Gary S. Collins

Lena Maier-Hein, Annika Reinke, Patrick Godau et al. · utoronto

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.

Annika Reinke, Minu D. Tizabi, Michael Baumgartner et al.

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.

Giovanni E. Cacciamani, Michael B. Eppler, Conner Ganjavi et al.

The swift progress and ubiquitous adoption of Generative AI (GAI), Generative Pre-trained Transformers (GPTs), and large language models (LLMs) like ChatGPT, have spurred queries about their ethical application, use, and disclosure in scholarly research and scientific productions. A few publishers and journals have recently created their own sets of rules; however, the absence of a unified approach may lead to a 'Babel Tower Effect,' potentially resulting in confusion rather than desired standardization. In response to this, we present the ChatGPT, Generative Artificial Intelligence, and Natural Large Language Models for Accountable Reporting and Use Guidelines (CANGARU) initiative, with the aim of fostering a cross-disciplinary global inclusive consensus on the ethical use, disclosure, and proper reporting of GAI/GPT/LLM technologies in academia. The present protocol consists of four distinct parts: a) an ongoing systematic review of GAI/GPT/LLM applications to understand the linked ideas, findings, and reporting standards in scholarly research, and to formulate guidelines for its use and disclosure, b) a bibliometric analysis of existing author guidelines in journals that mention GAI/GPT/LLM, with the goal of evaluating existing guidelines, analyzing the disparity in their recommendations, and identifying common rules that can be brought into the Delphi consensus process, c) a Delphi survey to establish agreement on the items for the guidelines, ensuring principled GAI/GPT/LLM use, disclosure, and reporting in academia, and d) the subsequent development and dissemination of the finalized guidelines and their supplementary explanation and elaboration documents.

Conner Ganjavi, Michael B. Eppler, Asli Pekcan et al.

We aim to determine the extent and content of guidance for authors regarding the use of generative-AI (GAI), Generative Pretrained models (GPTs) and Large Language Models (LLMs) powered tools among the top 100 academic publishers and journals in science. The websites of these publishers and journals were screened from between 19th and 20th May 2023. Among the largest 100 publishers, 17% provided guidance on the use of GAI, of which 12 (70.6%) were among the top 25 publishers. Among the top 100 journals, 70% have provided guidance on GAI. Of those with guidance, 94.1% of publishers and 95.7% of journals prohibited the inclusion of GAI as an author. Four journals (5.7%) explicitly prohibit the use of GAI in the generation of a manuscript, while 3 (17.6%) publishers and 15 (21.4%) journals indicated their guidance exclusively applies to the writing process. When disclosing the use of GAI, 42.8% of publishers and 44.3% of journals included specific disclosure criteria. There was variability in guidance of where to disclose the use of GAI, including in the methods, acknowledgments, cover letter, or a new section. There was also variability in how to access GAI guidance and the linking of journal and publisher instructions to authors. There is a lack of guidance by some top publishers and journals on the use of GAI by authors. Among those publishers and journals that provide guidance, there is substantial heterogeneity in the allowable uses of GAI and in how it should be disclosed, with this heterogeneity persisting among affiliated publishers and journals in some instances. The lack of standardization burdens authors and threatens to limit the effectiveness of these regulations. There is a need for standardized guidelines in order to protect the integrity of scientific output as GAI continues to grow in popularity.

Thomas Sounack, Raffaele Giancotti, Catherine A. Gao et al.

