Hunting imaging biomarkers in pulmonary fibrosis: Benchmarks of the AIIB23 challenge

Airway-related quantitative imaging biomarkers are crucial for examination, diagnosis, and prognosis in pulmonary diseases. However, the manual delineation of airway trees remains prohibitively time-consuming. While significant efforts have been made towards enhancing airway modelling, current public-available datasets concentrate on lung diseases with moderate morphological variations. The intricate honeycombing patterns present in the lung tissues of fibrotic lung disease patients exacerbate the challenges, often leading to various prediction errors. To address this issue, the 'Airway-Informed Quantitative CT Imaging Biomarker for Fibrotic Lung Disease 2023' (AIIB23) competition was organized in conjunction with the official 2023 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). The airway structures were meticulously annotated by three experienced radiologists. Competitors were encouraged to develop automatic airway segmentation models with high robustness and generalization abilities, followed by exploring the most correlated QIB of mortality prediction. A training set of 120 high-resolution computerised tomography (HRCT) scans were publicly released with expert annotations and mortality status. The online validation set incorporated 52 HRCT scans from patients with fibrotic lung disease and the offline test set included 140 cases from fibrosis and COVID-19 patients. The results have shown that the capacity of extracting airway trees from patients with fibrotic lung disease could be enhanced by introducing voxel-wise weighted general union loss and continuity loss. In addition to the competitive image biomarkers for prognosis, a strong airway-derived biomarker (Hazard ratio>1.5, p<0.0001) was revealed for survival prognostication compared with existing clinical measurements, clinician assessment and AI-based biomarkers.

PnPNet: Pull-and-Push Networks for Volumetric Segmentation with Boundary Confusion

Precise boundary segmentation of volumetric images is a critical task for image-guided diagnosis and computer-assisted intervention, especially for boundary confusion in clinical practice. However, U-shape networks cannot effectively resolve this challenge due to the lack of boundary shape constraints. Besides, existing methods of refining boundaries overemphasize the slender structure, which results in the overfitting phenomenon due to networks' limited abilities to model tiny objects. In this paper, we reconceptualize the mechanism of boundary generation by encompassing the interaction dynamics with adjacent regions. Moreover, we propose a unified network termed PnPNet to model shape characteristics of the confused boundary region. Core ingredients of PnPNet contain the pushing and pulling branches. Specifically, based on diffusion theory, we devise the semantic difference module (SDM) from the pushing branch to squeeze the boundary region. Explicit and implicit differential information inside SDM significantly boost representation abilities for inter-class boundaries. Additionally, motivated by the K-means algorithm, the class clustering module (CCM) from the pulling branch is introduced to stretch the intersected boundary region. Thus, pushing and pulling branches will shrink and enlarge the boundary uncertainty respectively. They furnish two adversarial forces to promote models to output a more precise delineation of boundaries. We carry out experiments on three challenging public datasets and one in-house dataset, containing three types of boundary confusion in model predictions. Experimental results demonstrate the superiority of PnPNet over other segmentation networks, especially on evaluation metrics of HD and ASSD. Besides, pushing and pulling branches can serve as plug-and-play modules to enhance classic U-shape baseline models. Codes are available.

Implicit Shape Modeling for Anatomical Structure Refinement of Volumetric Medical Images

Shape modeling of volumetric medical images is a critical task for quantitative analysis and surgical plans in computer-aided diagnosis. To relieve the burden of expert clinicians, the reconstructed shapes are widely acquired from deep learning models, e.g. Convolutional Neural Networks (CNNs), followed by marching cube algorithm. However, automatically obtaining reconstructed shapes can not always achieve perfect results due to the limited resolution of images and lack of shape prior constraints. In this paper, we design a unified framework for the refinement of medical image segmentation on top of an implicit neural network. Specifically, To learn a sharable shape prior from different instances within the same category in the training phase, the physical information of volumetric medical images are firstly utilized to construct the Physical-Informed Continuous Coordinate Transform (PICCT). PICCT transforms the input data in an aligned manner fed into the implicit shape modeling. To better learn shape representation, we introduce implicit shape constraints on top of the signed distance function (SDF) into the implicit shape modeling of both instances and latent template. For the inference phase, a template interaction module (TIM) is proposed to refine initial results produced by CNNs via deforming deep implicit templates with latent codes. Experimental results on three datasets demonstrated the superiority of our approach in shape refinement. The Chamfer Distance/Earth Mover's Distance achieved by the proposed method are 0.232/0.087 on the Liver dataset, 0.128/0.069 on the Pancreas dataset, and 0.417/0.100 on the Lung Lobe dataset.

