arXiv Machine Learning
TANGO: RNA Topology and Geometry Co-Design
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arXiv Machine Learning
3d ago
CocoRNA: Collective RNA Design with Cooperative Multi-agent Reinforcement Learning
CocoRNA is a cooperative multi-agent reinforcement learning framework that tackles RNA inverse design by breaking the problem into smaller sub‑problems solved collaboratively by multiple agents. A centralized critic provides global structural guidance during training, allowing the agents to jointly optimize their design strategies. Experiments on the Rfam dataset show that CocoRNA outperforms state‑of‑the‑art methods in both success rate and design speed, and additional tests on other biological sequence design tasks demonstrate its broad effectiveness.
arXiv Machine Learning
Sep 30
RNA Design via Conditioned Flow Matching and Finite-Policy Reinforcement Learning
arXiv:2609.36885v1 Announce Type: cross Abstract: RNA design aims to identify sequences that fold into specified secondary structures. Existing methods formulate the task as target-specific search or...
arXiv Machine Learning
Oct 12
MORAD: Reinforcement Learning with Multi-Objective Rewards for RNA Inverse Design
MORAD is an online reinforcement learning framework that trains a single shared policy for backbone‑conditioned RNA diffusion models, enabling structure‑conditioned RNA inverse design across diverse target backbones. It integrates backbone‑conditioned group sampling, group‑relative reward normalization, and a forward‑process diffusion objective, jointly optimizing six measurements—including tertiary geometry, base pairing, ensemble behavior, and sequence composition—by mapping each to a bounded desirability score and combining them with a weighted geometric mean. Compared to a tertiary‑structure‑only reward, MORAD improves 10 of 11 evaluation metrics, achieving significant gains in GDT‑TS, pairing MCC, and normalized ensemble defect, and surpasses existing methods such as RiboDiffusion, gRNAde, and RDesign on tertiary structural accuracy, secondary‑structure pairing, and thermodynamic quality.
arXiv Machine Learning
1d ago
Curriculum-Augmented GFlowNets For mRNA Sequence Generation
arXiv:2510.03811v2 Announce Type: replace Abstract: We develop an approach for the de novo synthesis of messenger RNA (mRNA) sequences encoding target proteins. This requires optimizing multiple biol...
arXiv AI
Oct 9
La-Ribo: RNA Co-Design via Geometry-Latent Flow Matching
La‑Ribo is a generative framework that jointly designs RNA nucleotide sequences and their three‑dimensional structures using geometry‑latent flow matching. It preserves a sparse phosphate‑sugar‑base scaffold while encoding nucleotide identity and local conformation in residue‑wise latent variables, which a shared flow network generates before an RNA‑specific decoder reconstructs all heavy atoms. The authors also built a large, quality‑controlled corpus of 168,561 RNA structures—combining experimental data with predictions from three folding models—to expand supervision, and demonstrate that La‑Ribo outperforms baselines in designability and co‑designability across sampling budgets and refolding models, while also enabling scaffold‑conditioned inverse folding without extra training.
arXiv Machine Learning
Oct 12
Scaling RNA Foundation Models through Iterative Refinement
Eco‑RNA is an 80‑million‑parameter RNA foundation model that introduces adjustable inference depth via learned iterative refinement. The shared, input‑conditioned Transformer core repeatedly refines sequence representations, with the number of iterations chosen after training to control effective depth. On the RNAGym fitness benchmark, increasing iterations from one to four improves Spearman correlation from 0.242 to 0.286, and at four iterations Eco‑RNA outperforms the 40‑billion‑parameter Evo 2 model across all aggregate fitness metrics, while also excelling in non‑coding RNA classification, secondary‑structure prediction, and chemical probing profile prediction.