arXiv subjects

Lequan Yu

Publications and source records attributed to Lequan Yu.

At least 37 records · Page 2Linked to original sources

arXiv2025

Proxy-Tuning: Tailoring Multimodal Autoregressive Models for Subject-Driven Image Generation

Multimodal autoregressive (AR) models, based on next-token prediction and transformer architecture, have demonstrated remarkable capabilities in various multimodal tasks including text-to-image (T2I) generation. Despite their strong performance in general T2I tasks, our research reveals that these models initially struggle with subject-driven image generation compared to dominant diffusion models. To address this limitation, we introduce Proxy-Tuning, leveraging diffusion models to enhance AR models' capabilities in subject-specific image generation. Our method reveals a striking weak-to-strong phenomenon: fine-tuned AR models consistently outperform their diffusion model supervisors in both subject fidelity and prompt adherence. We analyze this performance shift and identify scenarios where AR models excel, particularly in multi-subject compositions and contextual understanding. This work not only demonstrates impressive results in subject-driven AR image generation, but also unveils the potential of weak-to-strong generalization in the image generation domain, contributing to a deeper understanding of different architectures' strengths and limitations.

cs.CV↗

arXiv2025

Interpretable Multimodal Cancer Prototyping with Whole Slide Images and Incompletely Paired Genomics

Multimodal approaches that integrate histology and genomics hold strong potential for precision oncology. However, phenotypic and genotypic heterogeneity limits the quality of intra-modal representations and hinders effective inter-modal integration. Furthermore, most existing methods overlook real-world clinical scenarios where genomics may be partially missing or entirely unavailable. We propose a flexible multimodal prototyping framework to integrate whole slide images and incomplete genomics for precision oncology. Our approach has four key components: 1) Biological Prototyping using text prompting and prototype-wise weighting; 2) Multiview Alignment through sample- and distribution-wise alignments; 3) Bipartite Fusion to capture both shared and modality-specific information for multimodal fusion; and 4) Semantic Genomics Imputation to handle missing data. Extensive experiments demonstrate the consistent superiority of the proposed method compared to other state-of-the-art approaches on multiple downstream tasks. The code is available at https://github.com/helenypzhang/Interpretable-Multimodal-Prototyping.

cs.CV↗

arXiv2025

CTPD: Cross-Modal Temporal Pattern Discovery for Enhanced Multimodal Electronic Health Records Analysis

Integrating multimodal Electronic Health Records (EHR) data, such as numerical time series and free-text clinical reports, has great potential in predicting clinical outcomes. However, prior work has primarily focused on capturing temporal interactions within individual samples and fusing multimodal information, overlooking critical temporal patterns across patients. These patterns, such as trends in vital signs like abnormal heart rate or blood pressure, can indicate deteriorating health or an impending critical event. Similarly, clinical notes often contain textual descriptions that reflect these patterns. Identifying corresponding temporal patterns across different modalities is crucial for improving the accuracy of clinical outcome predictions, yet it remains a challenging task. To address this gap, we introduce a Cross-Modal Temporal Pattern Discovery (CTPD) framework, designed to efficiently extract meaningful cross-modal temporal patterns from multimodal EHR data. Our approach introduces shared initial temporal pattern representations which are refined using slot attention to generate temporal semantic embeddings. To ensure rich cross-modal temporal semantics in the learned patterns, we introduce a contrastive-based TPNCE loss for cross-modal alignment, along with two reconstruction losses to retain core information of each modality. Evaluations on two clinically critical tasks, 48-hour in-hospital mortality and 24-hour phenotype classification, using the MIMIC-III database demonstrate the superiority of our method over existing approaches.

cs.LG↗

arXiv2025

Cross-Modal Alignment via Variational Copula Modelling

Various data modalities are common in real-world applications (e.g., electronic health records, medical images and clinical notes in healthcare). It is essential to develop multimodal learning methods to aggregate various information from multiple modalities. The main challenge is how to appropriately align and fuse the representations of different modalities into a joint distribution. Existing methods mainly rely on concatenation or the Kronecker product, oversimplifying the interaction structure between modalities and indicating a need to model more complex interactions. Additionally, the joint distribution of latent representations with higher-order interactions is underexplored. Copula is a powerful statistical structure for modelling the interactions among variables, as it naturally bridges the joint distribution and marginal distributions of multiple variables. We propose a novel copula-driven multimodal learning framework, which focuses on learning the joint distribution of various modalities to capture the complex interactions among them. The key idea is to interpret the copula model as a tool to align the marginal distributions of the modalities efficiently. By assuming a Gaussian mixture distribution for each modality and a copula model on the joint distribution, our model can generate accurate representations for missing modalities. Extensive experiments on public MIMIC datasets demonstrate the superior performance of our model over other competitors. The code is available at https://github.com/HKU-MedAI/CMCM.

