Understanding metric-related pitfalls in image analysis validation

Validation metrics are key for tracking scientific progress and bridging the current chasm between artificial intelligence research and its translation into practice. However, increasing evidence shows that, particularly in image analysis, metrics are often chosen inadequately. Although 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 multistage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides a reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Although focused on biomedical image analysis, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. The work serves to enhance global comprehension of a key topic in image analysis validation.

Metrics reloaded: recommendations for image analysis validation

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. In biomedical image analysis, chosen performance metrics often do not reflect the domain interest, and thus fail to adequately measure scientific progress and hinder translation of ML techniques into practice. To overcome this, we created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. Developed by a large international consortium in a multistage Delphi process, it is based on the novel concept of a problem fingerprint-a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), dataset and algorithm output. On the basis of the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as classification tasks at image, object or pixel level, namely image-level classification, object detection, semantic segmentation and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. Its applicability is demonstrated for various biomedical use cases.

Efficient Photoacoustic Image Synthesis with Deep Learning

Photoacoustic imaging potentially allows for the real-time visualization of functional human tissue parameters such as oxygenation but is subject to a challenging underlying quantification problem. While in silico studies have revealed the great potential of deep learning (DL) methodology in solving this problem, the inherent lack of an efficient gold standard method for model training and validation remains a grand challenge. This work investigates whether DL can be leveraged to accurately and efficiently simulate photon propagation in biological tissue, enabling photoacoustic image synthesis. Our approach is based on estimating the initial pressure distribution of the photoacoustic waves from the underlying optical properties using a back-propagatable neural network trained on synthetic data. In proof-of-concept studies, we validated the performance of two complementary neural network architectures, namely a conventional U-Net-like model and a Fourier Neural Operator (FNO) network. Our in silico validation on multispectral human forearm images shows that DL methods can speed up image generation by a factor of 100 when compared to Monte Carlo simulations with 5×108 photons. While the FNO is slightly more accurate than the U-Net, when compared to Monte Carlo simulations performed with a reduced number of photons (5×106), both neural network architectures achieve equivalent accuracy. In contrast to Monte Carlo simulations, the proposed DL models can be used as inherently differentiable surrogate models in the photoacoustic image synthesis pipeline, allowing for back-propagation of the synthesis error and gradient-based optimization over the entire pipeline. Due to their efficiency, they have the potential to enable large-scale training data generation that can expedite the clinical application of photoacoustic imaging.

Sources of performance variability in deep learning-based polyp detection

PURPOSE

Validation metrics are a key prerequisite for the reliable tracking of scientific progress and for deciding on the potential clinical translation of methods. While recent initiatives aim to develop comprehensive theoretical frameworks for understanding metric-related pitfalls in image analysis problems, there is a lack of experimental evidence on the concrete effects of common and rare pitfalls on specific applications. We address this gap in the literature in the context of colon cancer screening.

METHODS

Our contribution is twofold. Firstly, we present the winning solution of the Endoscopy Computer Vision Challenge on colon cancer detection, conducted in conjunction with the IEEE International Symposium on Biomedical Imaging 2022. Secondly, we demonstrate the sensitivity of commonly used metrics to a range of hyperparameters as well as the consequences of poor metric choices.

RESULTS

Based on comprehensive validation studies performed with patient data from six clinical centers, we found all commonly applied object detection metrics to be subject to high inter-center variability. Furthermore, our results clearly demonstrate that the adaptation of standard hyperparameters used in the computer vision community does not generally lead to the clinically most plausible results. Finally, we present localization criteria that correspond well to clinical relevance.

CONCLUSION

We conclude from our study that (1) performance results in polyp detection are highly sensitive to various design choices, (2) common metric configurations do not reflect the clinical need and rely on suboptimal hyperparameters and (3) comparison of performance across datasets can be largely misleading. Our work could be a first step towards reconsidering common validation strategies in deep learning-based colonoscopy and beyond.

Labelling instructions matter in biomedical image analysis

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.

