Lanning Wei

Lanning Wei, Huan Zhao, Xiaohan Zheng et al. · tsinghua

Designing versatile graph learning approaches is important, considering the diverse graphs and tasks existing in real-world applications. Existing methods have attempted to achieve this target through automated machine learning techniques, pre-training and fine-tuning strategies, and large language models. However, these methods are not versatile enough for graph learning, as they work on either limited types of graphs or a single task. In this paper, we propose to explore versatile graph learning approaches with LLM-based agents, and the key insight is customizing the graph learning procedures for diverse graphs and tasks. To achieve this, we develop several LLM-based agents, equipped with diverse profiles, tools, functions and human experience. They collaborate to configure each procedure with task and data-specific settings step by step towards versatile solutions, and the proposed method is dubbed GL-Agent. By evaluating on diverse tasks and graphs, the correct results of the agent and its comparable performance showcase the versatility of the proposed method, especially in complex scenarios.The low resource cost and the potential to use open-source LLMs highlight the efficiency of GL-Agent.

Zhen Xu, Lanning Wei, Huan Zhao et al. · tsinghua

Graph structured data is ubiquitous in daily life and scientific areas and has attracted increasing attention. Graph Neural Networks (GNNs) have been proved to be effective in modeling graph structured data and many variants of GNN architectures have been proposed. However, much human effort is often needed to tune the architecture depending on different datasets. Researchers naturally adopt Automated Machine Learning on Graph Learning, aiming to reduce the human effort and achieve generally top-performing GNNs, but their methods focus more on the architecture search. To understand GNN practitioners' automated solutions, we organized AutoGraph Challenge at KDD Cup 2020, emphasizing on automated graph neural networks for node classification. We received top solutions especially from industrial tech companies like Meituan, Alibaba and Twitter, which are already open sourced on Github. After detailed comparisons with solutions from academia, we quantify the gaps between academia and industry on modeling scope, effectiveness and efficiency, and show that (1) academia AutoML for Graph solutions focus on GNN architecture search while industrial solutions, especially the winning ones in the KDD Cup, tend to obtain an overall solution (2) by neural architecture search only, academia solutions achieve on average 97.3% accuracy of industrial solutions (3) academia solutions are cheap to obtain with several GPU hours while industrial solutions take a few months' labors. Academic solutions also contain much fewer parameters.

Lanning Wei, Zhiqiang He, Huan Zhao et al. · tsinghua

In recent years, Graph Neural Networks (GNNs) have been popular in the graph classification task. Currently, shallow GNNs are more common due to the well-known over-smoothing problem facing deeper GNNs. However, they are sub-optimal without utilizing the information from distant nodes, i.e., the long-range dependencies. The mainstream methods in the graph classification task can extract the long-range dependencies either by designing the pooling operations or incorporating the higher-order neighbors, while they have evident drawbacks by modifying the original graph structure, which may result in information loss in graph structure learning. In this paper, by justifying the smaller influence of the over-smoothing problem in the graph classification task, we evoke the importance of stacking-based GNNs and then employ them to capture the long-range dependencies without modifying the original graph structure. To achieve this, two design needs are given for stacking-based GNNs, i.e., sufficient model depth and adaptive skip-connection schemes. By transforming the two design needs into designing data-specific inter-layer connections, we propose a novel approach with the help of neural architecture search (NAS), which is dubbed LRGNN (Long-Range Graph Neural Networks). Extensive experiments on five datasets show that the proposed LRGNN can achieve the best performance, and obtained data-specific GNNs with different depth and skip-connection schemes, which can better capture the long-range dependencies.

Xu Wang, Huan Zhao, Lanning Wei et al. · tsinghua

Aiming at two molecular graph datasets and one protein association subgraph dataset in OGB graph classification task, we design a graph neural network framework for graph classification task by introducing PAS(Pooling Architecture Search). At the same time, we improve it based on the GNN topology design method F2GNN to further design the feature selection and fusion strategies, so as to further improve the performance of the model in the graph property prediction task while overcoming the over smoothing problem of deep GNN training. Finally, a performance breakthrough is achieved on these three datasets, which is significantly better than other methods with fixed aggregate function. It is proved that the NAS method has high generalization ability for multiple tasks and the advantage of our method in processing graph property prediction tasks.

