Yilin Liu

Yilin Liu, Ruining Deng, Juming Xiong et al.

Eosinophilic esophagitis (EoE) is a chronic and relapsing disease characterized by esophageal inflammation. Symptoms of EoE include difficulty swallowing, food impaction, and chest pain which significantly impact the quality of life, resulting in nutritional impairments, social limitations, and psychological distress. The diagnosis of EoE is typically performed with a threshold (15 to 20) of eosinophils (Eos) per high-power field (HPF). Since the current counting process of Eos is a resource-intensive process for human pathologists, automatic methods are desired. Circle representation has been shown as a more precise, yet less complicated, representation for automatic instance cell segmentation such as CircleSnake approach. However, the CircleSnake was designed as a single-label model, which is not able to deal with multi-label scenarios. In this paper, we propose the multi-label CircleSnake model for instance segmentation on Eos. It extends the original CircleSnake model from a single-label design to a multi-label model, allowing segmentation of multiple object types. Experimental results illustrate the CircleSnake model's superiority over the traditional Mask R-CNN model and DeepSnake model in terms of average precision (AP) in identifying and segmenting eosinophils, thereby enabling enhanced characterization of EoE. This automated approach holds promise for streamlining the assessment process and improving diagnostic accuracy in EoE analysis. The source code has been made publicly available at https://github.com/yilinliu610730/EoE.

Juming Xiong, Yilin Liu, Ruining Deng et al.

Eosinophilic Esophagitis (EoE) is a chronic, immune/antigen-mediated esophageal disease, characterized by symptoms related to esophageal dysfunction and histological evidence of eosinophil-dominant inflammation. Owing to the intricate microscopic representation of EoE in imaging, current methodologies which depend on manual identification are not only labor-intensive but also prone to inaccuracies. In this study, we develop an open-source toolkit, named Open-EoE, to perform end-to-end whole slide image (WSI) level eosinophil (Eos) detection using one line of command via Docker. Specifically, the toolkit supports three state-of-the-art deep learning-based object detection models. Furthermore, Open-EoE further optimizes the performance by implementing an ensemble learning strategy, and enhancing the precision and reliability of our results. The experimental results demonstrated that the Open-EoE toolkit can efficiently detect Eos on a testing set with 289 WSIs. At the widely accepted threshold of >= 15 Eos per high power field (HPF) for diagnosing EoE, the Open-EoE achieved an accuracy of 91%, showing decent consistency with pathologist evaluations. This suggests a promising avenue for integrating machine learning methodologies into the diagnostic process for EoE. The docker and source code has been made publicly available at https://github.com/hrlblab/Open-EoE.

Yilin Liu, Jiang Li, Yunkui Pang et al.

Deep Image Prior (DIP) shows that some network architectures naturally bias towards smooth images and resist noises, a phenomenon known as spectral bias. Image denoising is an immediate application of this property. Although DIP has removed the requirement of large training sets, it still presents two practical challenges for denoising: architectural design and noise-fitting, which are often intertwined. Existing methods mostly handcraft or search for the architecture from a large design space, due to the lack of understanding on how the architectural choice corresponds to the image. In this study, we analyze from a frequency perspective to demonstrate that the unlearnt upsampling is the main driving force behind the denoising phenomenon in DIP. This finding then leads to strategies for estimating a suitable architecture for every image without a laborious search. Extensive experiments show that the estimated architectures denoise and preserve the textural details better than current methods with up to 95% fewer parameters. The under-parameterized nature also makes them especially robust to a higher level of noise.

Xiang Xu, Pradeep Kumar Jayaraman, Joseph G. Lambourne et al.

The boundary representation (B-Rep) is the standard data structure used in Computer-Aided Design (CAD) for defining solid models. Despite recent progress, directly generating B-Reps end-to-end with precise geometry and watertight topology remains a challenge. This paper presents AutoBrep, a novel Transformer model that autoregressively generates B-Reps with high quality and validity. AutoBrep employs a unified tokenization scheme that encodes both geometric and topological characteristics of a B-Rep model as a sequence of discrete tokens. Geometric primitives (i.e., surfaces and curves) are encoded as latent geometry tokens, and their structural relationships are defined as special topological reference tokens. Sequence order in AutoBrep naturally follows a breadth first traversal of the B-Rep face adjacency graph. At inference time, neighboring faces and edges along with their topological structure are progressively generated. Extensive experiments demonstrate the advantages of our unified representation when coupled with next-token prediction for B-Rep generation. AutoBrep outperforms baselines with better quality and watertightness. It is also highly scalable to complex solids with good fidelity and inference speed. We further show that autocompleting B-Reps is natively supported through our unified tokenization, enabling user-controllable CAD generation with minimal changes. Code is available at https://github.com/AutodeskAILab/AutoBrep.

Congzhang Shao, Quan Yuan, Guiyang Luo et al.

