OpenRaiser/Intern-Atlas huggingface dataset:
Task-Specific Sparse Feature Masks for Molecular Toxicity Prediction with Chemical Language Models
Venue: arXiv cs.CE 2025
Year: 2025

Reliable in silico molecular toxicity prediction is a cornerstone of modern drug discovery, offering a scalable alternative to experimental screening. However, the black-box nature of state-of-the-art models remains a significant barrier to adoption, as high-stakes safety decisions demand verifiable structural insights alongside predictive performance. To address this, we propose a novel multi-task learning (MTL) framework designed to jointly enhance accuracy and interpretability. Our architecture integrates a shared chemical language model with task-specific attention modules. By imposing an L1 sparsity penalty on these modules, the framework is constrained to focus on a minimal set of salient molecular fragments for each distinct toxicity endpoint. The resulting framework is trained end-to-end and is readily adaptable to various transformer-based backbones. Evaluated on the ClinTox, SIDER, and Tox21 benchmark datasets, our approach consistently outperforms both single-task and standard MTL baselines. Crucially, the sparse attention weights provide chemically intuitive visualizations that reveal the specific fragments influencing predictions, thereby enhancing insight into the model's decision-making process.
Capacity-Achieving Codes with Inverse-Ackermann-Depth Encoders
Venue: arXiv cs.IT 2025
Year: 2025

For any symmetric discrete memoryless channel with input and output alphabet of size $q$, where $q$ is a prime power, we prove that there exist error-correcting codes approaching channel capacity encodable by arithmetic circuits (with weighted addition gates) over $\mathbb{F}_q$ of size $O(n)$ and depth $α(n)$, where $α(n)$ is a version of the inverse Ackermann function. Our results suggest that certain capacity-achieving codes admit highly efficient encoding circuits that are both in linear size and of inverse-Ackermann depth. Our construction composes a linear code with constant rate and relative distance, based on the constructions of Gál, Hansen, Koucký, Pudlák, and Viola [IEEE Trans. Inform. Theory 59(10), 2013] and Drucker and Li [COCOON 2023], with an additional layer formed by a disperser graph whose edge weights are chosen uniformly at random.
DOS: Distilling Observable Softmaps of Zipfian Prototypes for Self-Supervised Point Representation
Venue: arXiv cs.CV 2025
Year: 2025

Recent advances in self-supervised learning (SSL) have shown tremendous potential for learning 3D point cloud representations without human annotations. However, SSL for 3D point clouds still faces critical challenges due to irregular geometry, shortcut-prone reconstruction, and unbalanced semantics distribution. In this work, we propose DOS (Distilling Observable Softmaps), a novel SSL framework that self-distills semantic relevance softmaps only at observable (unmasked) points. This strategy prevents information leakage from masked regions and provides richer supervision than discrete token-to-prototype assignments. To address the challenge of unbalanced semantics in an unsupervised setting, we introduce Zipfian prototypes and incorporate them using a modified Sinkhorn-Knopp algorithm, Zipf-Sinkhorn, which enforces a power-law prior over prototype usage and modulates the sharpness of the target softmap during training. DOS outperforms current state-of-the-art methods on semantic segmentation and 3D object detection across multiple benchmarks, including nuScenes, Waymo, SemanticKITTI, ScanNet, and ScanNet200, without relying on extra data or annotations. Our results demonstrate that observable-point softmaps distillation offers a scalable and effective paradigm for learning robust 3D representations.
Three methods, one problem: Classical and AI approaches to no-three-in-line
Venue: arXiv cs.AI 2025
Year: 2025

