Junwei Yang

Wei Ju, Zheng Fang, Yiyang Gu et al. · uw

Graph representation learning aims to effectively encode high-dimensional sparse graph-structured data into low-dimensional dense vectors, which is a fundamental task that has been widely studied in a range of fields, including machine learning and data mining. Classic graph embedding methods follow the basic idea that the embedding vectors of interconnected nodes in the graph can still maintain a relatively close distance, thereby preserving the structural information between the nodes in the graph. However, this is sub-optimal due to: (i) traditional methods have limited model capacity which limits the learning performance; (ii) existing techniques typically rely on unsupervised learning strategies and fail to couple with the latest learning paradigms; (iii) representation learning and downstream tasks are dependent on each other which should be jointly enhanced. With the remarkable success of deep learning, deep graph representation learning has shown great potential and advantages over shallow (traditional) methods, there exist a large number of deep graph representation learning techniques have been proposed in the past decade, especially graph neural networks. In this survey, we conduct a comprehensive survey on current deep graph representation learning algorithms by proposing a new taxonomy of existing state-of-the-art literature. Specifically, we systematically summarize the essential components of graph representation learning and categorize existing approaches by the ways of graph neural network architectures and the most recent advanced learning paradigms. Moreover, this survey also provides the practical and promising applications of deep graph representation learning. Last but not least, we state new perspectives and suggest challenging directions which deserve further investigations in the future.

Kimi Team, Tongtong Bai, Yifan Bai et al.

We introduce Kimi K2.5, an open-source multimodal agentic model designed to advance general agentic intelligence. K2.5 emphasizes the joint optimization of text and vision so that two modalities enhance each other. This includes a series of techniques such as joint text-vision pre-training, zero-vision SFT, and joint text-vision reinforcement learning. Building on this multimodal foundation, K2.5 introduces Agent Swarm, a self-directed parallel agent orchestration framework that dynamically decomposes complex tasks into heterogeneous sub-problems and executes them concurrently. Extensive evaluations show that Kimi K2.5 achieves state-of-the-art results across various domains including coding, vision, reasoning, and agentic tasks. Agent Swarm also reduces latency by up to $4.5\times$ over single-agent baselines. We release the post-trained Kimi K2.5 model checkpoint to facilitate future research and real-world applications of agentic intelligence.

Wei Ju, Junwei Yang, Meng Qu et al.

This paper studies semi-supervised graph classification, which is an important problem with various applications in social network analysis and bioinformatics. This problem is typically solved by using graph neural networks (GNNs), which yet rely on a large number of labeled graphs for training and are unable to leverage unlabeled graphs. We address the limitations by proposing the Kernel-based Graph Neural Network (KGNN). A KGNN consists of a GNN-based network as well as a kernel-based network parameterized by a memory network. The GNN-based network performs classification through learning graph representations to implicitly capture the similarity between query graphs and labeled graphs, while the kernel-based network uses graph kernels to explicitly compare each query graph with all the labeled graphs stored in a memory for prediction. The two networks are motivated from complementary perspectives, and thus combing them allows KGNN to use labeled graphs more effectively. We jointly train the two networks by maximizing their agreement on unlabeled graphs via posterior regularization, so that the unlabeled graphs serve as a bridge to let both networks mutually enhance each other. Experiments on a range of well-known benchmark datasets demonstrate that KGNN achieves impressive performance over competitive baselines.

Yiyang Gu, Junwei Yang, Junyu Luo et al.

