Abstract Biomedical image analysis algorithm validation depends on high-quality annotation of reference datasets, for which labelling instructions are key. Despite their importance, their optimization remains largely unexplored. Here we present a systematic study of labelling instructions and their impact on annotation quality in the field. Through comprehensive examination of professional practice and international competitions registered at the Medical Image Computing and Computer Assisted Intervention Society, the largest international society in the biomedical imaging field, we uncovered a discrepancy between annotators’ needs for labelling instructions and their current quality and availability. On the basis of an analysis of 14,040 images annotated by 156 annotators from four professional annotation companies and 708 Amazon Mechanical Turk crowdworkers using instructions with different information density levels, we further found that including exemplary images substantially boosts annotation performance compared with text-only descriptions, while solely extending text descriptions does not. Finally, professional annotators constantly outperform Amazon Mechanical Turk crowdworkers. Our study raises awareness for the need of quality standards in biomedical image analysis labelling instructions. 

/pdf/labelling-instructions-matter-in-biomedical-image-analysis-5h00ceew.pdf

Labelling instructions matter in biomedical image analysis

pdf/constrained-unsupervised-anomaly-segmentation-31ox4bwg.pdf

Constrained unsupervised anomaly segmentation

Real-world medical image segmentation has tremendous long-tailed complexity of objects, among which tail conditions correlate with relatively rare diseases and are clinically significant. A trustworthy medical AI algorithm should demonstrate its effectiveness on tail conditions to avoid clinically dangerous damage in these out-of-distribution (OOD) cases. In this paper, we adopt the concept of object queries in Mask Transformers to formulate semantic segmentation as a soft cluster assignment. The queries fit the feature-level cluster centers of inliers during training. Therefore, when performing inference on a medical image in real-world scenarios, the similarity between pixels and the queries detects and localizes OOD regions. We term this OOD localization as MaxQuery. Furthermore, the foregrounds of real-world medical images, whether OOD objects or inliers, are lesions. The difference between them is less than that between the foreground and background, possibly misleading the object queries to focus redundantly on the background. Thus, we propose a query-distribution (QD) loss to enforce clear boundaries between segmentation targets and other regions at the query level, improving the inlier segmentation and OOD indication. Our proposed framework is tested on two real-world segmentation tasks, i.e., segmentation of pancreatic and liver tumors, outperforming previous state-of-the-art algorithms by an average of 7.39% on AUROC, 14.69% on AUPR, and 13.79% on FPR95 for OOD localization. On the other hand, our framework improves the performance of inlier segmentation by an average of 5.27% DSC when compared with the leading baseline nnUNet.

pdf/devil-is-in-the-queries-advancing-mask-transformers-for-real-91iycqu9.pdf

Devil is in the Queries: Advancing Mask Transformers for Real-world Medical Image Segmentation and Out-of-Distribution Localization

The long-tailed distribution problem in medical image analysis reflects a high prevalence of common conditions and a low prevalence of rare ones, which poses a significant challenge in developing a unified model capable of identifying rare or novel tumor categories not encountered during training. In this paper, we propose a new zero-shot pan-tumor segmentation framework (ZePT) based on query-disentangling and self-prompting to segment unseen tumor categories beyond the training set. ZePT disentangles the object queries into two subsets and trains them in two stages. Initially, it learns a set of fundamental queries for organ segmentation through an object-aware feature grouping strategy, which gathers organ-level visual features. Subsequently, it refines the other set of advanced queries that focus on the auto-generated visual prompts for unseen tumor segmentation. Moreover, we introduce query-knowledge alignment at the feature level to enhance each query's discriminative representation and generalizability. Extensive experiments on various tumor segmentation tasks demonstrate the performance superiority of ZePT, which surpasses the previous counterparts and evidence the promising ability for zero-shot tumor segmentation in real-world settings. Codes will be made publicly available.

https://export.arxiv.org/pdf/2312.04964v2.pdf

ZePT: Zero-Shot Pan-Tumor Segmentation via Query-Disentangling and Self-Prompting

