arXiv subjects

Katie Allen

Publications and source records attributed to Katie Allen.

8 recordsLinked to original sources

arXiv2024

Multi-Resolution Histopathology Patch Graphs for Ovarian Cancer Subtyping

Computer vision models are increasingly capable of classifying ovarian epithelial cancer subtypes, but they differ from pathologists by processing small tissue patches at a single resolution. Multi-resolution graph models leverage the spatial relationships of patches at multiple magnifications, learning the context for each patch. In this study, we conduct the most thorough validation of a graph model for ovarian cancer subtyping to date. Seven models were tuned and trained using five-fold cross-validation on a set of 1864 whole slide images (WSIs) from 434 patients treated at Leeds Teaching Hospitals NHS Trust. The cross-validation models were ensembled and evaluated using a balanced hold-out test set of 100 WSIs from 30 patients, and an external validation set of 80 WSIs from 80 patients in the Transcanadian Study. The best-performing model, a graph model using 10x+20x magnification data, gave balanced accuracies of 73%, 88%, and 99% in cross-validation, hold-out testing, and external validation, respectively. However, this only exceeded the performance of attention-based multiple instance learning in external validation, with a 93% balanced accuracy. Graph models benefitted greatly from using the UNI foundation model rather than an ImageNet-pretrained ResNet50 for feature extraction, with this having a much greater effect on performance than changing the subsequent classification approach. The accuracy of the combined foundation model and multi-resolution graph network offers a step towards the clinical applicability of these models, with a new highest-reported performance for this task, though further validations are still required to ensure the robustness and usability of the models.

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arXiv2024

A Comprehensive Evaluation of Histopathology Foundation Models for Ovarian Cancer Subtype Classification

Large pretrained transformers are increasingly being developed as generalised foundation models which can underpin powerful task-specific artificial intelligence models. Histopathology foundation models show great promise across many tasks, but analyses have typically been limited by arbitrary hyperparameters that were not tuned to the specific task. We report the most rigorous single-task validation of histopathology foundation models to date, specifically in ovarian cancer morphological subtyping. Attention-based multiple instance learning classifiers were compared using three ImageNet-pretrained feature extractors and fourteen histopathology foundation models. The training set consisted of 1864 whole slide images from 434 ovarian carcinoma cases at Leeds Teaching Hospitals NHS Trust. Five-class classification performance was evaluated through five-fold cross-validation, and these cross-validation models were ensembled for hold-out testing and external validation on the Transcanadian Study and OCEAN Challenge datasets. The best-performing model used the H-optimus-0 foundation model, with five-class balanced accuracies of 89%, 97%, and 74% in the test sets. Normalisations and augmentations aided the performance of the ImageNet-pretrained ResNets, but these were still outperformed by 13 of the 14 foundation models. Hyperparameter tuning the downstream classifiers improved performance by a median 1.9% balanced accuracy, with many improvements being statistically significant. Histopathology foundation models offer a clear benefit to ovarian cancer subtyping, improving classification performance to a degree where clinical utility is tangible, albeit with an increased computational burden. Such models could provide a second opinion to histopathologists diagnosing challenging cases and may improve the accuracy, objectivity, and efficiency of pathological diagnoses overall.

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arXiv2023

Reducing Histopathology Slide Magnification Improves the Accuracy and Speed of Ovarian Cancer Subtyping

Artificial intelligence has found increasing use for ovarian cancer morphological subtyping from histopathology slides, but the optimal magnification for computational interpretation is unclear. Higher magnifications offer abundant cytological information, whereas lower magnifications give a broader histoarchitectural overview. Using attention-based multiple instance learning, we performed the most extensive analysis of ovarian cancer tissue magnifications to date, with data at six magnifications subjected to the same preprocessing, hyperparameter tuning, cross-validation and hold-out testing procedures. The lowest magnifications (1.25x and 2.5x) performed best in cross-validation, and intermediate magnifications (5x and 10x) performed best in hold-out testing (62% and 61% accuracy, respectively). Lower magnification models were also significantly faster, with the 5x model taking 5% as long to train and 31% as long to evaluate slides compared to 40x. This indicates that the standard usage of high magnifications for computational ovarian cancer subtyping may be unnecessary, with lower magnifications giving faster, more accurate alternatives.

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arXiv2023

Predicting Ovarian Cancer Treatment Response in Histopathology using Hierarchical Vision Transformers and Multiple Instance Learning

For many patients, current ovarian cancer treatments offer limited clinical benefit. For some therapies, it is not possible to predict patients' responses, potentially exposing them to the adverse effects of treatment without any therapeutic benefit. As part of the automated prediction of treatment effectiveness in ovarian cancer using histopathological images (ATEC23) challenge, we evaluated the effectiveness of deep learning to predict whether a course of treatment including the antiangiogenic drug bevacizumab could contribute to remission or prevent disease progression for at least 6 months in a set of 282 histopathology whole slide images (WSIs) from 78 ovarian cancer patients. Our approach used a pretrained Hierarchical Image Pyramid Transformer (HIPT) to extract region-level features and an attention-based multiple instance learning (ABMIL) model to aggregate features and classify whole slides. The optimal HIPT-ABMIL model had an internal balanced accuracy of 60.2% +- 2.9% and an AUC of 0.646 +- 0.033. Histopathology-specific model pretraining was found to be beneficial to classification performance, though hierarchical transformers were not, with a ResNet feature extractor achieving similar performance. Due to the dataset being small and highly heterogeneous, performance was variable across 5-fold cross-validation folds, and there were some extreme differences between validation and test set performance within folds. The model did not generalise well to tissue microarrays, with accuracy worse than random chance. It is not yet clear whether ovarian cancer WSIs contain information that can be used to accurately predict treatment response, with further validation using larger, higher-quality datasets required.

