arXiv subjects

Patrick Godau

Publications and source records attributed to Patrick Godau.

At least 19 recordsLinked to original sources

arXiv2026

Towards Global AI-Driven Cervical Cancer Screening

The global elimination of cervical cancer is a key public health goal set by the World Health Organization (WHO), with screening programs reducing mortality by up to 80%. However, access to experts and biopsy services is limited in low- to middle-income countries (LMICs). Deep learning (DL)-based algorithms offer promising support for screening, but most existing approaches have been developed and validated on private datasets from single countries. We present the first DL-based approach to cervical cancer screening validated on data from multiple countries. Technically, we phrase the problem of detecting and classifying lesions in colposcopy images as a multi-task learning problem, in which we simultaneously perform image-level classification and lesion segmentation. Our model was trained on a private data set of acid stain colposcopy images with manually generated lesion segmentation masks and corresponding histopathological results, employing extensive data augmentation to address image variability. In an in-distribution validation with pathology results serving as ground truth, our algorithm outperformed medical experts (Balanced Accuracy: 0.68 vs 0.64) in CIN1- (Cervical intraepithelial neoplasia grade 1 or lower) versus CIN2+ (grade 2 or higher) classification. External validation on four colposcopy data sets from four countries featuring radical differences in prevalence and patient characteristics yielded superior performance of our method compared to baseline methods. Performance variability across countries was high with AUC values ranging from 0.54 - 0.80. Overall, algorithm performance varied with age, transformation zone (cervical area most prone to lesion development), presence of comorbidities and pathognomonic signs, with comorbidities having by far the largest negative effect. Future work should focus on improving model robustness and generalizability.

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arXiv2026

A multi-center analysis of deep learning methods for video polyp detection and segmentation

Colonic polyps are well-recognized precursors to colorectal cancer (CRC), typically detected during colonoscopy. However, the variability in appearance, location, and size of these polyps complicates their detection and removal, leading to challenges in effective surveillance, intervention, and subsequently CRC prevention. The processes of colonoscopy surveillance and polyp removal are highly reliant on the expertise of gastroenterologists and occur within the complexities of the colonic structure. As a result, there is a high rate of missed detections and incomplete removal of colonic polyps, which can adversely impact patient outcomes. Recently, automated methods that use machine learning have been developed to enhance polyps detection and segmentation, thus helping clinical processes and reducing missed rates. These advancements highlight the potential for improving diagnostic accuracy in real-time applications, which ultimately facilitates more effective patient management. Furthermore, integrating sequence data and temporal information could significantly enhance the precision of these methods by capturing the dynamic nature of polyp growth and the changes that occur over time. To rigorously investigate these challenges, data scientists and experts gastroenterologists collaborated to compile a comprehensive dataset that spans multiple centers and diverse populations. This initiative aims to underscore the critical importance of incorporating sequence data and temporal information in the development of robust automated detection and segmentation methods. This study evaluates the applicability of deep learning techniques developed in real-time clinical colonoscopy tasks using sequence data, highlighting the critical role of temporal relationships between frames in improving diagnostic precision.

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arXiv2026

Performance uncertainty in medical image analysis: a large-scale investigation of confidence intervals

Performance uncertainty quantification is essential for reliable validation and eventual clinical translation of medical imaging artificial intelligence (AI). Confidence intervals (CIs) play a central role in this process by indicating how precise a reported performance estimate is. Yet, due to the limited amount of work examining CI behavior in medical imaging, the community remains largely unaware of how many diverse CI methods exist and how they behave in specific settings. The purpose of this study is to close this gap. To this end, we conducted a large-scale empirical analysis across a total of 24 segmentation and classification tasks, using 19 trained models per task group, a broad spectrum of commonly used performance metrics, multiple aggregation strategies, and several widely adopted CI methods. Reliability (coverage) and precision (width) of each CI method were estimated across all settings to characterize their dependence on study characteristics. Our analysis revealed five principal findings: 1) the sample size required for reliable CIs varies from a few dozens to several thousands of cases depending on study parameters; 2) CI behavior is strongly affected by the choice of performance metric; 3) aggregation strategy substantially influences the reliability of CIs, e.g. they require more observations for macro than for micro; 4) the machine learning problem (segmentation versus classification) modulates these effects; 5) different CI methods are not equally reliable and precise depending on the use case. Finally, we derived practical implications of this study in the form of a decision tree which shall prove useful to the community. This paves the way for future consensus guidelines on reporting performance uncertainty.

