ArticleProceedings of machine learning research2024
Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling.
Article in Proceedings of machine learning research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- Small variant calling in the era of long-read sequencing.Nature reviews. Genetics · 2026Review
- DeepGVS: a bimodal deep learning framework integrating coding-sequence and protein-structural representations for virulence factor prediction.Bioinformatics (Oxford, England) · 2026Article
- OrchAlign: orchestrated multimodal alignment for gene expression prediction.Bioinformatics (Oxford, England) · 2026Article
- From prompts to genomes: A constraint-first framework for AI-driven sequence design across life and viruses.PLoS computational biology · 2026Article
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- Review
- A unified benchmark of supervised and retrieval-based methods for viral genomic sequence classification.Scientific reports · 2026Article
- Balanced DNA interpolation improves learning of genetic distance-informed embeddings in plants.PLoS computational biology · 2026Article
- Multimodal deep learning enhances genomic risk prediction for cardiometabolic diseases.Briefings in bioinformatics · 2026Article
- LAMBDA: a prophage detection benchmark for genomic language models.NAR genomics and bioinformatics · 2026Article
- MOSAIC enables selective transfer and fairness-aware generalization in cross-species DNA methylation prediction.Nucleic acids research · 2026Article
- PI-Mamba: linear-time protein backbone generation via spectrally initialized flow matching.Bioinformatics (Oxford, England) · 2026Article
- Foundation models in omics research: a comprehensive survey.Briefings in bioinformatics · 2026Review
- EssTFNet: integration of adaptive time-frequency and DNA language models for interpretable human essential gene prediction.Briefings in bioinformatics · 2026Article
- Advancing bioinformatics with language models: components, applications, and perspectives.Briefings in bioinformatics · 2026Review
- CodonMoE: DNA language models for codon-dependent mRNA prediction.Bioinformatics (Oxford, England) · 2026Article
- Data-driven AI system for learning how to run transcript assemblers.Genome biology · 2026Article
- Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.Briefings in bioinformatics · 2026Review
- Scalable homology detection with ERAST.Nature biotechnology · 2026Article
- A survey on large language models in biology and chemistry.Experimental & molecular medicine · 2026Review
15 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of
Identifiers
40567809PMC12189541What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.