Self Pre-training with Topology- and Spatiality-aware Masked Autoencoders for 3D Medical Image Segmentation

Masked Autoencoders (MAEs) have been shown to be effective in pre-training Vision Transformers (ViTs) for natural and medical image analysis problems. By reconstructing missing pixel/voxel information in visible patches, a ViT encoder can aggregate contextual information for downstream tasks. But, existing MAE pre-training methods, which were specifically developed with the ViT architecture, lack the ability to capture geometric shape and spatial information, which is critical for medical image segmentation tasks. In this paper, we propose a novel extension of known MAEs for self pre-training (i.e., models pre-trained on the same target dataset) for 3D medical image segmentation. (1) We propose a new topological loss to preserve geometric shape information by computing topological signatures of both the input and reconstructed volumes, learning geometric shape information. (2) We introduce a pre-text task that predicts the positions of the centers and eight corners of 3D crops, enabling the MAE to aggregate spatial information. (3) We extend the MAE pre-training strategy to a hybrid state-of-the-art (SOTA) medical image segmentation architecture and co-pretrain it alongside the ViT. (4) We develop a fine-tuned model for downstream segmentation tasks by complementing the pre-trained ViT encoder with our pre-trained SOTA model. Extensive experiments on five public 3D segmentation datasets show the effectiveness of our new approach.

SHMC-Net: A Mask-guided Feature Fusion Network for Sperm Head Morphology Classification

Male infertility accounts for about one-third of global infertility cases. Manual assessment of sperm abnormalities through head morphology analysis encounters issues of observer variability and diagnostic discrepancies among experts. Its alternative, Computer-Assisted Semen Analysis (CASA), suffers from low-quality sperm images, small datasets, and noisy class labels. We propose a new approach for sperm head morphology classification, called SHMC-Net, which uses segmentation masks of sperm heads to guide the morphology classification of sperm images. SHMC-Net generates reliable segmentation masks using image priors, refines object boundaries with an efficient graph-based method, and trains an image network with sperm head crops and a mask network with the corresponding masks. In the intermediate stages of the networks, image and mask features are fused with a fusion scheme to better learn morphological features. To handle noisy class labels and regularize training on small datasets, SHMC-Net applies Soft Mixup to combine mixup augmentation and a loss function. We achieve state-of-the-art results on SCIAN and HuSHeM datasets, outperforming methods that use additional pre-training or costly ensembling techniques.

ConUNETR: A Conditional Transformer Network for 3D Micro-CT Embryonic Cartilage Segmentation

Studying the morphological development of cartilaginous and osseous structures is critical to the early detection of life-threatening skeletal dysmorphology. Embryonic cartilage undergoes rapid structural changes within hours, introducing biological variations and morphological shifts that limit the generalization of deep learning-based segmentation models that infer across multiple embryonic age groups. Obtaining individual models for each age group is expensive and less effective, while direct transfer (predicting an age unseen during training) suffers a potential performance drop due to morphological shifts. We propose a novel Transformer-based segmentation model with improved biological priors that better distills morphologically diverse information through conditional mechanisms. This enables a single model to accurately predict cartilage across multiple age groups. Experiments on the mice cartilage dataset show the superiority of our new model compared to other competitive segmentation models. Additional studies on a separate mice cartilage dataset with a distinct mutation show that our model generalizes well and effectively captures age-based cartilage morphology patterns.

RR-CP: Reliable-Region-Based Conformal Prediction for Trustworthy Medical Image Classification

Conformal prediction (CP) generates a set of predictions for a given test sample such that the prediction set almost always contains the true label (e.g., 99.5\% of the time). CP provides comprehensive predictions on possible labels of a given test sample, and the size of the set indicates how certain the predictions are (e.g., a set larger than one is `uncertain'). Such distinct properties of CP enable effective collaborations between human experts and medical AI models, allowing efficient intervention and quality check in clinical decision-making. In this paper, we propose a new method called Reliable-Region-Based Conformal Prediction (RR-CP), which aims to impose a stronger statistical guarantee so that the user-specified error rate (e.g., 0.5\%) can be achieved in the test time, and under this constraint, the size of the prediction set is optimized (to be small). We consider a small prediction set size an important measure only when the user-specified error rate is achieved. Experiments on five public datasets show that our RR-CP performs well: with a reasonably small-sized prediction set, it achieves the user-specified error rate (e.g., 0.5\%) significantly more frequently than exiting CP methods.

SwIPE: Efficient and Robust Medical Image Segmentation with Implicit Patch Embeddings

Modern medical image segmentation methods primarily use discrete representations in the form of rasterized masks to learn features and generate predictions. Although effective, this paradigm is spatially inflexible, scales poorly to higher-resolution images, and lacks direct understanding of object shapes. To address these limitations, some recent works utilized implicit neural representations (INRs) to learn continuous representations for segmentation. However, these methods often directly adopted components designed for 3D shape reconstruction. More importantly, these formulations were also constrained to either point-based or global contexts, lacking contextual understanding or local fine-grained details, respectively--both critical for accurate segmentation. To remedy this, we propose a novel approach, SwIPE (Segmentation with Implicit Patch Embeddings), that leverages the advantages of INRs and predicts shapes at the patch level--rather than at the point level or image level--to enable both accurate local boundary delineation and global shape coherence. Extensive evaluations on two tasks (2D polyp segmentation and 3D abdominal organ segmentation) show that SwIPE significantly improves over recent implicit approaches and outperforms state-of-the-art discrete methods with over 10x fewer parameters. Our method also demonstrates superior data efficiency and improved robustness to data shifts across image resolutions and datasets. Code is available on Github.

