arXiv subjects

Che Liu

Publications and source records attributed to Che Liu.

At least 55 records · Page 3Linked to original sources

arXiv2025

How Far Have Medical Vision-Language Models Come? A Comprehensive Benchmarking Study

Vision-Language Models (VLMs) trained on web-scale corpora excel at natural image tasks and are increasingly repurposed for healthcare; however, their competence in medical tasks remains underexplored. We present a comprehensive evaluation of open-source general-purpose and medically specialised VLMs, ranging from 3B to 72B parameters, across eight benchmarks: MedXpert, OmniMedVQA, PMC-VQA, PathVQA, MMMU, SLAKE, and VQA-RAD. To observe model performance across different aspects, we first separate it into understanding and reasoning components. Three salient findings emerge. First, large general-purpose models already match or surpass medical-specific counterparts on several benchmarks, demonstrating strong zero-shot transfer from natural to medical images. Second, reasoning performance is consistently lower than understanding, highlighting a critical barrier to safe decision support. Third, performance varies widely across benchmarks, reflecting differences in task design, annotation quality, and knowledge demands. No model yet reaches the reliability threshold for clinical deployment, underscoring the need for stronger multimodal alignment and more rigorous, fine-grained evaluation protocols.

cs.CV↗

arXiv2025

Dual form Complementary Masking for Domain-Adaptive Image Segmentation

Recent works have correlated Masked Image Modeling (MIM) with consistency regularization in Unsupervised Domain Adaptation (UDA). However, they merely treat masking as a special form of deformation on the input images and neglect the theoretical analysis, which leads to a superficial understanding of masked reconstruction and insufficient exploitation of its potential in enhancing feature extraction and representation learning. In this paper, we reframe masked reconstruction as a sparse signal reconstruction problem and theoretically prove that the dual form of complementary masks possesses superior capabilities in extracting domain-agnostic image features. Based on this compelling insight, we propose MaskTwins, a simple yet effective UDA framework that integrates masked reconstruction directly into the main training pipeline. MaskTwins uncovers intrinsic structural patterns that persist across disparate domains by enforcing consistency between predictions of images masked in complementary ways, enabling domain generalization in an end-to-end manner. Extensive experiments verify the superiority of MaskTwins over baseline methods in natural and biological image segmentation. These results demonstrate the significant advantages of MaskTwins in extracting domain-invariant features without the need for separate pre-training, offering a new paradigm for domain-adaptive segmentation.

cs.CV↗

arXiv2025

MEIT: Multimodal Electrocardiogram Instruction Tuning on Large Language Models for Report Generation

Electrocardiogram (ECG) is the primary non-invasive diagnostic tool for monitoring cardiac conditions and is crucial in assisting clinicians. Recent studies have concentrated on classifying cardiac conditions using ECG data but have overlooked ECG report generation, which is time-consuming and requires clinical expertise. To automate ECG report generation and ensure its versatility, we propose the Multimodal ECG Instruction Tuning (MEIT) framework, the first attempt to tackle ECG report generation with LLMs and multimodal instructions. To facilitate future research, we establish a benchmark to evaluate MEIT with various LLMs backbones across two large-scale ECG datasets. Our approach uniquely aligns the representations of the ECG signal and the report, and we conduct extensive experiments to benchmark MEIT with nine open-source LLMs using more than 800,000 ECG reports. MEIT's results underscore the superior performance of instruction-tuned LLMs, showcasing their proficiency in quality report generation, zero-shot capabilities, resilience to signal perturbation, and alignment with human expert evaluation. These findings emphasize the efficacy of MEIT and its potential for real-world clinical application.

cs.CL↗

arXiv2025

PlanMoGPT: Flow-Enhanced Progressive Planning for Text to Motion Synthesis

Recent advances in large language models (LLMs) have enabled breakthroughs in many multimodal generation tasks, but a significant performance gap still exists in text-to-motion generation, where LLM-based methods lag far behind non-LLM methods. We identify the granularity of motion tokenization as a critical bottleneck: fine-grained tokenization induces local dependency issues, where LLMs overemphasize short-term coherence at the expense of global semantic alignment, while coarse-grained tokenization sacrifices motion details. To resolve this issue, we propose PlanMoGPT, an LLM-based framework integrating progressive planning and flow-enhanced fine-grained motion tokenization. First, our progressive planning mechanism leverages LLMs' autoregressive capabilities to hierarchically generate motion tokens by starting from sparse global plans and iteratively refining them into full sequences. Second, our flow-enhanced tokenizer doubles the downsampling resolution and expands the codebook size by eight times, minimizing detail loss during discretization, while a flow-enhanced decoder recovers motion nuances. Extensive experiments on text-to-motion benchmarks demonstrate that it achieves state-of-the-art performance, improving FID scores by 63.8% (from 0.380 to 0.141) on long-sequence generation while enhancing motion diversity by 49.9% compared to existing methods. The proposed framework successfully resolves the diversity-quality trade-off that plagues current non-LLM approaches, establishing new standards for text-to-motion generation.

