# ProtSent: Protein Sentence Transformers

arXiv: https://arxiv.org/abs/2605.06830 · HTML: https://mlsanity.com/paper/2605.06830/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 29 references that are in the map.
- First posted on arXiv 7 May 2026.

## Builds on (most cited first, 4 of 4)

- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Making Monolingual Sentence Embeddings Multilingual using Knowledge Distillation](https://mlsanity.com/paper/2004.09813/) (2020)
- [Evaluating Protein Transfer Learning with TAPE](https://mlsanity.com/paper/1906.08230/) (2019)
- [Efficient Natural Language Response Suggestion for Smart Reply](https://mlsanity.com/paper/1705.00652/) (2017)

## Abstract (arXiv)

Protein language models (pLMs) produce per-residue representations that capture evolutionary and structural information, yet their mean-pooled sequence embeddings are not explicitly trained to reflect functional, evolutionary or structural similarity between proteins. We present Protein Sentence Transformers (ProtSent), a contrastive fine-tuning framework for adapting PLMs into general-purpose embedding models. ProtSent trains with MultipleNegativesRankingLoss across five protein-pair datasets: Pfam families, structurally derived hard negatives, AlphaFold DB structural pairs, and StringDB protein--protein interactions, and Deep Mutational Scanning data. We evaluate on 23~downstream tasks using frozen embeddings with a k-nearest-neighbor probe to measure embedding neighborhood quality. On ESM-2 150M, ProtSent improves 15 of 23 tasks, with gains of +105% on remote homology detection, +17% on variant effect prediction, and +19.9% Recall@1 on SCOPe-40 structural retrieval. The 35M variant improves 16 of 23 tasks with +40.5% on remote homology and +15.5% Recall@1 on SCOPe-40. Contrastive fine-tuning restructures the embedding space to better capture protein function and structure, without any task-specific supervision. We release the models, public data, and training recipe and code.