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Muhammad Muneeb

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Machine Learning Computation and Language Computer Vision eess.IV Genomics

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preprint2026arXiv

EFGPP: Exploratory framework for genotype-phenotype prediction

Predicting complex human traits from genetic data is challenging because different genetic, clinical, and molecular data sources often contain different parts of the signal. Here, we present EFGPP, a reproducible framework for generating, ranking, and combining multiple types of data for genotype-to-phenotype prediction. We applied EFGPP to migraine prediction using UK Biobank data from 733 individuals. The framework combined genotype-derived features, principal components, clinical and metabolomic covariates, and polygenic risk scores generated from migraine and depression GWAS using PLINK, PRSice-2, AnnoPred, and LDAK-GWAS. The best single data type achieved a test AUC of 0.644, while combining multiple data types improved performance to 0.688 using migraine-focused inputs and 0.663 using cross-trait depression-derived inputs. Genetic features alone did not outperform the covariates-only baseline, but genotype-derived features performed better than PRS alone, and depression-derived PRS showed useful predictive signal. Overall, EFGPP provides a practical proof-of-concept framework for prioritising and integrating heterogeneous genetic data sources for complex phenotype prediction.

preprint2025arXiv

An Empirical Analysis of Fine-Tuning Large Language Models on Bioinformatics Literature: PRSGPT and BioStarsGPT

Large language models (LLMs) often lack specialized knowledge for complex bioinformatics applications. We present a reproducible pipeline for fine-tuning LLMs on specialized bioinformatics data, demonstrated through two use cases: PRSGPT, focused on polygenic risk score (PRS) tools, and BioStarsGPT, trained on community forum discussions. The nine-step pipeline integrates diverse data sources, structured preprocessing, prompt-based question-answer (QA) generation (via Google Gemini), natural language inference (NLI) for quality control, semantic deduplication, clustering-based data splitting, and parameter-efficient fine-tuning using LoRA. We fine-tuned three LLMs (LLaMA-3.2-3B, Qwen2.5-7B, Gemma) and benchmarked them on over 14 lexical and semantic metrics. Qwen2.5-7B emerged as the best performer, with BLEU-4 and ROUGE-1 improvements of 82\% and 70\% for PRSGPT and 6\% and 18\% for BioStarsGPT, respectively. The open-source datasets produced include over 28,000 QA pairs for PRSGPT and 154,282 for BioStarsGPT. Human evaluation of PRSGPT yielded 61.9\% accuracy on the PRS tools comparison task, comparable to Google Gemini (61.4\%), but with richer methodological detail and accurate citations. BioStarsGPT demonstrated 59\% conceptual accuracy across 142 curated bioinformatics questions. Our pipeline enables scalable, domain-specific fine-tuning of LLMs. It enables privacy-preserving, locally deployable bioinformatics assistants, explores their practical applications, and addresses the challenges, limitations, and mitigation strategies associated with their development and use.

preprint2022arXiv

Deep learning pipeline for image classification on mobile phones

This article proposes and documents a machine-learning framework and tutorial for classifying images using mobile phones. Compared to computers, the performance of deep learning model performance degrades when deployed on a mobile phone and requires a systematic approach to find a model that performs optimally on both computers and mobile phones. By following the proposed pipeline, which consists of various computational tools, simple procedural recipes, and technical considerations, one can bring the power of deep learning medical image classification to mobile devices, potentially unlocking new domains of applications. The pipeline is demonstrated on four different publicly available datasets: COVID X-rays, COVID CT scans, leaves, and colorectal cancer. We used two application development frameworks: TensorFlow Lite (real-time testing) and Flutter (digital image testing) to test the proposed pipeline. We found that transferring deep learning models to a mobile phone is limited by hardware and classification accuracy drops. To address this issue, we proposed this pipeline to find an optimized model for mobile phones. Finally, we discuss additional applications and computational concerns related to deploying deep-learning models on phones, including real-time analysis and image preprocessing. We believe the associated documentation and code can help physicians and medical experts develop medical image classification applications for distribution.

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