arXiv subjects

Junwei Yang

Publications and source records attributed to Junwei Yang.

At least 19 recordsLinked to original sources

arXiv2026

Breaking the mutual exclusivity between metallicity and ferroelectricity in a non-polar covalent semiconductor via orbital selective doping

The mutual exclusion of ferroelectricity and metallic conductivity is a long-standing tenet because itinerant electrons screen long-range Coulomb forces that stabilize the bulk polar order. Here, we break this paradigm by heavily doping a non-polar covalent semiconductor of cubic silicon carbide (3C-SiC) with nitrogen. This introduces heavy electron doping, inducing metallicity and driving a structural transition from the non-polar F-43m to the polar R3m symmetry via the pseudo-Jahn-Teller effect. Remarkably, we provide direct, atomic-scale visualization of about 180{\deg} polarization reversal under an external voltage bias in a ferroelectric metal. The strongly directional character of antibonding orbitals occupied by conduction electrons prevents them from screening the local Si-C polarization, resulting in the coexistence of metallicity and ferroelectricity. Ferroelectric tunnel junctions demonstrate nonvolatile memory properties with a well-defined high-resistance state (HRS) and low-resistance state (LRS), an ultrahigh response speed (~50 ns), an ultralow operating voltage (1 V), an endurance exceeding 85927 cycles, and a projected retention time of 100 years. Our results provide a novel strategy for pioneering ferroelectricity in a metal, a new ferroelectric metal platform for exploring exotic properties, and a ferroelectric device with high performance that meets the requirements for low consumption and high-speed non-volatile devices.

cond-mat.mtrl-sci↗

arXiv2026

PerceptionBench: Evaluating Atomic Visual Perception in Multimodal Large Language Models

We introduce PerceptionBench, a benchmark specifically designed to evaluate the atomic visual perception capabilities of Multimodal Large Language Models (MLLMs). Existing benchmarks often fail to isolate perception: holistic evaluations conflate perceptual errors with failures in reasoning or domain knowledge, while application-driven benchmarks only cover narrow, fragmented domains shaped by heuristic designs. To address these limitations, PerceptionBench adopts a bottom-up approach: by diagnosing the earliest failure points in the responses of frontier MLLMs across 42 existing benchmarks, we construct an error taxonomy whose perception branch defines ten atomic perceptual capabilities. Guided by this taxonomy, we construct 3,000 verified questions with short, unambiguous answers, each isolating a single capability, with difficulty stemming from perception rather than reasoning or knowledge. Benchmark results across sixteen frontier MLLMs reveal that atomic perception remains largely unsolved---no model reaches 60\% accuracy, perception-related hallucination is the weakest capability on average, and similar overall scores conceal sharply divergent capability profiles. PerceptionBench thus provides a capability-level standard for measuring and diagnosing the visual perception boundaries of MLLMs.

cs.CV↗

arXiv2026

Illuminating Unified Multimodal Model for Free-form Interleaved Text-Image Generation

The advancement of generative AI models capable of producing text and image marks a critical step forward in the realm of multimodal intelligence, particularly for tasks involving the interleaving of both modalities. To advance this intelligence to the next stage, it is crucial for models to autonomously generate free-form interleaved text-image sequences. In this paper, we introduce ILLUME-X, an advanced unified multimodal paradigm that enables high-quality, free-form interleaved text-image generation by improving multimodal data efficiency and stabilizing the multimodal training process. ILLUME-X comprises three key components: (i) an expanded training data pipeline optimized for interleaved text-image generation, (ii) a progressive training strategy with self-adaptive objectives for free-length multimodal token sequences, and (iii) an objective and comprehensive evaluation method ILScore for interleaved text-image sequences. Notably, our ILLUME-X outperforms previous unified models across multiple interleaved text-image generation tasks like style transfer, image decomposition and storytelling.

cs.CV↗

arXiv2026

A multi-agent system for spine MRI report generation from multi-sequence imaging

Spinal pathology is a leading cause of pain and disability worldwide. Spine MRI is central to clinical evaluation, yet its interpretation remains complex and time-consuming, requiring integration of information across multiple imaging sequences and anatomical regions. Despite recent advances in automated MRI analysis, effectively combining multi-sequence data while preserving sequence-specific diagnostic information remains an open challenge. Here we present SpineAgent, a multi-agent framework for spine MRI report generation built upon a multi-sequence foundation model trained on routine clinical data from 32,047 patients and 453,683 MRI series, comprising a total of 13,441,191 MRI slices. To accommodate diverse modalities of sequences, we first pre-train two DINOv3-based encoders separately on T1- and T2-weighted sequences. We then introduce a continual training strategy that learns a synthesizer to embed images of other sequences using the T1 and T2 encoders, producing patient-level embedding that integrates various signals across MRI sequences. Using these embeddings, SpineAgent achieves state-of-the-art performance, and demonstrates strong generalizability under cross-manufacturer and cross-cohort evaluation. Beyond classification, SpineAgent enables pathology localization by identifying findings-relevant slices and segmenting pathological regions. It also supports multimodal image-report retrieval, providing a solid foundation for scalable and explainable MRI report generation. We further integrate these validated capabilities of SpineAgent into 37 specialized agents. Finally, we incorporate their outputs as structured tokens within a Medical Report Agent trained end-to-end for report generation. Through both automated metrics and expert evaluation by five radiologists, SpineAgent achieves leading performance in spine MRI report generation.