Large language models (LLMs) are increasingly applied to scientific research, yet existing evaluations often fail to reflect the fine-grained capabilities required in practice. Most benchmarks are manually curated or domain-generic, limiting scalability and alignment with real scientific use cases. In this paper, we propose a new framework named SciCustom to address the problem. It enables the custom construction of benchmarks from large-scale scientific data to evaluate application-specific scientific capabilities in LLMs. SciCustom first organizes scientific knowledge into ontology-grounded knowledge units with controlled granularity and trains a tagger to map large-scale data instances into this knowledge space. Given a custom requirement, relevant knowledge units are identified via voting-based multi-model consensus. These units enable relevance-aware benchmark retrieval via binary search, followed by proxy subset selection and data-grounded benchmark generation for efficient evaluation. Experiments in chemistry and healthcare demonstrate that SciCustom reveals fine-grained differences in LLM scientific capabilities that standard benchmarks overlook, while requiring neither expert annotation nor synthetic question generation. This work provides a scalable and application-aware foundation for benchmarking scientific capabilities in LLMs. The source code is available at https://github.com/yjwtheonly/SciCustom.

Junwei Yang, Ke Zhang, Zhaolin Cui et al.

Feature representation via self-supervised learning has reached remarkable success in image-level contrastive learning, which brings impressive performances on image classification tasks. While image-level feature representation mainly focuses on contrastive learning in single instance, it ignores the objective differences between pretext and downstream prediction tasks such as object detection and instance segmentation. In order to fully unleash the power of feature representation on downstream prediction tasks, we propose a new end-to-end self-supervised framework called InsCon, which is devoted to capturing multi-instance information and extracting cell-instance features for object recognition and localization. On the one hand, InsCon builds a targeted learning paradigm that applies multi-instance images as input, aligning the learned feature between corresponding instance views, which makes it more appropriate for multi-instance recognition tasks. On the other hand, InsCon introduces the pull and push of cell-instance, which utilizes cell consistency to enhance fine-grained feature representation for precise boundary localization. As a result, InsCon learns multi-instance consistency on semantic feature representation and cell-instance consistency on spatial feature representation. Experiments demonstrate the method we proposed surpasses MoCo v2 by 1.1% AP^{bb} on COCO object detection and 1.0% AP^{mk} on COCO instance segmentation using Mask R-CNN R50-FPN network structure with 90k iterations, 2.1% APbb on PASCAL VOC objection detection using Faster R-CNN R50-C4 network structure with 24k iterations.

Junyu Luo, Weizhi Zhang, Ye Yuan et al. · pku

The era of intelligent agents is upon us, driven by revolutionary advancements in large language models. Large Language Model (LLM) agents, with goal-driven behaviors and dynamic adaptation capabilities, potentially represent a critical pathway toward artificial general intelligence. This survey systematically deconstructs LLM agent systems through a methodology-centered taxonomy, linking architectural foundations, collaboration mechanisms, and evolutionary pathways. We unify fragmented research threads by revealing fundamental connections between agent design principles and their emergent behaviors in complex environments. Our work provides a unified architectural perspective, examining how agents are constructed, how they collaborate, and how they evolve over time, while also addressing evaluation methodologies, tool applications, practical challenges, and diverse application domains. By surveying the latest developments in this rapidly evolving field, we offer researchers a structured taxonomy for understanding LLM agents and identify promising directions for future research. The collection is available at https://github.com/luo-junyu/Awesome-Agent-Papers.

Kangjie Zheng, Siyu Long, Tianyu Lu et al.

Protein language models have demonstrated significant potential in the field of protein engineering. However, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the atom level. This limitation prevents us from fully exploiting the capabilities of protein language models for applications involving both proteins and small molecules. In this paper, we propose ESM-AA (ESM All-Atom), a novel approach that enables atom-scale and residue-scale unified molecular modeling. ESM-AA achieves this by pre-training on multi-scale code-switch protein sequences and utilizing a multi-scale position encoding to capture relationships among residues and atoms. Experimental results indicate that ESM-AA surpasses previous methods in protein-molecule tasks, demonstrating the full utilization of protein language models. Further investigations reveal that through unified molecular modeling, ESM-AA not only gains molecular knowledge but also retains its understanding of proteins. The source codes of ESM-AA are publicly released at https://github.com/zhengkangjie/ESM-AA.

