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Yihao Liu

Publications and source records attributed to Yihao Liu.

At least 127 records · Page 7Linked to original sources
arXiv2024

SAMM (Segment Any Medical Model): A 3D Slicer Integration to SAM

The Segment Anything Model (SAM) is a new image segmentation tool trained with the largest available segmentation dataset. The model has demonstrated that, with prompts, it can create high-quality masks for general images. However, the performance of the model on medical images requires further validation. To assist with the development, assessment, and application of SAM on medical images, we introduce Segment Any Medical Model (SAMM), an extension of SAM on 3D Slicer - an image processing and visualization software extensively used by the medical imaging community. This open-source extension to 3D Slicer and its demonstrations are posted on GitHub (https://github.com/bingogome/samm). SAMM achieves 0.6-second latency of a complete cycle and can infer image masks in nearly real-time.

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arXiv2023

Learning to See Low-Light Images via Feature Domain Adaptation

Raw low light image enhancement (LLIE) has achieved much better performance than the sRGB domain enhancement methods due to the merits of raw data. However, the ambiguity between noisy to clean and raw to sRGB mappings may mislead the single-stage enhancement networks. The two-stage networks avoid ambiguity by decoupling the two mappings but usually have large computing complexity. To solve this problem, we propose a single-stage network empowered by Feature Domain Adaptation (FDA) to decouple the denoising and color mapping tasks in raw LLIE. The denoising encoder is supervised by the clean raw image, and then the denoised features are adapted for the color mapping task by an FDA module. We propose a Lineformer to serve as the FDA, which can well explore the global and local correlations with fewer line buffers (friendly to the line-based imaging process). During inference, the raw supervision branch is removed. In this way, our network combines the advantage of a two-stage enhancement process with the efficiency of single-stage inference. Experiments on four benchmark datasets demonstrate that our method achieves state-of-the-art performance with fewer computing costs (60% FLOPs of the two-stage method DNF). Our codes will be released after the acceptance of this work.

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arXiv2023

LeCo: Lightweight Compression via Learning Serial Correlations

Lightweight data compression is a key technique that allows column stores to exhibit superior performance for analytical queries. Despite a comprehensive study on dictionary-based encodings to approach Shannon's entropy, few prior works have systematically exploited the serial correlation in a column for compression. In this paper, we propose LeCo (i.e., Learned Compression), a framework that uses machine learning to remove the serial redundancy in a value sequence automatically to achieve an outstanding compression ratio and decompression performance simultaneously. LeCo presents a general approach to this end, making existing (ad-hoc) algorithms such as Frame-of-Reference (FOR), Delta Encoding, and Run-Length Encoding (RLE) special cases under our framework. Our microbenchmark with three synthetic and six real-world data sets shows that a prototype of LeCo achieves a Pareto improvement on both compression ratio and random access speed over the existing solutions. When integrating LeCo into widely-used applications, we observe up to 5.2x speed up in a data analytical query in the Arrow columnar execution engine and a 16% increase in RocksDB's throughput.

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arXiv2023

Evaluating the Generalization Ability of Super-Resolution Networks

Performance and generalization ability are two important aspects to evaluate the deep learning models. However, research on the generalization ability of Super-Resolution (SR) networks is currently absent. Assessing the generalization ability of deep models not only helps us to understand their intrinsic mechanisms, but also allows us to quantitatively measure their applicability boundaries, which is important for unrestricted real-world applications. To this end, we make the first attempt to propose a Generalization Assessment Index for SR networks, namely SRGA. SRGA exploits the statistical characteristics of the internal features of deep networks to measure the generalization ability. Specially, it is a non-parametric and non-learning metric. To better validate our method, we collect a patch-based image evaluation set (PIES) that includes both synthetic and real-world images, covering a wide range of degradations. With SRGA and PIES dataset, we benchmark existing SR models on the generalization ability. This work provides insights and tools for future research on model generalization in low-level vision.

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arXiv2023

Cost-Intelligent Data Analytics in the Cloud

For decades, database research has focused on optimizing performance under fixed resources. As more and more database applications move to the public cloud, we argue that it is time to make cost a first-class citizen when solving database optimization problems. In this paper, we introduce the concept of cost intelligence and envision the architecture of a cloud data warehouse designed for that. We investigate two critical challenges to achieving cost intelligence in an analytical system: automatic resource deployment and cost-oriented auto-tuning. We describe our system architecture with an emphasis on the components that are missing in today's cloud data warehouses. Each of these new components represents unique research opportunities in this much-needed research area.

