OpenRaiser/Intern-Atlas huggingface dataset:
MSCoD: An Enhanced Bayesian Updating Framework with Multi-Scale Information Bottleneck and Cooperative Attention for Structure-Based Drug Design
Venue: arXiv cs.LG 2025
Year: 2025

Structure-Based Drug Design (SBDD) is a powerful strategy in computational drug discovery, utilizing three-dimensional protein structures to guide the design of molecules with improved binding affinity. However, capturing complex protein-ligand interactions across multiple scales remains challenging, as current methods often overlook the hierarchical organization and intrinsic asymmetry of these interactions. To address these limitations, we propose MSCoD, a novel Bayesian updating-based generative framework for structure-based drug design. In our MSCoD, Multi-Scale Information Bottleneck (MSIB) was developed, which enables semantic compression at multiple abstraction levels for efficient hierarchical feature extraction. Furthermore, a multi-head cooperative attention (MHCA) mechanism was developed, which employs asymmetric protein-to-ligand attention to capture diverse interaction types while addressing the dimensionality disparity between proteins and ligands. Empirical studies showed that MSCoD outperforms state-of-the-art methods on the benchmark dataset. Its real-world applicability is confirmed by case studies on difficult targets like KRAS G12D (7XKJ). Additionally, the MSIB and MHCA modules prove transferable, boosting the performance of GraphDTA on standard drug target affinity prediction benchmarks (Davis and Kiba). The code and data underlying this article are freely available at https://github.com/xulong0826/MSCoD.
WDformer: A Wavelet-based Differential Transformer Model for Time Series Forecasting
Venue: arXiv cs.LG 2025
Year: 2025

Time series forecasting has various applications, such as meteorological rainfall prediction, traffic flow analysis, financial forecasting, and operational load monitoring for various systems. Due to the sparsity of time series data, relying solely on time-domain or frequency-domain modeling limits the model's ability to fully leverage multi-domain information. Moreover, when applied to time series forecasting tasks, traditional attention mechanisms tend to over-focus on irrelevant historical information, which may introduce noise into the prediction process, leading to biased results. We proposed WDformer, a wavelet-based differential Transformer model. This study employs the wavelet transform to conduct a multi-resolution analysis of time series data. By leveraging the advantages of joint representation in the time-frequency domain, it accurately extracts the key information components that reflect the essential characteristics of the data. Furthermore, we apply attention mechanisms on inverted dimensions, allowing the attention mechanism to capture relationships between multiple variables. When performing attention calculations, we introduced the differential attention mechanism, which computes the attention score by taking the difference between two separate softmax attention matrices. This approach enables the model to focus more on important information and reduce noise. WDformer has achieved state-of-the-art (SOTA) results on multiple challenging real-world datasets, demonstrating its accuracy and effectiveness. Code is available at https://github.com/xiaowangbc/WDformer.
Machine Learning for Pattern Detection in Printhead Nozzle Logging
Venue: arXiv cs.LG 2025
Year: 2025

Correct identification of failure mechanisms is essential for manufacturers to ensure the quality of their products. Certain failures of printheads developed by Canon Production Printing can be identified from the behavior of individual nozzles, the states of which are constantly recorded and can form distinct patterns in terms of the number of failed nozzles over time, and in space in the nozzle grid. In our work, we investigate the problem of printhead failure classification based on a multifaceted dataset of nozzle logging and propose a Machine Learning classification approach for this problem. We follow the feature-based framework of time-series classification, where a set of time-based and spatial features was selected with the guidance of domain experts. Several traditional ML classifiers were evaluated, and the One-vs-Rest Random Forest was found to have the best performance. The proposed model outperformed an in-house rule-based baseline in terms of a weighted F1 score for several failure mechanisms.
Quantum est in Libris: Navigating Archives with GenAI, Uncovering Tension Between Preservation and Innovation
Venue: arXiv cs.DL 2025
Year: 2025