Lanning Wei, Zhiqiang He, Huan Zhao et al. · tsinghua

In recent years, Graph Neural Networks (GNNs) have been popular in graph representation learning which assumes the homophily property, i.e., the connected nodes have the same label or have similar features. However, they may fail to generalize into the heterophilous graphs which in the low/medium level of homophily. Existing methods tend to address this problem by enhancing the intra-class information extraction, i.e., either by designing better GNNs to improve the model effectiveness, or re-designing the graph structures to incorporate more potential intra-class nodes from distant hops. Despite the success, we observe two aspects that can be further improved: (a) enhancing the ego feature information extraction from node itself which is more reliable in extracting the intra-class information; (b) designing node-wise GNNs can better adapt to the nodes with different homophily ratios. In this paper, we propose a novel method IIE-GNN (Intra-class Information Enhanced Graph Neural Networks) to achieve two improvements. A unified framework is proposed based on the literature, in which the intra-class information from the node itself and neighbors can be extracted based on seven carefully designed blocks. With the help of neural architecture search (NAS), we propose a novel search space based on the framework, and then provide an architecture predictor to design GNNs for each node. We further conduct experiments to show that IIE-GNN can improve the model performance by designing node-wise GNNs to enhance intra-class information extraction.

Jintian Zhang, Kewei Xu, Jingsheng Zheng et al.

LLMs and Agents have achieved impressive progress in code generation, mathematical reasoning, and scientific discovery. However, existing benchmarks primarily measure correctness, overlooking the diversity of methods behind solutions. True innovation depends not only on producing correct answers but also on the originality of the approach. We present InnoGym, the first benchmark and framework designed to systematically evaluate the innovation potential of AI agents. InnoGym introduces two complementary metrics: performance gain, which measures improvement over the best-known solutions, and novelty, which captures methodological differences from prior approaches. The benchmark includes 18 carefully curated tasks from real-world engineering and scientific domains, each standardized through resource filtering, evaluator validation, and solution collection. In addition, we provide iGym, a unified execution environment for reproducible and long-horizon evaluations. Extensive experiments show that while some agents produce novel approaches, their lack of robustness limits performance gains. These results highlight a key gap between creativity and effectiveness, underscoring the need for benchmarks that evaluate both.

Tiwei Bie, Maosong Cao, Xiang Cao et al.

While LLaDA2.0 showcased the scaling potential of 100B-level block-diffusion models and their inherent parallelization, the delicate equilibrium between decoding speed and generation quality has remained an elusive frontier. Today, we unveil LLaDA2.1, a paradigm shift designed to transcend this trade-off. By seamlessly weaving Token-to-Token (T2T) editing into the conventional Mask-to-Token (M2T) scheme, we introduce a joint, configurable threshold-decoding scheme. This structural innovation gives rise to two distinct personas: the Speedy Mode (S Mode), which audaciously lowers the M2T threshold to bypass traditional constraints while relying on T2T to refine the output; and the Quality Mode (Q Mode), which leans into conservative thresholds to secure superior benchmark performances with manageable efficiency degrade. Furthering this evolution, underpinned by an expansive context window, we implement the first large-scale Reinforcement Learning (RL) framework specifically tailored for dLLMs, anchored by specialized techniques for stable gradient estimation. This alignment not only sharpens reasoning precision but also elevates instruction-following fidelity, bridging the chasm between diffusion dynamics and complex human intent. We culminate this work by releasing LLaDA2.1-Mini (16B) and LLaDA2.1-Flash (100B). Across 33 rigorous benchmarks, LLaDA2.1 delivers strong task performance and lightning-fast decoding speed. Despite its 100B volume, on coding tasks it attains an astounding 892 TPS on HumanEval+, 801 TPS on BigCodeBench, and 663 TPS on LiveCodeBench.

Yujie Luo, Xiangyuan Ru, Kangwei Liu et al.

We introduce OneKE, a dockerized schema-guided knowledge extraction system, which can extract knowledge from the Web and raw PDF Books, and support various domains (science, news, etc.). Specifically, we design OneKE with multiple agents and a configure knowledge base. Different agents perform their respective roles, enabling support for various extraction scenarios. The configure knowledge base facilitates schema configuration, error case debugging and correction, further improving the performance. Empirical evaluations on benchmark datasets demonstrate OneKE's efficacy, while case studies further elucidate its adaptability to diverse tasks across multiple domains, highlighting its potential for broad applications. We have open-sourced the Code at https://github.com/zjunlp/OneKE and released a Video at http://oneke.openkg.cn/demo.mp4.

Yixin Ou, Yujie Luo, Jingsheng Zheng et al.

