arXiv subjects

Yikang Liu

Publications and source records attributed to Yikang Liu.

At least 19 recordsLinked to original sources

arXiv2025

RAU: Reference-based Anatomical Understanding with Vision Language Models

Anatomical understanding, which is the ability to identify, localize, or segment anatomical structures, is critical in medical image analysis; however, its progress is constrained by the scarcity of expert-labeled data. A promising remedy is to leverage an annotated reference image to guide the interpretation of an unlabeled target. Although recent vision-language models (VLMs) exhibit non-trivial visual reasoning, their reference-based understanding and fine-grained localization remain limited. We introduce RAU, a framework for reference-based anatomical understanding with VLMs. We first show that a VLM learns to identify anatomical regions through relative spatial reasoning between reference and target images, trained on a moderately sized dataset. We validate this capability through visual question answering (VQA) and bounding box prediction. Next, we demonstrate that the VLM-derived spatial cues can be seamlessly integrated with the fine-grained segmentation capability of SAM2, enabling localization and pixel-level segmentation of small anatomical regions, such as vessel segments. Across two in-distribution and two out-of-distribution datasets, RAU consistently outperforms a SAM2 fine-tuning baseline using the same memory setup, yielding more accurate segmentations and more reliable localization. More importantly, its generalization ability to unseen modalities makes it scalable to unseen datasets, a property crucial for medical image applications. To the best of our knowledge, RAU is the first to explore the capability of VLMs for reference-based identification, localization, and segmentation of anatomical structures in medical images. Its promising performance highlights the potential of VLM-driven approaches for anatomical understanding in automated clinical workflows.

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arXiv2025

Math Natural Language Inference: this should be easy!

We ask whether contemporary LLMs are able to perform natural language inference (NLI) tasks on mathematical texts. We call this the Math NLI problem. We construct a corpus of Math NLI pairs whose premises are from extant mathematical text and whose hypotheses and gold labels were provided by people with experience in both research-level mathematics and also in the NLI field. We also investigate the quality of corpora using the same premises but whose hypotheses are provided by LLMs themselves. We not only investigate the performance but also the inter-group consistency of the diverse group of LLMs. We have both positive and negative findings. Among our positive findings: in some settings, using a majority vote of LLMs is approximately equivalent to using human-labeled data in the Math NLI area. On the negative side: LLMs still struggle with mathematical language. They occasionally fail at even basic inferences. Current models are not as prone to hypothesis-only "inference" in our data the way the previous generation had been. In addition to our findings, we also provide our corpora as data to support future work on Math NLI.

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arXiv2025

Translationese-index: Using Likelihood Ratios for Graded and Generalizable Measurement of Translationese

Translationese refers to linguistic properties that usually occur in translated texts. Previous works study translationese by framing it as a binary classification between original texts and translated texts. In this paper, we argue that translationese should be graded instead of binary and propose the first measure for translationese -- the translationese-index (T-index), computed from the likelihood ratios of two contrastively fine-tuned language models (LMs). We use synthesized translations and translations in the wild to evaluate T-index's generalizability in cross-domain settings and its validity against human judgments. Our results show that T-index can generalize to unseen genres, authors, and language pairs. Moreover, T-index computed using two 0.5B LMs fine-tuned on only 1-5k pairs of synthetic data can effectively capture translationese, as demonstrated by alignment with human pointwise ratings and pairwise judgments. Additionally, the correlation between T-index and existing machine translation (MT) quality estimation (QE) metrics such as BLEU and COMET is low, suggesting that T-index is not covered by these metrics and can serve as a complementary metric in MT QE.

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arXiv2025

Adapting Vision Foundation Models for Real-time Ultrasound Image Segmentation

We propose a novel approach that adapts hierarchical vision foundation models for real-time ultrasound image segmentation. Existing ultrasound segmentation methods often struggle with adaptability to new tasks, relying on costly manual annotations, while real-time approaches generally fail to match state-of-the-art performance. To overcome these limitations, we introduce an adaptive framework that leverages the vision foundation model Hiera to extract multi-scale features, interleaved with DINOv2 representations to enhance visual expressiveness. These enriched features are then decoded to produce precise and robust segmentation. We conduct extensive evaluations on six public datasets and one in-house dataset, covering both cardiac and thyroid ultrasound segmentation. Experiments show that our approach outperforms state-of-the-art methods across multiple datasets and excels with limited supervision, surpassing nnUNet by over 20\% on average in the 1\% and 10\% data settings. Our method achieves $\sim$77 FPS inference speed with TensorRT on a single GPU, enabling real-time clinical applications.

cs.CV↗

arXiv2025

Leveraging Diffusion Model and Image Foundation Model for Improved Correspondence Matching in Coronary Angiography

