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Article
Open AccessAuthor Correction: Prediction of recurrence risk in endometrial cancer with multimodal deep learning
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Article
Open AccessAuthor Correction: Pathway level subty** identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer
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Article
Open AccessPrediction of recurrence risk in endometrial cancer with multimodal deep learning
Predicting distant recurrence of endometrial cancer (EC) is crucial for personalized adjuvant treatment. The current gold standard of combined pathological and molecular profiling is costly, hampering implemen...
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Article
Open AccessImage-based consensus molecular subty** in rectal cancer biopsies and response to neoadjuvant chemoradiotherapy
The development of deep learning (DL) models to predict the consensus molecular subtypes (CMS) from histopathology images (imCMS) is a promising and cost-effective strategy to support patient stratification. H...
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Article
Open AccessPathway level subty** identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer
Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal c...
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Article
Open AccessSwiss digital pathology recommendations: results from a Delphi process conducted by the Swiss Digital Pathology Consortium of the Swiss Society of Pathology
Integration of digital pathology (DP) into clinical diagnostic workflows is increasingly receiving attention as new hardware and software become available. To facilitate the adoption of DP, the Swiss Digital P...
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Article
Open AccessNational digital pathology projects in Switzerland: A 2023 update
The Swiss Digital Pathology Consortium (SDiPath) was founded in 2018 as a working group of the Swiss Society for Pathology with the aim of networking, training, and promoting digital pathology (DP) at a nation...
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Article
Open AccessDigital image analysis and artificial intelligence in pathology diagnostics—the Swiss view
Digital pathology (DP) is increasingly entering routine clinical pathology diagnostics. As digitization of the routine caseload advances, implementation of digital image analysis algorithms and artificial inte...
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Article
Open AccessCombinational expression of tumor testis antigens NY-ESO-1, MAGE-A3, and MAGE-A4 predicts response to immunotherapy in mucosal melanoma patients
Immunotherapy using immune checkpoint inhibitors (ICI) has revolutionized cancer treatment in recent years, particularly in melanoma. While response to immunotherapy is associated with high tumor mutational b...
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Chapter and Conference Paper
Joint Prediction of Response to Therapy, Molecular Traits, and Spatial Organisation in Colorectal Cancer Biopsies
Existing methods for interpretability of model predictions are largely based on technical insights and are not linked to clinical context. We use the question of predicting response to radiotherapy in colorect...
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Chapter and Conference Paper
Fine-Grained Hard-Negative Mining: Generalizing Mitosis Detection with a Fifth of the MIDOG 2022 Dataset
Making histopathology image classifiers robust to a wide range of real-world variability is a challenging task. Here, we describe a candidate deep learning solution for the Mitosis Domain Generalization Challe...
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Article
Open AccessAutomated causal inference in application to randomized controlled clinical trials
Randomized controlled trials (RCTs) are considered the gold standard for testing causal hypotheses in the clinical domain; however, the investigation of prognostic variables of patient outcome in a hypothesize...
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Article
Open AccessTertiary lymphoid structures critical for prognosis in endometrial cancer patients
B-cells play a key role in cancer suppression, particularly when aggregated in tertiary lymphoid structures (TLS). Here, we investigate the role of B-cells and TLS in endometrial cancer (EC). Single cell RNA-s...
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Chapter and Conference Paper
Enhancing Local Context of Histology Features in Vision Transformers
Predicting complete response to radiotherapy in rectal cancer patients using deep learning approaches from morphological features extracted from histology biopsies provides a quick, low-cost and effective way ...
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Chapter and Conference Paper
Rotation Invariance and Extensive Data Augmentation: A Strategy for the MItosis DOmain Generalization (MIDOG) Challenge
Automated detection of mitotic figures in histopathology images is a challenging task: here, we present the different steps that describe the strategy we applied to participate in the MIDOG 2021 competition. T...
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Article
Open AccessTwo distinct immunopathological profiles in autopsy lungs of COVID-19
Coronavirus Disease 19 (COVID-19) is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has grown to a worldwide pandemic with substantial mortality. Immune med...
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Article
Publisher Correction: Uncoupling protein 2 reprograms the tumor microenvironment to support the anti-tumor immune cycle
In the version of this article initially published, the bars were not aligned with the data points or horizontal axis labels in Fig. 5d, and the labels along each horizontal axis of Fig. 5j–l indicating the pr...
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Article
Open AccessPrecision immunoprofiling by image analysis and artificial intelligence
Clinical success of immunotherapy is driving the need for new prognostic and predictive assays to inform patient selection and stratification. This requirement can be met by a combination of computational path...
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Article
Uncoupling protein 2 reprograms the tumor microenvironment to support the anti-tumor immune cycle
Immune checkpoint blockade therapy has shifted the paradigm for cancer treatment. However, the majority of patients lack effective responses due to insufficient T cell infiltration in tumors. Here we show that...
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Article
The evolutionary landscape of colorectal tumorigenesis
The evolutionary events that cause colorectal adenomas (benign) to progress to carcinomas (malignant) remain largely undetermined. Using multi-region genome and exome sequencing of 24 benign and malignant colo...
