Cover Image

Entropy, Disagreement, and the Limits of Foundation Models in Genomics

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Rochkoulets, Maxime, Vrček, Lovro, Šikić, Mile
Format:	Preprint
Published:	2026
Subjects:	Machine Learning Computation and Language Genomics
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

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)

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

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

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

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

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

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

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

OmniGenBench: A Modular Platform for Reproducible Genomic Foundation Models Benchmarking
by: Yang, Heng, et al.
Published: (2025)

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

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

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

PlantBiMoE: A Bidirectional Foundation Model with SparseMoE for Plant Genomes
by: Lin, Kepeng, et al.
Published: (2025)

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

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

Cancer-inspired Genomics Mapper Model for the Generation of Synthetic DNA Sequences with Desired Genomics Signatures
by: Lazebnik, Teddy, et al.
Published: (2023)

Absorb & Escape: Overcoming Single Model Limitations in Generating Genomic Sequences
by: Li, Zehui, et al.
Published: (2024)

A Phylogenetic Approach to Genomic Language Modeling
by: Albors, Carlos, et al.
Published: (2025)

How Private Are DNA Embeddings? Inverting Foundation Model Representations of Genomic Sequences
by: Ouaari, Sofiane, et al.
Published: (2026)

Whole-Genome Phenotype Prediction with Machine Learning: Open Problems in Bacterial Genomics
by: James, Tamsin, 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)

HAD: Hybrid Architecture Distillation Outperforms Teacher in Genomic Sequence Modeling
by: Yang, Hexiong, et al.
Published: (2025)

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

Leveraging State Space Models in Long Range Genomics
by: Popov, Matvei, et al.
Published: (2025)

Statistical Linear Models in Virus Genomic Alignment-free Classification: Application to Hepatitis C Viruses
by: Remita, Amine M., et al.
Published: (2019)

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

Towards Applying Large Language Models to Complement Single-Cell Foundation Models
by: Palayew, Steven, et al.
Published: (2025)

Semantically Rich Local Dataset Generation for Explainable AI in Genomics
by: Barbosa, Pedro, et al.
Published: (2024)

A Misclassification Network-Based Method for Comparative Genomic Analysis
by: He, Wan, et al.
Published: (2024)

Contrastive Deep Learning for Variant Detection in Wastewater Genomic Sequencing
by: Chinda, Adele, et al.
Published: (2025)

JanusDNA: A Powerful Bi-directional Hybrid DNA Foundation Model
by: Duan, Qihao, et al.
Published: (2025)

Discovering Interpretable Biological Concepts in Single-cell RNA-seq Foundation Models
by: Claye, Charlotte, et al.
Published: (2025)

Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability
by: Liang, Yuheng, et al.
Published: (2026)

Enhancing Downstream Analysis in Genome Sequencing: Species Classification While Basecalling
by: Kodra, Riselda, et al.
Published: (2025)

Whole Genome Transformer for Gene Interaction Effects in Microbiome Habitat Specificity
by: Li, Zhufeng, et al.
Published: (2024)

Understanding the Natural Language of DNA using Encoder-Decoder Foundation Models with Byte-level Precision
by: Malusare, Aditya, et al.
Published: (2023)

Explainable AI in Genomics: Transcription Factor Binding Site Prediction with Mixture of Experts
by: Tripathi, Aakash, et al.
Published: (2025)

Embedding Is (Almost) All You Need: Retrieval-Augmented Inference for Generalizable Genomic Prediction Tasks
by: Datta, Nirjhor, et al.
Published: (2025)

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