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arXiv2025

MedAgentBoard: Benchmarking Multi-Agent Collaboration with Conventional Methods for Diverse Medical Tasks

The rapid advancement of Large Language Models (LLMs) has stimulated interest in multi-agent collaboration for addressing complex medical tasks. However, the practical advantages of multi-agent collaboration approaches remain insufficiently understood. Existing evaluations often lack generalizability, failing to cover diverse tasks reflective of real-world clinical practice, and frequently omit rigorous comparisons against both single-LLM-based and established conventional methods. To address this critical gap, we introduce MedAgentBoard, a comprehensive benchmark for the systematic evaluation of multi-agent collaboration, single-LLM, and conventional approaches. MedAgentBoard encompasses four diverse medical task categories: (1) medical (visual) question answering, (2) lay summary generation, (3) structured Electronic Health Record (EHR) predictive modeling, and (4) clinical workflow automation, across text, medical images, and structured EHR data. Our extensive experiments reveal a nuanced landscape: while multi-agent collaboration demonstrates benefits in specific scenarios, such as enhancing task completeness in clinical workflow automation, it does not consistently outperform advanced single LLMs (e.g., in textual medical QA) or, critically, specialized conventional methods that generally maintain better performance in tasks like medical VQA and EHR-based prediction. MedAgentBoard offers a vital resource and actionable insights, emphasizing the necessity of a task-specific, evidence-based approach to selecting and developing AI solutions in medicine. It underscores that the inherent complexity and overhead of multi-agent collaboration must be carefully weighed against tangible performance gains. All code, datasets, detailed prompts, and experimental results are open-sourced at https://medagentboard.netlify.app/.

cs.AI↗

arXiv2025

Variational Polya Tree

Density estimation is essential for generative modeling, particularly with the rise of modern neural networks. While existing methods capture complex data distributions, they often lack interpretability and uncertainty quantification. Bayesian nonparametric methods, especially the \polya tree, offer a robust framework that addresses these issues by accurately capturing function behavior over small intervals. Traditional techniques like Markov chain Monte Carlo (MCMC) face high computational complexity and scalability limitations, hindering the use of Bayesian nonparametric methods in deep learning. To tackle this, we introduce the variational \polya tree (VPT) model, which employs stochastic variational inference to compute posterior distributions. This model provides a flexible, nonparametric Bayesian prior that captures latent densities and works well with stochastic gradient optimization. We also leverage the joint distribution likelihood for a more precise variational posterior approximation than traditional mean-field methods. We evaluate the model performance on both real data and images, and demonstrate its competitiveness with other state-of-the-art deep density estimation methods. We also explore its ability in enhancing interpretability and uncertainty quantification. Code is available at https://github.com/howardchanth/var-polya-tree.

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arXiv2025

Amplifying Prominent Representations in Multimodal Learning via Variational Dirichlet Process

Developing effective multimodal fusion approaches has become increasingly essential in many real-world scenarios, such as health care and finance. The key challenge is how to preserve the feature expressiveness in each modality while learning cross-modal interactions. Previous approaches primarily focus on the cross-modal alignment, while over-emphasis on the alignment of marginal distributions of modalities may impose excess regularization and obstruct meaningful representations within each modality. The Dirichlet process (DP) mixture model is a powerful Bayesian non-parametric method that can amplify the most prominent features by its richer-gets-richer property, which allocates increasing weights to them. Inspired by this unique characteristic of DP, we propose a new DP-driven multimodal learning framework that automatically achieves an optimal balance between prominent intra-modal representation learning and cross-modal alignment. Specifically, we assume that each modality follows a mixture of multivariate Gaussian distributions and further adopt DP to calculate the mixture weights for all the components. This paradigm allows DP to dynamically allocate the contributions of features and select the most prominent ones, leveraging its richer-gets-richer property, thus facilitating multimodal feature fusion. Extensive experiments on several multimodal datasets demonstrate the superior performance of our model over other competitors. Ablation analysis further validates the effectiveness of DP in aligning modality distributions and its robustness to changes in key hyperparameters. Code is anonymously available at https://github.com/HKU-MedAI/DPMM.git

