1,720,953 research outputs found
Towards clinically reliable artificial intelligence for prostate cancer pathology
No full textHistopathological assessment of prostate biopsies plays a central role in determining patient prognosis and guiding treatment decisions. This evaluation is typically performed by pathologists using the Gleason scoring system on hematoxylin and eosin (H&E) stained tissue sections. However, the process is subjective and prone to significant intra- and inter-pathologist variability, which can result in under- and over-treatment of patients. In cases where a definitive diagnosis cannot be made from H&E slides alone, additional immunohistochemical (IHC) staining is often used to confirm malignancy, though this introduces added cost, time, and workload. The digitisation of prostate biopsies into Whole Slide Images (WSIs) and the application of Artificial Intelligence (AI) have shown great potential to support pathologists by improving diagnostic consistency and reducing variability. Deep learning models, in particular, have demonstrated diagnostic performance comparable to that of expert pathologists. Yet, real-world deployment remains limited due to a lack of protocolised studies assessing model generalisability different laboratories, whole slide scanners, patient populations and clinically challenging cases. More recently, foundation models have shown promising pan-cancer detection capabilities, including prostate cancer, but evidence on their performance in disease-specific diagnostics is limited. This thesis addresses these gaps by developing and validating AI models for prostate cancer diagnosis with a focus on generalisability, clinical integration, and potential applications such as reducing reliance on IHC.In Study I, we developed software for accessing the .isyntax WSI format, which is the proprietary format of the Philips UFS scanner-the first scanner to obtain U.S. Food and Drug Administration clearance. Accessing these digital images allowed us to use them in subsequent studies to train AI models. In Study II, we evaluated the use of physical colour calibration for reducing scanner-induced colour variability in WSIs, with the goal of assessing the model's performance across cohorts digitised by different scanner vendors. Colour calibration showed superior performance over colour normalisation techniques, improving cancer detection and Gleason grading performance. In Study III, we have pre-registered a study protocol for the development and retrospective validation of an improved, weakly supervised AI model for diagnostic assessment of digitised prostate biopsies, and in Study IV, we have developed and validated the model rigorously following the predefined protocol. To our knowledge, this represents the largest retrospective validation of an AI model for such a purpose, including approximately 100,000 digitised core needle biopsies from 7,342 patients spanning across 15 laboratories in 11 countries. The model was trained end-to-end and showed excellent generalisation capabilities, achieving pathologist-level diagnosis and grading across international cohorts (i.e., external or internal validation with respect to the scanner used for digitisation and clinical laboratory). We compared the developed model, which we refer to as task-specific (TS), with the foundation models (FM), UNI and Virchow2. Given the potential of FMs as few- shot learners, we investigated whether their performance improves with increased prostate pathology training data. Results showed a consistent improvement in Gleason scoring across all validation cohorts for all models when more prostate pathology training data were available. We further assessed performance across different scanners and clinically challenging cases, observing improvements with increased task-specific training data. Notably, foundation models used up to 35 times more energy than the TS model during model prediction, raising concerns about their sustainability. In Study V, we used our in-house TS model for an important clinical challenge: reducing IHC staining in prostate cancer. Using a sensitivity-prioritised scenario, we retrospectively evaluated the model's performance on H&E-stained biopsies from international cohorts, selecting cases where pathologists had originally assessed the H&E-stained biopsy alongside the IHC. By lowering the malignancy classification threshold to prioritise sensitivity, the model identified all malignant slides without a single false negative, while reducing IHC usage up to 44.4% across international cohorts.To conclude, the constituent papers of this thesis address important and timely challenges in digital pathology, paving the way for future prospective clinical trials of AI models in real-world settings. These efforts support the broader integration of AI-assisted diagnostics into routine clinical practice, with the ultimate goal of reducing variability in histopathological assessment and enhancing patient care.List of scientific papersI. Mulliqi N*, Kartasalo K*, Olsson H, Ji X, Egevad L, Eklund M, Ruusuvuori P. OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology. Bioinformatics 2021 Aug 6;37(21):3995-3997.https://doi.org/10.1093/bioinformatics/btab578II. Ji X, Salmon R, Mulliqi N, Khan U, Wang Y, Blilie A, Olsson H, Pedersen BG, Sørensen KD, Ulhøi BP, Kjosavik SR, Janssen EAM, Rantalainen M, Egevad L, Ruusuvuori P, Eklund M, Kartasalo K. Physical Color Calibration of Digital Pathology Scanners for Robust Artificial Intelligence-Assisted Cancer Diagnosis. Modern Pathology 2025 Jan 16;38(5):100715.https://doi.org/10.1016/j.modpat.2025.100715III. Mulliqi N, Blilie A, Ji X, Szolnoky K, Olsson H, Titus M, Gonzalez GM, Boman SE, Valkonen M, Gudlaugsson E, Kjosavik SR, Asenjo J, Gambacorta M, Libretti P, Braun M, Kordek R, Łowicki R, Hotakainen K, Väre P, Pedersen BG, Sørensen KD, Ulhøi BP, Rantalainen M, Ruusuvuori P, Delahunt B, Samaratunga H, Tsuzuki T, Janssen EAM, Egevad L, Kartasalo K, Eklund M. Study Protocol: Development and Retrospective Validation of an Artificial Intelligence System for Diagnostic Assessment of Prostate Biopsies. medRxiv 2024.07.04.24309948. [Manuscript Preprint]https://doi.org/10.1101/2024.07.04.24309948IV. Mulliqi N, Blilie A, Ji X, Szolnoky K, Olsson H, Boman SE, Titus M, Gonzalez GM, Mielcarz JA, Valkonen M, Gudlaugsson E, Kjosavik SR, Asenjo J, Gambacorta M, Libretti P, Braun M, Kordek R, Łowicki R, Hotakainen K, Väre P, Pedersen BG, Sørensen KD, Ulhøi BP, Ruusuvuori P, Delahunt B, Samaratunga H, Tsuzuki T, Janssen EAM, Egevad L, Eklund M, Kartasalo K. Foundation Models - A Panacea for Artificial Intelligence in Pathology? arXiv:2502.21264v2 [cs.CV]. [Manuscript Preprint]https://doi.org/10.48550/arXiv.2502.21264V. Blilie A*, Mulliqi N*, Ji X, Szolnoky K, Boman SE, Titus M, Gonzalez GM, Asenjo J, Gambacorta M, Libretti P, Gudlaugsson E, Kjosavik SR, Egevad L, Janssen EAM, Eklund M, Kartasalo K. Artificial Intelligence- Assisted Prostate Cancer Diagnosis for Reduced Use of Immunohistochemistry. arXiv:2504.00979v1 [cs.CV]. [Manuscript Preprint]https://doi.org/10.48550/arXiv.2504.00979* Authors contributed equally</p
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Author Under Sail The Imagination of Jack London, 1893-1902
No full textIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Intro -- Title Page -- Copyright Page -- Dedication -- Contents -- Acknowledgments -- Introduction -- 1. Spirit Truth -- 2. From Absorption to Theatricality and Back Again -- 3. "I Will Build a New Present" -- 4. Sons as Authors -- 5. Fathers as Publishers -- 6. The Daughter as Author -- 7. Lovers as Authors -- 8. At Sea with the Family -- 9. Yellow News, Yellow Stories -- 10. The Return Home -- Notes -- Bibliography -- Index -- About Jay WilliamsIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
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