The No-Three-In-Line problem asks for the maximum number of points that can be placed on an n by n grid with no three collinear, representing a famous problem in combinatorial geometry. While classical methods like Integer Linear Programming (ILP) guarantee optimal solutions, they face exponential scaling with grid size, and recent advances in machine learning offer promising alternatives for pattern-based approximation. This paper presents the first systematic comparison of classical optimization and AI approaches to this problem, evaluating their performance against traditional algorithms. We apply PatternBoost transformer learning and reinforcement learning (PPO) to this problem for the first time, comparing them against ILP. ILP achieves provably optimal solutions up to 19 by 19 grids, while PatternBoost matches optimal performance up to 14 by 14 grids with 96% test loss reduction. PPO achieves perfect solutions on 10 by 10 grids but fails at 11 by 11 grids, where constraint violations prevent valid configurations. These results demonstrate that classical optimization remains essential for exact solutions while AI methods offer competitive performance on smaller instances, with hybrid approaches presenting the most promising direction for scaling to larger problem sizes.
Contiguous Storage of Grid Data for Heterogeneous Computing
Venue: arXiv cs.CE 2025
Year: 2025

Structured Cartesian grids are a fundamental component in numerical simulations. Although these grids facilitate straightforward discretization schemes, their naïve use in sparse domains leads to excessive memory overhead and inefficient computation. Existing frameworks address are primarily optimized for CPU execution and exhibit performance bottlenecks on GPU architectures due to limited parallelism and high memory access latency. This work presents a redesigned storage architecture optimized for GPU compatibility and efficient execution across heterogeneous platforms. By abstracting low-level GPU-specific details and adopting a unified programming model based on SYCL, the proposed data structure enables seamless integration across host and device environments. This architecture simplifies GPU programming for end-users while improving scalability and portability in sparse-grid and gird-particle coupling numerical simulations.
Capacitive Touchscreens at Risk: Recovering Handwritten Trajectory on Smartphone via Electromagnetic Emanations
Venue: arXiv cs.CR 2025
Year: 2025

This paper reveals and exploits a critical security vulnerability: the electromagnetic (EM) side channel of capacitive touchscreens leaks sufficient information to recover fine-grained, continuous handwriting trajectories. We present Touchscreen Electromagnetic Side-channel Leakage Attack (TESLA), a non-contact attack framework that captures EM signals generated during on-screen writing and regresses them into two-dimensional (2D) handwriting trajectories in real time. Extensive evaluations across a variety of commercial off-the-shelf (COTS) smartphones show that TESLA achieves 77% character recognition accuracy and a Jaccard index of 0.74, demonstrating its capability to recover highly recognizable motion trajectories that closely resemble the original handwriting under realistic attack conditions.
Building Patient Journeys in Hebrew: A Language Model for Clinical Timeline Extraction
Venue: arXiv cs.CL 2025
Year: 2025

We present a new Hebrew medical language model designed to extract structured clinical timelines from electronic health records, enabling the construction of patient journeys. Our model is based on DictaBERT 2.0 and continually pre-trained on over five million de-identified hospital records. To evaluate its effectiveness, we introduce two new datasets -- one from internal medicine and emergency departments, and another from oncology -- annotated for event temporal relations. Our results show that our model achieves strong performance on both datasets. We also find that vocabulary adaptation improves token efficiency and that de-identification does not compromise downstream performance, supporting privacy-conscious model development. The model is made available for research use under ethical restrictions.
TSkel-Mamba: Temporal Dynamic Modeling via State Space Model for Human Skeleton-based Action Recognition
Venue: arXiv cs.CV 2025
Year: 2025

Skeleton-based action recognition has garnered significant attention in the computer vision community. Inspired by the recent success of the selective state-space model (SSM) Mamba in modeling 1D temporal sequences, we propose TSkel-Mamba, a hybrid Transformer-Mamba framework that effectively captures both spatial and temporal dynamics. In particular, our approach leverages Spatial Transformer for spatial feature learning while utilizing Mamba for temporal modeling. Mamba, however, employs separate SSM blocks for individual channels, which inherently limits its ability to model inter-channel dependencies. To better adapt Mamba for skeleton data and enhance Mamba`s ability to model temporal dependencies, we introduce a Temporal Dynamic Modeling (TDM) block, which is a versatile plug-and-play component that integrates a novel Multi-scale Temporal Interaction (MTI) module. The MTI module employs multi-scale Cycle operators to capture cross-channel temporal interactions, a critical factor in action recognition. Extensive experiments on NTU-RGB+D 60, NTU-RGB+D 120, NW-UCLA and UAV-Human datasets demonstrate that TSkel-Mamba achieves state-of-the-art performance while maintaining low inference time, making it both efficient and highly effective.
Parametric Numerical Integration with (Differential) Machine Learning
Venue: arXiv cs.LG 2025
Year: 2025