cs.CV↗

arXiv2026

SciCustom: A Framework for Custom Evaluation of Scientific Capabilities in Large Language Models

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.

cs.CL↗

arXiv2025

Analysis of Contagion in China's Stock Market: A Hawkes Process Perspective

This study explores contagion in the Chinese stock market using Hawkes processes to analyze autocorrelation and cross-correlation in multivariate time series data. We examine whether market indices exhibit trending behavior and whether sector indices influence one another. By fitting self-exciting and inhibitory Hawkes processes to daily returns of indices like the Shanghai Composite, Shenzhen Component, and ChiNext, as well as sector indices (CSI Consumer, Healthcare, and Financial), we identify long-term dependencies and trending patterns, including upward, downward, and oversold rebound trends. Results show that during high trading activity, sector indices tend to sustain their trends, while low activity periods exhibit strong sector rotation. This research models stock price movements using spatiotemporal Hawkes processes, leveraging conditional intensity functions to explain sector rotation, advancing the understanding of financial contagion.

q-fin.ST↗

arXiv2025

Failure Makes the Agent Stronger: Enhancing Accuracy through Structured Reflection for Reliable Tool Interactions

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.

cs.CV↗

arXiv2025

ILLUME+: Illuminating Unified MLLM with Dual Visual Tokenization and Diffusion Refinement

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/.

cs.CV↗

arXiv2025

Large Language Model Agent: A Survey on Methodology, Applications and Challenges

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.

cs.CL↗

arXiv2025

ExLM: Rethinking the Impact of [MASK] Tokens in Masked Language Models

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.

cs.CL↗

arXiv2024

ILLUME: Illuminating Your LLMs to See, Draw, and Self-Enhance

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.

cs.CV↗

arXiv2024

SMI-Editor: Edit-based SMILES Language Model with Fragment-level Supervision

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.

cs.LG↗

arXiv2024

Towards Graph Contrastive Learning: A Survey and Beyond

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.

cs.LG↗

arXiv2024

ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling

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.

q-bio.BM↗

arXiv2023

Dual-Domain Multi-Contrast MRI Reconstruction with Synthesis-based Fusion Network

Purpose: To develop an efficient dual-domain reconstruction framework for multi-contrast MRI, with the focus on minimising cross-contrast misalignment in both the image and the frequency domains to enhance optimisation. Theory and Methods: Our proposed framework, based on deep learning, facilitates the optimisation for under-sampled target contrast using fully-sampled reference contrast that is quicker to acquire. The method consists of three key steps: 1) Learning to synthesise data resembling the target contrast from the reference contrast; 2) Registering the multi-contrast data to reduce inter-scan motion; and 3) Utilising the registered data for reconstructing the target contrast. These steps involve learning in both domains with regularisation applied to ensure their consistency. We also compare the reconstruction performance with existing deep learning-based methods using a dataset of brain MRI scans. Results: Extensive experiments demonstrate the superiority of our proposed framework, for up to an 8-fold acceleration rate, compared to state-of-the-art algorithms. Comprehensive analysis and ablation studies further present the effectiveness of the proposed components. Conclusion:Our dual-domain framework offers a promising approach to multi-contrast MRI reconstruction. It can also be integrated with existing methods to further enhance the reconstruction.

eess.IV↗

arXiv2023

Unsupervised Adaptive Implicit Neural Representation Learning for Scan-Specific MRI Reconstruction

In recent studies on MRI reconstruction, advances have shown significant promise for further accelerating the MRI acquisition. Most state-of-the-art methods require a large amount of fully-sampled data to optimise reconstruction models, which is impractical and expensive under certain clinical settings. On the other hand, for unsupervised scan-specific reconstruction methods, overfitting is likely to happen due to insufficient supervision, while restrictions on acceleration rates and under-sampling patterns further limit their applicability. To this end, we propose an unsupervised, adaptive coarse-to-fine framework that enhances reconstruction quality without being constrained by the sparsity levels or patterns in under-sampling. The framework employs an implicit neural representation for scan-specific MRI reconstruction, learning a mapping from multi-dimensional coordinates to their corresponding signal intensities. Moreover, we integrate a novel learning strategy that progressively refines the use of acquired k-space signals for self-supervision. This approach effectively adjusts the proportion of supervising signals from unevenly distributed information across different frequency bands, thus mitigating the issue of overfitting while improving the overall reconstruction. Comprehensive evaluation on a public dataset, including both 2D and 3D data, has shown that our method outperforms current state-of-the-art scan-specific MRI reconstruction techniques, for up to 8-fold under-sampling.

eess.IV↗

arXiv2023

A Comprehensive Survey on Deep Graph Representation Learning

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.

cs.LG↗

arXiv2022

MetaFill: Text Infilling for Meta-Path Generation on Heterogeneous Information Networks

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.

cs.CL↗