AURORA:Automated Training Framework of Universal Process Reward Models via Ensemble Prompting and Reverse Verification

The reasoning capabilities of advanced large language models (LLMs) like o1 have revolutionized artificial intelligence applications. Nevertheless, evaluating and optimizing complex reasoning processes remain significant challenges due to diverse policy distributions and the inherent limitations of human effort and accuracy. In this paper, we present AURORA, a novel automated framework for training universal process reward models (PRMs) using ensemble prompting and reverse verification. The framework employs a two-phase approach: First, it uses diverse prompting strategies and ensemble methods to perform automated annotation and evaluation of processes, ensuring robust assessments for reward learning. Second, it leverages practical reference answers for reverse verification, enhancing the model's ability to validate outputs and improving training accuracy. To assess the framework's performance, we extend beyond the existing ProcessBench benchmark by introducing UniversalBench, which evaluates reward predictions across full trajectories under diverse policy distribtion with long Chain-of-Thought (CoT) outputs. Experimental results demonstrate that AURORA enhances process evaluation accuracy, improves PRMs' accuracy for diverse policy distributions and long-CoT responses. The project will be open-sourced at https://auroraprm.github.io/. The Universal-PRM-7B is available at https://huggingface.co/infly/Universal-PRM-7B.

Equivariant Masked Position Prediction for Efficient Molecular Representation

Graph neural networks (GNNs) have shown considerable promise in computational chemistry. However, the limited availability of molecular data raises concerns regarding GNNs' ability to effectively capture the fundamental principles of physics and chemistry, which constrains their generalization capabilities. To address this challenge, we introduce a novel self-supervised approach termed Equivariant Masked Position Prediction (EMPP), grounded in intramolecular potential and force theory. Unlike conventional attribute masking techniques, EMPP formulates a nuanced position prediction task that is more well-defined and enhances the learning of quantum mechanical features. EMPP also bypasses the approximation of the Gaussian mixture distribution commonly used in denoising methods, allowing for more accurate acquisition of physical properties. Experimental results indicate that EMPP significantly enhances performance of advanced molecular architectures, surpassing state-of-the-art self-supervised approaches. Our code is released in https://github.com/ajy112/EMPP.

SCP-116K: A High-Quality Problem-Solution Dataset and a Generalized Pipeline for Automated Extraction in the Higher Education Science Domain

Recent breakthroughs in large language models (LLMs) exemplified by the impressive mathematical and scientific reasoning capabilities of the o1 model have spotlighted the critical importance of high-quality training data in advancing LLM performance across STEM disciplines. While the mathematics community has benefited from a growing body of curated datasets, the scientific domain at the higher education level has long suffered from a scarcity of comparable resources. To address this gap, we present SCP-116K, a new large-scale dataset of 116,756 high-quality problem-solution pairs, automatically extracted from heterogeneous sources using a streamlined and highly generalizable pipeline. Our approach involves stringent filtering to ensure the scientific rigor and educational level of the extracted materials, while maintaining adaptability for future expansions or domain transfers. By openly releasing both the dataset and the extraction pipeline, we seek to foster research on scientific reasoning, enable comprehensive performance evaluations of new LLMs, and lower the barrier to replicating the successes of advanced models like o1 in the broader science community. We believe SCP-116K will serve as a critical resource, catalyzing progress in high-level scientific reasoning tasks and promoting further innovations in LLM development. The dataset and code are publicly available at https://github.com/AQA6666/SCP-116K-open.

