# PlantBiMoE: A Bidirectional Foundation Model with SparseMoE for Plant Genomes

arXiv: https://arxiv.org/abs/2512.07113 · HTML: https://mlsanity.com/paper/2512.07113/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 27 references that are in the map.
- First posted on arXiv 8 Dec 2025.

## Builds on (most cited first, 10 of 10)

- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Outrageously Large Neural Networks: The Sparsely-Gated Mixture-of-Experts Layer](https://mlsanity.com/paper/1701.06538/) (2017)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling](https://mlsanity.com/paper/1412.3555/) (2014)
- [GLU Variants Improve Transformer](https://mlsanity.com/paper/2002.05202/) (2020)
- [Sigmoid-Weighted Linear Units for Neural Network Function Approximation in Reinforcement Learning](https://mlsanity.com/paper/1702.03118/) (2017)
- [Few-Shot Parameter-Efficient Fine-Tuning is Better and Cheaper than In-Context Learning](https://mlsanity.com/paper/2205.05638/) (2022)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome](https://mlsanity.com/paper/2306.15006/) (2023)
- [Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling](https://mlsanity.com/paper/2403.03234/) (2024)

## Abstract (arXiv)

Understanding the underlying linguistic rules of plant genomes remains a fundamental challenge in computational biology. Recent advances including AgroNT and PDLLMs have made notable progress although, they suffer from excessive parameter size and limited ability to model the bidirectional nature of DNA strands respectively. To address these limitations, we propose PlantBiMoE, a lightweight and expressive plant genome language model that integrates bidirectional Mamba and a Sparse Mixture-of-Experts (SparseMoE) framework. The bidirectional Mamba enables the model to effectively capture structural dependencies across both the forward and reverse DNA strands, while SparseMoE significantly reduces the number of active parameters, improving computational efficiency without sacrificing modeling capacity. We evaluated and tested our model on the Modified Plants Genome Benchmark (MPGB), an enhanced genomic benchmark, which consolidates 31 datasets across 11 representative tasks, with input sequence lengths ranging from 50 to 6,000 bp. Experimental results demonstrate that PlantBiMoE achieves the best performance on 20 out of 31 datasets and the average best when comparing with existing models. In summary, all above results demonstrate that our model can effectively represent plant genomic sequences, serving as a robust computational tool for diverse genomic tasks, while making substantive contributions to plant genomics, gene editing, and synthetic biology. The code is available at: https://github.com/HUST-Keep-Lin/PlantBiMoE