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arXiv2025

Current validation practice undermines surgical AI development

Surgical data science (SDS) is rapidly advancing, yet clinical adoption of artificial intelligence (AI) in surgery remains limited, with inadequate validation as an important contributing factor. Existing validation practices often neglect the temporal and hierarchical structure of intraoperative videos, yielding misleading or clinically irrelevant results. We introduce a comprehensive catalogue of validation pitfalls in AI-based surgical video analysis, derived from a multi-stage Delphi process with 92 international experts. Pitfalls span three categories: (1) data, (2) metric selection/configuration, and (3) aggregation and reporting. A systematic review of surgical AI papers reveals that these pitfalls are widespread. Experiments on surgical video datasets show that ignoring temporal and hierarchical data structures can understate uncertainty, obscure critical failure modes, and alter algorithm rankings. To address these shortcomings, we provide consensus-based best practices compiled. Together, this work provides an evidence-based framework for rigorous validation of surgical video analysis algorithms, guiding benchmarking, reporting, regulatory review, and clinical translation.

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arXiv2025

Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop

Artificial intelligence holds immense promise for transforming biology, yet a lack of standardized, cross domain, benchmarks undermines our ability to build robust, trustworthy models. Here, we present insights from a recent workshop that convened machine learning and computational biology experts across imaging, transcriptomics, proteomics, and genomics to tackle this gap. We identify major technical and systemic bottlenecks such as data heterogeneity and noise, reproducibility challenges, biases, and the fragmented ecosystem of publicly available resources and propose a set of recommendations for building benchmarking frameworks that can efficiently compare ML models of biological systems across tasks and data modalities. By promoting high quality data curation, standardized tooling, comprehensive evaluation metrics, and open, collaborative platforms, we aim to accelerate the development of robust benchmarks for AI driven Virtual Cells. These benchmarks are crucial for ensuring rigor, reproducibility, and biological relevance, and will ultimately advance the field toward integrated models that drive new discoveries, therapeutic insights, and a deeper understanding of cellular systems.

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arXiv2025

Challenging Vision-Language Models with Surgical Data: A New Dataset and Broad Benchmarking Study

While traditional computer vision models have historically struggled to generalize to endoscopic domains, the emergence of foundation models has shown promising cross-domain performance. In this work, we present the first large-scale study assessing the capabilities of Vision Language Models (VLMs) for endoscopic tasks with a specific focus on laparoscopic surgery. Using a diverse set of state-of-the-art models, multiple surgical datasets, and extensive human reference annotations, we address three key research questions: (1) Can current VLMs solve basic perception tasks on surgical images? (2) Can they handle advanced frame-based endoscopic scene understanding tasks? and (3) How do specialized medical VLMs compare to generalist models in this context? Our results reveal that VLMs can effectively perform basic surgical perception tasks, such as object counting and localization, with performance levels comparable to general domain tasks. However, their performance deteriorates significantly when the tasks require medical knowledge. Notably, we find that specialized medical VLMs currently underperform compared to generalist models across both basic and advanced surgical tasks, suggesting that they are not yet optimized for the complexity of surgical environments. These findings highlight the need for further advancements to enable VLMs to handle the unique challenges posed by surgery. Overall, our work provides important insights for the development of next-generation endoscopic AI systems and identifies key areas for improvement in medical visual language models.

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arXiv2025

False Promises in Medical Imaging AI? Assessing Validity of Outperformance Claims

Performance comparisons are fundamental in medical imaging Artificial Intelligence (AI) research, often driving claims of superiority based on relative improvements in common performance metrics. However, such claims frequently rely solely on empirical mean performance. In this paper, we investigate whether newly proposed methods genuinely outperform the state of the art by analyzing a representative cohort of medical imaging papers. We quantify the probability of false claims based on a Bayesian approach that leverages reported results alongside empirically estimated model congruence to estimate whether the relative ranking of methods is likely to have occurred by chance. According to our results, the majority (>80%) of papers claims outperformance when introducing a new method. Our analysis further revealed a high probability (>5%) of false outperformance claims in 86% of classification papers and 53% of segmentation papers. These findings highlight a critical flaw in current benchmarking practices: claims of outperformance in medical imaging AI are frequently unsubstantiated, posing a risk of misdirecting future research efforts.