Aneumo: A Large-Scale Comprehensive Synthetic Dataset of Aneurysm Hemodynamics

Intracranial aneurysm (IA) is a common cerebrovascular disease that is usually asymptomatic but may cause severe subarachnoid hemorrhage (SAH) if ruptured. Although clinical practice is usually based on individual factors and morphological features of the aneurysm, its pathophysiology and hemodynamic mechanisms remain controversial. To address the limitations of current research, this study constructed a comprehensive hemodynamic dataset of intracranial aneurysms. The dataset is based on 466 real aneurysm models, and 10,000 synthetic models were generated by resection and deformation operations, including 466 aneurysm-free models and 9,534 deformed aneurysm models. The dataset also provides medical image-like segmentation mask files to support insightful analysis. In addition, the dataset contains hemodynamic data measured at eight steady-state flow rates (0.001 to 0.004 kg/s), including critical parameters such as flow velocity, pressure, and wall shear stress, providing a valuable resource for investigating aneurysm pathogenesis and clinical prediction. This dataset will help advance the understanding of the pathologic features and hemodynamic mechanisms of intracranial aneurysms and support in-depth research in related fields. Dataset hosted at https://github.com/Xigui-Li/Aneumo.

An Attentive Dual-Encoder Framework Leveraging Multimodal Visual and Semantic Information for Automatic OSAHS Diagnosis

Obstructive sleep apnea-hypopnea syndrome (OSAHS) is a common sleep disorder caused by upper airway blockage, leading to oxygen deprivation and disrupted sleep. Traditional diagnosis using polysomnography (PSG) is expensive, time-consuming, and uncomfortable. Existing deep learning methods using facial image analysis lack accuracy due to poor facial feature capture and limited sample sizes. To address this, we propose a multimodal dual encoder model that integrates visual and language inputs for automated OSAHS diagnosis. The model balances data using randomOverSampler, extracts key facial features with attention grids, and converts physiological data into meaningful text. Cross-attention combines image and text data for better feature extraction, and ordered regression loss ensures stable learning. Our approach improves diagnostic efficiency and accuracy, achieving 91.3% top-1 accuracy in a four-class severity classification task, demonstrating state-of-the-art performance. Code will be released upon acceptance.

Centaur: Bridging the Impossible Trinity of Privacy, Efficiency, and Performance in Privacy-Preserving Transformer Inference

As pre-trained models, like Transformers, are increasingly deployed on cloud platforms for inference services, the privacy concerns surrounding model parameters and inference data are becoming more acute. Current Privacy-Preserving Transformer Inference (PPTI) frameworks struggle with the "impossible trinity" of privacy, efficiency, and performance. For instance, Secure Multi-Party Computation (SMPC)-based solutions offer strong privacy guarantees but come with significant inference overhead and performance trade-offs. On the other hand, PPTI frameworks that use random permutations achieve inference efficiency close to that of plaintext and maintain accurate results but require exposing some model parameters and intermediate results, thereby risking substantial privacy breaches. Addressing this "impossible trinity" with a single technique proves challenging. To overcome this challenge, we propose Centaur, a novel hybrid PPTI framework. Unlike existing methods, Centaur protects model parameters with random permutations and inference data with SMPC, leveraging the structure of Transformer models. By designing a series of efficient privacy-preserving algorithms, Centaur leverages the strengths of both techniques to achieve a better balance between privacy, efficiency, and performance in PPTI. We comprehensively evaluate the effectiveness of Centaur on various types of Transformer models and datasets. Experimental results demonstrate that the privacy protection capabilities offered by Centaur can withstand various existing model inversion attack methods. In terms of performance and efficiency, Centaur not only maintains the same performance as plaintext inference but also improves inference speed by $5.0-30.4$ times.

Personalize to generalize: Towards a universal medical multi-modality generalization through personalization

The differences among medical imaging modalities, driven by distinct underlying principles, pose significant challenges for generalization in multi-modal medical tasks. Beyond modality gaps, individual variations, such as differences in organ size and metabolic rate, further impede a model's ability to generalize effectively across both modalities and diverse populations. Despite the importance of personalization, existing approaches to multi-modal generalization often neglect individual differences, focusing solely on common anatomical features. This limitation may result in weakened generalization in various medical tasks. In this paper, we unveil that personalization is critical for multi-modal generalization. Specifically, we propose an approach to achieve personalized generalization through approximating the underlying personalized invariant representation ${X}_h$ across various modalities by leveraging individual-level constraints and a learnable biological prior. We validate the feasibility and benefits of learning a personalized ${X}_h$, showing that this representation is highly generalizable and transferable across various multi-modal medical tasks. Extensive experimental results consistently show that the additionally incorporated personalization significantly improves performance and generalization across diverse scenarios, confirming its effectiveness.

