HQColon: A Hybrid Interactive Machine Learning Pipeline for High Quality Colon Labeling and Segmentation

High-resolution colon segmentation is crucial for clinical and research applications, such as digital twins and personalized medicine. However, the leading open-source abdominal segmentation tool, TotalSegmentator, struggles with accuracy for the colon, which has a complex and variable shape, requiring time-intensive labeling. Here, we present the first fully automatic high-resolution colon segmentation method. To develop it, we first created a high resolution colon dataset using a pipeline that combines region growing with interactive machine learning to efficiently and accurately label the colon on CT colonography (CTC) images. Based on the generated dataset consisting of 435 labeled CTC images we trained an nnU-Net model for fully automatic colon segmentation. Our fully automatic model achieved an average symmetric surface distance of 0.2 mm (vs. 4.0 mm from TotalSegmentator) and a 95th percentile Hausdorff distance of 1.0 mm (vs. 18 mm from TotalSegmentator). Our segmentation accuracy substantially surpasses TotalSegmentator. We share our trained model and pipeline code, providing the first and only open-source tool for high-resolution colon segmentation. Additionally, we created a large-scale dataset of publicly available high-resolution colon labels.

Enhancing predictive imaging biomarker discovery through treatment effect analysis

Identifying predictive biomarkers, which forecast individual treatment effectiveness, is crucial for personalized medicine and informs decision-making across diverse disciplines. These biomarkers are extracted from pre-treatment data, often within randomized controlled trials, and have to be distinguished from prognostic biomarkers, which are independent of treatment assignment. Our study focuses on the discovery of predictive imaging biomarkers, aiming to leverage pre-treatment images to unveil new causal relationships. Previous approaches relied on labor-intensive handcrafted or manually derived features, which may introduce biases. In response, we present a new task of discovering predictive imaging biomarkers directly from the pre-treatment images to learn relevant image features. We propose an evaluation protocol for this task to assess a model's ability to identify predictive imaging biomarkers and differentiate them from prognostic ones. It employs statistical testing and a comprehensive analysis of image feature attribution. We explore the suitability of deep learning models originally designed for estimating the conditional average treatment effect (CATE) for this task, which previously have been primarily assessed for the precision of CATE estimation, overlooking the evaluation of imaging biomarker discovery. Our proof-of-concept analysis demonstrates promising results in discovering and validating predictive imaging biomarkers from synthetic outcomes and real-world image datasets.

Clockwork Diffusion: Efficient Generation With Model-Step Distillation

This work aims to improve the efficiency of text-to-image diffusion models. While diffusion models use computationally expensive UNet-based denoising operations in every generation step, we identify that not all operations are equally relevant for the final output quality. In particular, we observe that UNet layers operating on high-res feature maps are relatively sensitive to small perturbations. In contrast, low-res feature maps influence the semantic layout of the final image and can often be perturbed with no noticeable change in the output. Based on this observation, we propose Clockwork Diffusion, a method that periodically reuses computation from preceding denoising steps to approximate low-res feature maps at one or more subsequent steps. For multiple baselines, and for both text-to-image generation and image editing, we demonstrate that Clockwork leads to comparable or improved perceptual scores with drastically reduced computational complexity. As an example, for Stable Diffusion v1.5 with 8 DPM++ steps we save 32% of FLOPs with negligible FID and CLIP change.

Prediction of post-radiotherapy recurrence volumes in head and neck squamous cell carcinoma using 3D U-Net segmentation

Locoregional recurrences (LRR) are still a frequent site of treatment failure for head and neck squamous cell carcinoma (HNSCC) patients. Identification of high risk subvolumes based on pretreatment imaging is key to biologically targeted radiation therapy. We investigated the extent to which a Convolutional neural network (CNN) is able to predict LRR volumes based on pre-treatment 18F-fluorodeoxyglucose positron emission tomography (FDG-PET)/computed tomography (CT) scans in HNSCC patients and thus the potential to identify biological high risk volumes using CNNs. For 37 patients who had undergone primary radiotherapy for oropharyngeal squamous cell carcinoma, five oncologists contoured the relapse volumes on recurrence CT scans. Datasets of pre-treatment FDG-PET/CT, gross tumour volume (GTV) and contoured relapse for each of the patients were randomly divided into training (n=23), validation (n=7) and test (n=7) datasets. We compared a CNN trained from scratch, a pre-trained CNN, a SUVmax threshold approach, and using the GTV directly. The SUVmax threshold method included 5 out of the 7 relapse origin points within a volume of median 4.6 cubic centimetres (cc). Both the GTV contour and best CNN segmentations included the relapse origin 6 out of 7 times with median volumes of 28 and 18 cc respectively. The CNN included the same or greater number of relapse volume POs, with significantly smaller relapse volumes. Our novel findings indicate that CNNs may predict LRR, yet further work on dataset development is required to attain clinically useful prediction accuracy.