Large Language Model (LLM) agents have shown great potential in addressing real-world data science problems. LLM-driven data science agents promise to automate the entire machine learning pipeline, yet their real-world effectiveness remains limited. Existing frameworks depend on rigid, pre-defined workflows and inflexible coding strategies; consequently, they excel only on relatively simple, classical problems and fail to capture the empirical expertise that human practitioners bring to complex, innovative tasks. In this work, we introduce AutoMind, an adaptive, knowledgeable LLM-agent framework that overcomes these deficiencies through three key advances: (1) a curated expert knowledge base that grounds the agent in domain expert knowledge, (2) an agentic knowledgeable tree search algorithm that strategically explores possible solutions, and (3) a self-adaptive coding strategy that dynamically tailors code generation to task complexity. Evaluations on two automated data science benchmarks demonstrate that AutoMind delivers superior performance versus state-of-the-art baselines. Additional analyses confirm favorable effectiveness, efficiency, and qualitative solution quality, highlighting AutoMind as an efficient and robust step toward fully automated data science. Code is at https://github.com/innovatingAI/AutoMind.

Yuxin Ma, Lun Du, Lanning Wei et al.

Diffusion-based large language models (dLLMs) have emerged as a promising alternative to autoregressive (AR) LLMs, leveraging denoising-based generation to enable inherent parallelism. Even more and more open-sourced dLLM models emerge, yet their widespread adoption remains constrained by the lack of a standardized and efficient inference framework. We present dInfer, an efficient and extensible framework for dLLM inference. dInfer decomposes the inference pipeline into four modular components--model, diffusion iteration manager, decoding strategy, and KV-cache manager--and integrates novel algorithms for each component alongside system-level optimizations. Through this combination of algorithmic innovations and system enhancements, dInfer achieves substantial efficiency gains without compromising output quality on LLaDA-MoE. At batch size 1, it surpasses 1,100 tokens per second on HumanEval and averages over 800 tokens per second across six benchmarks on $8\times$ H800 GPUs. Compared to prior systems, dInfer delivers a $10\times$ speedup over Fast-dLLM while maintaining similar model performance. Even compared to the AR model (with a comparable number of activation parameters and performance) QWen2.5-3B, which is highly optimized with the latest vLLM inference engine, dInfer still delivers a $2$-$3\times$ speedup. The implementation of dInfer is open-sourced at https://github.com/inclusionAI/dInfer.

Yujie Luo, Zhuoyun Yu, Xuehai Wang et al.

Replicating AI research is a crucial yet challenging task for large language model (LLM) agents. Existing approaches often struggle to generate executable code, primarily due to insufficient background knowledge and the limitations of retrieval-augmented generation (RAG) methods, which fail to capture latent technical details hidden in referenced papers. Furthermore, previous approaches tend to overlook valuable implementation-level code signals and lack structured knowledge representations that support multi-granular retrieval and reuse. To overcome these challenges, we propose Executable Knowledge Graphs (xKG), a modular and pluggable knowledge base that automatically integrates technical insights, code snippets, and domain-specific knowledge extracted from scientific literature. When integrated into three agent frameworks with two different LLMs, xKG shows substantial performance gains (10.9% with o3-mini) on PaperBench, demonstrating its effectiveness as a general and extensible solution for automated AI research replication. Code will released at https://github.com/zjunlp/xKG.

Da Zheng, Lun Du, Junwei Su et al.

Problem-solving has been a fundamental driver of human progress in numerous domains. With advancements in artificial intelligence, Large Language Models (LLMs) have emerged as powerful tools capable of tackling complex problems across diverse domains. Unlike traditional computational systems, LLMs combine raw computational power with an approximation of human reasoning, allowing them to generate solutions, make inferences, and even leverage external computational tools. However, applying LLMs to real-world problem-solving presents significant challenges, including multi-step reasoning, domain knowledge integration, and result verification. This survey explores the capabilities and limitations of LLMs in complex problem-solving, examining techniques including Chain-of-Thought (CoT) reasoning, knowledge augmentation, and various LLM-based and tool-based verification techniques. Additionally, we highlight domain-specific challenges in various domains, such as software engineering, mathematical reasoning and proving, data analysis and modeling, and scientific research. The paper further discusses the fundamental limitations of the current LLM solutions and the future directions of LLM-based complex problems solving from the perspective of multi-step reasoning, domain knowledge integration and result verification.

Fengqi Zhu, Zebin You, Yipeng Xing et al.

