Artificial intelligence for genomic science: a scoping review of concepts, architectures, applications, and open challenges
Abstract
Introduction: Artificial intelligence (AI) is becoming central to genomics and multi-omics, but its concepts, architectures, applications, evaluation standards, and translational requirements remain fragmented. This scoping review mapped how AI is defined and operationalized in genomic science, including machine learning, deep learning, graph-based methods, foundation models, and large language models, and synthesized their data modalities, applications, evaluation practices, interpretability strategies, and governance challenges.
Methods: We conducted a PRISMA-ScR scoping review with Joanna Briggs Institute guidance. Eligible studies applied AI to genomics or closely allied omics in research, clinical, or public health contexts. MEDLINE/PubMed, Embase, and supplementary registers were searched from January 2001 to 3 September 2025 without language restrictions. Records were screened in duplicate, and standardized items were extracted, including AI concept or method family, omics modality, task, metrics, interpretability, governance, and deployment considerations. Methodological reporting and quality were appraised using design-appropriate JBI tools and summarized descriptively as a normalized 0%-100% checklist-fulfillment index.
Results: From 3,785 records, 1,040 studies were included. Publication remained sparse until 2017 and then expanded steeply, with more than 90% appearing from 2018 onward. The normalized JBI checklist-fulfillment index was modest overall (mean 35.3%,…
How strong is the evidence?
Evidence Hub reads this as a systematic review. Its evidence level is 1 of 5 (Highest · pooled evidence). Pooled evidence from several studies sits at the top of the evidence pyramid.
Read the paper
Related studies
- Active Learning during Federated Learning for Object Detection
- Fairness-aware federated learning
- Decentralized Federated Learning
- Building a Personally Identifiable Information Recognizer in a Privacy Preserved Manner Using Automated Annotation and Federated Learning
- Preservation of Patient Level Privacy: Federated Classification and Calibration Models
- Efficient explainable federated learning
Go deeper in Evidence Hub
Evidence Hub adds a study data sheet (design, sample size, evidence level, key numbers), an AI summary and a chat grounded in the paper's text.