Zequn Liu, Kefei Duan, Junwei Yang et al.

Heterogeneous Information Network (HIN) is essential to study complicated networks containing multiple edge types and node types. Meta-path, a sequence of node types and edge types, is the core technique to embed HINs. Since manually curating meta-paths is time-consuming, there is a pressing need to develop automated meta-path generation approaches. Existing meta-path generation approaches cannot fully exploit the rich textual information in HINs, such as node names and edge type names. To address this problem, we propose MetaFill, a text-infilling-based approach for meta-path generation. The key idea of MetaFill is to formulate meta-path identification problem as a word sequence infilling problem, which can be advanced by Pretrained Language Models (PLMs). We observed the superior performance of MetaFill against existing meta-path generation methods and graph embedding methods that do not leverage meta-paths in both link prediction and node classification on two real-world HIN datasets. We further demonstrated how MetaFill can accurately classify edges in the zero-shot setting, where existing approaches cannot generate any meta-paths. MetaFill exploits PLMs to generate meta-paths for graph embedding, opening up new avenues for language model applications in graph analysis.

Wei Ju, Yifan Wang, Yifang Qin et al. · pku

In recent years, deep learning on graphs has achieved remarkable success in various domains. However, the reliance on annotated graph data remains a significant bottleneck due to its prohibitive cost and time-intensive nature. To address this challenge, self-supervised learning (SSL) on graphs has gained increasing attention and has made significant progress. SSL enables machine learning models to produce informative representations from unlabeled graph data, reducing the reliance on expensive labeled data. While SSL on graphs has witnessed widespread adoption, one critical component, Graph Contrastive Learning (GCL), has not been thoroughly investigated in the existing literature. Thus, this survey aims to fill this gap by offering a dedicated survey on GCL. We provide a comprehensive overview of the fundamental principles of GCL, including data augmentation strategies, contrastive modes, and contrastive optimization objectives. Furthermore, we explore the extensions of GCL to other aspects of data-efficient graph learning, such as weakly supervised learning, transfer learning, and related scenarios. We also discuss practical applications spanning domains such as drug discovery, genomics analysis, recommender systems, and finally outline the challenges and potential future directions in this field.

Chunwei Wang, Guansong Lu, Junwei Yang et al.

In this paper, we introduce ILLUME, a unified multimodal large language model (MLLM) that seamlessly integrates multimodal understanding and generation capabilities within a single large language model through a unified next-token prediction formulation. To address the large dataset size typically required for image-text alignment, we propose to enhance data efficiency through the design of a vision tokenizer that incorporates semantic information and a progressive multi-stage training procedure. This approach reduces the dataset size to just 15M for pretraining -- over four times fewer than what is typically needed -- while achieving competitive or even superior performance with existing unified MLLMs, such as Janus. Additionally, to promote synergistic enhancement between understanding and generation capabilities, which is under-explored in previous works, we introduce a novel self-enhancing multimodal alignment scheme. This scheme supervises the MLLM to self-assess the consistency between text descriptions and self-generated images, facilitating the model to interpret images more accurately and avoid unrealistic and incorrect predictions caused by misalignment in image generation. Based on extensive experiments, our proposed ILLUME stands out and competes with state-of-the-art unified MLLMs and specialized models across various benchmarks for multimodal understanding, generation, and editing.

Runhui Huang, Chunwei Wang, Junwei Yang et al.