Partition-based K-space Synthesis for Multi-contrast Parallel Imaging

Multi-contrast magnetic resonance imaging is a significant and essential medical imaging technique.However, multi-contrast imaging has longer acquisition time and is easy to cause motion artifacts. In particular, the acquisition time for a T2-weighted image is prolonged due to its longer repetition time (TR). On the contrary, T1-weighted image has a shorter TR. Therefore,utilizing complementary information across T1 and T2-weighted image is a way to decrease the overall imaging time. Previous T1-assisted T2 reconstruction methods have mostly focused on image domain using whole-based image fusion approaches. The image domain reconstruction method has the defects of high computational complexity and limited flexibility. To address this issue, we propose a novel multi-contrast imaging method called partition-based k-space synthesis (PKS) which can achieve super reconstruction quality of T2-weighted image by feature fusion. Concretely, we first decompose fully-sampled T1 k-space data and under-sampled T2 k-space data into two sub-data, separately. Then two new objects are constructed by combining the two sub-T1/T2 data. After that, the two new objects as the whole data to realize the reconstruction of T2-weighted image. Finally, the objective T2 is synthesized by extracting the sub-T2 data of each part. Experimental results showed that our combined technique can achieve comparable or better results than using traditional k-space parallel imaging(SAKE) that processes each contrast independently.

Accurate Airway Tree Segmentation in CT Scans via Anatomy-aware Multi-class Segmentation and Topology-guided Iterative Learning

Intrathoracic airway segmentation in computed tomography (CT) is a prerequisite for various respiratory disease analyses such as chronic obstructive pulmonary disease (COPD), asthma and lung cancer. Unlike other organs with simpler shapes or topology, the airway's complex tree structure imposes an unbearable burden to generate the "ground truth" label (up to 7 or 3 hours of manual or semi-automatic annotation on each case). Most of the existing airway datasets are incompletely labeled/annotated, thus limiting the completeness of computer-segmented airway. In this paper, we propose a new anatomy-aware multi-class airway segmentation method enhanced by topology-guided iterative self-learning. Based on the natural airway anatomy, we formulate a simple yet highly effective anatomy-aware multi-class segmentation task to intuitively handle the severe intra-class imbalance of the airway. To solve the incomplete labeling issue, we propose a tailored self-iterative learning scheme to segment toward the complete airway tree. For generating pseudo-labels to achieve higher sensitivity , we introduce a novel breakage attention map and design a topology-guided pseudo-label refinement method by iteratively connecting breaking branches commonly existed from initial pseudo-labels. Extensive experiments have been conducted on four datasets including two public challenges. The proposed method ranked 1st in both EXACT'09 challenge using average score and ATM'22 challenge on weighted average score. In a public BAS dataset and a private lung cancer dataset, our method significantly improves previous leading approaches by extracting at least (absolute) 7.5% more detected tree length and 4.0% more tree branches, while maintaining similar precision.

Multi-aspect Repetition Suppression and Content Moderation of Large Language Models

Natural language generation is one of the most impactful fields in NLP, and recent years have witnessed its evolution brought about by large language models (LLMs). As the key instrument for writing assistance applications, they are generally prone to replicating or extending offensive content provided in the input. In low-resource data regime, they can also lead to repetitive outputs (Holtzman et al., 2019) [1]. Usually, offensive content and repetitions are mitigated with post-hoc methods, including n-gram level blocklists, top-k and nucleus sampling. In this paper, we introduce a combination of exact and non-exact repetition suppression using token and sequence level unlikelihood loss, repetition penalty during training, inference, and post-processing respectively. We further explore multi-level unlikelihood loss to the extent that it endows the model with abilities to avoid generating offensive words and phrases from the beginning. Finally, with comprehensive experiments, we demonstrate that our proposed methods work exceptionally in controlling the repetition and content quality of LLM outputs.