cs.CV↗

arXiv2025

Beyond Distillation: Pushing the Limits of Medical LLM Reasoning with Minimalist Rule-Based RL

Improving performance on complex tasks and enabling interpretable decision making in large language models (LLMs), especially for clinical applications, requires effective reasoning. Yet this remains challenging without supervised fine-tuning (SFT) on costly chain-of-thought (CoT) data distilled from closed-source models (e.g., GPT-4o). In this work, we present AlphaMed, the first medical LLM to show that reasoning capability can emerge purely through reinforcement learning (RL), using minimalist rule-based rewards on public multiple-choice QA datasets, without relying on SFT or distilled CoT data. AlphaMed achieves state-of-the-art results on six medical QA benchmarks, outperforming models trained with conventional SFT+RL pipelines. On challenging benchmarks (e.g., MedXpert), AlphaMed even surpasses larger or closed-source models such as DeepSeek-V3-671B and Claude-3.5-Sonnet. To understand the factors behind this success, we conduct a comprehensive data-centric analysis guided by three questions: (i) Can minimalist rule-based RL incentivize reasoning without distilled CoT supervision? (ii) How do dataset quantity and diversity impact reasoning? (iii) How does question difficulty shape the emergence and generalization of reasoning? Our findings show that dataset informativeness is a key driver of reasoning performance, and that minimalist RL on informative, multiple-choice QA data is effective at inducing reasoning without CoT supervision. We also observe divergent trends across benchmarks, underscoring limitations in current evaluation and the need for more challenging, reasoning-oriented medical QA benchmarks.

cs.CL↗

arXiv2025

BOTM: Echocardiography Segmentation via Bi-directional Optimal Token Matching

Existed echocardiography segmentation methods often suffer from anatomical inconsistency challenge caused by shape variation, partial observation and region ambiguity with similar intensity across 2D echocardiographic sequences, resulting in false positive segmentation with anatomical defeated structures in challenging low signal-to-noise ratio conditions. To provide a strong anatomical guarantee across different echocardiographic frames, we propose a novel segmentation framework named BOTM (Bi-directional Optimal Token Matching) that performs echocardiography segmentation and optimal anatomy transportation simultaneously. Given paired echocardiographic images, BOTM learns to match two sets of discrete image tokens by finding optimal correspondences from a novel anatomical transportation perspective. We further extend the token matching into a bi-directional cross-transport attention proxy to regulate the preserved anatomical consistency within the cardiac cyclic deformation in temporal domain. Extensive experimental results show that BOTM can generate stable and accurate segmentation outcomes (e.g. -1.917 HD on CAMUS2H LV, +1.9% Dice on TED), and provide a better matching interpretation with anatomical consistency guarantee.

cs.CV↗

arXiv2025

NOVA: A Benchmark for Anomaly Localization and Clinical Reasoning in Brain MRI

In many real-world applications, deployed models encounter inputs that differ from the data seen during training. Out-of-distribution detection identifies whether an input stems from an unseen distribution, while open-world recognition flags such inputs to ensure the system remains robust as ever-emerging, previously $unknown$ categories appear and must be addressed without retraining. Foundation and vision-language models are pre-trained on large and diverse datasets with the expectation of broad generalization across domains, including medical imaging. However, benchmarking these models on test sets with only a few common outlier types silently collapses the evaluation back to a closed-set problem, masking failures on rare or truly novel conditions encountered in clinical use. We therefore present $NOVA$, a challenging, real-life $evaluation-only$ benchmark of $\sim$900 brain MRI scans that span 281 rare pathologies and heterogeneous acquisition protocols. Each case includes rich clinical narratives and double-blinded expert bounding-box annotations. Together, these enable joint assessment of anomaly localisation, visual captioning, and diagnostic reasoning. Because NOVA is never used for training, it serves as an $extreme$ stress-test of out-of-distribution generalisation: models must bridge a distribution gap both in sample appearance and in semantic space. Baseline results with leading vision-language models (GPT-4o, Gemini 2.0 Flash, and Qwen2.5-VL-72B) reveal substantial performance drops across all tasks, establishing NOVA as a rigorous testbed for advancing models that can detect, localize, and reason about truly unknown anomalies.