We study the impact of different loss functions on lesion segmentation from medical images. Although the Cross-Entropy (CE) loss is the most popular option when dealing with natural images, for biomedical image segmentation the soft Dice loss is often preferred due to its ability to handle imbalanced scenarios. On the other hand, the combination of both functions has also been successfully applied in this kind of tasks. A much less studied problem is the generalization ability of all these losses in the presence of Out-of-Distribution (OoD) data. This refers to samples appearing in test time that are drawn from a different distribution than training images. In our case, we train our models on images that always contain lesions, but in test time we also have lesion-free samples. We analyze the impact of the minimization of different loss functions on in-distribution performance, but also its ability to generalize to OoD data, via comprehensive experiments on polyp segmentation from endoscopic images and ulcer segmentation from diabetic feet images. Our findings are surprising: CE-Dice loss combinations that excel in segmenting in-distribution images have a poor performance when dealing with OoD data, which leads us to recommend the adoption of the CE loss for this kind of problems, due to its robustness and ability to generalize to OoD samples. Code associated to our experiments can be found at https://github.com/agaldran/lesion_losses_ood .

On the Optimal Combination of Cross-Entropy and Soft Dice Losses for Lesion Segmentation with Out-of-Distribution Robustness

Detecting Out-of-Distribution (OoD) data is one of the greatest challenges in safe and robust deployment of machine learning algorithms in medicine. When the algorithms encounter cases that deviate from the distribution of the training data, they often produce incorrect and over-confident predictions. OoD detection algorithms aim to catch erroneous predictions in advance by analysing the data distribution and detecting potential instances of failure. Moreover, flagging OoD cases may support human readers in identifying incidental findings. Due to the increased interest in OoD algorithms, benchmarks for different domains have recently been established. In the medical imaging domain, for which reliable predictions are often essential, an open benchmark has been missing. We introduce the Medical-Out-Of-Distribution-Analysis-Challenge (MOOD) as an open, fair, and unbiased benchmark for OoD methods in the medical imaging domain. The analysis of the submitted algorithms shows that performance has a strong positive correlation with the perceived difficulty, and that all algorithms show a high variance for different anomalies, making it yet hard to recommend them for clinical practice. We also see a strong correlation between challenge ranking and performance on a simple toy test set, indicating that this might be a valuable addition as a proxy dataset during anomaly detection algorithm development.

https://ieeexplore.ieee.org/ielx7/42/4359023/09762702.pdf

MOOD 2020: A Public Benchmark for Out-of-Distribution Detection and Localization on Medical Images

To balance the annotation labor and the granularity of supervision, single-frame annotation has been introduced in temporal action localization. It provides a rough temporal location for an action but implicitly overstates the supervision from the annotated-frame during training, leading to the confusion between actions and backgrounds, i.e., action incompleteness and background false positives. To tackle the two challenges, in this work, we present the Snippet Classification model and the Dilation-Erosion module. In the Dilation-Erosion module, we expand the potential action segments with a loose criterion to alleviate the problem of action incompleteness and then remove the background from the potential action segments to alleviate the problem of action incompleteness. Relying on the single-frame annotation and the output of the snippet classification, the Dilation-Erosion module mines pseudo snippet-level ground-truth, hard backgrounds and evident backgrounds, which in turn further trains the Snippet Classification model. It forms a cyclic dependency. Furthermore, we propose a new embedding loss to aggregate the features of action instances with the same label and separate the features of actions from backgrounds. Experiments on THUMOS14 and ActivityNet 1.2 validate the effectiveness of the proposed method. Code has been made publicly available ( https://github.com/LingJun123/single-frame-TAL ).

pdf/dilation-erosion-for-single-frame-supervised-temporal-action-22m2bojz.pdf

Dilation-erosion for single-frame supervised temporal action localization

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MOOD 2020: A Public Benchmark for Out-of-Distribution Detection and Localization on Medical Images

Dilation-erosion for single-frame supervised temporal action localization