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arXiv2025

A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

cs.CL↗

arXiv2025

HealthFlow: A Self-Evolving AI Agent with Meta Planning for Autonomous Healthcare Research

The rapid proliferation of scientific knowledge presents a grand challenge: transforming this vast repository of information into an active engine for discovery, especially in high-stakes domains like healthcare. Current AI agents, however, are constrained by static, predefined strategies, limiting their ability to navigate the complex, evolving ecosystem of scientific research. This paper introduces HealthFlow, a self-evolving AI agent that overcomes this limitation through a novel meta-level evolution mechanism. HealthFlow autonomously refines its high-level problem-solving policies by distilling procedural successes and failures into a durable, structured knowledge base, enabling it to learn not just how to use tools, but how to strategize. To anchor our research and provide a community resource, we introduce EHRFlowBench, a new benchmark featuring complex health data analysis tasks systematically derived from peer-reviewed scientific literature. Our experiments demonstrate that HealthFlow's self-evolving approach significantly outperforms state-of-the-art agent frameworks. This work offers a new paradigm for intelligent systems that can learn to operationalize the procedural knowledge embedded in scientific content, marking a critical step toward more autonomous and effective AI for healthcare scientific discovery.

cs.AI↗

arXiv2025

ClinicRealm: Re-evaluating Large Language Models with Conventional Machine Learning for Non-Generative Clinical Prediction Tasks

Large Language Models (LLMs) are increasingly deployed in medicine. However, their utility in non-generative clinical prediction, often presumed inferior to specialized models, remains under-evaluated, leading to ongoing debate within the field and potential for misuse, misunderstanding, or over-reliance due to a lack of systematic benchmarking. Our ClinicRealm study addresses this by benchmarking 15 GPT-style LLMs, 5 BERT-style models, and 11 traditional methods on unstructured clinical notes and structured Electronic Health Records (EHR), while also assessing their reasoning, reliability, and fairness. Key findings reveal a significant shift: for clinical note predictions, leading LLMs (e.g., DeepSeek-V3.1-Think, GPT-5) in zero-shot settings now decisively outperform finetuned BERT models. On structured EHRs, while specialized models excel with ample data, advanced LLMs (e.g., GPT-5, DeepSeek-V3.1-Think) show potent zero-shot capabilities, often surpassing conventional models in data-scarce settings. Notably, leading open-source LLMs can match or exceed proprietary counterparts. These results provide compelling evidence that modern LLMs are competitive tools for non-generative clinical prediction, particularly with unstructured text and offering data-efficient structured data options, thus necessitating a re-evaluation of model selection strategies. This research should serve as an important insight for medical informaticists, AI developers, and clinical researchers, potentially prompting a reassessment of current assumptions and inspiring new approaches to LLM application in predictive healthcare.

cs.CL↗

arXiv2025

MedMMV: A Controllable Multimodal Multi-Agent Framework for Reliable and Verifiable Clinical Reasoning

Recent progress in multimodal large language models (MLLMs) has demonstrated promising performance on medical benchmarks and in preliminary trials as clinical assistants. Yet, our pilot audit of diagnostic cases uncovers a critical failure mode: instability in early evidence interpretation precedes hallucination, creating branching reasoning trajectories that cascade into globally inconsistent conclusions. This highlights the need for clinical reasoning agents that constrain stochasticity and hallucination while producing auditable decision flows. We introduce MedMMV, a controllable multimodal multi-agent framework for reliable and verifiable clinical reasoning. MedMMV stabilizes reasoning through diversified short rollouts, grounds intermediate steps in a structured evidence graph under the supervision of a Hallucination Detector, and aggregates candidate paths with a Combined Uncertainty scorer. On six medical benchmarks, MedMMV improves accuracy by up to 12.7% and, more critically, demonstrates superior reliability. Blind physician evaluations confirm that MedMMV substantially increases reasoning truthfulness without sacrificing informational content. By controlling instability through a verifiable, multi-agent process, our framework provides a robust path toward deploying trustworthy AI systems in high-stakes domains like clinical decision support.

