Johannes Raffler
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View article: Large language model processing capabilities of ChatGPT 4.0 to generate molecular tumor board recommendations—a critical evaluation on real world data
Large language model processing capabilities of ChatGPT 4.0 to generate molecular tumor board recommendations—a critical evaluation on real world data Open
Background Large language models (LLMs) like ChatGPT 4.0 hold promise for enhancing clinical decision-making in precision oncology, particularly within molecular tumor boards (MTBs). This study assesses ChatGPT 4.0’s performance in generat…
View article: Use of Client-Side Machine Learning Models for Privacy-Preserving Healthcare Predictions – A Deployment Case Study
Use of Client-Side Machine Learning Models for Privacy-Preserving Healthcare Predictions – A Deployment Case Study Open
Introduction: Machine learning (ML) and deep learning (DL) models in healthcare traditionally rely on server-centric architectures, where sensitive patient data is transmitted to external servers for processing via frameworks like Flask, r…
View article: Do explainable <scp>AI</scp> (<scp>XAI</scp>) methods improve the acceptance of <scp>AI</scp> in clinical practice? An evaluation of <scp>XAI</scp> methods on Gleason grading
Do explainable <span>AI</span> (<span>XAI</span>) methods improve the acceptance of <span>AI</span> in clinical practice? An evaluation of <span>XAI</span> methods on Gleason grading Open
This work aimed to evaluate both the usefulness and user acceptance of five gradient‐based explainable artificial intelligence (XAI) methods in the use case of a prostate carcinoma clinical decision support system environment. In addition,…
View article: User Experience and Trust Improvement Evaluation on Healthcare oriented Explainable Artificial Intelligence Interventions: Systematic Review (Preprint)
User Experience and Trust Improvement Evaluation on Healthcare oriented Explainable Artificial Intelligence Interventions: Systematic Review (Preprint) Open
BACKGROUND The field of artificial intelligence (AI) has expanded rapidly in recent years. Generally, AI is viewed as a “black box” since understanding how it came to its presented solution is nearly impossible, which causes mistrust amon…
View article: Bridging Data Silos in Oncology with Modular Software for Federated Analysis on Fast Healthcare Interoperability Resources: Multisite Implementation Study
Bridging Data Silos in Oncology with Modular Software for Federated Analysis on Fast Healthcare Interoperability Resources: Multisite Implementation Study Open
Background Real-world data (RWD) from sources like administrative claims, electronic health records, and cancer registries offer insights into patient populations beyond the tightly regulated environment of randomized controlled trials. To…
View article: Bridging Data Silos in Oncology with Modular Software for Federated Analysis on FHIR: A Multisite Implementation Study (Preprint)
Bridging Data Silos in Oncology with Modular Software for Federated Analysis on FHIR: A Multisite Implementation Study (Preprint) Open
BACKGROUND Real-world data (RWD) from sources like administrative claims, electronic health records, and cancer registries offer insights into patient populations beyond the tightly regulated environment of randomized controlled trials. T…
View article: Assessing the Performance of Deep Learning for Automated Gleason Grading in Prostate Cancer
Assessing the Performance of Deep Learning for Automated Gleason Grading in Prostate Cancer Open
Prostate cancer is a dominant health concern calling for advanced diagnostic tools. Utilizing digital pathology and artificial intelligence, this study explores the potential of 11 deep neural network architectures for automated Gleason gr…
View article: The HuMet Repository: Watching human metabolism at work
The HuMet Repository: Watching human metabolism at work Open
View article: Assessing the Performance of Deep Learning for Automated Gleason Grading in Prostate Cancer
Assessing the Performance of Deep Learning for Automated Gleason Grading in Prostate Cancer Open
Prostate cancer is a dominant health concern calling for advanced diagnostic tools. Utilizing digital pathology and artificial intelligence, this study explores the potential of 11 deep neural network architectures for automated Gleason gr…
View article: DeepGleason: a System for Automated Gleason Grading of Prostate Cancer using Deep Neural Networks
DeepGleason: a System for Automated Gleason Grading of Prostate Cancer using Deep Neural Networks Open
Advances in digital pathology and artificial intelligence (AI) offer promising opportunities for clinical decision support and enhancing diagnostic workflows. Previous studies already demonstrated AI's potential for automated Gleason gradi…
View article: The HuMet Repository: Watching human metabolism at work
The HuMet Repository: Watching human metabolism at work Open
The human metabolism constantly responds to stimuli such as food intake, fasting, exercise, and stress, triggering adaptive biochemical processes across multiple metabolic pathways. To understand the role of these processes and disruptions…
View article: Artificial intelligence and digital biomarker in precision pathology guiding immune therapy selection and precision oncology
Artificial intelligence and digital biomarker in precision pathology guiding immune therapy selection and precision oncology Open
