4 papers
AnnotateMissense: a genome-wide annotation and benchmarking framework for missense pathogenicity prediction
Muhammad Muneeb, David B. Ascher
Missense variant interpretation remains challenging because pathogenicity depends on heterogeneous evidence from population frequency, evolutionary conservation, transcript context…
Benchmarking Heritability Estimation Strategies Across 86 Configurations and Their Downstream Effect on Polygenic Risk Score Performance
Muhammad Muneeb, David B. Ascher
Objective: SNP heritability estimates vary substantially across estimation strategies, yet the downstream consequences for polygenic risk score (PRS) construction remain poorly cha…
An Empirical Analysis of Fine-Tuning Large Language Models on Bioinformatics Literature: PRSGPT and BioStarsGPT
Muhammad Muneeb, David B. Ascher
Large language models (LLMs) often lack specialized knowledge for complex bioinformatics applications. We present a reproducible pipeline for fine-tuning LLMs on specialized bioinf…
Comparative Analysis of 47 Context-Based Question Answer Models Across 8 Diverse Datasets
Muhammad Muneeb, David B. Ascher, Ahsan Baidar Bakht
Context-based question answering (CBQA) models provide more accurate and relevant answers by considering the contextual information. They effectively extract specific information g…