OpenCoder: The Open Cookbook for Top-Tier Code Large Language Models

Large language models (LLMs) for code have become indispensable in various domains, including code generation, reasoning tasks and agent systems.While open-access code LLMs are increasingly approaching the performance levels of proprietary models, high-quality code LLMs suitable for rigorous scientific investigation, particularly those with reproducible data processing pipelines and transparent training protocols, remain limited. The scarcity is due to various challenges, including resource constraints, ethical considerations, and the competitive advantages of keeping models advanced. To address the gap, we introduce OpenCoder, a top-tier code LLM that not only achieves performance comparable to leading models but also serves as an ``open cookbook'' for the research community. Unlike most prior efforts, we release not only model weights and inference code, but also the reproducible training data, complete data processing pipeline, rigorous experimental ablation results, and detailed training protocols for open scientific research. Through this comprehensive release, we identify the key ingredients for building a top-tier code LLM: (1) code optimized heuristic rules for data cleaning and methods for data deduplication, (2) recall of text corpus related to code and (3) high-quality synthetic data in both annealing and supervised fine-tuning stages. By offering this level of openness, we aim to broaden access to all aspects of a top-tier code LLM, with OpenCoder serving as both a powerful model and an open foundation to accelerate research, and enable reproducible advancements in code AI.

4D Diffusion for Dynamic Protein Structure Prediction with Reference Guided Motion Alignment

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and the expanded availability of experimental 3D protein structures have accelerated structure prediction, the dynamic nature of protein structures has received limited attention. This study introduces an innovative 4D diffusion model incorporating molecular dynamics (MD) simulation data to learn dynamic protein structures. Our approach is distinguished by the following components: (1) a unified diffusion model capable of generating dynamic protein structures, including both the backbone and side chains, utilizing atomic grouping and side-chain dihedral angle predictions; (2) a reference network that enhances structural consistency by integrating the latent embeddings of the initial 3D protein structures; and (3) a motion alignment module aimed at improving temporal structural coherence across multiple time steps. To our knowledge, this is the first diffusion-based model aimed at predicting protein trajectories across multiple time steps simultaneously. Validation on benchmark datasets demonstrates that our model exhibits high accuracy in predicting dynamic 3D structures of proteins containing up to 256 amino acids over 32 time steps, effectively capturing both local flexibility in stable states and significant conformational changes.

Dynamic PDB: A New Dataset and a SE(3) Model Extension by Integrating Dynamic Behaviors and Physical Properties in Protein Structures

Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed to the limited availability, diversity, and heterogeneity of dynamic protein datasets. To address this gap, we propose to enhance existing prestigious static 3D protein structural databases, such as the Protein Data Bank (PDB), by integrating dynamic data and additional physical properties. Specifically, we introduce a large-scale dataset, Dynamic PDB, encompassing approximately 12.6K proteins, each subjected to all-atom molecular dynamics (MD) simulations lasting 1 microsecond to capture conformational changes. Furthermore, we provide a comprehensive suite of physical properties, including atomic velocities and forces, potential and kinetic energies of proteins, and the temperature of the simulation environment, recorded at 1 picosecond intervals throughout the simulations. For benchmarking purposes, we evaluate state-of-the-art methods on the proposed dataset for the task of trajectory prediction. To demonstrate the value of integrating richer physical properties in the study of protein dynamics and related model design, we base our approach on the SE(3) diffusion model and incorporate these physical properties into the trajectory prediction process. Preliminary results indicate that this straightforward extension of the SE(3) model yields improved accuracy, as measured by MAE and RMSD, when the proposed physical properties are taken into consideration.