Cover Image

Explainable AI Methods for Multi-Omics Analysis: A Survey

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Hussein, Ahmad, Prasad, Mukesh, Braytee, Ali
Format:	Preprint
Published:	2024
Subjects:	Genomics Artificial Intelligence Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Multi-Omic and Quantum Machine Learning Integration for Lung Subtypes Classification
by: Saggi, Mandeep Kaur, et al.
Published: (2024)

Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification
by: Liu, Zicheng, et al.
Published: (2025)

eDOC: Explainable Decoding Out-of-domain Cell Types with Evidential Learning
by: Wu, Chaochen, et al.
Published: (2024)

Dy-mer: An Explainable DNA Sequence Representation Scheme using Dictionary Learning
by: Peng, Zhiyuan, et al.
Published: (2024)

Artificial Intelligence and Deep Learning Algorithms for Epigenetic Sequence Analysis: A Review for Epigeneticists and AI Experts
by: Tahir, Muhammad, et al.
Published: (2025)

F5C-finder: An Explainable and Ensemble Biological Language Model for Predicting 5-Formylcytidine Modifications on mRNA
by: Wang, Guohao, et al.
Published: (2024)

OmicsCL: Unsupervised Contrastive Learning for Cancer Subtype Discovery and Survival Stratification
by: Karagoz, Atahan
Published: (2025)

BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool
by: Ramos, Vicente, et al.
Published: (2025)

A Multi-Label Temporal Convolutional Framework for Transcription Factor Binding Characterization
by: Demurtas, Pietro, et al.
Published: (2026)

Omni-DNA: A Unified Genomic Foundation Model for Cross-Modal and Multi-Task Learning
by: Li, Zehui, et al.
Published: (2025)

Toward a Team of AI-made Scientists for Scientific Discovery from Gene Expression Data
by: Liu, Haoyang, et al.
Published: (2024)

SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics
by: Zhao, Suyuan, et al.
Published: (2025)

UniPTMs: The First Unified Multi-type PTM Site Prediction Model via Master-Slave Architecture-Based Multi-Stage Fusion Strategy and Hierarchical Contrastive Loss
by: Lin, Yiyu, et al.
Published: (2025)

Vision Transformers with Autoencoders and Explainable AI for Cancer Patient Risk Stratification Using Whole Slide Imaging
by: Hussein, Ahmad, et al.
Published: (2025)

Multi-Dimensional Spectral Geometry of Biological Knowledge in Single-Cell Transformer Representations
by: Kendiukhov, Ihor
Published: (2026)

GenoTEX: An LLM Agent Benchmark for Automated Gene Expression Data Analysis
by: Liu, Haoyang, et al.
Published: (2024)

DOGMA: Weaving Structural Information into Data-centric Single-cell Transcriptomics Analysis
by: Zhang, Ru, et al.
Published: (2026)

Knowledge-guided Contextual Gene Set Analysis Using Large Language Models
by: Wang, Zhizheng, et al.
Published: (2025)

Machine Learning-Based Genomic Linguistic Analysis (Gene Sequence Feature Learning): A Case Study on Predicting Heavy Metal Response Genes in Rice
by: Yang, Ruiqi, et al.
Published: (2025)

Soft-Evidence Fused Graph Neural Network for Cancer Driver Gene Identification across Multi-View Biological Graphs
by: Chen, Bang, et al.
Published: (2025)

Exploring the Potentials and Challenges of Using Large Language Models for the Analysis of Transcriptional Regulation of Long Non-coding RNAs
by: Wang, Wei, et al.
Published: (2024)

Nearest Neighbor CCP-Based Molecular Sequence Analysis
by: Ali, Sarwan, et al.
Published: (2024)

Foundation Models for AI-Enabled Biological Design
by: Moldwin, Asher, et al.
Published: (2025)

PRAGA: Prototype-aware Graph Adaptive Aggregation for Spatial Multi-modal Omics Analysis
by: Huang, Xinlei, et al.
Published: (2024)

GenoMAS: A Multi-Agent Framework for Scientific Discovery via Code-Driven Gene Expression Analysis
by: Liu, Haoyang, et al.
Published: (2025)

GenoBERT: A Language Model for Accurate Genotype Imputation
by: Huang, Lei, et al.
Published: (2026)

Celler:A Genomic Language Model for Long-Tailed Single-Cell Annotation
by: Zhao, Huan, et al.
Published: (2025)

A step toward a reinforcement learning de novo genome assembler
by: Padovani, Kleber, et al.
Published: (2021)

SeqMate: A Novel Large Language Model Pipeline for Automating RNA Sequencing
by: Mondal, Devam, et al.
Published: (2024)

Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN
by: Refahi, Mohammad Saleh, et al.
Published: (2025)

PhenoGnet: A Graph-Based Contrastive Learning Framework for Disease Similarity Prediction
by: Baminiwatte, Ranga, et al.
Published: (2025)

HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model
by: Ma, Mingqian, et al.
Published: (2025)

A Novel cVAE-Augmented Deep Learning Framework for Pan-Cancer RNA-Seq Classification
by: Polepalli, Vinil
Published: (2025)

scSiameseClu: A Siamese Clustering Framework for Interpreting single-cell RNA Sequencing Data
by: Xu, Ping, et al.
Published: (2025)

Comparative Analysis of Multi-Omics Integration Using Advanced Graph Neural Networks for Cancer Classification
by: Alharbi, Fadi, et al.
Published: (2024)

SynLeaF: A Dual-Stage Multimodal Fusion Framework for Synthetic Lethality Prediction Across Pan- and Single-Cancer Contexts
by: Xing, Zheming, et al.
Published: (2026)

MLOmics: Cancer Multi-Omics Database for Machine Learning
by: Yang, Ziwei, et al.
Published: (2024)

Fusing Sequence Motifs and Pan-Genomic Features: Antimicrobial Resistance Prediction using an Explainable Lightweight 1D CNN-XGBoost Ensemble
by: Siddiqui, Md. Saiful Bari, et al.
Published: (2025)

Phenome-Wide Multi-Omics Integration Uncovers Distinct Archetypes of Human Aging
by: Li, Huifa, et al.
Published: (2025)

OmicsLM: A Multimodal Large Language Model for Multi-Sample Omics Reasoning
by: Sypetkowski, Maciej, et al.
Published: (2026)