eess.IV↗

arXiv2025

MedVLM-R1: Incentivizing Medical Reasoning Capability of Vision-Language Models (VLMs) via Reinforcement Learning

Reasoning is a critical frontier for advancing medical image analysis, where transparency and trustworthiness play a central role in both clinician trust and regulatory approval. Although Medical Visual Language Models (VLMs) show promise for radiological tasks, most existing VLMs merely produce final answers without revealing the underlying reasoning. To address this gap, we introduce MedVLM-R1, a medical VLM that explicitly generates natural language reasoning to enhance transparency and trustworthiness. Instead of relying on supervised fine-tuning (SFT), which often suffers from overfitting to training distributions and fails to foster genuine reasoning, MedVLM-R1 employs a reinforcement learning framework that incentivizes the model to discover human-interpretable reasoning paths without using any reasoning references. Despite limited training data (600 visual question answering samples) and model parameters (2B), MedVLM-R1 boosts accuracy from 55.11% to 78.22% across MRI, CT, and X-ray benchmarks, outperforming larger models trained on over a million samples. It also demonstrates robust domain generalization under out-of-distribution tasks. By unifying medical image analysis with explicit reasoning, MedVLM-R1 marks a pivotal step toward trustworthy and interpretable AI in clinical practice. Inference model is available at: https://huggingface.co/JZPeterPan/MedVLM-R1.

cs.CV↗

arXiv2025

Spin squeezing in an ensemble of nitrogen-vacancy centers in diamond

Spin squeezed states provide a seminal example of how the structure of quantum mechanical correlations can be controlled to produce metrologically useful entanglement. Such squeezed states have been demonstrated in a wide variety of artificial quantum systems ranging from atoms in optical cavities to trapped ion crystals. By contrast, despite their numerous advantages as practical sensors, spin ensembles in solid-state materials have yet to be controlled with sufficient precision to generate targeted entanglement such as spin squeezing. In this work, we present the first experimental demonstration of spin squeezing in a solid-state spin system. Our experiments are performed on a strongly-interacting ensemble of nitrogen-vacancy (NV) color centers in diamond at room temperature, and squeezing (-0.5 $\pm$ 0.1 dB) is generated by the native magnetic dipole-dipole interaction between NVs. In order to generate and detect squeezing in a solid-state spin system, we overcome a number of key challenges of broad experimental and theoretical interest. First, we develop a novel approach, using interaction-enabled noise spectroscopy, to characterize the quantum projection noise in our system without directly resolving the spin probability distribution. Second, noting that the random positioning of spin defects severely limits the generation of spin squeezing, we implement a pair of strategies aimed at isolating the dynamics of a relatively ordered sub-ensemble of NV centers. Our results open the door to entanglement-enhanced metrology using macroscopic ensembles of optically active spins in solids.

quant-ph↗

arXiv2025

MEDA: Dynamic KV Cache Allocation for Efficient Multimodal Long-Context Inference

Long-context Multimodal Large Language Models (MLLMs) that incorporate long text-image and text-video modalities, demand substantial resources as their multimodal Key-Value (KV) caches grow with increasing input lengths, challenging inference efficiency. Existing methods for KV cache compression, in both text-only and multimodal LLMs, have neglected attention density variations across layers, thus often adopting uniform or progressive reduction strategies for layer-wise cache allocation. In this work, we propose MEDA, a dynamic layer-wise KV cache allocation method for efficient multimodal long-context inference. As its core, MEDA utilizes cross-modal attention entropy to determine the KV cache size at each MLLMs layer. Given the dynamically allocated KV cache size at each layer, MEDA also employs a KV pair selection scheme to identify which KV pairs to select and a KV pair merging strategy that merges the selected and non-selected ones to preserve information from the entire context. MEDA achieves up to 72% KV cache memory reduction and 2.82 times faster decoding speed, while maintaining or enhancing performance on various multimodal tasks in long-context settings, including multi-images and long-video scenarios. Our code is released at https://github.com/AIoT-MLSys-Lab/MEDA.

cs.CL↗

arXiv2025

Enhancing Abnormality Grounding for Vision Language Models with Knowledge Descriptions