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arXiv2023

MomentaMorph: Unsupervised Spatial-Temporal Registration with Momenta, Shooting, and Correction

Tagged magnetic resonance imaging (tMRI) has been employed for decades to measure the motion of tissue undergoing deformation. However, registration-based motion estimation from tMRI is difficult due to the periodic patterns in these images, particularly when the motion is large. With a larger motion the registration approach gets trapped in a local optima, leading to motion estimation errors. We introduce a novel "momenta, shooting, and correction" framework for Lagrangian motion estimation in the presence of repetitive patterns and large motion. This framework, grounded in Lie algebra and Lie group principles, accumulates momenta in the tangent vector space and employs exponential mapping in the diffeomorphic space for rapid approximation towards true optima, circumventing local optima. A subsequent correction step ensures convergence to true optima. The results on a 2D synthetic dataset and a real 3D tMRI dataset demonstrate our method's efficiency in estimating accurate, dense, and diffeomorphic 2D/3D motion fields amidst large motion and repetitive patterns.

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arXiv2023

EVD Surgical Guidance with Retro-Reflective Tool Tracking and Spatial Reconstruction using Head-Mounted Augmented Reality Device

Augmented Reality (AR) has been used to facilitate surgical guidance during External Ventricular Drain (EVD) surgery, reducing the risks of misplacement in manual operations. During this procedure, the key challenge is accurately estimating the spatial relationship between pre-operative images and actual patient anatomy in AR environment. This research proposes a novel framework utilizing Time of Flight (ToF) depth sensors integrated in commercially available AR Head Mounted Devices (HMD) for precise EVD surgical guidance. As previous studies have proven depth errors for ToF sensors, we first assessed their properties on AR-HMDs. Subsequently, a depth error model and patient-specific parameter identification method are introduced for accurate surface information. A tracking pipeline combining retro-reflective markers and point clouds is then proposed for accurate head tracking. The head surface is reconstructed using depth data for spatial registration, avoiding fixing tracking targets rigidly on the patient's skull. Firstly, $7.580\pm 1.488 mm$ depth value error was revealed on human skin, indicating the significance of depth correction. Our results showed that the error was reduced by over $85\%$ using proposed depth correction method on head phantoms in different materials. Meanwhile, the head surface reconstructed with corrected depth data achieved sub-millimetre accuracy. An experiment on sheep head revealed $0.79 mm$ reconstruction error. Furthermore, a user study was conducted for the performance in simulated EVD surgery, where five surgeons performed nine k-wire injections on a head phantom with virtual guidance. Results of this study revealed $2.09 \pm 0.16 mm$ translational accuracy and $2.97\pm 0.91$ degree orientational accuracy.

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arXiv2023

On Finite Difference Jacobian Computation in Deformable Image Registration

Producing spatial transformations that are diffeomorphic is a key goal in deformable image registration. As a diffeomorphic transformation should have positive Jacobian determinant |J| everywhere, the number of voxels with |J|<0 has been used to test for diffeomorphism and also to measure the irregularity of the transformation. For digital transformations, |J| is commonly approximated using a central difference, but this strategy can yield positive |J|'s for transformations that are clearly not diffeomorphic -- even at the voxel resolution level. To show this, we first investigate the geometric meaning of different finite difference approximations of |J|. We show that to determine if a deformation is diffeomorphic for digital images, the use of any individual finite difference approximation of |J| is insufficient. We further demonstrate that for a 2D transformation, four unique finite difference approximations of |J|'s must be positive to ensure that the entire domain is invertible and free of folding at the pixel level. For a 3D transformation, ten unique finite differences approximations of |J|'s are required to be positive. Our proposed digital diffeomorphism criteria solves several errors inherent in the central difference approximation of |J| and accurately detects non-diffeomorphic digital transformations. The source code of this work is available at https://github.com/yihao6/digital_diffeomorphism.

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arXiv2023

DRIMET: Deep Registration for 3D Incompressible Motion Estimation in Tagged-MRI with Application to the Tongue

Tagged magnetic resonance imaging~(MRI) has been used for decades to observe and quantify the detailed motion of deforming tissue. However, this technique faces several challenges such as tag fading, large motion, long computation times, and difficulties in obtaining diffeomorphic incompressible flow fields. To address these issues, this paper presents a novel unsupervised phase-based 3D motion estimation technique for tagged MRI. We introduce two key innovations. First, we apply a sinusoidal transformation to the harmonic phase input, which enables end-to-end training and avoids the need for phase interpolation. Second, we propose a Jacobian determinant-based learning objective to encourage incompressible flow fields for deforming biological tissues. Our method efficiently estimates 3D motion fields that are accurate, dense, and approximately diffeomorphic and incompressible. The efficacy of the method is assessed using human tongue motion during speech, and includes both healthy controls and patients that have undergone glossectomy. We show that the method outperforms existing approaches, and also exhibits improvements in speed, robustness to tag fading, and large tongue motion. The code is available: https://github.com/jasonbian97/DRIMET-tagged-MRI