"Quantum est in libris" explores the intersection of the archaic and the modern. On one side, there are manuscript materials from the Estonian National Museum's (ERM) more than century-old archive describing the life experiences of Estonian people; on the other side, there is technology that transforms these materials into a dynamic and interactive experience. Connecting technology and cultural heritage is the visitor, who turns texts into inputs for a screen sculpture. Historical narratives are visually brought to life through the contemporary technological language. Because the video AI models we employed, Runway Gen-3 and Gen-4, have not previously interacted with Estonian heritage, we can observe how machines today "read the world" and create future heritage. "Quantum est in libris" introduces an exciting yet unsettling new dimension to the concept of cultural heritage: in a world where data are fluid and interpretations unstable, heritage status becomes fragile. In the digital environment, heritage issues are no longer just about preservation and transmission, but also about representation of the media, machine creativity, and interpretive error. Who or what shapes memory processes and memory spaces, and how?
A Weather Foundation Model for the Power Grid
Venue: arXiv cs.LG 2025
Year: 2025

Weather foundation models (WFMs) have recently set new benchmarks in global forecast skill, yet their concrete value for the weather-sensitive infrastructure that powers modern society remains largely unexplored. In this study, we fine-tune Silurian AI's 1.5B-parameter WFM, Generative Forecasting Transformer (GFT), on a rich archive of Hydro-Québec asset observations--including transmission-line weather stations, wind-farm met-mast streams, and icing sensors--to deliver hyper-local, asset-level forecasts for five grid-critical variables: surface temperature, precipitation, hub-height wind speed, wind-turbine icing risk, and rime-ice accretion on overhead conductors. Across 6-72 h lead times, the tailored model surpasses state-of-the-art NWP benchmarks, trimming temperature mean absolute error (MAE) by 15%, total-precipitation MAE by 35%, and lowering wind speed MAE by 15%. Most importantly, it attains an average precision score of 0.72 for day-ahead rime-ice detection, a capability absent from existing operational systems, which affords several hours of actionable warning for potentially catastrophic outage events. These results show that WFMs, when post-trained with small amounts of high-fidelity, can serve as a practical foundation for next-generation grid-resilience intelligence.
Toward Causal-Visual Programming: Enhancing Agentic Reasoning in Low-Code Environments
Venue: arXiv cs.AI 2025
Year: 2025

Large language model (LLM) agents are increasingly capable of orchestrating complex tasks in low-code environments. However, these agents often exhibit hallucinations and logical inconsistencies because their inherent reasoning mechanisms rely on probabilistic associations rather than genuine causal understanding. This paper introduces a new programming paradigm: Causal-Visual Programming (CVP), designed to address this fundamental issue by explicitly introducing causal structures into the workflow design. CVP allows users to define a simple "world model" for workflow modules through an intuitive low-code interface, effectively creating a Directed Acyclic Graph (DAG) that explicitly defines the causal relationships between modules. This causal graph acts as a crucial constraint during the agent's reasoning process, anchoring its decisions to a user-defined causal structure and significantly reducing logical errors and hallucinations by preventing reliance on spurious correlations. To validate the effectiveness of CVP, we designed a synthetic experiment that simulates a common real-world problem: a distribution shift between the training and test environments. Our results show that a causally anchored model maintained stable accuracy in the face of this shift, whereas a purely associative baseline model that relied on probabilistic correlations experienced a significant performance drop. The primary contributions of this study are: a formal definition of causal structures for workflow modules; the proposal and implementation of a CVP framework that anchors agent reasoning to a user-defined causal graph; and empirical evidence demonstrating the framework's effectiveness in enhancing agent robustness and reducing errors caused by causal confusion in dynamic environments. CVP offers a viable path toward building more interpretable, reliable, and trustworthy AI agents.
AI in Pakistani Schools: Adoption, Usage, and Perceived Impact among Educators
Venue: arXiv cs.CY 2025
Year: 2025