We introduce LLaDA-MoE, a large language diffusion model with the Mixture-of-Experts (MoE) architecture, trained from scratch on approximately 20T tokens. LLaDA-MoE achieves competitive performance with significantly reduced computational overhead by maintaining a 7B-parameter capacity while activating only 1.4B parameters during inference. Our empirical evaluation reveals that LLaDA-MoE achieves state-of-the-art performance among diffusion language models with larger parameters, surpassing previous diffusion language models LLaDA, LLaDA 1.5, and Dream across multiple benchmarks. The instruct-tuned model LLaDA-MoE-7B-A1B-Instruct demonstrates capabilities comparable to Qwen2.5-3B-Instruct in knowledge understanding, code generation, mathematical reasoning, agent and alignment tasks, despite using fewer active parameters. Our results show that integrating a sparse MoE architecture into the training objective of masked diffusion language models still brings out MoE's strengths under efficient inference with few active parameters, and opens ample room for further exploration of diffusion language models. LLaDA-MoE models are available at Huggingface.

Lanning Wei, Jun Gao, Huan Zhao et al.

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

Mingyang Zhou, Quanming Yao, Lun Du et al.

Reproducing machine learning papers is essential for scientific progress but remains challenging for both humans and automated agents. Existing agent-based methods often struggle to fully and accurately reproduce implementation details such as mathematical formulas and algorithmic logic. Previous studies show that reflection with explicit feedback improves agent performance. However, current paper reproduction methods fail to effectively adopt this strategy. This gap mainly arises from the diverse paper patterns, complex method modules, and varied configurations encountered in research papers. Motivated by how humans use systematic checklists to efficiently debug complex code, we propose \textbf{RePro}, a \textbf{Re}flective Paper-to-Code \textbf{Repro}duction framework that automatically extracts a paper's fingerprint, referring to a comprehensive set of accurate and atomic criteria serving as high-quality supervisory signals. The framework first generates code based on the extracted information, and then leverages the fingerprint within iterative verification and refinement loop. This approach systematically detects discrepancies and produces targeted revisions to align generated code with the paper's implementation details. Extensive experiments on the PaperBench Code-Dev benchmark have been conducted, RePro achieves 13.0\% performance gap over baselines, and it correctly revises complex logical and mathematical criteria in reflecting, on which the effectiveness is obvious.

Xiaohan Zheng, Lanning Wei, Yong Li et al.

Effective decision-making on networks often relies on learning from graph-structured data, where Graph Neural Networks (GNNs) play a central role, but they take efforts to configure and tune. In this demo, we propose LLMNet, showing how to design GNN automated through Large Language Models. Our system develops a set of agents that construct graph-related knowlege bases and then leverages Retrieval-Augmented Generation (RAG) to support automated configuration and refinement of GNN models through a knowledge-guided evolution process. These agents, equipped with specialized knowledge bases, extract insights into tasks and graph structures by interacting with the knowledge bases. Empirical results show LLMNet excels in twelve datasets across three graph learning tasks, validating its effectiveness of GNN model designing.

Juzheng Zhang, Lanning Wei, Zhen Xu et al.

Link prediction is a fundamental task in graph learning, inherently shaped by the topology of the graph. While traditional heuristics are grounded in graph topology, they encounter challenges in generalizing across diverse graphs. Recent research efforts have aimed to leverage the potential of heuristics, yet a unified formulation accommodating both local and global heuristics remains undiscovered. Drawing insights from the fact that both local and global heuristics can be represented by adjacency matrix multiplications, we propose a unified matrix formulation to accommodate and generalize various heuristics. We further propose the Heuristic Learning Graph Neural Network (HL-GNN) to efficiently implement the formulation. HL-GNN adopts intra-layer propagation and inter-layer connections, allowing it to reach a depth of around 20 layers with lower time complexity than GCN. Extensive experiments on the Planetoid, Amazon, and OGB datasets underscore the effectiveness and efficiency of HL-GNN. It outperforms existing methods by a large margin in prediction performance. Additionally, HL-GNN is several orders of magnitude faster than heuristic-inspired methods while requiring only a few trainable parameters. The case study further demonstrates that the generalized heuristics and learned weights are highly interpretable.

