieving remarkable accuracy and generalization. Comprehensive experiments on multiple keypoint detection benchmarks demonstrate its state-of-the-art performance, underscoring its potential as a unified solution for fine-grained image understanding and its transformative implications for human-AI interaction.
MSA at ImageCLEF 2025 Multimodal Reasoning: Multilingual Multimodal Reasoning With Ensemble Vision Language Models
Venue: arXiv cs.CL 2025
Year: 2025

We present a robust ensemble-based system for multilingual multimodal reasoning, designed for the ImageCLEF 2025 EXAMS V challenge. Our approach integrates Gemini 2.5 Flash for visual description, Gemini 1.5 Pro for caption refinement and consistency checks, and Gemini 2.5 Pro as a reasoner which handles final answer selection, all coordinated through carefully engineered few-shot and zero-shot prompts. We conducted an extensive ablation study, training several large language models (Gemini 2.5 Flash, Phi 4, Gemma 3, Mistral) on an English dataset and its multilingual augmented version. Additionally, we evaluated Gemini 2.5 Flash in a zero-shot setting for comparison and found it to substantially outperform the trained models. Prompt design also proved critical: enforcing concise, language-normalized formats and prohibiting explanatory text boosted model accuracy on the English validation set from 55.9% to 61.7%. On the official leaderboard, our system (Team MSA) achieved first place overall in the multilingual track with 81.4% accuracy, and led 11 out of 13 individual language tracks, with top results such as 95.07% for Croatian and 92.12% for Italian. These findings highlight that lightweight OCR-VLM ensembles, when paired with precise prompt strategies and cross-lingual augmentation, can outperform heavier end-to-end models in high-stakes, multilingual educational settings.
FacialMotionID: Identifying Users of Mixed Reality Headsets using Abstract Facial Motion Representations
Venue: arXiv cs.CR 2025
Year: 2025

Facial motion capture in mixed reality headsets enables real-time avatar animation, allowing users to convey non-verbal cues during virtual interactions. However, as facial motion data constitutes a behavioral biometric, its use raises novel privacy concerns. With mixed reality systems becoming more immersive and widespread, understanding whether face motion data can lead to user identification or inference of sensitive attributes is increasingly important. To address this, we conducted a study with 116 participants using three types of headsets across three sessions, collecting facial, eye, and head motion data during verbal and non-verbal tasks. The data used is not raw video, but rather, abstract representations that are used to animate digital avatars. Our analysis shows that individuals can be re-identified from this data with up to 98% balanced accuracy, are even identifiable across device types, and that emotional states can be inferred with up to 86% accuracy. These results underscore the potential privacy risks inherent in face motion tracking in mixed reality environments.