Artificial Intelligence (AI) is increasingly permeating classrooms worldwide, yet its adoption in schools of developing countries remains under-explored. This paper investigates AI adoption, usage patterns, and perceived impact in Pakistani K-12 schools based on a survey of 125 educators. The questionnaire covered educator's familiarity with AI, frequency and modes of use, and attitudes toward AI's benefits and challenges. Results reveal a generally positive disposition towards AI: over two-thirds of teachers expressed willingness to adopt AI tools given proper support and many have begun integrating AI for lesson planning and content creation. However, AI usage is uneven - while about one-third of respondents actively use AI tools frequently, others remain occasional users. Content generation emerged as the most common AI application, whereas AI-driven grading and feedback are rarely used. Teachers reported moderate improvements in student engagement and efficiency due to AI, but also voiced concerns about equitable access. These findings highlight both the enthusiasm for AI's potential in Pakistan's schools and the need for training and infrastructure to ensure inclusive and effective implementation.
Scaling Behaviors of LLM Reinforcement Learning Post-Training: An Empirical Study in Mathematical Reasoning
Venue: arXiv cs.LG 2025
Year: 2025

While scaling laws for large language models (LLMs) during pre-training have been extensively studied, their behavior under reinforcement learning (RL) post-training remains largely unexplored. This paper presents a systematic empirical investigation of scaling behaviors in RL-based post-training, with a particular focus on mathematical reasoning. Based on a set of experiments across the full Qwen2.5 dense model series (0.5B to 72B), we characterize how model scale, data volume, and computational budget interact to shape performance. Our analysis leads to four key findings: 1. Larger models consistently exhibit superior learning efficiency on both compute and data metrics. 2. The relationship between test loss, compute, and data can be modeled by a predictive power-law which is robust across both base and instruction-tuned models. 3. Although larger models exhibit higher learning efficiency, the analytical learning efficiency term k(N) in the power-law reveals a latent saturation trend in learning efficiency as model size continues to increase. 4. In data-constrained regimes, repeated reuse of high-quality data proves highly effective, as final performance is primarily governed by the total number of optimization steps rather than the uniqueness of samples. Collectively, these results provide a principled foundation and practical guidelines for efficiently scaling the reasoning capabilities of LLMs through RL post-training.
LUMA: Low-Dimension Unified Motion Alignment with Dual-Path Anchoring for Text-to-Motion Diffusion Model
Venue: arXiv cs.CV 2025
Year: 2025

While current diffusion-based models, typically built on U-Net architectures, have shown promising results on the text-to-motion generation task, they still suffer from semantic misalignment and kinematic artifacts. Through analysis, we identify severe gradient attenuation in the deep layers of the network as a key bottleneck, leading to insufficient learning of high-level features. To address this issue, we propose \textbf{LUMA} (\textit{\textbf{L}ow-dimension \textbf{U}nified \textbf{M}otion \textbf{A}lignment}), a text-to-motion diffusion model that incorporates dual-path anchoring to enhance semantic alignment. The first path incorporates a lightweight MoCLIP model trained via contrastive learning without relying on external data, offering semantic supervision in the temporal domain. The second path introduces complementary alignment signals in the frequency domain, extracted from low-frequency DCT components known for their rich semantic content. These two anchors are adaptively fused through a temporal modulation mechanism, allowing the model to progressively transition from coarse alignment to fine-grained semantic refinement throughout the denoising process. Experimental results on HumanML3D and KIT-ML demonstrate that LUMA achieves state-of-the-art performance, with FID scores of 0.035 and 0.123, respectively. Furthermore, LUMA accelerates convergence by 1.4$\times$ compared to the baseline, making it an efficient and scalable solution for high-fidelity text-to-motion generation.
SARM: Stage-Aware Reward Modeling for Long Horizon Robot Manipulation
Venue: arXiv cs.RO 2025
Year: 2025