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arXiv2024

Beyond Knowledge Silos: Task Fingerprinting for Democratization of Medical Imaging AI

The field of medical imaging AI is currently undergoing rapid transformations, with methodical research increasingly translated into clinical practice. Despite these successes, research suffers from knowledge silos, hindering collaboration and progress: Existing knowledge is scattered across publications and many details remain unpublished, while privacy regulations restrict data sharing. In the spirit of democratizing of AI, we propose a framework for secure knowledge transfer in the field of medical image analysis. The key to our approach is dataset "fingerprints", structured representations of feature distributions, that enable quantification of task similarity. We tested our approach across 71 distinct tasks and 12 medical imaging modalities by transferring neural architectures, pretraining, augmentation policies, and multi-task learning. According to comprehensive analyses, our method outperforms traditional methods for identifying relevant knowledge and facilitates collaborative model training. Our framework fosters the democratization of AI in medical imaging and could become a valuable tool for promoting faster scientific advancement.

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arXiv2024

PitVis-2023 Challenge: Workflow Recognition in videos of Endoscopic Pituitary Surgery

The field of computer vision applied to videos of minimally invasive surgery is ever-growing. Workflow recognition pertains to the automated recognition of various aspects of a surgery: including which surgical steps are performed; and which surgical instruments are used. This information can later be used to assist clinicians when learning the surgery; during live surgery; and when writing operation notes. The Pituitary Vision (PitVis) 2023 Challenge tasks the community to step and instrument recognition in videos of endoscopic pituitary surgery. This is a unique task when compared to other minimally invasive surgeries due to the smaller working space, which limits and distorts vision; and higher frequency of instrument and step switching, which requires more precise model predictions. Participants were provided with 25-videos, with results presented at the MICCAI-2023 conference as part of the Endoscopic Vision 2023 Challenge in Vancouver, Canada, on 08-Oct-2023. There were 18-submissions from 9-teams across 6-countries, using a variety of deep learning models. A commonality between the top performing models was incorporating spatio-temporal and multi-task methods, with greater than 50% and 10% macro-F1-score improvement over purely spacial single-task models in step and instrument recognition respectively. The PitVis-2023 Challenge therefore demonstrates state-of-the-art computer vision models in minimally invasive surgery are transferable to a new dataset, with surgery specific techniques used to enhance performance, progressing the field further. Benchmark results are provided in the paper, and the dataset is publicly available at: https://doi.org/10.5522/04/26531686.

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arXiv2023

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.

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arXiv2023

Deployment of Image Analysis Algorithms under Prevalence Shifts

Domain gaps are among the most relevant roadblocks in the clinical translation of machine learning (ML)-based solutions for medical image analysis. While current research focuses on new training paradigms and network architectures, little attention is given to the specific effect of prevalence shifts on an algorithm deployed in practice. Such discrepancies between class frequencies in the data used for a method's development/validation and that in its deployment environment(s) are of great importance, for example in the context of artificial intelligence (AI) democratization, as disease prevalences may vary widely across time and location. Our contribution is twofold. First, we empirically demonstrate the potentially severe consequences of missing prevalence handling by analyzing (i) the extent of miscalibration, (ii) the deviation of the decision threshold from the optimum, and (iii) the ability of validation metrics to reflect neural network performance on the deployment population as a function of the discrepancy between development and deployment prevalence. Second, we propose a workflow for prevalence-aware image classification that uses estimated deployment prevalences to adjust a trained classifier to a new environment, without requiring additional annotated deployment data. Comprehensive experiments based on a diverse set of 30 medical classification tasks showcase the benefit of the proposed workflow in generating better classifier decisions and more reliable performance estimates compared to current practice.