Background The currently available immunotherapies already changed the strategy how many cancers are treated from first to last line. Understanding even the most complex heterogeneity in tumor tissue and mapping the spatial cartography of …
View article: Rare and common genetic determinants of metabolic individuality and their effects on human health
Rare and common genetic determinants of metabolic individuality and their effects on human health Open
View article: Dynamic patterns of postprandial metabolic responses to three dietary challenges
Dynamic patterns of postprandial metabolic responses to three dietary challenges Open
Food intake triggers extensive changes in the blood metabolome. The kinetics of these changes depend on meal composition and on intrinsic, health-related characteristics of each individual, making the assessment of changes in the postprand…
View article: Mapping the proteo-genomic convergence of human diseases
Mapping the proteo-genomic convergence of human diseases Open
Detangling gene-disease connections Many diseases are at least partially due to genetic causes that are not always understood or targetable with specific treatments. To provide insight into the biology of various human diseases as well as …
View article: A Predictive Model for Progression of CKD to Kidney Failure Based on Routine Laboratory Tests
A Predictive Model for Progression of CKD to Kidney Failure Based on Routine Laboratory Tests Open
View article: Plasma metabolites to profile pathways in noncommunicable disease multimorbidity
Plasma metabolites to profile pathways in noncommunicable disease multimorbidity Open
View article: Author Correction: Genetic architecture of host proteins involved in SARS-CoV-2 infection
Author Correction: Genetic architecture of host proteins involved in SARS-CoV-2 infection Open
View article: A cross-platform approach identifies genetic regulators of human metabolism and health
A cross-platform approach identifies genetic regulators of human metabolism and health Open
View article: Genetic architecture of host proteins involved in SARS-CoV-2 infection
Genetic architecture of host proteins involved in SARS-CoV-2 infection Open
View article: Genetic architecture of host proteins interacting with SARS-CoV-2
Genetic architecture of host proteins interacting with SARS-CoV-2 Open
Strategies to develop therapeutics for SARS-CoV-2 infection may be informed by experimental identification of viral-host protein interactions in cellular assays and measurement of host response proteins in COVID-19 patients. Identification…
View article: Cross-platform genetic discovery of small molecule products of metabolism and application to clinical outcomes
Cross-platform genetic discovery of small molecule products of metabolism and application to clinical outcomes Open
Circulating levels of small molecules or metabolites are highly heritable, but the impact of genetic differences in metabolism on human health is not well understood. In this cross-platform, genome-wide meta-analysis of 174 metabolite leve…
View article: Genetic studies of urinary metabolites illuminate mechanisms of detoxification and excretion in humans
Genetic studies of urinary metabolites illuminate mechanisms of detoxification and excretion in humans Open
View article: Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels
Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels Open
Saliva, as a biofluid, is inexpensive and non-invasive to obtain, and provides a vital tool to investigate oral health and its interaction with systemic health conditions. There is growing interest in salivary biomarkers for systemic disea…
View article: Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels
Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels Open
Saliva, as a biofluid, is inexpensive and non-invasive to obtain, and provides a vital tool to investigate oral health and its interaction with systemic health conditions. There is growing interest in salivary biomarkers for systemic disea…
View article: Datenbasierte Funktionsvorhersage krankheitsrelevanter genetischer Varianten
Datenbasierte Funktionsvorhersage krankheitsrelevanter genetischer Varianten Open
View article: Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies
Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies Open
Missing data in untargeted MS-based metabolomics data occur for various reasons. Based on our results, we recommend that KNN-based imputation is performed on observations with variable pre-selection since it showed robust results in all ev…
View article: HitPickV2: a web server to predict targets of chemical compounds
HitPickV2: a web server to predict targets of chemical compounds Open
Motivation The identification of protein targets of novel compounds is essential to understand compounds’ mechanisms of action leading to biological effects. Experimental methods to determine these protein targets are usually slow, costly …
View article: Genome-Wide Association Studies of Metabolite Concentrations (mGWAS): Relevance for Nephrology
Genome-Wide Association Studies of Metabolite Concentrations (mGWAS): Relevance for Nephrology Open
View article: Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies
Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies Open
BACKGROUND Untargeted mass spectrometry (MS)-based metabolomics data often contain missing values that reduce statistical power and can introduce bias in epidemiological studies. However, a systematic assessment of the various sources of m…