In this work, we introduce a machine/deep learning methodology to solve parametric integrals. Besides classical machine learning approaches, we consider a differential learning framework that incorporates derivative information during training, emphasizing its advantageous properties. Our study covers three representative problem classes: statistical functionals (including moments and cumulative distribution functions), approximation of functions via Chebyshev expansions, and integrals arising directly from differential equations. These examples range from smooth closed-form benchmarks to challenging numerical integrals. Across all cases, the differential machine learning-based approach consistently outperforms standard architectures, achieving lower mean squared error, enhanced scalability, and improved sample efficiency.
Parallax: Runtime Parallelization for Operator Fallbacks in Heterogeneous Edge Systems
Venue: arXiv cs.DC 2025
Year: 2025

The growing demand for real-time DNN applications on edge devices necessitates faster inference of increasingly complex models. Although many devices include specialized accelerators (e.g., mobile GPUs), dynamic control-flow operators and unsupported kernels often fall back to CPU execution. Existing frameworks handle these fallbacks poorly, leaving CPU cores idle and causing high latency and memory spikes. We introduce Parallax, a framework that accelerates mobile DNN inference without model refactoring or custom operator implementations. Parallax first partitions the computation DAG to expose parallelism, then employs branch-aware memory management with dedicated arenas and buffer reuse to reduce runtime footprint. An adaptive scheduler executes branches according to device memory constraints, meanwhile, fine-grained subgraph control enables heterogeneous inference of dynamic models. By evaluating on five representative DNNs across three different mobile devices, Parallax achieves up to 46% latency reduction, maintains controlled memory overhead (26.5% on average), and delivers up to 30% energy savings compared with state-of-the-art frameworks, offering improvements aligned with the responsiveness demands of real-time mobile inference.
A Multi-Criteria Automated MLOps Pipeline for Cost-Effective Cloud-Based Classifier Retraining in Response to Data Distribution Shifts
Venue: arXiv cs.LG 2025
Year: 2025

The performance of machine learning (ML) models often deteriorates when the underlying data distribution changes over time, a phenomenon known as data distribution drift. When this happens, ML models need to be retrained and redeployed. ML Operations (MLOps) is often manual, i.e., humans trigger the process of model retraining and redeployment. In this work, we present an automated MLOps pipeline designed to address neural network classifier retraining in response to significant data distribution changes. Our MLOps pipeline employs multi-criteria statistical techniques to detect distribution shifts and triggers model updates only when necessary, ensuring computational efficiency and resource optimization. We demonstrate the effectiveness of our framework through experiments on several benchmark anomaly detection data sets, showing significant improvements in model accuracy and robustness compared to traditional retraining strategies. Our work provides a foundation for deploying more reliable and adaptive ML systems in dynamic real-world settings, where data distribution changes are common.
Infinity and Beyond: Compositional Alignment in VAR and Diffusion T2I Models
Venue: arXiv cs.CV 2025
Year: 2025