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arXiv2023

Self-distillation for surgical action recognition

Surgical scene understanding is a key prerequisite for contextaware decision support in the operating room. While deep learning-based approaches have already reached or even surpassed human performance in various fields, the task of surgical action recognition remains a major challenge. With this contribution, we are the first to investigate the concept of self-distillation as a means of addressing class imbalance and potential label ambiguity in surgical video analysis. Our proposed method is a heterogeneous ensemble of three models that use Swin Transfomers as backbone and the concepts of self-distillation and multi-task learning as core design choices. According to ablation studies performed with the CholecT45 challenge data via cross-validation, the biggest performance boost is achieved by the usage of soft labels obtained by self-distillation. External validation of our method on an independent test set was achieved by providing a Docker container of our inference model to the challenge organizers. According to their analysis, our method outperforms all other solutions submitted to the latest challenge in the field. Our approach thus shows the potential of self-distillation for becoming an important tool in medical image analysis applications.

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arXiv2023

CholecTriplet2022: Show me a tool and tell me the triplet -- an endoscopic vision challenge for surgical action triplet detection

Formalizing surgical activities as triplets of the used instruments, actions performed, and target anatomies is becoming a gold standard approach for surgical activity modeling. The benefit is that this formalization helps to obtain a more detailed understanding of tool-tissue interaction which can be used to develop better Artificial Intelligence assistance for image-guided surgery. Earlier efforts and the CholecTriplet challenge introduced in 2021 have put together techniques aimed at recognizing these triplets from surgical footage. Estimating also the spatial locations of the triplets would offer a more precise intraoperative context-aware decision support for computer-assisted intervention. This paper presents the CholecTriplet2022 challenge, which extends surgical action triplet modeling from recognition to detection. It includes weakly-supervised bounding box localization of every visible surgical instrument (or tool), as the key actors, and the modeling of each tool-activity in the form of triplet. The paper describes a baseline method and 10 new deep learning algorithms presented at the challenge to solve the task. It also provides thorough methodological comparisons of the methods, an in-depth analysis of the obtained results across multiple metrics, visual and procedural challenges; their significance, and useful insights for future research directions and applications in surgery.

eess.IV↗

arXiv2023

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.

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arXiv2022

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.

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arXiv2022

Sources of performance variability in deep learning-based polyp detection

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. Our contribution is twofold. Firstly, we present the winning solution of the Endoscopy computer vision challenge (EndoCV) on colon cancer detection, conducted in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2022. Secondly, we demonstrate the sensitivity of commonly used metrics to a range of hyperparameters as well as the consequences of poor metric choices. 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. Our work could be a first step towards reconsidering common validation strategies in automatic colon cancer screening applications.

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arXiv2022

Metrics reloaded: Recommendations for image analysis validation

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, our large international expert consortium created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. The framework was developed in a multi-stage Delphi process and 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), data set and algorithm output. Based on 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 a classification task 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, which also provides a point of access to explore weaknesses, strengths and specific recommendations for the most common validation metrics. The broad applicability of our framework across domains is demonstrated by an instantiation for various biological and medical image analysis use cases.

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arXiv2021

Task Fingerprinting for Meta Learning in Biomedical Image Analysis

Shortage of annotated data is one of the greatest bottlenecks in biomedical image analysis. Meta learning studies how learning systems can increase in efficiency through experience and could thus evolve as an important concept to overcome data sparsity. However, the core capability of meta learning-based approaches is the identification of similar previous tasks given a new task - a challenge largely unexplored in the biomedical imaging domain. In this paper, we address the problem of quantifying task similarity with a concept that we refer to as task fingerprinting. The concept involves converting a given task, represented by imaging data and corresponding labels, to a fixed-length vector representation. In fingerprint space, different tasks can be directly compared irrespective of their data set sizes, types of labels or specific resolutions. An initial feasibility study in the field of surgical data science (SDS) with 26 classification tasks from various medical and non-medical domains suggests that task fingerprinting could be leveraged for both (1) selecting appropriate data sets for pretraining and (2) selecting appropriate architectures for a new task. Task fingerprinting could thus become an important tool for meta learning in SDS and other fields of biomedical image analysis.

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