# Splicing Up Your Predictions with RNA Contrastive Learning

arXiv: https://arxiv.org/abs/2310.08738 · HTML: https://mlsanity.com/paper/2310.08738/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 61 references that are in the map.
- First posted on arXiv 12 Oct 2023.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [mixup: Beyond Empirical Risk Minimization](https://mlsanity.com/paper/1710.09412/) (2017)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs](https://mlsanity.com/paper/1606.00915/) (2016)
- [CutMix: Regularization Strategy to Train Strong Classifiers with Localizable Features](https://mlsanity.com/paper/1905.04899/) (2019)
- [VICReg: Variance-Invariance-Covariance Regularization for Self-Supervised Learning](https://mlsanity.com/paper/2105.04906/) (2021)
- [A Cookbook of Self-Supervised Learning](https://mlsanity.com/paper/2304.12210/) (2023)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [Decoupled Contrastive Learning](https://mlsanity.com/paper/2110.06848/) (2021)
- [DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome](https://mlsanity.com/paper/2306.15006/) (2023)
- [On the duality between contrastive and non-contrastive self-supervised learning](https://mlsanity.com/paper/2206.02574/) (2022)
- [Pushing the limits of self-supervised ResNets: Can we outperform supervised learning without labels on ImageNet?](https://mlsanity.com/paper/2201.05119/) (2022)
- [Reverse Engineering Self-Supervised Learning](https://mlsanity.com/paper/2305.15614/) (2023)
- [Evolution Is All You Need: Phylogenetic Augmentation for Contrastive Learning](https://mlsanity.com/paper/2012.13475/) (2020)

## Abstract (arXiv)

In the face of rapidly accumulating genomic data, our understanding of the RNA regulatory code remains incomplete. Recent self-supervised methods in other domains have demonstrated the ability to learn rules underlying the data-generating process such as sentence structure in language. Inspired by this, we extend contrastive learning techniques to genomic data by utilizing functional similarities between sequences generated through alternative splicing and gene duplication. Our novel dataset and contrastive objective enable the learning of generalized RNA isoform representations. We validate their utility on downstream tasks such as RNA half-life and mean ribosome load prediction. Our pre-training strategy yields competitive results using linear probing on both tasks, along with up to a two-fold increase in Pearson correlation in low-data conditions. Importantly, our exploration of the learned latent space reveals that our contrastive objective yields semantically meaningful representations, underscoring its potential as a valuable initialization technique for RNA property prediction.