Achieving compositional alignment between textual descriptions and generated images - covering objects, attributes, and spatial relationships - remains a core challenge for modern text-to-image (T2I) models. Although diffusion-based architectures have been widely studied, the compositional behavior of emerging Visual Autoregressive (VAR) models is still largely unexamined. We benchmark six diverse T2I systems - SDXL, PixArt-$α$, Flux-Dev, Flux-Schnell, Infinity-2B, and Infinity-8B - across the full T2I-CompBench++ and GenEval suites, evaluating alignment in color and attribute binding, spatial relations, numeracy, and complex multi-object prompts. Across both benchmarks, Infinity-8B achieves the strongest overall compositional alignment, while Infinity-2B also matches or exceeds larger diffusion models in several categories, highlighting favorable efficiency-performance trade-offs. In contrast, SDXL and PixArt-$α$ show persistent weaknesses in attribute-sensitive and spatial tasks. These results provide the first systematic comparison of VAR and diffusion approaches to compositional alignment and establish unified baselines for the future development of the T2I model.
SSL-MedSAM2: A Semi-supervised Medical Image Segmentation Framework Powered by Few-shot Learning of SAM2
Venue: arXiv cs.CV 2025
Year: 2025

Despite the success of deep learning based models in medical image segmentation, most state-of-the-art (SOTA) methods perform fully-supervised learning, which commonly rely on large scale annotated training datasets. However, medical image annotation is highly time-consuming, hindering its clinical applications. Semi-supervised learning (SSL) has been emerged as an appealing strategy in training with limited annotations, largely reducing the labelling cost. We propose a novel SSL framework SSL-MedSAM2, which contains a training-free few-shot learning branch TFFS-MedSAM2 based on the pretrained large foundation model Segment Anything Model 2 (SAM2) for pseudo label generation, and an iterative fully-supervised learning branch FSL-nnUNet based on nnUNet for pseudo label refinement. The results on MICCAI2025 challenge CARE-LiSeg (Liver Segmentation) demonstrate an outstanding performance of SSL-MedSAM2 among other methods. The average dice scores on the test set in GED4 and T1 MRI are 0.9710 and 0.9648 respectively, and the Hausdorff distances are 20.07 and 21.97 respectively. The code is available via https://github.com/naisops/SSL-MedSAM2/tree/main.
Fully Inductive Node Representation Learning via Graph View Transformation
Venue: arXiv cs.LG 2025
Year: 2025

Generalizing a pretrained model to unseen datasets without retraining is an essential step toward a foundation model. However, achieving such cross-dataset, fully inductive inference is difficult in graph-structured data where feature spaces vary widely in both dimensionality and semantics. Any transformation in the feature space can easily violate the inductive applicability to unseen datasets, strictly limiting the design space of a graph model. In this work, we introduce the view space, a novel representational axis in which arbitrary graphs can be naturally encoded in a unified manner. We then propose Graph View Transformation (GVT), a node- and feature-permutation-equivariant mapping in the view space. GVT serves as the building block for Recurrent GVT, a fully inductive model for node representation learning. Pretrained on OGBN-Arxiv and evaluated on 27 node-classification benchmarks, Recurrent GVT outperforms GraphAny, the prior fully inductive graph model, by +8.93% and surpasses 12 individually tuned GNNs by at least +3.30%. These results establish the view space as a principled and effective ground for fully inductive node representation learning.
Atomic Action Slicing: Planner-Aligned Options for Generalist VLA Agents
Venue: arXiv cs.LG 2025
Year: 2025

Current vision-language-action (VLA) models generalize poorly, particularly when tasks require new compositions of skills or objects. We introduce Atomic Action Slicing (AAS), a planner-aligned approach that decomposes long-horizon demonstrations into short, typed atomic actions that are easier for planners to use and policies to learn. Using LIBERO demonstrations, AAS produces a validated dataset of 2,124 atomic segments labeled with action type, temporal span, and confidence. A stronger segmenter (Gemini 2.5 Pro) closely matches planner-defined plans and remains robust under keyframe jitter, while smaller models perform worse on multi-object tasks. Fine-tuning CLIP-RT+ on our atomic dataset improves task success from 94.2% to 95.3% on LIBERO-Goal and 83.8% to 88.8% on LIBERO-Long. We publicly release the GATE-VLAP dataset on HuggingFace(https://huggingface.co/datasets/gate-institute/GATE-VLAP-datasets)
FirecREST v2: lessons learned from redesigning an API for scalable HPC resource access
Venue: arXiv cs.DC 2025
Year: 2025