Accurate correspondence matching in coronary angiography images is crucial for reconstructing 3D coronary artery structures, which is essential for precise diagnosis and treatment planning of coronary artery disease (CAD). Traditional matching methods for natural images often fail to generalize to X-ray images due to inherent differences such as lack of texture, lower contrast, and overlapping structures, compounded by insufficient training data. To address these challenges, we propose a novel pipeline that generates realistic paired coronary angiography images using a diffusion model conditioned on 2D projections of 3D reconstructed meshes from Coronary Computed Tomography Angiography (CCTA), providing high-quality synthetic data for training. Additionally, we employ large-scale image foundation models to guide feature aggregation, enhancing correspondence matching accuracy by focusing on semantically relevant regions and keypoints. Our approach demonstrates superior matching performance on synthetic datasets and effectively generalizes to real-world datasets, offering a practical solution for this task. Furthermore, our work investigates the efficacy of different foundation models in correspondence matching, providing novel insights into leveraging advanced image foundation models for medical imaging applications.

cs.CV↗

arXiv2025

DiffDenoise: Self-Supervised Medical Image Denoising with Conditional Diffusion Models

Many self-supervised denoising approaches have been proposed in recent years. However, these methods tend to overly smooth images, resulting in the loss of fine structures that are essential for medical applications. In this paper, we propose DiffDenoise, a powerful self-supervised denoising approach tailored for medical images, designed to preserve high-frequency details. Our approach comprises three stages. First, we train a diffusion model on noisy images, using the outputs of a pretrained Blind-Spot Network as conditioning inputs. Next, we introduce a novel stabilized reverse sampling technique, which generates clean images by averaging diffusion sampling outputs initialized with a pair of symmetric noises. Finally, we train a supervised denoising network using noisy images paired with the denoised outputs generated by the diffusion model. Our results demonstrate that DiffDenoise outperforms existing state-of-the-art methods in both synthetic and real-world medical image denoising tasks. We provide both a theoretical foundation and practical insights, demonstrating the method's effectiveness across various medical imaging modalities and anatomical structures.

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arXiv2024

Label-Efficient Data Augmentation with Video Diffusion Models for Guidewire Segmentation in Cardiac Fluoroscopy

The accurate segmentation of guidewires in interventional cardiac fluoroscopy videos is crucial for computer-aided navigation tasks. Although deep learning methods have demonstrated high accuracy and robustness in wire segmentation, they require substantial annotated datasets for generalizability, underscoring the need for extensive labeled data to enhance model performance. To address this challenge, we propose the Segmentation-guided Frame-consistency Video Diffusion Model (SF-VD) to generate large collections of labeled fluoroscopy videos, augmenting the training data for wire segmentation networks. SF-VD leverages videos with limited annotations by independently modeling scene distribution and motion distribution. It first samples the scene distribution by generating 2D fluoroscopy images with wires positioned according to a specified input mask, and then samples the motion distribution by progressively generating subsequent frames, ensuring frame-to-frame coherence through a frame-consistency strategy. A segmentation-guided mechanism further refines the process by adjusting wire contrast, ensuring a diverse range of visibility in the synthesized image. Evaluation on a fluoroscopy dataset confirms the superior quality of the generated videos and shows significant improvements in guidewire segmentation.

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arXiv2024

A Systematic Assessment of Language Models with Linguistic Minimal Pairs in Chinese

We present ZhoBLiMP, the largest linguistic minimal pair benchmark for Chinese, with over 100 paradigms, ranging from topicalization to the \textit{Ba} construction. We then train from scratch a suite of Chinese language models (LMs) with different tokenizers, parameter sizes, and token volumes, to study the learning curves of LMs on Chinese. To mitigate the biases introduced by unequal lengths of the sentences in a minimal pair, we propose a new metric named sub-linear length normalized log-probabilities (SLLN-LP). Using SLLN-LP as the metric, our results show that \textsc{Anaphor}, \textsc{Quantifiers}, and \textsc{Ellipsis} in Chinese are difficult for LMs even up to 32B parameters, and that SLLN-LP successfully mitigates biases in ZhoBLiMP, JBLiMP and BLiMP. We conclude that future evaluations should be more carefully designed to consider the intricate relations between linking functions, LMs, and targeted minimal pairs.

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arXiv2024

Auxiliary Input in Training: Incorporating Catheter Features into Deep Learning Models for ECG-Free Dynamic Coronary Roadmapping

Dynamic coronary roadmapping is a technology that overlays the vessel maps (the "roadmap") extracted from an offline image sequence of X-ray angiography onto a live stream of X-ray fluoroscopy in real-time. It aims to offer navigational guidance for interventional surgeries without the need for repeated contrast agent injections, thereby reducing the risks associated with radiation exposure and kidney failure. The precision of the roadmaps is contingent upon the accurate alignment of angiographic and fluoroscopic images based on their cardiac phases, as well as precise catheter tip tracking. The former ensures the selection of a roadmap that closely matches the vessel shape in the current frame, while the latter uses catheter tips as reference points to adjust for translational motion between the roadmap and the present vessel tree. Training deep learning models for both tasks is challenging and underexplored. However, incorporating catheter features into the models could offer substantial benefits, given humans heavily rely on catheters to complete the tasks. To this end, we introduce a simple but effective method, auxiliary input in training (AIT), and demonstrate that it enhances model performance across both tasks, outperforming baseline methods in knowledge incorporation and transfer learning.