cs.AI↗

arXiv2025

Large Material Gaussian Model for Relightable 3D Generation

The increasing demand for 3D assets across various industries necessitates efficient and automated methods for 3D content creation. Leveraging 3D Gaussian Splatting, recent large reconstruction models (LRMs) have demonstrated the ability to efficiently achieve high-quality 3D rendering by integrating multiview diffusion for generation and scalable transformers for reconstruction. However, existing models fail to produce the material properties of assets, which is crucial for realistic rendering in diverse lighting environments. In this paper, we introduce the Large Material Gaussian Model (MGM), a novel framework designed to generate high-quality 3D content with Physically Based Rendering (PBR) materials, ie, albedo, roughness, and metallic properties, rather than merely producing RGB textures with uncontrolled light baking. Specifically, we first fine-tune a new multiview material diffusion model conditioned on input depth and normal maps. Utilizing the generated multiview PBR images, we explore a Gaussian material representation that not only aligns with 2D Gaussian Splatting but also models each channel of the PBR materials. The reconstructed point clouds can then be rendered to acquire PBR attributes, enabling dynamic relighting by applying various ambient light maps. Extensive experiments demonstrate that the materials produced by our method not only exhibit greater visual appeal compared to baseline methods but also enhance material modeling, thereby enabling practical downstream rendering applications.

cs.CV↗

arXiv2025

C$^2$MIL: Synchronizing Semantic and Topological Causalities in Multiple Instance Learning for Robust and Interpretable Survival Analysis

Graph-based Multiple Instance Learning (MIL) is widely used in survival analysis with Hematoxylin and Eosin (H\&E)-stained whole slide images (WSIs) due to its ability to capture topological information. However, variations in staining and scanning can introduce semantic bias, while topological subgraphs that are not relevant to the causal relationships can create noise, resulting in biased slide-level representations. These issues can hinder both the interpretability and generalization of the analysis. To tackle this, we introduce a dual structural causal model as the theoretical foundation and propose a novel and interpretable dual causal graph-based MIL model, C$^2$MIL. C$^2$MIL incorporates a novel cross-scale adaptive feature disentangling module for semantic causal intervention and a new Bernoulli differentiable causal subgraph sampling method for topological causal discovery. A joint optimization strategy combining disentangling supervision and contrastive learning enables simultaneous refinement of both semantic and topological causalities. Experiments demonstrate that C$^2$MIL consistently improves generalization and interpretability over existing methods and can serve as a causal enhancement for diverse MIL baselines. The code is available at https://github.com/mimic0127/C2MIL.

cs.CV↗

arXiv2025

HyperPath: Knowledge-Guided Hyperbolic Semantic Hierarchy Modeling for WSI Analysis

Pathology is essential for cancer diagnosis, with multiple instance learning (MIL) widely used for whole slide image (WSI) analysis. WSIs exhibit a natural hierarchy -- patches, regions, and slides -- with distinct semantic associations. While some methods attempt to leverage this hierarchy for improved representation, they predominantly rely on Euclidean embeddings, which struggle to fully capture semantic hierarchies. To address this limitation, we propose HyperPath, a novel method that integrates knowledge from textual descriptions to guide the modeling of semantic hierarchies of WSIs in hyperbolic space, thereby enhancing WSI classification. Our approach adapts both visual and textual features extracted by pathology vision-language foundation models to the hyperbolic space. We design an Angular Modality Alignment Loss to ensure robust cross-modal alignment, while a Semantic Hierarchy Consistency Loss further refines feature hierarchies through entailment and contradiction relationships and thus enhance semantic coherence. The classification is performed with geodesic distance, which measures the similarity between entities in the hyperbolic semantic hierarchy. This eliminates the need for linear classifiers and enables a geometry-aware approach to WSI analysis. Extensive experiments show that our method achieves superior performance across tasks compared to existing methods, highlighting the potential of hyperbolic embeddings for WSI analysis.

cs.CV↗

arXiv2025

From Token to Rhythm: A Multi-Scale Approach for ECG-Language Pretraining

Electrocardiograms (ECGs) play a vital role in monitoring cardiac health and diagnosing heart diseases. However, traditional deep learning approaches for ECG analysis rely heavily on large-scale manual annotations, which are both time-consuming and resource-intensive to obtain. To overcome this limitation, self-supervised learning (SSL) has emerged as a promising alternative, enabling the extraction of robust ECG representations that can be efficiently transferred to various downstream tasks. While previous studies have explored SSL for ECG pretraining and multi-modal ECG-language alignment, they often fail to capture the multi-scale nature of ECG signals. As a result, these methods struggle to learn generalized representations due to their inability to model the hierarchical structure of ECG data. To address this gap, we introduce MELP, a novel Multi-scale ECG-Language Pretraining (MELP) model that fully leverages hierarchical supervision from ECG-text pairs. MELP first pretrains a cardiology-specific language model to enhance its understanding of clinical text. It then applies three levels of cross-modal supervision-at the token, beat, and rhythm levels-to align ECG signals with textual reports, capturing structured information across different time scales. We evaluate MELP on three public ECG datasets across multiple tasks, including zero-shot ECG classification, linear probing, and transfer learning. Experimental results demonstrate that MELP outperforms existing SSL methods, underscoring its effectiveness and adaptability across diverse clinical applications. Our code is available at https://github.com/HKU-MedAI/MELP.