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arXiv2023

HACA3: A Unified Approach for Multi-site MR Image Harmonization

The lack of standardization is a prominent issue in magnetic resonance (MR) imaging. This often causes undesired contrast variations in the acquired images due to differences in hardware and acquisition parameters. In recent years, image synthesis-based MR harmonization with disentanglement has been proposed to compensate for the undesired contrast variations. Despite the success of existing methods, we argue that three major improvements can be made. First, most existing methods are built upon the assumption that multi-contrast MR images of the same subject share the same anatomy. This assumption is questionable, since different MR contrasts are specialized to highlight different anatomical features. Second, these methods often require a fixed set of MR contrasts for training (e.g., both T1-weighted and T2-weighted images), limiting their applicability. Lastly, existing methods are generally sensitive to imaging artifacts. In this paper, we present Harmonization with Attention-based Contrast, Anatomy, and Artifact Awareness (HACA3), a novel approach to address these three issues. HACA3 incorporates an anatomy fusion module that accounts for the inherent anatomical differences between MR contrasts. Furthermore, HACA3 is also robust to imaging artifacts and can be trained and applied to any set of MR contrasts. HACA3 is developed and evaluated on diverse MR datasets acquired from 21 sites with varying field strengths, scanner platforms, and acquisition protocols. Experiments show that HACA3 achieves state-of-the-art performance under multiple image quality metrics. We also demonstrate the applicability and versatility of HACA3 on downstream tasks including white matter lesion segmentation and longitudinal volumetric analyses.

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arXiv2023

Unknown Sniffer for Object Detection: Don't Turn a Blind Eye to Unknown Objects

The recently proposed open-world object and open-set detection have achieved a breakthrough in finding never-seen-before objects and distinguishing them from known ones. However, their studies on knowledge transfer from known classes to unknown ones are not deep enough, resulting in the scanty capability for detecting unknowns hidden in the background. In this paper, we propose the unknown sniffer (UnSniffer) to find both unknown and known objects. Firstly, the generalized object confidence (GOC) score is introduced, which only uses known samples for supervision and avoids improper suppression of unknowns in the background. Significantly, such confidence score learned from known objects can be generalized to unknown ones. Additionally, we propose a negative energy suppression loss to further suppress the non-object samples in the background. Next, the best box of each unknown is hard to obtain during inference due to lacking their semantic information in training. To solve this issue, we introduce a graph-based determination scheme to replace hand-designed non-maximum suppression (NMS) post-processing. Finally, we present the Unknown Object Detection Benchmark, the first publicly benchmark that encompasses precision evaluation for unknown detection to our knowledge. Experiments show that our method is far better than the existing state-of-the-art methods.

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arXiv2023

Masked Image Training for Generalizable Deep Image Denoising

When capturing and storing images, devices inevitably introduce noise. Reducing this noise is a critical task called image denoising. Deep learning has become the de facto method for image denoising, especially with the emergence of Transformer-based models that have achieved notable state-of-the-art results on various image tasks. However, deep learning-based methods often suffer from a lack of generalization ability. For example, deep models trained on Gaussian noise may perform poorly when tested on other noise distributions. To address this issue, we present a novel approach to enhance the generalization performance of denoising networks, known as masked training. Our method involves masking random pixels of the input image and reconstructing the missing information during training. We also mask out the features in the self-attention layers to avoid the impact of training-testing inconsistency. Our approach exhibits better generalization ability than other deep learning models and is directly applicable to real-world scenarios. Additionally, our interpretability analysis demonstrates the superiority of our method.

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arXiv2023

Spatially-varying Regularization with Conditional Transformer for Unsupervised Image Registration

In the past, optimization-based registration models have used spatially-varying regularization to account for deformation variations in different image regions. However, deep learning-based registration models have mostly relied on spatially-invariant regularization. Here, we introduce an end-to-end framework that uses neural networks to learn a spatially-varying deformation regularizer directly from data. The hyperparameter of the proposed regularizer is conditioned into the network, enabling easy tuning of the regularization strength. The proposed method is built upon a Transformer-based model, but it can be readily adapted to any network architecture. We thoroughly evaluated the proposed approach using publicly available datasets and observed a significant performance improvement while maintaining smooth deformation. The source code of this work will be made available after publication.

