# Scaling RNA Foundation Models through Iterative Refinement

arXiv: https://arxiv.org/abs/2610.13106 · HTML: https://mlsanity.com/paper/2610.13106/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 46 references that are in the map.
- First posted on arXiv 9 Oct 2026.

## Builds on (most cited first, 21 of 21)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [ALBERT: A Lite BERT for Self-supervised Learning of Language Representations](https://mlsanity.com/paper/1909.11942/) (2019)
- [GLU Variants Improve Transformer](https://mlsanity.com/paper/2002.05202/) (2020)
- [GQA: Training Generalized Multi-Query Transformer Models from Multi-Head Checkpoints](https://mlsanity.com/paper/2305.13245/) (2023)
- [Large Language Monkeys: Scaling Inference Compute with Repeated Sampling](https://mlsanity.com/paper/2407.21787/) (2024)
- [Universal Transformers](https://mlsanity.com/paper/1807.03819/) (2018)
- [Scaling up Test-Time Compute with Latent Reasoning: A Recurrent Depth Approach](https://mlsanity.com/paper/2502.05171/) (2025)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [Mixture-of-Recursions: Learning Dynamic Recursive Depths for Adaptive Token-Level Computation](https://mlsanity.com/paper/2507.10524/) (2025)
- [Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling](https://mlsanity.com/paper/2403.03234/) (2024)
- [Parcae: Scaling Laws For Stable Looped Language Models](https://mlsanity.com/paper/2604.12946/) (2026)
- [RiNALMo: General-Purpose RNA Language Models Can Generalize Well on Structure Prediction Tasks](https://mlsanity.com/paper/2403.00043/) (2024)
- [Stabilizing Recurrent Dynamics for Test-Time Scalable Latent Reasoning in Looped Language Models](https://mlsanity.com/paper/2605.26733/) (2026)
- [Accurate RNA 3D structure prediction using a language model-based deep learning approach](https://mlsanity.com/paper/2207.01586/) (2022)
- [SpiralFormer: Looped Transformers Can Learn Hierarchical Dependencies via Multi-Resolution Recursion](https://mlsanity.com/paper/2602.11698/) (2026)
- [Recursive Inference Scaling: A Winning Path to Scalable Inference in Language and Multimodal Systems](https://mlsanity.com/paper/2502.07503/) (2025)
- [Think Shallow, Solve Deep: Controlling Recurrent Dynamics for Reliable Test-Time Depth](https://mlsanity.com/paper/2608.18222/) (2026)
- [ncRNA Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1905.06515/) (2019)
- [DeepLoop: Depth Scaling for Looped Transformers](https://mlsanity.com/paper/2607.13491/) (2026)
- [Scalable Deep Learning for RNA Secondary Structure Prediction](https://mlsanity.com/paper/2307.10073/) (2023)

## Abstract (arXiv)

Biological function in RNA is encoded across scales, from local sequence motifs to long-range structural dependencies. Conventional RNA foundation models couple parameter capacity and inference depth within a fixed architecture, prescribing a fixed computation graph for each inference. Here we present Eco-RNA, an 80M-parameter RNA foundation model that makes inference depth adjustable through learned iterative refinement. Its shared, input-conditioned Transformer core refines sequence representations through repeated application. The iteration count is selected after training and controls effective depth at fixed model parameters. We train across recurrent depths with masked reconstruction, state regularization, and a one-sided loss that anchors deeper reconstruction to a shallow reference. On the 70-assay RNAGym fitness benchmark, increasing refinement from one to four iterations raises aggregate absolute Spearman correlation from 0.242 to 0.286, with the gain retained through eight iterations. At four iterations, Eco-RNA surpasses the current SOTA Evo 2 40B on all three aggregate fitness metrics despite 500x fewer parameters. Its iteration configurations advance the compute-performance Pareto frontier among the evaluated models. It also outperforms the evaluated baselines in non-coding RNA family classification, RNA secondary-structure prediction, and chemical probing profile prediction. These results establish internal inference computation as an effective scaling dimension for RNA foundation models.