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arXiv2024

Retrieval-augmented Few-shot Medical Image Segmentation with Foundation Models

Medical image segmentation is crucial for clinical decision-making, but the scarcity of annotated data presents significant challenges. Few-shot segmentation (FSS) methods show promise but often require training on the target domain and struggle to generalize across different modalities. Similarly, adapting foundation models like the Segment Anything Model (SAM) for medical imaging has limitations, including the need for finetuning and domain-specific adaptation. To address these issues, we propose a novel method that adapts DINOv2 and Segment Anything Model 2 (SAM 2) for retrieval-augmented few-shot medical image segmentation. Our approach uses DINOv2's feature as query to retrieve similar samples from limited annotated data, which are then encoded as memories and stored in memory bank. With the memory attention mechanism of SAM 2, the model leverages these memories as conditions to generate accurate segmentation of the target image. We evaluated our framework on three medical image segmentation tasks, demonstrating superior performance and generalizability across various modalities without the need for any retraining or finetuning. Overall, this method offers a practical and effective solution for few-shot medical image segmentation and holds significant potential as a valuable annotation tool in clinical applications.

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arXiv2024

MELA: Multilingual Evaluation of Linguistic Acceptability

In this work, we present the largest benchmark to date on linguistic acceptability: Multilingual Evaluation of Linguistic Acceptability -- MELA, with 46K samples covering 10 languages from a diverse set of language families. We establish LLM baselines on this benchmark, and investigate cross-lingual transfer in acceptability judgements with XLM-R. In pursuit of multilingual interpretability, we conduct probing experiments with fine-tuned XLM-R to explore the process of syntax capability acquisition. Our results show that GPT-4o exhibits a strong multilingual ability, outperforming fine-tuned XLM-R, while open-source multilingual models lag behind by a noticeable gap. Cross-lingual transfer experiments show that transfer in acceptability judgment is non-trivial: 500 Icelandic fine-tuning examples lead to 23 MCC performance in a completely unrelated language -- Chinese. Results of our probing experiments indicate that training on MELA improves the performance of XLM-R on syntax-related tasks. Our data is available at https://github.com/sjtu-compling/MELA.

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arXiv2024

Clinically Feasible Diffusion Reconstruction for Highly-Accelerated Cardiac Cine MRI

The currently limited quality of accelerated cardiac cine reconstruction may potentially be improved by the emerging diffusion models, but the clinically unacceptable long processing time poses a challenge. We aim to develop a clinically feasible diffusion-model-based reconstruction pipeline to improve the image quality of cine MRI. A multi-in multi-out diffusion enhancement model together with fast inference strategies were developed to be used in conjunction with a reconstruction model. The diffusion reconstruction reduced spatial and temporal blurring in prospectively undersampled clinical data, as validated by experts inspection. The 1.5s per video processing time enabled the approach to be applied in clinical scenarios.

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arXiv2024

Spatiotemporal Diffusion Model with Paired Sampling for Accelerated Cardiac Cine MRI

Current deep learning reconstruction for accelerated cardiac cine MRI suffers from spatial and temporal blurring. We aim to improve image sharpness and motion delineation for cine MRI under high undersampling rates. A spatiotemporal diffusion enhancement model conditional on an existing deep learning reconstruction along with a novel paired sampling strategy was developed. The diffusion model provided sharper tissue boundaries and clearer motion than the original reconstruction in experts evaluation on clinical data. The innovative paired sampling strategy substantially reduced artificial noises in the generative results.

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arXiv2024

Federated Data Model

In artificial intelligence (AI), especially deep learning, data diversity and volume play a pivotal role in model development. However, training a robust deep learning model often faces challenges due to data privacy, regulations, and the difficulty of sharing data between different locations, especially for medical applications. To address this, we developed a method called the Federated Data Model (FDM). This method uses diffusion models to learn the characteristics of data at one site and then creates synthetic data that can be used at another site without sharing the actual data. We tested this approach with a medical image segmentation task, focusing on cardiac magnetic resonance images from different hospitals. Our results show that models trained with this method perform well both on the data they were originally trained on and on data from other sites. This approach offers a promising way to train accurate and privacy-respecting AI models across different locations.

