Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent-of-Origin-based Detection (POD) method

Abstract Background Mosaic somatic alterations are present in all multi-cellular organisms, but the physiological effects of low-level mosaicism are largely unknown. Most mosaic alterations remain undetectable with current analytical approaches, although the presence of such alterations is increasingly implicated as causative for disease. Results Here, we present the Parent-of-Origin-based Detection (POD) method for chromosomal abnormality detection in trio-based SNP microarray data. Our software implementation, triPOD, was benchmarked using a simulated dataset, outperformed comparable software for sensitivity of abnormality detection, and displayed substantial improvement in the detection of low-level mosaicism while maintaining comparable specificity. Examples of low-level mosaic abnormalities from a large autism dataset demonstrate the benefits of the increased sensitivity provided by triPOD. The triPOD analyses showed robustness across multiple types of Illumina microarray chips. Two large, clinically-relevant datasets were characterized and compared. Conclusions Our method and software provide a significant advancement in the ability to detect low-level mosaic abnormalities, thereby opening new avenues for research into the implications of mosaicism in pathogenic and non-pathogenic processes. </jats:sec

Fuzzy Rules for Explaining Deep Neural Network Decisions (FuzRED)

This paper introduces a novel approach to explainable artificial intelligence (XAI) that enhances interpretability by combining local insights from Shapley additive explanations (SHAP)&mdash;a widely adopted XAI tool&mdash;with global explanations expressed as fuzzy association rules. By employing fuzzy association rules, our method enables AI systems to generate explanations that closely resemble human reasoning, delivering intuitive and comprehensible insights into system behavior. We present the FuzRED methodology and evaluate its performance on models trained across three diverse datasets: two classification tasks (spam identification and phishing link detection), and one reinforcement learning task involving robot navigation. Compared to the Anchors method FuzRED offers at least one order of magnitude faster execution time (minutes vs. hours) while producing easily interpretable rules that enhance human understanding of AI decision making

Crystal Cube: Forecasting Disruptive Events

Disruptive events within a country can have global repercussions, creating a need for the anticipation and planning of these events. Crystal Cube (CC) is a novel approach to forecasting disruptive political events at least one month into the future. The system uses a recurrent neural network and a novel measure of event similarity between past and current events. We also introduce the innovative Thermometer of Irregular Leadership Change (ILC). We present an evaluation of CC in predicting ILC for 167 countries and show promising results in forecasting events one to twelve months in advance. We compare CC results with results using a random forest as well as previous work