Multi-site, Multi-domain Airway Tree Modeling (ATM'22): A Public Benchmark for Pulmonary Airway Segmentation

Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolution. Since EXACT'09 pulmonary airway segmentation, limited effort has been directed to quantitative comparison of newly emerged algorithms driven by the maturity of deep learning based approaches and clinical drive for resolving finer details of distal airways for early intervention of pulmonary diseases. Thus far, public annotated datasets are extremely limited, hindering the development of data-driven methods and detailed performance evaluation of new algorithms. To provide a benchmark for the medical imaging community, we organized the Multi-site, Multi-domain Airway Tree Modeling (ATM'22), which was held as an official challenge event during the MICCAI 2022 conference. ATM'22 provides large-scale CT scans with detailed pulmonary airway annotation, including 500 CT scans (300 for training, 50 for validation, and 150 for testing). The dataset was collected from different sites and it further included a portion of noisy COVID-19 CTs with ground-glass opacity and consolidation. Twenty-three teams participated in the entire phase of the challenge and the algorithms for the top ten teams are reviewed in this paper. Quantitative and qualitative results revealed that deep learning models embedded with the topological continuity enhancement achieved superior performance in general. ATM'22 challenge holds as an open-call design, the training data and the gold standard evaluation are available upon successful registration via its homepage.

Low-rank Tensor Assisted K-space Generative Model for Parallel Imaging Reconstruction

Although recent deep learning methods, especially generative models, have shown good performance in fast magnetic resonance imaging, there is still much room for improvement in high-dimensional generation. Considering that internal dimensions in score-based generative models have a critical impact on estimating the gradient of the data distribution, we present a new idea, low-rank tensor assisted k-space generative model (LR-KGM), for parallel imaging reconstruction. This means that we transform original prior information into high-dimensional prior information for learning. More specifically, the multi-channel data is constructed into a large Hankel matrix and the matrix is subsequently folded into tensor for prior learning. In the testing phase, the low-rank rotation strategy is utilized to impose low-rank constraints on tensor output of the generative network. Furthermore, we alternately use traditional generative iterations and low-rank high-dimensional tensor iterations for reconstruction. Experimental comparisons with the state-of-the-arts demonstrated that the proposed LR-KGM method achieved better performance.

Generative Modeling in Sinogram Domain for Sparse-view CT Reconstruction

The radiation dose in computed tomography (CT) examinations is harmful for patients but can be significantly reduced by intuitively decreasing the number of projection views. Reducing projection views usually leads to severe aliasing artifacts in reconstructed images. Previous deep learning (DL) techniques with sparse-view data require sparse-view/full-view CT image pairs to train the network with supervised manners. When the number of projection view changes, the DL network should be retrained with updated sparse-view/full-view CT image pairs. To relieve this limitation, we present a fully unsupervised score-based generative model in sinogram domain for sparse-view CT reconstruction. Specifically, we first train a score-based generative model on full-view sinogram data and use multi-channel strategy to form highdimensional tensor as the network input to capture their prior distribution. Then, at the inference stage, the stochastic differential equation (SDE) solver and data-consistency step were performed iteratively to achieve fullview projection. Filtered back-projection (FBP) algorithm was used to achieve the final image reconstruction. Qualitative and quantitative studies were implemented to evaluate the presented method with several CT data. Experimental results demonstrated that our method achieved comparable or better performance than the supervised learning counterparts.

Differentiable Topology-Preserved Distance Transform for Pulmonary Airway Segmentation

Detailed pulmonary airway segmentation is a clinically important task for endobronchial intervention and treatment of peripheral lung cancer lesions. Convolutional Neural Networks (CNNs) are promising tools for medical image analysis but have been performing poorly for cases when there is a significantly imbalanced feature distribution, which is true for the airway data as the trachea and principal bronchi dominate most of the voxels whereas the lobar bronchi and distal segmental bronchi occupy only a small proportion. In this paper, we propose a Differentiable Topology-Preserved Distance Transform (DTPDT) framework to improve the performance of airway segmentation. A Topology-Preserved Surrogate (TPS) learning strategy is first proposed to equalize the training progress within-class distribution. Furthermore, a Convolutional Distance Transform (CDT) is designed to identify the breakage phenomenon with improved sensitivity, minimizing the variation of the distance map between the prediction and ground-truth. The proposed method is validated with the publicly available reference airway segmentation datasets.