We present ILLUME+ that leverages dual visual tokenization and a diffusion decoder to improve both deep semantic understanding and high-fidelity image generation. Existing unified models have struggled to simultaneously handle the three fundamental capabilities in a unified model: understanding, generation, and editing. Models like Chameleon and EMU3 utilize VQGAN for image discretization, due to the lack of deep semantic interaction, they lag behind specialist models like LLaVA in visual understanding tasks. To mitigate this, LaViT and ILLUME employ semantic encoders for tokenization, but they struggle with image editing due to poor texture preservation. Meanwhile, Janus series decouples the input and output image representation, limiting their abilities to seamlessly handle interleaved image-text understanding and generation. In contrast, ILLUME+ introduces a unified dual visual tokenizer, DualViTok, which preserves both fine-grained textures and text-aligned semantics while enabling a coarse-to-fine image representation strategy for multimodal understanding and generation. Additionally, we employ a diffusion model as the image detokenizer for enhanced generation quality and efficient super-resolution. ILLUME+ follows a continuous-input, discrete-output scheme within the unified MLLM and adopts a progressive training procedure that supports dynamic resolution across the vision tokenizer, MLLM, and diffusion decoder. This design allows for flexible and efficient context-aware image editing and generation across diverse tasks. ILLUME+ (3B) exhibits competitive performance against existing unified MLLMs and specialized models across multimodal understanding, generation, and editing benchmarks. With its strong performance, ILLUME+ provides a scalable and versatile foundation for future multimodal applications. Project Page: https://illume-unified-mllm.github.io/.

Kangjie Zheng, Siyue Liang, Junwei Yang et al.

SMILES, a crucial textual representation of molecular structures, has garnered significant attention as a foundation for pre-trained language models (LMs). However, most existing pre-trained SMILES LMs focus solely on the single-token level supervision during pre-training, failing to fully leverage the substructural information of molecules. This limitation makes the pre-training task overly simplistic, preventing the models from capturing richer molecular semantic information. Moreover, during pre-training, these SMILES LMs only process corrupted SMILES inputs, never encountering any valid SMILES, which leads to a train-inference mismatch. To address these challenges, we propose SMI-Editor, a novel edit-based pre-trained SMILES LM. SMI-Editor disrupts substructures within a molecule at random and feeds the resulting SMILES back into the model, which then attempts to restore the original SMILES through an editing process. This approach not only introduces fragment-level training signals, but also enables the use of valid SMILES as inputs, allowing the model to learn how to reconstruct complete molecules from these incomplete structures. As a result, the model demonstrates improved scalability and an enhanced ability to capture fragment-level molecular information. Experimental results show that SMI-Editor achieves state-of-the-art performance across multiple downstream molecular tasks, and even outperforming several 3D molecular representation models.

Junhao Su, Yuanliang Wan, Junwei Yang et al.

Tool-augmented large language models (LLMs) are usually trained with supervised imitation or coarse-grained reinforcement learning that optimizes single tool calls. Current self-reflection practices rely on heuristic prompts or one-way reasoning: the model is urged to 'think more' instead of learning error diagnosis and repair. This is fragile in multi-turn interactions; after a failure the model often repeats the same mistake. We propose structured reflection, which turns the path from error to repair into an explicit, controllable, and trainable action. The agent produces a short yet precise reflection: it diagnoses the failure using evidence from the previous step and then proposes a correct, executable follow-up call. For training we combine DAPO and GSPO objectives with a reward scheme tailored to tool use, optimizing the stepwise strategy Reflect, then Call, then Final. To evaluate, we introduce Tool-Reflection-Bench, a lightweight benchmark that programmatically checks structural validity, executability, parameter correctness, and result consistency. Tasks are built as mini trajectories of erroneous call, reflection, and corrected call, with disjoint train and test splits. Experiments on BFCL v3 and Tool-Reflection-Bench show large gains in multi-turn tool-call success and error recovery, and a reduction of redundant calls. These results indicate that making reflection explicit and optimizing it directly improves the reliability of tool interaction and offers a reproducible path for agents to learn from failure.

Kangjie Zheng, Junwei Yang, Siyue Liang et al.