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arXiv2023

Deformable Cross-Attention Transformer for Medical Image Registration

Transformers have recently shown promise for medical image applications, leading to an increasing interest in developing such models for medical image registration. Recent advancements in designing registration Transformers have focused on using cross-attention (CA) to enable a more precise understanding of spatial correspondences between moving and fixed images. Here, we propose a novel CA mechanism that computes windowed attention using deformable windows. In contrast to existing CA mechanisms that require intensive computational complexity by either computing CA globally or locally with a fixed and expanded search window, the proposed deformable CA can selectively sample a diverse set of features over a large search window while maintaining low computational complexity. The proposed model was extensively evaluated on multi-modal, mono-modal, and atlas-to-patient registration tasks, demonstrating promising performance against state-of-the-art methods and indicating its effectiveness for medical image registration. The source code for this work will be available after publication.

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arXiv2023

Automated Ventricle Parcellation and Evan's Ratio Computation in Pre- and Post-Surgical Ventriculomegaly

Normal pressure hydrocephalus~(NPH) is a brain disorder associated with enlarged ventricles and multiple cognitive and motor symptoms. The degree of ventricular enlargement can be measured using magnetic resonance images~(MRIs) and characterized quantitatively using the Evan's ratio (ER). Automatic computation of ER is desired to avoid the extra time and variations associated with manual measurements on MRI. Because shunt surgery is often used to treat NPH, it is necessary that this process be robust to image artifacts caused by the shunt and related implants. In this paper, we propose a 3D regions-of-interest aware (ROI-aware) network for segmenting the ventricles. The method achieves state-of-the-art performance on both pre-surgery MRIs and post-surgery MRIs with artifacts. Based on our segmentation results, we also describe an automated approach to compute ER from these results. Experimental results on multiple datasets demonstrate the potential of the proposed method to assist clinicians in the diagnosis and management of NPH.

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arXiv2023

A latent space for unsupervised MR image quality control via artifact assessment

Image quality control (IQC) can be used in automated magnetic resonance (MR) image analysis to exclude erroneous results caused by poorly acquired or artifact-laden images. Existing IQC methods for MR imaging generally require human effort to craft meaningful features or label large datasets for supervised training. The involvement of human labor can be burdensome and biased, as labeling MR images based on their quality is a subjective task. In this paper, we propose an automatic IQC method that evaluates the extent of artifacts in MR images without supervision. In particular, we design an artifact encoding network that learns representations of artifacts based on contrastive learning. We then use a normalizing flow to estimate the density of learned representations for unsupervised classification. Our experiments on large-scale multi-cohort MR datasets show that the proposed method accurately detects images with high levels of artifacts, which can inform downstream analysis tasks about potentially flawed data.

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arXiv2022

CP3: Unifying Point Cloud Completion by Pretrain-Prompt-Predict Paradigm

Point cloud completion aims to predict complete shape from its partial observation. Current approaches mainly consist of generation and refinement stages in a coarse-to-fine style. However, the generation stage often lacks robustness to tackle different incomplete variations, while the refinement stage blindly recovers point clouds without the semantic awareness. To tackle these challenges, we unify point cloud Completion by a generic Pretrain-Prompt-Predict paradigm, namely CP3. Inspired by prompting approaches from NLP, we creatively reinterpret point cloud generation and refinement as the prompting and predicting stages, respectively. Then, we introduce a concise self-supervised pretraining stage before prompting. It can effectively increase robustness of point cloud generation, by an Incompletion-Of-Incompletion (IOI) pretext task. Moreover, we develop a novel Semantic Conditional Refinement (SCR) network at the predicting stage. It can discriminatively modulate multi-scale refinement with the guidance of semantics. Finally, extensive experiments demonstrate that our CP3 outperforms the state-of-the-art methods with a large margin.

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arXiv2022

Cross-identity Video Motion Retargeting with Joint Transformation and Synthesis

In this paper, we propose a novel dual-branch Transformation-Synthesis network (TS-Net), for video motion retargeting. Given one subject video and one driving video, TS-Net can produce a new plausible video with the subject appearance of the subject video and motion pattern of the driving video. TS-Net consists of a warp-based transformation branch and a warp-free synthesis branch. The novel design of dual branches combines the strengths of deformation-grid-based transformation and warp-free generation for better identity preservation and robustness to occlusion in the synthesized videos. A mask-aware similarity module is further introduced to the transformation branch to reduce computational overhead. Experimental results on face and dance datasets show that TS-Net achieves better performance in video motion retargeting than several state-of-the-art models as well as its single-branch variants. Our code is available at https://github.com/nihaomiao/WACV23_TSNet.

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