Search bioRxiv⌕ Search

Biology subjects

Malekpour, S. A.

Publications and source records attributed to Malekpour, S. A..

2 recordsLinked to original sources

Interpretable Predictive Modeling for Medical Data Using Boolean Rule-aware Regression

PurposeIn clinical practice, accurate prediction of disease risk must be accompanied by transparent, human-understandable explanations to support diagnostic confidence, guide therapeutic decisions, and meet ethical and regulatory standards. While deep neural networks achieve high predictive performance in tasks such as cancer detection and diabetes risk stratification, their black-box nature prevents clinicians from understanding the reasoning behind predictions, severely limiting trust and safe integration into patient care. MethodsWe present Regression-Based Boolean Rule (RBBR), a framework that automatically derives clinically interpretable Boolean rules directly from patient data. RBBR generates human-readable conjunctions (logical AND combinations) of up to three clinical features, transforms them into inputs for ridge regression to predict binary or multi-class disease outcomes, estimates rule importance via regularized coefficients, and selects the most parsimonious and predictive rule sets using the Bayesian Information Criterion. ResultsApplied to six real-world medical datasets (lung cancer screening and staging, Wisconsin and diagnostic breast cancer, heart failure, and early-stage diabetes risk), RBBR consistently produced concise, clinically meaningful rules - e.g., gender-specific symptom combinations in diabetes, distinct histopathological subpopulations in breast cancer, and symptom-risk factor interactions in lung cancer - with strong explanatory power (R2 up to 0.92) and competitive discrimination. ConclusionBy delivering logical, transparent decision rules aligned with clinical reasoning (if symptom A and B, then high risk), RBBR bridges the gap between predictive accuracy and bedside usability, enabling clinicians to validate predictions, identify high-risk patients, stratify subpopulations, and enhance shared decision-making in routine care.

bioinformatics↗

Inferring the selective history of CNVs using a maximum likelihood model

Copy number variations (CNVs) - structural variations generated by deletion and/or duplication that result in change in DNA dosage - are prevalent in nature. CNVs can drastically affect the phenotype of an organism and have been shown to be both involved in genetic disorders and be used as raw material in adaptive evolution. Unlike single-nucleotide variations, the often large and varied effects of CNVs on phenotype hinders our ability to infer their selective advantage based on the population genetics data. Here, we present a likelihood-based approach, dubbed PoMoCNV, that estimates the evolutionary parameters of CNVs based on population genetics data. As a case study, we analyze the genomics data of 40 strains of Caenorhabditis elegans, representing four different populations. We take advantage of the data on chromatin accessibility to interpret the evolutionary parameters of CNVs inferred by PoMoCNV. We further test the reliability of PoMoCNV by estimating the evolutionary parameters of CNVs for mutation-accumulation experiments in C. elegans with varying levels of genetic drift. SignificanceInferring the evolutionary parameters of copy number variations (CNVs) based on population genetics data is crucial to understand their role in evolution. However, given the diversity in the size and effects of CNVs, such inference poses a challenge. We developed a likelihood-based approach called PoMoCNV to address this issue.

bioinformatics↗