Localise to segment: crop to improve organ at risk segmentation accuracy

Increased organ at risk segmentation accuracy is required to reduce cost and complications for patients receiving radiotherapy treatment. Some deep learning methods for the segmentation of organs at risk use a two stage process where a localisation network first crops an image to the relevant region and then a locally specialised network segments the cropped organ of interest. We investigate the accuracy improvements brought about by such a localisation stage by comparing to a single-stage baseline network trained on full resolution images. We find that localisation approaches can improve both training time and stability and a two stage process involving both a localisation and organ segmentation network provides a significant increase in segmentation accuracy for the spleen, pancreas and heart from the Medical Segmentation Decathlon dataset. We also observe increased benefits of localisation for smaller organs. Source code that recreates the main results is available at \href{https://github.com/Abe404/localise_to_segment}{this https URL}.

Transformer Utilization in Medical Image Segmentation Networks

Owing to success in the data-rich domain of natural images, Transformers have recently become popular in medical image segmentation. However, the pairing of Transformers with convolutional blocks in varying architectural permutations leaves their relative effectiveness to open interpretation. We introduce Transformer Ablations that replace the Transformer blocks with plain linear operators to quantify this effectiveness. With experiments on 8 models on 2 medical image segmentation tasks, we explore -- 1) the replaceable nature of Transformer-learnt representations, 2) Transformer capacity alone cannot prevent representational replaceability and works in tandem with effective design, 3) The mere existence of explicit feature hierarchies in transformer blocks is more beneficial than accompanying self-attention modules, 4) Major spatial downsampling before Transformer modules should be used with caution.

MedNeXt: Transformer-driven Scaling of ConvNets for Medical Image Segmentation

There has been exploding interest in embracing Transformer-based architectures for medical image segmentation. However, the lack of large-scale annotated medical datasets make achieving performances equivalent to those in natural images challenging. Convolutional networks, in contrast, have higher inductive biases and consequently, are easily trainable to high performance. Recently, the ConvNeXt architecture attempted to modernize the standard ConvNet by mirroring Transformer blocks. In this work, we improve upon this to design a modernized and scalable convolutional architecture customized to challenges of data-scarce medical settings. We introduce MedNeXt, a Transformer-inspired large kernel segmentation network which introduces - 1) A fully ConvNeXt 3D Encoder-Decoder Network for medical image segmentation, 2) Residual ConvNeXt up and downsampling blocks to preserve semantic richness across scales, 3) A novel technique to iteratively increase kernel sizes by upsampling small kernel networks, to prevent performance saturation on limited medical data, 4) Compound scaling at multiple levels (depth, width, kernel size) of MedNeXt. This leads to state-of-the-art performance on 4 tasks on CT and MRI modalities and varying dataset sizes, representing a modernized deep architecture for medical image segmentation.

Understanding metric-related pitfalls in image analysis validation

Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation.

Neural Image Compression with a Diffusion-Based Decoder

Diffusion probabilistic models have recently achieved remarkable success in generating high quality image and video data. In this work, we build on this class of generative models and introduce a method for lossy compression of high resolution images. The resulting codec, which we call DIffuson-based Residual Augmentation Codec (DIRAC),is the first neural codec to allow smooth traversal of the rate-distortion-perception tradeoff at test time, while obtaining competitive performance with GAN-based methods in perceptual quality. Furthermore, while sampling from diffusion probabilistic models is notoriously expensive, we show that in the compression setting the number of steps can be drastically reduced.

Explicit Temporal Embedding in Deep Generative Latent Models for Longitudinal Medical Image Synthesis

Medical imaging plays a vital role in modern diagnostics and treatment. The temporal nature of disease or treatment progression often results in longitudinal data. Due to the cost and potential harm, acquiring large medical datasets necessary for deep learning can be difficult. Medical image synthesis could help mitigate this problem. However, until now, the availability of GANs capable of synthesizing longitudinal volumetric data has been limited. To address this, we use the recent advances in latent space-based image editing to propose a novel joint learning scheme to explicitly embed temporal dependencies in the latent space of GANs. This, in contrast to previous methods, allows us to synthesize continuous, smooth, and high-quality longitudinal volumetric data with limited supervision. We show the effectiveness of our approach on three datasets containing different longitudinal dependencies. Namely, modeling a simple image transformation, breathing motion, and tumor regression, all while showing minimal disentanglement. The implementation is made available online at https://github.com/julschoen/Temp-GAN.