Introducing FirecREST v2, the next generation of our open-source RESTful API for programmatic access to HPC resources. FirecREST v2 delivers a 100x performance improvement over its predecessor. This paper explores the lessons learned from redesigning FirecREST from the ground up, with a focus on integrating enhanced security and high throughput as core requirements. We provide a detailed account of our systematic performance testing methodology, highlighting common bottlenecks in proxy-based APIs with intensive I/O operations. Key design and architectural changes that enabled these performance gains are presented. Finally, we demonstrate the impact of these improvements, supported by independent peer validation, and discuss opportunities for further improvements.
Automating Historical Insight Extraction from Large-Scale Newspaper Archives via Neural Topic Modeling
Venue: arXiv cs.CL 2025
Year: 2025

Extracting coherent and human-understandable themes from large collections of unstructured historical newspaper archives presents significant challenges due to topic evolution, Optical Character Recognition (OCR) noise, and the sheer volume of text. Traditional topic-modeling methods, such as Latent Dirichlet Allocation (LDA), often fall short in capturing the complexity and dynamic nature of discourse in historical texts. To address these limitations, we employ BERTopic. This neural topic-modeling approach leverages transformerbased embeddings to extract and classify topics, which, despite its growing popularity, still remains underused in historical research. Our study focuses on articles published between 1955 and 2018, specifically examining discourse on nuclear power and nuclear safety. We analyze various topic distributions across the corpus and trace their temporal evolution to uncover long-term trends and shifts in public discourse. This enables us to more accurately explore patterns in public discourse, including the co-occurrence of themes related to nuclear power and nuclear weapons and their shifts in topic importance over time. Our study demonstrates the scalability and contextual sensitivity of BERTopic as an alternative to traditional approaches, offering richer insights into historical discourses extracted from newspaper archives. These findings contribute to historical, nuclear, and social-science research while reflecting on current limitations and proposing potential directions for future work.
From Verification Burden to Trusted Collaboration: Design Goals for LLM-Assisted Literature Reviews
Venue: arXiv cs.HC 2025
Year: 2025

Large Language Models (LLMs) are increasingly embedded in academic writing practices. Although numerous studies have explored how researchers employ these tools for scientific writing, their concrete implementation, limitations, and design challenges within the literature review process remain underexplored. In this paper, we report a user study with researchers across multiple disciplines to characterize current practices, benefits, and \textit{pain points} in using LLMs to investigate related work. We identified three recurring gaps: (i) lack of trust in outputs, (ii) persistent verification burden, and (iii) requiring multiple tools. This motivates our proposal of six design goals and a high-level framework that operationalizes them through improved related papers visualization, verification at every step, and human-feedback alignment with generation-guided explanations. Overall, by grounding our work in the practical, day-to-day needs of researchers, we designed a framework that addresses these limitations and models real-world LLM-assisted writing, advancing trust through verifiable actions and fostering practical collaboration between researchers and AI systems.
A Relational Model of Neighborhood Mobility: The Role of Amenities and Cultural Alignment
Venue: arXiv cs.SI 2025
Year: 2025

Why are some neighborhoods strongly connected while others remain isolated? Although standard explanations focus on demographics, economics, and geography, movement across the city may also depend on cultural styles and amenity mix. This study proposes a relational, cross-national model in which local culture and amenity mix alignment creates a "soft infrastructure" of urban mobility, i.e., symbolic cues and functional features that shape expectations about the character of places. Using ~650 million Google Places reviews to measure co-visitation between U.S. ZIP codes and ~30 million Canadian change-of-address to track residential mobility, results show that neighborhoods with similar cultural styles and amenities are significantly more connected. These effects persist even after controlling for race, income, education, politics, housing costs, and distance. Urban cohesion and segregation depend not only on who lives where or how far apart neighborhoods are, but on the shared cultural and material ecologies that structure movement across the city.