Polyp and Surgical Instrument Segmentation with Double Encoder-Decoder Networks

This paper describes a solution for the MedAI competition, in which participants were required to segment both polyps and surgical instruments from endoscopic images. Our approach relies on a double encoder-decoder neural network which we have previously applied for polyp segmentation, but with a series of enhancements: a more powerful encoder architecture, an improved optimization procedure, and the post-processing of segmentations based on tempered model ensembling. Experimental results show that our method produces segmentations that show a good agreement with manual delineations provided by medical experts.

Data-Centric Label Smoothing for Explainable Glaucoma Screening from Eye Fundus Images

As current computing capabilities increase, modern machine learning and computer vision system tend to increase in complexity, mostly by means of larger models and advanced optimization strategies. Although often neglected, in many problems there is also much to be gained by considering potential improvements in understanding and better leveraging already-available training data, including annotations. This so-called data-centric approach can lead to substantial performance increases, sometimes beyond what can be achieved by larger models. In this paper we adopt such an approach for the task of justifiable glaucoma screening from retinal images. In particular, we focus on how to combine information from multiple annotators of different skills into a tailored label smoothing scheme that allows us to better employ a large collection of fundus images, instead of discarding samples suffering from inter-rater variability. Internal validation results indicate that our bespoke label smoothing approach surpasses the performance of a standard resnet50 model and also the same model trained with conventional label smoothing techniques, in particular for the multi-label scenario of predicting clinical reasons of glaucoma likelihood in a highly imbalanced screening context. Our code is made available at github.com/agaldran/justraigs .

Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neuro-vascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited public datasets with annotations on CoW anatomy, especially for CTA. Therefore we organized the TopCoW Challenge in 2023 with the release of an annotated CoW dataset and invited submissions worldwide for the CoW segmentation task, which attracted over 140 registered participants from four continents. TopCoW dataset was the first public dataset with voxel-level annotations for CoW's 13 vessel components, made possible by virtual-reality (VR) technology. It was also the first dataset with paired MRA and CTA from the same patients. TopCoW challenge aimed to tackle the CoW characterization problem as a multiclass anatomical segmentation task with an emphasis on topological metrics. The top performing teams managed to segment many CoW components to Dice scores around 90%, but with lower scores for communicating arteries and rare variants. There were also topological mistakes for predictions with high Dice scores. Additional topological analysis revealed further areas for improvement in detecting certain CoW components and matching CoW variant's topology accurately. TopCoW represented a first attempt at benchmarking the CoW anatomical segmentation task for MRA and CTA, both morphologically and topologically.

Performance Metrics for Probabilistic Ordinal Classifiers

Ordinal classification models assign higher penalties to predictions further away from the true class. As a result, they are appropriate for relevant diagnostic tasks like disease progression prediction or medical image grading. The consensus for assessing their categorical predictions dictates the use of distance-sensitive metrics like the Quadratic-Weighted Kappa score or the Expected Cost. However, there has been little discussion regarding how to measure performance of probabilistic predictions for ordinal classifiers. In conventional classification, common measures for probabilistic predictions are Proper Scoring Rules (PSR) like the Brier score, or Calibration Errors like the ECE, yet these are not optimal choices for ordinal classification. A PSR named Ranked Probability Score (RPS), widely popular in the forecasting field, is more suitable for this task, but it has received no attention in the image analysis community. This paper advocates the use of the RPS for image grading tasks. In addition, we demonstrate a counter-intuitive and questionable behavior of this score, and propose a simple fix for it. Comprehensive experiments on four large-scale biomedical image grading problems over three different datasets show that the RPS is a more suitable performance metric for probabilistic ordinal predictions. Code to reproduce our experiments can be found at https://github.com/agaldran/prob_ord_metrics .

Why is the winner the best?

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

Multi-Head Multi-Loss Model Calibration

Delivering meaningful uncertainty estimates is essential for a successful deployment of machine learning models in the clinical practice. A central aspect of uncertainty quantification is the ability of a model to return predictions that are well-aligned with the actual probability of the model being correct, also known as model calibration. Although many methods have been proposed to improve calibration, no technique can match the simple, but expensive approach of training an ensemble of deep neural networks. In this paper we introduce a form of simplified ensembling that bypasses the costly training and inference of deep ensembles, yet it keeps its calibration capabilities. The idea is to replace the common linear classifier at the end of a network by a set of heads that are supervised with different loss functions to enforce diversity on their predictions. Specifically, each head is trained to minimize a weighted Cross-Entropy loss, but the weights are different among the different branches. We show that the resulting averaged predictions can achieve excellent calibration without sacrificing accuracy in two challenging datasets for histopathological and endoscopic image classification. Our experiments indicate that Multi-Head Multi-Loss classifiers are inherently well-calibrated, outperforming other recent calibration techniques and even challenging Deep Ensembles' performance. Code to reproduce our experiments can be found at \url{https://github.com/agaldran/mhml_calibration} .

AIROGS: Artificial Intelligence for RObust Glaucoma Screening Challenge

The early detection of glaucoma is essential in preventing visual impairment. Artificial intelligence (AI) can be used to analyze color fundus photographs (CFPs) in a cost-effective manner, making glaucoma screening more accessible. While AI models for glaucoma screening from CFPs have shown promising results in laboratory settings, their performance decreases significantly in real-world scenarios due to the presence of out-of-distribution and low-quality images. To address this issue, we propose the Artificial Intelligence for Robust Glaucoma Screening (AIROGS) challenge. This challenge includes a large dataset of around 113,000 images from about 60,000 patients and 500 different screening centers, and encourages the development of algorithms that are robust to ungradable and unexpected input data. We evaluated solutions from 14 teams in this paper, and found that the best teams performed similarly to a set of 20 expert ophthalmologists and optometrists. The highest-scoring team achieved an area under the receiver operating characteristic curve of 0.99 (95% CI: 0.98-0.99) for detecting ungradable images on-the-fly. Additionally, many of the algorithms showed robust performance when tested on three other publicly available datasets. These results demonstrate the feasibility of robust AI-enabled glaucoma screening.

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.

Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Class Adaptive Network Calibration

Recent studies have revealed that, beyond conventional accuracy, calibration should also be considered for training modern deep neural networks. To address miscalibration during learning, some methods have explored different penalty functions as part of the learning objective, alongside a standard classification loss, with a hyper-parameter controlling the relative contribution of each term. Nevertheless, these methods share two major drawbacks: 1) the scalar balancing weight is the same for all classes, hindering the ability to address different intrinsic difficulties or imbalance among classes; and 2) the balancing weight is usually fixed without an adaptive strategy, which may prevent from reaching the best compromise between accuracy and calibration, and requires hyper-parameter search for each application. We propose Class Adaptive Label Smoothing (CALS) for calibrating deep networks, which allows to learn class-wise multipliers during training, yielding a powerful alternative to common label smoothing penalties. Our method builds on a general Augmented Lagrangian approach, a well-established technique in constrained optimization, but we introduce several modifications to tailor it for large-scale, class-adaptive training. Comprehensive evaluation and multiple comparisons on a variety of benchmarks, including standard and long-tailed image classification, semantic segmentation, and text classification, demonstrate the superiority of the proposed method. The code is available at https://github.com/by-liu/CALS.