eess.SP↗

arXiv2025

AssetDropper: Asset Extraction via Diffusion Models with Reward-Driven Optimization

Recent research on generative models has primarily focused on creating product-ready visual outputs; however, designers often favor access to standardized asset libraries, a domain that has yet to be significantly enhanced by generative capabilities. Although open-world scenes provide ample raw materials for designers, efficiently extracting high-quality, standardized assets remains a challenge. To address this, we introduce AssetDropper, the first framework designed to extract assets from reference images, providing artists with an open-world asset palette. Our model adeptly extracts a front view of selected subjects from input images, effectively handling complex scenarios such as perspective distortion and subject occlusion. We establish a synthetic dataset of more than 200,000 image-subject pairs and a real-world benchmark with thousands more for evaluation, facilitating the exploration of future research in downstream tasks. Furthermore, to ensure precise asset extraction that aligns well with the image prompts, we employ a pre-trained reward model to fulfill a closed-loop with feedback. We design the reward model to perform an inverse task that pastes the extracted assets back into the reference sources, which assists training with additional consistency and mitigates hallucination. Extensive experiments show that, with the aid of reward-driven optimization, AssetDropper achieves the state-of-the-art results in asset extraction. Project page: AssetDropper.github.io.

cs.CV↗

arXiv2025

StyleAR: Customizing Multimodal Autoregressive Model for Style-Aligned Text-to-Image Generation

In the current research landscape, multimodal autoregressive (AR) models have shown exceptional capabilities across various domains, including visual understanding and generation. However, complex tasks such as style-aligned text-to-image generation present significant challenges, particularly in data acquisition. In analogy to instruction-following tuning for image editing of AR models, style-aligned generation requires a reference style image and prompt, resulting in a text-image-to-image triplet where the output shares the style and semantics of the input. However, acquiring large volumes of such triplet data with specific styles is considerably more challenging than obtaining conventional text-to-image data used for training generative models. To address this issue, we propose StyleAR, an innovative approach that combines a specially designed data curation method with our proposed AR models to effectively utilize text-to-image binary data for style-aligned text-to-image generation. Our method synthesizes target stylized data using a reference style image and prompt, but only incorporates the target stylized image as the image modality to create high-quality binary data. To facilitate binary data training, we introduce a CLIP image encoder with a perceiver resampler that translates the image input into style tokens aligned with multimodal tokens in AR models and implement a style-enhanced token technique to prevent content leakage which is a common issue in previous work. Furthermore, we mix raw images drawn from large-scale text-image datasets with stylized images to enhance StyleAR's ability to extract richer stylistic features and ensure style consistency. Extensive qualitative and quantitative experiments demonstrate our superior performance.

cs.CV↗

arXiv2025

Feature Preserving Shrinkage on Bayesian Neural Networks via the R2D2 Prior

Bayesian neural networks (BNNs) treat neural network weights as random variables, which aim to provide posterior uncertainty estimates and avoid overfitting by performing inference on the posterior weights. However, the selection of appropriate prior distributions remains a challenging task, and BNNs may suffer from catastrophic inflated variance or poor predictive performance when poor choices are made for the priors. Existing BNN designs apply different priors to weights, while the behaviours of these priors make it difficult to sufficiently shrink noisy signals or they are prone to overshrinking important signals in the weights. To alleviate this problem, we propose a novel R2D2-Net, which imposes the R^2-induced Dirichlet Decomposition (R2D2) prior to the BNN weights. The R2D2-Net can effectively shrink irrelevant coefficients towards zero, while preventing key features from over-shrinkage. To approximate the posterior distribution of weights more accurately, we further propose a variational Gibbs inference algorithm that combines the Gibbs updating procedure and gradient-based optimization. This strategy enhances stability and consistency in estimation when the variational objective involving the shrinkage parameters is non-convex. We also analyze the evidence lower bound (ELBO) and the posterior concentration rates from a theoretical perspective. Experiments on both natural and medical image classification and uncertainty estimation tasks demonstrate satisfactory performance of our method.

cs.LG↗