Masked Language Models (MLMs) have achieved remarkable success in many self-supervised representation learning tasks. MLMs are trained by randomly masking portions of the input sequences with [MASK] tokens and learning to reconstruct the original content based on the remaining context. This paper explores the impact of [MASK] tokens on MLMs. Analytical studies show that masking tokens can introduce the corrupted semantics problem, wherein the corrupted context may convey multiple, ambiguous meanings. This problem is also a key factor affecting the performance of MLMs on downstream tasks. Based on these findings, we propose a novel enhanced-context MLM, ExLM. Our approach expands [MASK] tokens in the input context and models the dependencies between these expanded states. This enhancement increases context capacity and enables the model to capture richer semantic information, effectively mitigating the corrupted semantics problem during pre-training. Experimental results demonstrate that ExLM achieves significant performance improvements in both text modeling and SMILES modeling tasks. Further analysis confirms that ExLM enriches semantic representations through context enhancement, and effectively reduces the semantic multimodality commonly observed in MLMs.

Junwei Yang, Xiao-Xin Li, Feihong Liu et al.

Recent studies on T1-assisted MRI reconstruction for under-sampled images of other modalities have demonstrated the potential of further accelerating MRI acquisition of other modalities. Most of the state-of-the-art approaches have achieved improvement through the development of network architectures for fixed under-sampling patterns, without fully exploiting the complementary information between modalities. Although existing under-sampling pattern learning algorithms can be simply modified to allow the fully-sampled T1-weighted MR image to assist the pattern learning, no significant improvement on the reconstruction task can be achieved. To this end, we propose an iterative framework to optimize the under-sampling pattern for MRI acquisition of another modality that can complement the fully-sampled T1-weighted MR image at different under-sampling factors, while jointly optimizing the T1-assisted MRI reconstruction model. Specifically, our proposed method exploits the difference of latent information between the two modalities for determining the sampling patterns that can maximize the assistance power of T1-weighted MR image in improving the MRI reconstruction. We have demonstrated superior performance of our learned under-sampling patterns on a public dataset, compared to commonly used under-sampling patterns and state-of-the-art methods that can jointly optimize both the reconstruction network and the under-sampling pattern, up to 8-fold under-sampling factor.

Jin Zhu, Chuan Tan, Junwei Yang et al.

Single image super-resolution (SISR) aims to obtain a high-resolution output from one low-resolution image. Currently, deep learning-based SISR approaches have been widely discussed in medical image processing, because of their potential to achieve high-quality, high spatial resolution images without the cost of additional scans. However, most existing methods are designed for scale-specific SR tasks and are unable to generalise over magnification scales. In this paper, we propose an approach for medical image arbitrary-scale super-resolution (MIASSR), in which we couple meta-learning with generative adversarial networks (GANs) to super-resolve medical images at any scale of magnification in (1, 4]. Compared to state-of-the-art SISR algorithms on single-modal magnetic resonance (MR) brain images (OASIS-brains) and multi-modal MR brain images (BraTS), MIASSR achieves comparable fidelity performance and the best perceptual quality with the smallest model size. We also employ transfer learning to enable MIASSR to tackle SR tasks of new medical modalities, such as cardiac MR images (ACDC) and chest computed tomography images (COVID-CT). The source code of our work is also public. Thus, MIASSR has the potential to become a new foundational pre-/post-processing step in clinical image analysis tasks such as reconstruction, image quality enhancement, and segmentation.

Ashwini Pokle, Roberto Martín-Martín, Patrick Goebel et al.

We present a navigation system that combines ideas from hierarchical planning and machine learning. The system uses a traditional global planner to compute optimal paths towards a goal, and a deep local trajectory planner and velocity controller to compute motion commands. The latter components of the system adjust the behavior of the robot through attention mechanisms such that it moves towards the goal, avoids obstacles, and respects the space of nearby pedestrians. Both the structure of the proposed deep models and the use of attention mechanisms make the system's execution interpretable. Our simulation experiments suggest that the proposed architecture outperforms baselines that try to map global plan information and sensor data directly to velocity commands. In comparison to a hand-designed traditional navigation system, the proposed approach showed more consistent performance.