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.

Promoting Equality in Large Language Models: Identifying and Mitigating the Implicit Bias based on Bayesian Theory

Large language models (LLMs) are trained on extensive text corpora, which inevitably include biased information. Although techniques such as Affective Alignment can mitigate some negative impacts of these biases, existing prompt-based attack methods can still extract these biases from the model's weights. Moreover, these biases frequently appear subtly when LLMs are prompted to perform identical tasks across different demographic groups, thereby camouflaging their presence. To address this issue, we have formally defined the implicit bias problem and developed an innovative framework for bias removal based on Bayesian theory, Bayesian-Theory based Bias Removal (BTBR). BTBR employs likelihood ratio screening to pinpoint data entries within publicly accessible biased datasets that represent biases inadvertently incorporated during the LLM training phase. It then automatically constructs relevant knowledge triples and expunges bias information from LLMs using model editing techniques. Through extensive experimentation, we have confirmed the presence of the implicit bias problem in LLMs and demonstrated the effectiveness of our BTBR approach.

Imagen 3

We introduce Imagen 3, a latent diffusion model that generates high quality images from text prompts. We describe our quality and responsibility evaluations. Imagen 3 is preferred over other state-of-the-art (SOTA) models at the time of evaluation. In addition, we discuss issues around safety and representation, as well as methods we used to minimize the potential harm of our models.

FuXi Weather: An end-to-end machine learning weather data assimilation and forecasting system

Operational numerical weather prediction systems consist of three fundamental components: the global observing system for data collection, data assimilation for generating initial conditions, and the forecasting model to predict future weather conditions. While NWP have undergone a quiet revolution, with forecast skills progressively improving over the past few decades, their advancement has slowed due to challenges such as high computational costs and the complexities associated with assimilating an increasing volume of observational data and managing finer spatial grids. Advances in machine learning offer an alternative path towards more efficient and accurate weather forecasts. The rise of machine learning based weather forecasting models has also spurred the development of machine learning based DA models or even purely machine learning based weather forecasting systems. This paper introduces FuXi Weather, an end-to-end machine learning based weather forecasting system. FuXi Weather employs specialized data preprocessing and multi-modal data fusion techniques to integrate information from diverse sources under all-sky conditions, including microwave sounders from 3 polar-orbiting satellites and radio occultation data from Global Navigation Satellite System. Operating on a 6-hourly DA and forecasting cycle, FuXi Weather independently generates robust and accurate 10-day global weather forecasts at a spatial resolution of 0.25\textdegree. It surpasses the European Centre for Medium-range Weather Forecasts high-resolution forecasts in terms of predictability, extending the skillful forecast lead times for several key weather variables such as the geopotential height at 500 hPa from 9.25 days to 9.5 days. The system's high computational efficiency and robust performance, even with limited observations, demonstrates its potential as a promising alternative to traditional NWP systems.

Thought-Like-Pro: Enhancing Reasoning of Large Language Models through Self-Driven Prolog-based Chain-of-Though

Large language models (LLMs) have shown exceptional performance as general-purpose assistants, excelling across a variety of reasoning tasks. This achievement represents a significant step toward achieving artificial general intelligence (AGI). Despite these advancements, the effectiveness of LLMs often hinges on the specific prompting strategies employed, and there remains a lack of a robust framework to facilitate learning and generalization across diverse reasoning tasks. To address these challenges, we introduce a novel learning framework, THOUGHT-LIKE-PRO In this framework, we utilize imitation learning to imitate the Chain-of-Thought (CoT) process which is verified and translated from reasoning trajectories generated by a symbolic Prolog logic engine. This framework proceeds in a self-driven manner, that enables LLMs to formulate rules and statements from given instructions and leverage the symbolic Prolog engine to derive results. Subsequently, LLMs convert Prolog-derived successive reasoning trajectories into natural language CoT for imitation learning. Our empirical findings indicate that our proposed approach substantially enhances the reasoning abilities of LLMs and demonstrates robust generalization across out-of-distribution reasoning tasks.

Struct-X: Enhancing Large Language Models Reasoning with Structured Data

Structured data, rich in logical and relational information, has the potential to enhance the reasoning abilities of large language models (LLMs). Still, its integration poses a challenge due to the risk of overwhelming LLMs with excessive tokens and irrelevant context information. To address this, we propose Struct-X, a novel framework that operates through five key phases: ``read-model-fill-reflect-reason'' efficiently enabling LLMs to utilize structured data. It begins by encoding structured data into a topological space using graph embeddings, followed by filling in missing entity information with knowledge retrieval modules, and filtering out irrelevant tokens via a self-supervised module. The final phase involves constructing a topological network with selected tokens to further reduce the total token length for more effective LLM inference. Additionally, Struct-X includes an Auxiliary Module trained to generate prompts, aiding LLMs in analyzing structured data. Extensive experiments on benchmarks, including the knowledge graph question-answer task and the long document reading comprehension task, show that Struct-X notably improves LLM reasoning, demonstrating the effectiveness of structured data augmentation in improving LLM inference with complex input context.

Sign is Not a Remedy: Multiset-to-Multiset Message Passing for Learning on Heterophilic Graphs

Graph Neural Networks (GNNs) have gained significant attention as a powerful modeling and inference method, especially for homophilic graph-structured data. To empower GNNs in heterophilic graphs, where adjacent nodes exhibit dissimilar labels or features, Signed Message Passing (SMP) has been widely adopted. However, there is a lack of theoretical and empirical analysis regarding the limitations of SMP. In this work, we unveil some potential pitfalls of SMP and their remedies. We first identify two limitations of SMP: undesirable representation update for multi-hop neighbors and vulnerability against oversmoothing issues. To overcome these challenges, we propose a novel message passing function called Multiset to Multiset GNN(M2M-GNN). Our theoretical analyses and extensive experiments demonstrate that M2M-GNN effectively alleviates the aforementioned limitations of SMP, yielding superior performance in comparison

AI2Apps: A Visual IDE for Building LLM-based AI Agent Applications

We introduce AI2Apps, a Visual Integrated Development Environment (Visual IDE) with full-cycle capabilities that accelerates developers to build deployable LLM-based AI agent Applications. This Visual IDE prioritizes both the Integrity of its development tools and the Visuality of its components, ensuring a smooth and efficient building experience.On one hand, AI2Apps integrates a comprehensive development toolkit ranging from a prototyping canvas and AI-assisted code editor to agent debugger, management system, and deployment tools all within a web-based graphical user interface. On the other hand, AI2Apps visualizes reusable front-end and back-end code as intuitive drag-and-drop components. Furthermore, a plugin system named AI2Apps Extension (AAE) is designed for Extensibility, showcasing how a new plugin with 20 components enables web agent to mimic human-like browsing behavior. Our case study demonstrates substantial efficiency improvements, with AI2Apps reducing token consumption and API calls when debugging a specific sophisticated multimodal agent by approximately 90% and 80%, respectively. The AI2Apps, including an online demo, open-source code, and a screencast video, is now publicly accessible.