# Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers

arXiv: https://arxiv.org/abs/2411.08909 · HTML: https://mlsanity.com/paper/2411.08909/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Core SSM architectures for language, one of 10 directions in State-space sequence models (S4, Mamba).
- Builds on 58 of its 120 references that are in the map.
- First posted on arXiv 29 Oct 2024.

## Placed in

- State-space sequence models (S4, Mamba) / [Core SSM architectures for language](https://mlsanity.com/ssm/core-ssm-architectures-for-language/)

## Builds on (most cited first, 30 of 58)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention](https://mlsanity.com/paper/2006.16236/) (2020)
- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Transformers are SSMs: Generalized Models and Efficient Algorithms Through Structured State Space Duality](https://mlsanity.com/paper/2405.21060/) (2024)
- [Vision Mamba: Efficient Visual Representation Learning with Bidirectional State Space Model](https://mlsanity.com/paper/2401.09417/) (2024)
- [Link Prediction Based on Graph Neural Networks](https://mlsanity.com/paper/1802.09691/) (2018)
- [RWKV: Reinventing RNNs for the Transformer Era](https://mlsanity.com/paper/2305.13048/) (2023)
- [How Contextual are Contextualized Word Representations? Comparing the Geometry of BERT, ELMo, and GPT-2 Embeddings](https://mlsanity.com/paper/1909.00512/) (2019)
- [HiPPO: Recurrent Memory with Optimal Polynomial Projections](https://mlsanity.com/paper/2008.07669/) (2020)
- [DeepGCNs: Can GCNs Go as Deep as CNNs?](https://mlsanity.com/paper/1904.03751/) (2019)
- [Masked Label Prediction: Unified Message Passing Model for Semi-Supervised Classification](https://mlsanity.com/paper/2009.03509/) (2020)
- [Hungry Hungry Hippos: Towards Language Modeling with State Space Models](https://mlsanity.com/paper/2212.14052/) (2022)
- [Jamba: A Hybrid Transformer-Mamba Language Model](https://mlsanity.com/paper/2403.19887/) (2024)
- [Hyena Hierarchy: Towards Larger Convolutional Language Models](https://mlsanity.com/paper/2302.10866/) (2023)
- [Massive Activations in Large Language Models](https://mlsanity.com/paper/2402.17762/) (2024)
- [Representation Degeneration Problem in Training Natural Language Generation Models](https://mlsanity.com/paper/1907.12009/) (2019)
- [Benefits of depth in neural networks](https://mlsanity.com/paper/1602.04485/) (2016)
- [DeeperGCN: All You Need to Train Deeper GCNs](https://mlsanity.com/paper/2006.07739/) (2020)
- [Evaluating Protein Transfer Learning with TAPE](https://mlsanity.com/paper/1906.08230/) (2019)
- [LinkBERT: Pretraining Language Models with Document Links](https://mlsanity.com/paper/2203.15827/) (2022)
- [Simple linear attention language models balance the recall-throughput tradeoff](https://mlsanity.com/paper/2402.18668/) (2024)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [An Empirical Study of Mamba-based Language Models](https://mlsanity.com/paper/2406.07887/) (2024)

## Built on by (most cited first, 1 of 1)

- [Language Models for Controllable DNA Sequence Design](https://mlsanity.com/paper/2507.19523/) (2025)

## Abstract (arXiv)

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built upon selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and up to 30% and 16% improvements on protein downstream tasks compared to Transformer-based ESM-2 when trained with 100B and 1T tokens, respectively. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g., structured state space models) in learning universal protein representations and incorporating molecular interaction contexts contained in biological graphs.