Keep Your Friends Close & Enemies Farther: Debiasing Contrastive Learning with Spatial Priors in 3D Radiology Images

Understanding of spatial attributes is central to effective 3D radiology image analysis where crop-based learning is the de facto standard. Given an image patch, its core spatial properties (e.g., position & orientation) provide helpful priors on expected object sizes, appearances, and structures through inherent anatomical consistencies. Spatial correspondences, in particular, can effectively gauge semantic similarities between inter-image regions, while their approximate extraction requires no annotations or overbearing computational costs. However, recent 3D contrastive learning approaches either neglect correspondences or fail to maximally capitalize on them. To this end, we propose an extensible 3D contrastive framework (Spade, for Spatial Debiasing) that leverages extracted correspondences to select more effective positive & negative samples for representation learning. Our method learns both globally invariant and locally equivariant representations with downstream segmentation in mind. We also propose separate selection strategies for global & local scopes that tailor to their respective representational requirements. Compared to recent state-of-the-art approaches, Spade shows notable improvements on three downstream segmentation tasks (CT Abdominal Organ, CT Heart, MR Heart).

A Point in the Right Direction: Vector Prediction for Spatially-aware Self-supervised Volumetric Representation Learning

High annotation costs and limited labels for dense 3D medical imaging tasks have recently motivated an assortment of 3D self-supervised pretraining methods that improve transfer learning performance. However, these methods commonly lack spatial awareness despite its centrality in enabling effective 3D image analysis. More specifically, position, scale, and orientation are not only informative but also automatically available when generating image crops for training. Yet, to date, no work has proposed a pretext task that distills all key spatial features. To fulfill this need, we develop a new self-supervised method, VectorPOSE, which promotes better spatial understanding with two novel pretext tasks: Vector Prediction (VP) and Boundary-Focused Reconstruction (BFR). VP focuses on global spatial concepts (i.e., properties of 3D patches) while BFR addresses weaknesses of recent reconstruction methods to learn more effective local representations. We evaluate VectorPOSE on three 3D medical image segmentation tasks, showing that it often outperforms state-of-the-art methods, especially in limited annotation settings.

ConvFormer: Combining CNN and Transformer for Medical Image Segmentation

Convolutional neural network (CNN) based methods have achieved great successes in medical image segmentation, but their capability to learn global representations is still limited due to using small effective receptive fields of convolution operations. Transformer based methods are capable of modelling long-range dependencies of information for capturing global representations, yet their ability to model local context is lacking. Integrating CNN and Transformer to learn both local and global representations while exploring multi-scale features is instrumental in further improving medical image segmentation. In this paper, we propose a hierarchical CNN and Transformer hybrid architecture, called ConvFormer, for medical image segmentation. ConvFormer is based on several simple yet effective designs. (1) A feed forward module of Deformable Transformer (DeTrans) is re-designed to introduce local information, called Enhanced DeTrans. (2) A residual-shaped hybrid stem based on a combination of convolutions and Enhanced DeTrans is developed to capture both local and global representations to enhance representation ability. (3) Our encoder utilizes the residual-shaped hybrid stem in a hierarchical manner to generate feature maps in different scales, and an additional Enhanced DeTrans encoder with residual connections is built to exploit multi-scale features with feature maps of different scales as input. Experiments on several datasets show that our ConvFormer, trained from scratch, outperforms various CNN- or Transformer-based architectures, achieving state-of-the-art performance.

Unsupervised Feature Clustering Improves Contrastive Representation Learning for Medical Image Segmentation

Self-supervised instance discrimination is an effective contrastive pretext task to learn feature representations and address limited medical image annotations. The idea is to make features of transformed versions of the same images similar while forcing all other augmented images' representations to contrast. However, this instance-based contrastive learning leaves performance on the table by failing to maximize feature affinity between images with similar content while counter-productively pushing their representations apart. Recent improvements on this paradigm (e.g., leveraging multi-modal data, different images in longitudinal studies, spatial correspondences) either relied on additional views or made stringent assumptions about data properties, which can sacrifice generalizability and applicability. To address this challenge, we propose a new self-supervised contrastive learning method that uses unsupervised feature clustering to better select positive and negative image samples. More specifically, we produce pseudo-classes by hierarchically clustering features obtained by an auto-encoder in an unsupervised manner, and prevent destructive interference during contrastive learning by avoiding the selection of negatives from the same pseudo-class. Experiments on 2D skin dermoscopic image segmentation and 3D multi-class whole heart CT segmentation demonstrate that our method outperforms state-of-the-art self-supervised contrastive techniques on these tasks.

Improving Human Sperm Head Morphology Classification with Unsupervised Anatomical Feature Distillation

With rising male infertility, sperm head morphology classification becomes critical for accurate and timely clinical diagnosis. Recent deep learning (DL) morphology analysis methods achieve promising benchmark results, but leave performance and robustness on the table by relying on limited and possibly noisy class labels. To address this, we introduce a new DL training framework that leverages anatomical and image priors from human sperm microscopy crops to extract useful features without additional labeling cost. Our core idea is to distill sperm head information with reliably-generated pseudo-masks and unsupervised spatial prediction tasks. The predicted foreground masks from this distillation step are then leveraged to regularize and reduce image and label noise in the tuning stage. We evaluate our new approach on two public sperm datasets and achieve state-of-the-art performances (e.g. 65.9% SCIAN accuracy and 96.5% HuSHeM accuracy).