Analytical code is essential for reproducing diagnostic and prognostic prediction model research, yet code availability in the published literature remains limited. While the TRIPOD statements set standards for reporting prediction model methods, they do not define explicit standards for repository structure and documentation. This review quantifies current code-sharing practices to inform the development of TRIPOD-Code, a TRIPOD extension reporting guideline focused on code sharing. We conducted a scoping review of PubMed-indexed articles citing TRIPOD or TRIPOD+AI as of Aug 11, 2025, restricted to studies retrievable via the PubMed Central Open Access API. Eligible studies developed, updated, or validated multivariable prediction models. A large language model-assisted pipeline was developed to screen articles and extract code availability statements and repository links. Repositories were assessed with the same LLM against 14 predefined reproducibility-related features. Our code is made publicly available. Among 3,967 eligible articles, 12.2% included code sharing statements. Code sharing increased over time, reaching 15.8% in 2025, and was higher among TRIPOD+AI-citing studies than TRIPOD-citing studies. Sharing prevalence varied widely by journal and country. Repository assessment showed substantial heterogeneity in reproducibility features: most repositories contained a README file (80.5%), but fewer specified dependencies (37.6%; version-constrained 21.6%) or were modular (42.4%). In prediction model research, code sharing remains relatively uncommon, and when shared, often falls short of being reusable. These findings provide an empirical baseline for the TRIPOD-Code extension and underscore the need for clearer expectations beyond code availability, including documentation, dependency specification, licensing, and executable structure.

Ben Van Calster, Gary S. Collins, Andrew J. Vickers et al.

A myriad of measures to illustrate performance of predictive artificial intelligence (AI) models have been proposed in the literature. Selecting appropriate performance measures is essential for predictive AI models that are developed to be used in medical practice, because poorly performing models may harm patients and lead to increased costs. We aim to assess the merits of classic and contemporary performance measures when validating predictive AI models for use in medical practice. We focus on models with a binary outcome. We discuss 32 performance measures covering five performance domains (discrimination, calibration, overall, classification, and clinical utility) along with accompanying graphical assessments. The first four domains cover statistical performance, the fifth domain covers decision-analytic performance. We explain why two key characteristics are important when selecting which performance measures to assess: (1) whether the measure's expected value is optimized when it is calculated using the correct probabilities (i.e., a "proper" measure), and (2) whether they reflect either purely statistical performance or decision-analytic performance by properly considering misclassification costs. Seventeen measures exhibit both characteristics, fourteen measures exhibited one characteristic, and one measure possessed neither characteristic (the F1 measure). All classification measures (such as classification accuracy and F1) are improper for clinically relevant decision thresholds other than 0.5 or the prevalence. We recommend the following measures and plots as essential to report: AUROC, calibration plot, a clinical utility measure such as net benefit with decision curve analysis, and a plot with probability distributions per outcome category.

João Matos, Ben Van Calster, Leo Anthony Celi et al.

Predictive artificial intelligence (AI) offers an opportunity to improve clinical practice and patient outcomes, but risks perpetuating biases if fairness is inadequately addressed. However, the definition of "fairness" remains unclear. We conducted a scoping review to identify and critically appraise fairness metrics for clinical predictive AI. We defined a "fairness metric" as a measure quantifying whether a model discriminates (societally) against individuals or groups defined by sensitive attributes. We searched five databases (2014-2024), screening 820 records, to include 41 studies, and extracted 62 fairness metrics. Metrics were classified by performance-dependency, model output level, and base performance metric, revealing a fragmented landscape with limited clinical validation and overreliance on threshold-dependent measures. Eighteen metrics were explicitly developed for healthcare, including only one clinical utility metric. Our findings highlight conceptual challenges in defining and quantifying fairness and identify gaps in uncertainty quantification, intersectionality, and real-world applicability. Future work should prioritise clinically meaningful metrics.

Annika Reinke, Minu D. Tizabi, Carole H. Sudre et al.

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation. Performance metrics are particularly key for meaningful, objective, and transparent performance assessment and validation of the used automatic algorithms, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. These are typically related to (1) the disregard of inherent metric properties, such as the behaviour in the presence of class imbalance or small target structures, (2) the disregard of inherent data set properties, such as the non-independence of the test cases, and (3) the disregard of the actual biomedical domain interest that the metrics should reflect. This living dynamically document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. In this context, it focuses on biomedical image analysis problems that can be phrased as image-level classification, semantic segmentation, instance segmentation, or object detection task. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts from more than 60 institutions worldwide.