Visual Language Models (VLMs) have demonstrated impressive capabilities in visual grounding tasks. However, their effectiveness in the medical domain, particularly for abnormality detection and localization within medical images, remains underexplored. A major challenge is the complex and abstract nature of medical terminology, which makes it difficult to directly associate pathological anomaly terms with their corresponding visual features. In this work, we introduce a novel approach to enhance VLM performance in medical abnormality detection and localization by leveraging decomposed medical knowledge. Instead of directly prompting models to recognize specific abnormalities, we focus on breaking down medical concepts into fundamental attributes and common visual patterns. This strategy promotes a stronger alignment between textual descriptions and visual features, improving both the recognition and localization of abnormalities in medical images.We evaluate our method on the 0.23B Florence-2 base model and demonstrate that it achieves comparable performance in abnormality grounding to significantly larger 7B LLaVA-based medical VLMs, despite being trained on only 1.5% of the data used for such models. Experimental results also demonstrate the effectiveness of our approach in both known and previously unseen abnormalities, suggesting its strong generalization capabilities.

cs.CV↗

arXiv2025

T3D: Advancing 3D Medical Vision-Language Pre-training by Learning Multi-View Visual Consistency

While 3D visual self-supervised learning (vSSL) shows promising results in capturing visual representations, it overlooks the clinical knowledge from radiology reports. Meanwhile, 3D medical vision-language pre-training (MedVLP) remains underexplored due to the lack of a large-scale, publicly available 3D medical image-report dataset. To bridge this gap, we introduce **CT-3DVLP**, the first and largest **public** 3D volume-report dataset, establishing a comprehensive benchmark for 3D MedVLP research. Meanwhile, we propose the **T3D** framework, which enhances 3D MedVLP beyond naive CLIP-style alignment that directly pairs volumes with reports but neglects local visual representations. Instead, we introduce **Text-informed Multi-view Alignment (TMA)**, a novel approach that clusters volumetric data while enforcing consistency across different views of the same volume-report pair. TMA integrates textual features into fine-grained visual representations, ensuring contextual coherence across views. We evaluate T3D across multiple downstream tasks in both unimodal and cross-modal settings, including zero-shot and fine-tuned classification, cross-modal retrieval, report generation, and semantic segmentation. Our results show that T3D consistently outperforms existing vSSL and multimodal methods, demonstrating superior zero-shot and fine-tuning capabilities and setting a new benchmark for 3D medical image understanding.

cs.CV↗

arXiv2025

Argus: Benchmarking and Enhancing Vision-Language Models for 3D Radiology Report Generation

Automatic radiology report generation holds significant potential to streamline the labor-intensive process of report writing by radiologists, particularly for 3D radiographs such as CT scans. While CT scans are critical for clinical diagnostics, they remain less explored compared to 2D radiographs. To date, there has been no comprehensive benchmark for 3D radiograph report generation (3DRRG), nor sufficient investigation into the optimal training strategies for Vision Language Models (VLMs) in this context, particularly with respect to vision encoder choices, visual token compression, and model scaling. In this work, we make three key contributions. We curate **CT-3DRRG**, the largest **publicly** available 3D CT-report dataset, establishing a robust and diverse benchmark for evaluating VLM performance on 3DRRG. Furthermore, we propose a comprehensive training recipe for building high-performing VLMs for 3DRRG, exploring key factors such as vision encoder pretraining strategies, visual token compression, and the impact of data & model scale. Guided by these findings, we introduce **Argus**, a state-of-the-art family of VLMs that achieve superior performance across different model sizes and input 3D medical image resolutions, efficiently processing high-resolution 3D images up to $512 \times 512 \times 256$[^1].

cs.CV↗

arXiv2025

Can Medical Vision-Language Pre-training Succeed with Purely Synthetic Data?

Medical Vision-Language Pre-training (MedVLP) has made significant progress in enabling zero-shot tasks for medical image understanding. However, training MedVLP models typically requires large-scale datasets with paired, high-quality image-text data, which are scarce in the medical domain. Recent advancements in Large Language Models (LLMs) and diffusion models have made it possible to generate large-scale synthetic image-text pairs. This raises the question: "Can MedVLP succeed using purely synthetic data?" To address this, we use off-the-shelf generative models to create synthetic radiology reports and paired Chest X-ray (CXR) images, and propose an automated pipeline to build a diverse, high-quality synthetic dataset, enabling a rigorous study that isolates model and training settings, focusing entirely from the data perspective. Our results show that MedVLP models trained exclusively on synthetic data outperform those trained on real data by 3.8% in averaged AUC on zero-shot classification. Moreover, using a combination of synthetic and real data leads to a further improvement of 9.07%. Additionally, MedVLP models trained on synthetic or mixed data consistently outperform those trained on real data in zero-shot grounding, as well as in fine-tuned classification and segmentation tasks. Our analysis suggests MedVLP trained on well-designed synthetic data can outperform models trained on real datasets, which may be limited by low-quality samples and long-tailed distributions.