Lanning Wei, Huan Zhao, Zhiqiang He

In recent years, Graph Neural Networks (GNNs) have shown superior performance on diverse real-world applications. To improve the model capacity, besides designing aggregation operations, GNN topology design is also very important. In general, there are two mainstream GNN topology design manners. The first one is to stack aggregation operations to obtain the higher-level features but easily got performance drop as the network goes deeper. Secondly, the multiple aggregation operations are utilized in each layer which provides adequate and independent feature extraction stage on local neighbors while are costly to obtain the higher-level information. To enjoy the benefits while alleviating the corresponding deficiencies of these two manners, we learn to design the topology of GNNs in a novel feature fusion perspective which is dubbed F$^2$GNN. To be specific, we provide a feature fusion perspective in designing GNN topology and propose a novel framework to unify the existing topology designs with feature selection and fusion strategies. Then we develop a neural architecture search method on top of the unified framework which contains a set of selection and fusion operations in the search space and an improved differentiable search algorithm. The performance gains on eight real-world datasets demonstrate the effectiveness of F$^2$GNN. We further conduct experiments to show that F$^2$GNN can improve the model capacity while alleviating the deficiencies of existing GNN topology design manners, especially alleviating the over-smoothing problem, by utilizing different levels of features adaptively.

Lanning Wei, Huan Zhao, Zhiqiang He

In recent years, Graph Neural Networks (GNNs) have shown superior performance on diverse applications on real-world datasets. To improve the model capacity and alleviate the over-smoothing problem, several methods proposed to incorporate the intermediate layers by layer-wise connections. However, due to the highly diverse graph types, the performance of existing methods vary on diverse graphs, leading to a need for data-specific layer-wise connection methods. To address this problem, we propose a novel framework LLC (Learn Layer-wise Connections) based on neural architecture search (NAS) to learn adaptive connections among intermediate layers in GNNs. LLC contains one novel search space which consists of 3 types of blocks and learnable connections, and one differentiable search algorithm to enable the efficient search process. Extensive experiments on five real-world datasets are conducted, and the results show that the searched layer-wise connections can not only improve the performance but also alleviate the over-smoothing problem.

Lanning Wei, Huan Zhao, Quanming Yao et al.

Graph classification is an important problem with applications across many domains, like chemistry and bioinformatics, for which graph neural networks (GNNs) have been state-of-the-art (SOTA) methods. GNNs are designed to learn node-level representation based on neighborhood aggregation schemes, and to obtain graph-level representation, pooling methods are applied after the aggregation operation in existing GNN models to generate coarse-grained graphs. However,due to highly diverse applications of graph classification, and the performance of existing pooling methods vary on different graphs. In other words, it is a challenging problem to design a universal pooling architecture to perform well in most cases, leading to a demand for data-specific pooling methods in real-world applications. To address this problem, we propose to use neural architecture search (NAS) to search for adaptive pooling architectures for graph classification. Firstly we designed a unified framework consisting of four modules: Aggregation, Pooling, Readout, and Merge, which can cover existing human-designed pooling methods for graph classification. Based on this framework, a novel search space is designed by incorporating popular operations in human-designed architectures. Then to enable efficient search, a coarsening strategy is proposed to continuously relax the search space, thus a differentiable search method can be adopted. Extensive experiments on six real-world datasets from three domains are conducted, and the results demonstrate the effectiveness and efficiency of the proposed framework.

Huan Zhao, Lanning Wei, Quanming Yao

Recent years have witnessed the popularity of Graph Neural Networks (GNN) in various scenarios. To obtain optimal data-specific GNN architectures, researchers turn to neural architecture search (NAS) methods, which have made impressive progress in discovering effective architectures in convolutional neural networks. Two preliminary works, GraphNAS and Auto-GNN, have made first attempt to apply NAS methods to GNN. Despite the promising results, there are several drawbacks in expressive capability and search efficiency of GraphNAS and Auto-GNN due to the designed search space. To overcome these drawbacks, we propose the SNAG framework (Simplified Neural Architecture search for Graph neural networks), consisting of a novel search space and a reinforcement learning based search algorithm. Extensive experiments on real-world datasets demonstrate the effectiveness of the SNAG framework compared to human-designed GNNs and NAS methods, including GraphNAS and Auto-GNN.

Zhenqian Shen, Yongqi Zhang, Lanning Wei et al.

Machine learning (ML) methods have been developing rapidly, but configuring and selecting proper methods to achieve a desired performance is increasingly difficult and tedious. To address this challenge, automated machine learning (AutoML) has emerged, which aims to generate satisfactory ML configurations for given tasks in a data-driven way. In this paper, we provide a comprehensive survey on this topic. We begin with the formal definition of AutoML and then introduce its principles, including the bi-level learning objective, the learning strategy, and the theoretical interpretation. Then, we summarize the AutoML practices by setting up the taxonomy of existing works based on three main factors: the search space, the search algorithm, and the evaluation strategy. Each category is also explained with the representative methods. Then, we illustrate the principles and practices with exemplary applications from configuring ML pipeline, one-shot neural architecture search, and integration with foundation models. Finally, we highlight the emerging directions of AutoML and conclude the survey.