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arXiv2023

Generative Adversarial Networks for Stain Normalisation in Histopathology

The rapid growth of digital pathology in recent years has provided an ideal opportunity for the development of artificial intelligence-based tools to improve the accuracy and efficiency of clinical diagnoses. One of the significant roadblocks to current research is the high level of visual variability across digital pathology images, causing models to generalise poorly to unseen data. Stain normalisation aims to standardise the visual profile of digital pathology images without changing the structural content of the images. In this chapter, we explore different techniques which have been used for stain normalisation in digital pathology, with a focus on approaches which utilise generative adversarial networks (GANs). Typically, GAN-based methods outperform non-generative approaches but at the cost of much greater computational requirements. However, it is not clear which method is best for stain normalisation in general, with different GAN and non-GAN approaches outperforming each other in different scenarios and according to different performance metrics. This is an ongoing field of study as researchers aim to identify a method which efficiently and effectively normalises pathology images to make AI models more robust and generalisable.

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arXiv2023

Artificial Intelligence in Ovarian Cancer Histopathology: A Systematic Review

Purpose - To characterise and assess the quality of published research evaluating artificial intelligence (AI) methods for ovarian cancer diagnosis or prognosis using histopathology data. Methods - A search of PubMed, Scopus, Web of Science, CENTRAL, and WHO-ICTRP was conducted up to 19/05/2023. The inclusion criteria required that research evaluated AI on histopathology images for diagnostic or prognostic inferences in ovarian cancer. The risk of bias was assessed using PROBAST. Information about each model of interest was tabulated and summary statistics were reported. PRISMA 2020 reporting guidelines were followed. Results - 1573 records were identified, of which 45 were eligible for inclusion. There were 80 models of interest, including 37 diagnostic models, 22 prognostic models, and 21 models with other diagnostically relevant outcomes. Models were developed using 1-1375 slides from 1-776 ovarian cancer patients. Model outcomes included treatment response (11/80), malignancy status (10/80), stain quantity (9/80), and histological subtype (7/80). All models were found to be at high or unclear risk of bias overall, with most research having a high risk of bias in the analysis and a lack of clarity regarding participants and predictors in the study. Research frequently suffered from insufficient reporting and limited validation using small sample sizes. Conclusion - Limited research has been conducted on the application of AI to histopathology images for diagnostic or prognostic purposes in ovarian cancer, and none of the associated models have been demonstrated to be ready for real-world implementation. Key aspects to help ensure clinical translation include more transparent and comprehensive reporting of data provenance and modelling approaches, as well as improved quantitative performance evaluation using cross-validation and external validations.

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arXiv2023

Efficient subtyping of ovarian cancer histopathology whole slide images using active sampling in multiple instance learning

Weakly-supervised classification of histopathology slides is a computationally intensive task, with a typical whole slide image (WSI) containing billions of pixels to process. We propose Discriminative Region Active Sampling for Multiple Instance Learning (DRAS-MIL), a computationally efficient slide classification method using attention scores to focus sampling on highly discriminative regions. We apply this to the diagnosis of ovarian cancer histological subtypes, which is an essential part of the patient care pathway as different subtypes have different genetic and molecular profiles, treatment options, and patient outcomes. We use a dataset of 714 WSIs acquired from 147 epithelial ovarian cancer patients at Leeds Teaching Hospitals NHS Trust to distinguish the most common subtype, high-grade serous carcinoma, from the other four subtypes (low-grade serous, endometrioid, clear cell, and mucinous carcinomas) combined. We demonstrate that DRAS-MIL can achieve similar classification performance to exhaustive slide analysis, with a 3-fold cross-validated AUC of 0.8679 compared to 0.8781 with standard attention-based MIL classification. Our approach uses at most 18% as much memory as the standard approach, while taking 33% of the time when evaluating on a GPU and only 14% on a CPU alone. Reducing prediction time and memory requirements may benefit clinical deployment and the democratisation of AI, reducing the extent to which computational hardware limits end-user adoption.

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arXiv2021

Decoding gender differences: Intellectual profiles of children with specific learning disabilities

There has been a significant amount of debate around gender differences in intellectual functioning, however, most of this research concerns typically developing populations and lacks research into atypically developing populations and those with specific learning disabilities (SLD). To address this, we examined performance on the WISC-IV in children with SLDs (N=1238, N female= 539, Age range = 7-16 years). We further divided the sample into those with specific deficits in reading, mathematics, and those with mixed disorder. Results indicate that gender predicts significant differences in the working memory index and processing speed index only, indicating a small but significant female superiority. Results also show different profiles for the different disorders investigated, with some gender differences emerging. The most prominent gender difference appears to be in the coding subtest indicating a female advantage, particularly in those with SLDs with mathematical difficulties. We discuss the theoretical and clinical implications of the findings.

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