Large-scale robot learning has recently shown promise for enabling robots to perform complex tasks by integrating perception, control, and language understanding. Yet, it struggles with long-horizon, contact-rich manipulation such as deformable object handling, where demonstration quality is inconsistent. Reward modeling offers a natural solution: by providing grounded progress signals, it transforms noisy demonstrations into stable supervision that generalizes across diverse trajectories. We introduce a stage-aware, video-based reward modeling framework that jointly predicts high-level task stages and fine-grained progress. Reward labels are automatically derived from natural language subtask annotations, ensuring consistent progress estimation across variable-length demonstrations. This design overcomes frame-index labeling, which fails in variable-duration tasks like folding a T-shirt. Our reward model demonstrates robustness to variability, generalization to out-of-distribution settings, and strong utility for policy training. Building on it, we propose Reward-Aligned Behavior Cloning (RA-BC), which filters high-quality data and reweights samples by reward. Experiments show the reward model alone outperforms baselines on validation and real robot rollouts. Integrated into RA-BC, our approach achieves 83% success on folding T-shirts from the flattened state and 67% from the crumpled state -- far surpassing vanilla behavior cloning, which attains only 8% and 0% success. Overall, our results highlight reward modeling as a key enabler for scalable, annotation-efficient, and robust imitation learning in long-horizon manipulation.
On the Shape of Latent Variables in a Denoising VAE-MoG: A Posterior Sampling-Based Study
Venue: arXiv cs.LG 2025
Year: 2025

In this work, we explore the latent space of a denoising variational autoencoder with a mixture-of-Gaussians prior (VAE-MoG), trained on gravitational wave data from event GW150914. To evaluate how well the model captures the underlying structure, we use Hamiltonian Monte Carlo (HMC) to draw posterior samples conditioned on clean inputs, and compare them to the encoder's outputs from noisy data. Although the model reconstructs signals accurately, statistical comparisons reveal a clear mismatch in the latent space. This shows that strong denoising performance doesn't necessarily mean the latent representations are reliable highlighting the importance of using posterior-based validation when evaluating generative models.
Computational Design and Single-Wire Sensing of 3D Printed Objects with Integrated Capacitive Touchpoints
Venue: arXiv cs.GR 2025
Year: 2025

Producing interactive 3D printed objects currently requires laborious 3D design and post-instrumentation with off-the-shelf electronics. Multi-material 3D printing using conductive PLA presents opportunities to mitigate these challenges. We present a computational design pipeline that embeds multiple capacitive touchpoints into any 3D model that has a closed mesh without self-intersection. With our pipeline, users define touchpoints on the 3D object's surface to indicate interactive regions. Our pipeline then automatically generates a conductive path to connect the touch regions. This path is optimized to output unique resistor-capacitor delays when each region is touched, resulting in all regions being able to be sensed through a double-wire or single-wire connection. We illustrate our approach's utility with five computational and sensing performance evaluations (achieving 93.35% mean accuracy for single-wire) and six application examples. Our sensing technique supports existing uses (e.g., prototyping) and highlights the growing promise to produce interactive devices entirely with 3D printing. Project website: https://github.com/d-rep-lab/3dp-singlewire-sensing
Adaptive Test-Time Reasoning via Reward-Guided Dual-Phase Search
Venue: arXiv cs.AI 2025
Year: 2025

Large Language Models (LLMs) have achieved significant advances in reasoning tasks. A key approach is tree-based search with verifiers, which expand candidate reasoning paths and use reward models to guide pruning and selection. Although effective in improving accuracy, these methods are not optimal in terms of efficiency: they perform simple decomposition on the reasoning process, but ignore the planning-execution nature of tasks such as math reasoning or code generation. This results in inefficient exploration of reasoning process. To address this, we propose a dual-phase test-time scaling framework that explicitly separates reasoning into planning and execution, and performs search over the two phases individually. Specifically, we decompose reasoning trajectories and develop reward models for each phase, enabling the search to explore and prune plans and executions separately. We further introduce a dynamic budget allocation mechanism that adaptively redistributes sampling effort based on reward feedback, allowing early stopping on confident steps and reallocation of computation to more challenging parts of the reasoning process. Experiments on both mathematical reasoning and code generation benchmarks demonstrate that our approach consistently improves accuracy while reducing redundant computation.
CoTaP: Compliant Task Pipeline and Reinforcement Learning of Its Controller with Compliance Modulation
Venue: arXiv cs.RO 2025
Year: 2025