Collaborative perception improves task performance by expanding the perception range through information sharing among agents. . Immutable heterogeneity poses a significant challenge in collaborative perception, as participating agents may employ different and fixed perception models. This leads to domain gaps in the intermediate features shared among agents, consequently degrading collaborative performance. Aligning the features of all agents to a common representation can eliminate domain gaps with low training cost. However, in existing methods, the common representation is designated as the representation of a specific agent, making it difficult for agents with significant domain discrepancies from this specific agent to achieve proper alignment. This paper proposes NegoCollab, a heterogeneous collaboration method based on the negotiated common representation. It introduces a negotiator during training to derive the common representation from the local representations of each modality's agent, effectively reducing the inherent domain gap with the various local representations. In NegoCollab, the mutual transformation of features between the local representation space and the common representation space is achieved by a pair of sender and receiver. To better align local representations to the common representation containing multimodal information, we introduce structural alignment loss and pragmatic alignment loss in addition to the distribution alignment loss to supervise the training. This enables the knowledge in the common representation to be fully distilled into the sender.

Juming Xiong, Ethan H. Nguyen, Yilin Liu et al.

Recently, circle representation has been introduced for medical imaging, designed specifically to enhance the detection of instance objects that are spherically shaped (e.g., cells, glomeruli, and nuclei). Given its outstanding effectiveness in instance detection, it is compelling to consider the application of circle representation for segmenting instance medical objects. In this study, we introduce CircleSnake, a simple end-to-end segmentation approach that utilizes circle contour deformation for segmenting ball-shaped medical objects at the instance level. The innovation of CircleSnake lies in these three areas: (1) It substitutes the complex bounding box-to-octagon contour transformation with a more consistent and rotation-invariant bounding circle-to-circle contour adaptation. This adaptation specifically targets ball-shaped medical objects. (2) The circle representation employed in CircleSnake significantly reduces the degrees of freedom to two, compared to eight in the octagon representation. This reduction enhances both the robustness of the segmentation performance and the rotational consistency of the method. (3) CircleSnake is the first end-to-end deep instance segmentation pipeline to incorporate circle representation, encompassing consistent circle detection, circle contour proposal, and circular convolution in a unified framework. This integration is achieved through the novel application of circular graph convolution within the context of circle detection and instance segmentation. In practical applications, such as the detection of glomeruli, nuclei, and eosinophils in pathological images, CircleSnake has demonstrated superior performance and greater rotation invariance when compared to benchmarks. The code has been made publicly available: https://github.com/hrlblab/CircleSnake.

Lei Chen, Yilin Liu, Yue Li et al.

Visual cues are essential in computer-mediated communication. It is especially important when communication happens in a collaboration scenario that requires focusing several users' attention on aspecific object among other similar ones. This paper explores the effect of visual cues on pointing tasks in co-located Augmented Reality (AR) collaboration. A user study (N = 32, 16 pairs) was conducted to compare two types of visual cues: Pointing Line (PL)and Moving Track (MT). Both are head-based visual techniques.Through a series of collaborative pointing tasks on objects with different states (static and dynamic) and density levels (low, mediumand high), the results showed that PL was better on task performance and usability, but MT was rated higher on social presenceand user preference. Based on our results, some design implicationsare provided for pointing tasks in co-located AR collaboration.

Yilin Liu, Ke Xie, Hui Huang

The drone navigation requires the comprehensive understanding of both visual and geometric information in the 3D world. In this paper, we present a Visual-Geometric Fusion Network(VGF-Net), a deep network for the fusion analysis of visual/geometric data and the construction of 2.5D height maps for simultaneous drone navigation in novel environments. Given an initial rough height map and a sequence of RGB images, our VGF-Net extracts the visual information of the scene, along with a sparse set of 3D keypoints that capture the geometric relationship between objects in the scene. Driven by the data, VGF-Net adaptively fuses visual and geometric information, forming a unified Visual-Geometric Representation. This representation is fed to a new Directional Attention Model(DAM), which helps enhance the visual-geometric object relationship and propagates the informative data to dynamically refine the height map and the corresponding keypoints. An entire end-to-end information fusion and mapping system is formed, demonstrating remarkable robustness and high accuracy on the autonomous drone navigation across complex indoor and large-scale outdoor scenes. The dataset can be found in http://vcc.szu.edu.cn/research/2021/VGFNet.

Yilin Liu, Gengyan Zhao, Brendon M. Nacewicz et al.

Recent advances in deep learning have improved the segmentation accuracy of subcortical brain structures, which would be useful in neuroimaging studies of many neurological disorders. However, most of the previous deep learning work does not investigate the specific difficulties that exist in segmenting extremely small but important brain regions such as the amygdala and its subregions. To tackle this challenging task, a novel 3D Bayesian fully convolutional neural network was developed to apply a dilated dualpathway approach that retains fine details and utilizes both local and more global contextual information to automatically segment the amygdala and its subregions at high precision. The proposed method provides insights on network design and sampling strategy that target segmentations of small 3D structures. In particular, this study confirms that a large context, enabled by a large field of view, is beneficial for segmenting small objects; furthermore, precise contextual information enabled by dilated convolutions allows for better boundary localization, which is critical for examining the morphology of the structure. In addition, it is demonstrated that the uncertainty information estimated from our network may be leveraged to identify atypicality in data. Our method was compared with two state-of-the-art deep learning models and a traditional multi-atlas approach, and exhibited excellent performance as measured both by Dice overlap as well as average symmetric surface distance. To the best of our knowledge, this work is the first deep learning-based approach that targets the subregions of the amygdala.