Cover Image

OmniGenBench: A Modular Platform for Reproducible Genomic Foundation Models Benchmarking

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Yang, Heng, Cole, Jack, Li, Yuan, Chen, Renzhi, Min, Geyong, Li, Ke
Format:	Preprint
Published:	2025
Subjects:	Genomics Computation and Language
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

OmniGenBench: Automating Large-scale in-silico Benchmarking for Genomic Foundation Models
by: Yang, Heng, et al.
Published: (2024)

Bridging Sequence-Structure Alignment in RNA Foundation Models
by: Yang, Heng, et al.
Published: (2024)

GENERator: A Long-Context Generative Genomic Foundation Model
by: Wu, Wei, et al.
Published: (2025)

GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models
by: Liu, Zicheng, et al.
Published: (2024)

GenomeQA: Benchmarking General Large Language Models for Genome Sequence Understanding
by: Long, Weicai, et al.
Published: (2026)

PhageBench: Can LLMs Understand Raw Bacteriophage Genomes?
by: Hou, Yusen, et al.
Published: (2026)

DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome
by: Zhou, Zhihan, et al.
Published: (2023)

Entropy, Disagreement, and the Limits of Foundation Models in Genomics
by: Rochkoulets, Maxime, et al.
Published: (2026)

PathoLM: Identifying pathogenicity from the DNA sequence through the Genome Foundation Model
by: Dip, Sajib Acharjee, et al.
Published: (2024)

Gene42: Long-Range Genomic Foundation Model With Dense Attention
by: Vishniakov, Kirill, et al.
Published: (2025)

Large Language Models in Bioinformatics: A Survey
by: Wang, Zhenyu, et al.
Published: (2025)

Single-Cell Omics Arena: A Benchmark Study for Large Language Models on Cell Type Annotation Using Single-Cell Data
by: Liu, Junhao, et al.
Published: (2024)

Mind the Gap No More: Achieving Zero-Gap Multimodal Integration via One Tokenizer
by: Li, Yanan, et al.
Published: (2026)

GeneMamba: An Efficient and Effective Foundation Model on Single Cell Data
by: Qi, Cong, et al.
Published: (2025)

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

Large Language Models in Plant Biology
by: Lam, Hilbert Yuen In, et al.
Published: (2024)

DNACHUNKER: Learnable Tokenization for DNA Language Models
by: Kim, Taewon, et al.
Published: (2026)

Knowledge-Driven Feature Selection and Engineering for Genotype Data with Large Language Models
by: Lee, Joseph, et al.
Published: (2024)

GeneSUM: Large Language Model-based Gene Summary Extraction
by: Chen, Zhijian, et al.
Published: (2024)

Leveraging Natural Language Processing to Unravel the Mystery of Life: A Review of NLP Approaches in Genomics, Transcriptomics, and Proteomics
by: Rannon, Ella, et al.
Published: (2025)

Open World Knowledge Aided Single-Cell Foundation Model with Robust Cross-Modal Cell-Language Pre-training
by: Wang, Haoran, et al.
Published: (2026)

GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information
by: Jin, Qiao, et al.
Published: (2023)

OmniGenBench: A Benchmark for Omnipotent Multimodal Generation across 50+ Tasks
by: Wang, Jiayu, et al.
Published: (2025)

METAGENE-1: Metagenomic Foundation Model for Pandemic Monitoring
by: Liu, Ollie, et al.
Published: (2025)

scReader: Prompting Large Language Models to Interpret scRNA-seq Data
by: Li, Cong, et al.
Published: (2024)

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

Poisoning the Genome: Targeted Backdoor Attacks on DNA Foundation Models
by: Koilakos, Charalampos, et al.
Published: (2026)

Estimating Reproducibility in Genome-Wide Association Studies
by: Jiang, Wei, et al.
Published: (2015)

Cross-Species Antimicrobial Resistance Prediction from Genomic Foundation Models
by: Tai, Huilin
Published: (2026)

The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids.
by: May, Samuel A, et al.
Published: (2025)

Beyond Conditional Computation: Retrieval-Augmented Genomic Foundation Models with Gengram
by: Xu, Huinan, et al.
Published: (2026)

Generative Language Models on Nucleotide Sequences of Human Genes
by: Ihtiyar, Musa Nuri, et al.
Published: (2023)

Genome-Factory: A Library for Tuning, Deploying, and Interpreting Genomic Foundation Models
by: Wu, Weimin, et al.
Published: (2025)

Can Large Language Models Replace Data Scientists in Biomedical Research?
by: Wang, Zifeng, et al.
Published: (2024)

SPACE: Your Genomic Profile Predictor is a Powerful DNA Foundation Model
by: Yang, Zhao, et al.
Published: (2025)

OGU: A Toolbox for Better Utilising Organelle Genomic Data.
by: Wu, Ping, et al.
Published: (2025)

A Chromosome-level Assembly and Functional Genomic Resources for the Model Annelid Capitella teleta.
by: Davies, Billie E, et al.
Published: (2026)

Hecate: A Modular Genomic Compressor
by: Szewczyk, Kamila, et al.
Published: (2026)

Gosling Designer: a Platform to Democratize Construction and Sharing of Genomics Data Visualization Tools
by: L'Yi, Sehi, et al.
Published: (2025)

MBGD: Microbial Genome Database for Comparative Analysis Featuring Enhanced Functionality to Characterize Gene and Genome Functions Through Large-scale Orthology Analysis.
by: Uchiyama, Ikuo, et al.
Published: (2025)