Humanoid whole-body locomotion control is a critical approach for humanoid robots to leverage their inherent advantages. Learning-based control methods derived from retargeted human motion data provide an effective means of addressing this issue. However, because most current human datasets lack measured force data, and learning-based robot control is largely position-based, achieving appropriate compliance during interaction with real environments remains challenging. This paper presents Compliant Task Pipeline (CoTaP): a pipeline that leverages compliance information in the learning-based structure of humanoid robots. A two-stage dual-agent reinforcement learning framework combined with model-based compliance control for humanoid robots is proposed. In the training process, first a base policy with a position-based controller is trained; then in the distillation, the upper-body policy is combined with model-based compliance control, and the lower-body agent is guided by the base policy. In the upper-body control, adjustable task-space compliance can be specified and integrated with other controllers through compliance modulation on the symmetric positive definite (SPD) manifold, ensuring system stability. We validated the feasibility of the proposed strategy in simulation, primarily comparing the responses to external disturbances under different compliance settings.
Joint Embeddings Go Temporal
Venue: arXiv cs.LG 2025
Year: 2025

Self-supervised learning has seen great success recently in unsupervised representation learning, enabling breakthroughs in natural language and image processing. However, these methods often rely on autoregressive and masked modeling, which aim to reproduce masked information in the input, which can be vulnerable to the presence of noise or confounding variables. To address this problem, Joint-Embedding Predictive Architectures (JEPA) has been introduced with the aim to perform self-supervised learning in the latent space. To leverage these advancements in the domain of time series, we introduce Time Series JEPA (TS-JEPA), an architecture specifically adapted for time series representation learning. We validate TS-JEPA on both classification and forecasting, showing that it can match or surpass current state-of-the-art baselines on different standard datasets. Notably, our approach demonstrates a strong performance balance across diverse tasks, indicating its potential as a robust foundation for learning general representations. Thus, this work lays the groundwork for developing future time series foundation models based on Joint Embedding.
SimulRAG: Simulator-based RAG for Grounding LLMs in Long-form Scientific QA
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) show promise in solving scientific problems. They can help generate long-form answers for scientific questions, which are crucial for comprehensive understanding of complex phenomena that require detailed explanations spanning multiple interconnected concepts and evidence. However, LLMs often suffer from hallucination, especially in the challenging task of long-form scientific question answering. Retrieval-Augmented Generation (RAG) approaches can ground LLMs by incorporating external knowledge sources to improve trustworthiness. In this context, scientific simulators, which play a vital role in validating hypotheses, offer a particularly promising retrieval source to mitigate hallucination and enhance answer factuality. However, existing RAG approaches cannot be directly applied for scientific simulation-based retrieval due to two fundamental challenges: how to retrieve from scientific simulators, and how to efficiently verify and update long-form answers. To overcome these challenges, we propose the simulator-based RAG framework (SimulRAG) and provide a long-form scientific QA benchmark covering climate science and epidemiology with ground truth verified by both simulations and human annotators. In this framework, we propose a generalized simulator retrieval interface to transform between textual and numerical modalities. We further design a claim-level generation method that utilizes uncertainty estimation scores and simulator boundary assessment (UE+SBA) to efficiently verify and update claims. Extensive experiments demonstrate SimulRAG outperforms traditional RAG baselines by 30.4% in informativeness and 16.3% in factuality. UE+SBA further improves efficiency and quality for claim-level generation.