Photoacoustic image synthesis with generative adversarial networks

Photoacoustic tomography (PAT) has the potential to recover morphological and functional tissue properties with high spatial resolution. However, previous attempts to solve the optical inverse problem with supervised machine learning were hampered by the absence of labeled reference data. While this bottleneck has been tackled by simulating training data, the domain gap between real and simulated images remains an unsolved challenge. We propose a novel approach to PAT image synthesis that involves subdividing the challenge of generating plausible simulations into two disjoint problems: (1) Probabilistic generation of realistic tissue morphology, and (2) pixel-wise assignment of corresponding optical and acoustic properties. The former is achieved with Generative Adversarial Networks (GANs) trained on semantically annotated medical imaging data. According to a validation study on a downstream task our approach yields more realistic synthetic images than the traditional model-based approach and could therefore become a fundamental step for deep learning-based quantitative PAT (qPAT).

Semantic segmentation of multispectral photoacoustic images using deep learning

Photoacoustic (PA) imaging has the potential to revolutionize functional medical imaging in healthcare due to the valuable information on tissue physiology contained in multispectral photoacoustic measurements. Clinical translation of the technology requires conversion of the high-dimensional acquired data into clinically relevant and interpretable information. In this work, we present a deep learning-based approach to semantic segmentation of multispectral photoacoustic images to facilitate image interpretability. Manually annotated photoacoustic and ultrasound imaging data are used as reference and enable the training of a deep learning-based segmentation algorithm in a supervised manner. Based on a validation study with experimentally acquired data from 16 healthy human volunteers, we show that automatic tissue segmentation can be used to create powerful analyses and visualizations of multispectral photoacoustic images. Due to the intuitive representation of high-dimensional information, such a preprocessing algorithm could be a valuable means to facilitate the clinical translation of photoacoustic imaging.

Surgical data science - from concepts toward clinical translation

Recent developments in data science in general and machine learning in particular have transformed the way experts envision the future of surgery. Surgical Data Science (SDS) is a new research field that aims to improve the quality of interventional healthcare through the capture, organization, analysis and modeling of data. While an increasing number of data-driven approaches and clinical applications have been studied in the fields of radiological and clinical data science, translational success stories are still lacking in surgery. In this publication, we shed light on the underlying reasons and provide a roadmap for future advances in the field. Based on an international workshop involving leading researchers in the field of SDS, we review current practice, key achievements and initiatives as well as available standards and tools for a number of topics relevant to the field, namely (1) infrastructure for data acquisition, storage and access in the presence of regulatory constraints, (2) data annotation and sharing and (3) data analytics. We further complement this technical perspective with (4) a review of currently available SDS products and the translational progress from academia and (5) a roadmap for faster clinical translation and exploitation of the full potential of SDS, based on an international multi-round Delphi process.

Common Pitfalls and Recommendations for Grand Challenges in Medical Artificial Intelligence

With the impact of artificial intelligence (AI) algorithms on medical research on the rise, the importance of competitions for comparative validation of algorithms, so-called challenges, has been steadily increasing, to a point at which challenges can be considered major drivers of research, particularly in the biomedical image analysis domain. Given their importance, high quality, transparency, and interpretability of challenges is essential for good scientific practice and meaningful validation of AI algorithms, for instance towards clinical translation. This mini-review presents several issues related to the design, execution, and interpretation of challenges in the biomedical domain and provides best-practice recommendations. PATIENT SUMMARY: This paper presents recommendations on how to reliably compare the usefulness of new artificial intelligence methods for analysis of medical images.

Heidelberg colorectal data set for surgical data science in the sensor operating room

Image-based tracking of medical instruments is an integral part of surgical data science applications. Previous research has addressed the tasks of detecting, segmenting and tracking medical instruments based on laparoscopic video data. However, the proposed methods still tend to fail when applied to challenging images and do not generalize well to data they have not been trained on. This paper introduces the Heidelberg Colorectal (HeiCo) data set - the first publicly available data set enabling comprehensive benchmarking of medical instrument detection and segmentation algorithms with a specific emphasis on method robustness and generalization capabilities. Our data set comprises 30 laparoscopic videos and corresponding sensor data from medical devices in the operating room for three different types of laparoscopic surgery. Annotations include surgical phase labels for all video frames as well as information on instrument presence and corresponding instance-wise segmentation masks for surgical instruments (if any) in more than 10,000 individual frames. The data has successfully been used to organize international competitions within the Endoscopic Vision Challenges 2017 and 2019.