cs.CV↗

arXiv2025

Knowledge-enhanced Multimodal ECG Representation Learning with Arbitrary-Lead Inputs

Recent advances in multimodal ECG representation learning center on aligning ECG signals with paired free-text reports. However, suboptimal alignment persists due to the complexity of medical language and the reliance on a full 12-lead setup, which is often unavailable in under-resourced settings. To tackle these issues, we propose **K-MERL**, a knowledge-enhanced multimodal ECG representation learning framework. **K-MERL** leverages large language models to extract structured knowledge from free-text reports and employs a lead-aware ECG encoder with dynamic lead masking to accommodate arbitrary lead inputs. Evaluations on six external ECG datasets show that **K-MERL** achieves state-of-the-art performance in zero-shot classification and linear probing tasks, while delivering an average **16%** AUC improvement over existing methods in partial-lead zero-shot classification.

cs.LG↗

arXiv2025

BP-GPT: Auditory Neural Decoding Using fMRI-prompted LLM

Decoding language information from brain signals represents a vital research area within brain-computer interfaces, particularly in the context of deciphering the semantic information from the fMRI signal. Although existing work uses LLM to achieve this goal, their method does not use an end-to-end approach and avoids the LLM in the mapping of fMRI-to-text, leaving space for the exploration of the LLM in auditory decoding. In this paper, we introduce a novel method, the Brain Prompt GPT (BP-GPT). By using the brain representation that is extracted from the fMRI as a prompt, our method can utilize GPT-2 to decode fMRI signals into stimulus text. Further, we introduce the text prompt and align the fMRI prompt to it. By introducing the text prompt, our BP-GPT can extract a more robust brain prompt and promote the decoding of pre-trained LLM. We evaluate our BP-GPT on the open-source auditory semantic decoding dataset and achieve a significant improvement up to 4.61 on METEOR and 2.43 on BERTScore across all the subjects compared to the state-of-the-art method. The experimental results demonstrate that using brain representation as a prompt to further drive LLM for auditory neural decoding is feasible and effective. The code is available at https://github.com/1994cxy/BP-GPT.

cs.HC↗

arXiv2025

Machine learning for modelling unstructured grid data in computational physics: a review

Unstructured grid data are essential for modelling complex geometries and dynamics in computational physics. Yet, their inherent irregularity presents significant challenges for conventional machine learning (ML) techniques. This paper provides a comprehensive review of advanced ML methodologies designed to handle unstructured grid data in high-dimensional dynamical systems. Key approaches discussed include graph neural networks, transformer models with spatial attention mechanisms, interpolation-integrated ML methods, and meshless techniques such as physics-informed neural networks. These methodologies have proven effective across diverse fields, including fluid dynamics and environmental simulations. This review is intended as a guidebook for computational scientists seeking to apply ML approaches to unstructured grid data in their domains, as well as for ML researchers looking to address challenges in computational physics. It places special focus on how ML methods can overcome the inherent limitations of traditional numerical techniques and, conversely, how insights from computational physics can inform ML development. To support benchmarking, this review also provides a summary of open-access datasets of unstructured grid data in computational physics. Finally, emerging directions such as generative models with unstructured data, reinforcement learning for mesh generation, and hybrid physics-data-driven paradigms are discussed to inspire future advancements in this evolving field.

cs.LG↗

arXiv2024

EVOR: Evolving Retrieval for Code Generation

Recently the retrieval-augmented generation (RAG) has been successfully applied in code generation. However, existing pipelines for retrieval-augmented code generation (RACG) employ static knowledge bases with a single source, limiting the adaptation capabilities of Large Language Models (LLMs) to domains they have insufficient knowledge of. In this work, we develop a novel pipeline, EVOR, that employs the synchronous evolution of both queries and diverse knowledge bases. On two realistic settings where the external knowledge is required to solve code generation tasks, we compile four new datasets associated with frequently updated libraries and long-tail programming languages, named EVOR-BENCH. Extensive experiments demonstrate that EVOR achieves two to four times of execution accuracy compared to other methods such as Reflexion (Shinn et al., 2024), DocPrompting (Zhou et al., 2023), etc. We demonstrate that EVOR is flexible and can be easily combined with them to achieve further improvement. Further analysis reveals that EVOR benefits from the synchronous evolution of queries and documents and the diverse information sources in the knowledge base. We hope that our studies will inspire more insights into the design of advanced RACG pipelines in future research. Our model, code, and data are available at https://arks-codegen.github.io.

cs.CL↗