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arXiv2023

ArguGPT: evaluating, understanding and identifying argumentative essays generated by GPT models

AI generated content (AIGC) presents considerable challenge to educators around the world. Instructors need to be able to detect such text generated by large language models, either with the naked eye or with the help of some tools. There is also growing need to understand the lexical, syntactic and stylistic features of AIGC. To address these challenges in English language teaching, we first present ArguGPT, a balanced corpus of 4,038 argumentative essays generated by 7 GPT models in response to essay prompts from three sources: (1) in-class or homework exercises, (2) TOEFL and (3) GRE writing tasks. Machine-generated texts are paired with roughly equal number of human-written essays with three score levels matched in essay prompts. We then hire English instructors to distinguish machine essays from human ones. Results show that when first exposed to machine-generated essays, the instructors only have an accuracy of 61% in detecting them. But the number rises to 67% after one round of minimal self-training. Next, we perform linguistic analyses of these essays, which show that machines produce sentences with more complex syntactic structures while human essays tend to be lexically more complex. Finally, we test existing AIGC detectors and build our own detectors using SVMs and RoBERTa. Results suggest that a RoBERTa fine-tuned with the training set of ArguGPT achieves above 90% accuracy in both essay- and sentence-level classification. To the best of our knowledge, this is the first comprehensive analysis of argumentative essays produced by generative large language models. Machine-authored essays in ArguGPT and our models will be made publicly available at https://github.com/huhailinguist/ArguGPT

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arXiv2023

Enhancing Cardiac MRI Segmentation via Classifier-Guided Two-Stage Network and All-Slice Information Fusion Transformer

Cardiac Magnetic Resonance imaging (CMR) is the gold standard for assessing cardiac function. Segmenting the left ventricle (LV), right ventricle (RV), and LV myocardium (MYO) in CMR images is crucial but time-consuming. Deep learning-based segmentation methods have emerged as effective tools for automating this process. However, CMR images present additional challenges due to irregular and varying heart shapes, particularly in basal and apical slices. In this study, we propose a classifier-guided two-stage network with an all-slice fusion transformer to enhance CMR segmentation accuracy, particularly in basal and apical slices. Our method was evaluated on extensive clinical datasets and demonstrated better performance in terms of Dice score compared to previous CNN-based and transformer-based models. Moreover, our method produces visually appealing segmentation shapes resembling human annotations and avoids common issues like holes or fragments in other models' segmentations.

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arXiv2023

Computationally Efficient 3D MRI Reconstruction with Adaptive MLP

Compared with 2D MRI, 3D MRI provides superior volumetric spatial resolution and signal-to-noise ratio. However, it is more challenging to reconstruct 3D MRI images. Current methods are mainly based on convolutional neural networks (CNN) with small kernels, which are difficult to scale up to have sufficient fitting power for 3D MRI reconstruction due to the large image size and GPU memory constraint. Furthermore, MRI reconstruction is a deconvolution problem, which demands long-distance information that is difficult to capture by CNNs with small convolution kernels. The multi-layer perceptron (MLP) can model such long-distance information, but it requires a fixed input size. In this paper, we proposed Recon3DMLP, a hybrid of CNN modules with small kernels for low-frequency reconstruction and adaptive MLP (dMLP) modules with large kernels to boost the high-frequency reconstruction, for 3D MRI reconstruction. We further utilized the circular shift operation based on MRI physics such that dMLP accepts arbitrary image size and can extract global information from the entire FOV. We also propose a GPU memory efficient data fidelity module that can reduce $>$50$\%$ memory. We compared Recon3DMLP with other CNN-based models on a high-resolution (HR) 3D MRI dataset. Recon3DMLP improves HR 3D reconstruction and outperforms several existing CNN-based models under similar GPU memory consumption, which demonstrates that Recon3DMLP is a practical solution for HR 3D MRI reconstruction.

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arXiv2023

An Unsupervised Framework for Joint MRI Super Resolution and Gibbs Artifact Removal

The k-space data generated from magnetic resonance imaging (MRI) is only a finite sampling of underlying signals. Therefore, MRI images often suffer from low spatial resolution and Gibbs ringing artifacts. Previous studies tackled these two problems separately, where super resolution methods tend to enhance Gibbs artifacts, whereas Gibbs ringing removal methods tend to blur the images. It is also a challenge that high resolution ground truth is hard to obtain in clinical MRI. In this paper, we propose an unsupervised learning framework for both MRI super resolution and Gibbs artifacts removal without using high resolution ground truth. Furthermore, we propose regularization methods to improve the model's generalizability across out-of-distribution MRI images. We evaluated our proposed methods with other state-of-the-art methods on eight MRI datasets with various contrasts and anatomical structures. Our method not only achieves the best SR performance but also significantly reduces the Gibbs artifacts. Our method also demonstrates good generalizability across different datasets, which is beneficial to clinical applications where training data are usually scarce and biased.

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