% Key papers for Biological sequence transformers (scime atlas, https://atlas.scime.ai). Authors are not included: add them from the paper pages.

@inproceedings{icml2022_learning_40770,
  title = {{Learning inverse folding from millions of predicted structures}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2022},
  url = {https://icml.cc/virtual/2022/poster/16885},
}

@inproceedings{iclr2021_transformer_30519,
  title = {{Transformer protein language models are unsupervised structure learners}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2021},
  url = {https://iclr.cc/virtual/2021/poster/3016},
}

@inproceedings{iclr2021_bertology_30410,
  title = {{BERTology Meets Biology: Interpreting Attention in Protein Language Models}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2021},
  url = {https://iclr.cc/virtual/2021/poster/3057},
}

@inproceedings{iclr2024_saprot_33681,
  title = {{SaProt: Protein Language Modeling with Structure-aware Vocabulary}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/19394},
}

@inproceedings{neurips2019_levenshtein_58542,
  title = {{Levenshtein Transformer}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2019},
  url = {https://nips.cc/virtual/2019/poster/14112},
}

@inproceedings{iclr2024_dnabert_35250,
  title = {{DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genomes}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/17823},
}

@inproceedings{iclr2024_cellplm_33854,
  title = {{CellPLM: Pre-training of Cell Language Model Beyond Single Cells}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/19221},
}

@inproceedings{iclr2023_pifold_33175,
  title = {{PiFold: Toward effective and efficient protein inverse folding}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2023},
  url = {https://iclr.cc/virtual/2023/poster/11386},
}

@inproceedings{neurips2023_poet_66585,
  title = {{PoET: A generative model of protein families as sequences-of-sequences}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2023},
  url = {https://nips.cc/virtual/2023/poster/73032},
}

@inproceedings{neurips2017_plan_56571,
  title = {{Plan, Attend, Generate: Planning for Sequence-to-Sequence Models}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2017},
  url = {https://nips.cc/virtual/2017/poster/9322},
}

@inproceedings{neurips2021_co_62141,
  title = {{Co-evolution Transformer for Protein Contact Prediction}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2021},
  url = {https://nips.cc/virtual/2021/poster/27506},
}

@inproceedings{aaai2025_foldtoken_9215,
  title = {{FoldToken: Learning Protein Language via Vector Quantization and Beyond}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2025},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/31998},
}

@inproceedings{icml2022_retroformer_41090,
  title = {{Retroformer: Pushing the Limits of End-to-end Retrosynthesis Transformer}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2022},
  url = {https://icml.cc/virtual/2022/poster/18129},
}

@inproceedings{icml2024_multimodal_43386,
  title = {{Multimodal Prototyping for cancer survival prediction}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/35066},
}

@inproceedings{neurips2024_protein_72636,
  title = {{Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/94745},
}

@inproceedings{iclr2024_de_33781,
  title = {{De novo Protein Design Using Geometric Vector Field Networks}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/19294},
}

@inproceedings{aaai2026_nucel_99861,
  title = {{NucEL: Single-Nucleotide ELECTRA-Style Genomic Pre-training for Efficient and Interpretable Representations}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2026},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/36982},
}

@inproceedings{icml2024_vqdna_43727,
  title = {{VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2024},
  url = {https://icml.cc/virtual/2024/poster/34725},
}

@inproceedings{neurips2025_traversal_75498,
  title = {{Traversal Verification for Speculative Tree Decoding}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=8nOMhDFpkU},
}

@inproceedings{aaai2025_genauction_9309,
  title = {{GenAuction: A Generative Auction for Online Advertising}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2025},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/33348},
}

@inproceedings{icml2025_curriculum_47588,
  title = {{Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/45008},
}

@inproceedings{icml2025_ppdiff_48134,
  title = {{PPDiff: Diffusing in Hybrid Sequence-Structure Space for Protein-Protein Complex Design}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/44475},
}

@inproceedings{icml2026_dnahnet_49884,
  title = {{dnaHNet: A Scalable and Hierarchical Foundation Model for Genomic Sequence Learning}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=6pN2KNCspk},
}

@inproceedings{icml2026_ldarnet_55043,
  title = {{LDARNet: DNA Adaptive Representation Network with Learnable Tokenization for Genomic Modeling}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=v4hQnJn6aN},
}

@inproceedings{icml2026_induction_55090,
  title = {{Induction Meets Biology: Mechanisms of Repeat Detection in Protein Language Models}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=vPUInIYURl},
}

@inproceedings{neurips2025_stree_78008,
  title = {{STree: Speculative Tree Decoding for Hybrid State Space Models}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=a95Vd41o1u},
}

@inproceedings{iclr2026_patchdna_85078,
  title = {{PatchDNA: A Flexible and Biologically-Informed Alternative to Tokenization for DNA}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2026},
  url = {https://openreview.net/forum?id=AFZeojzjoG},
}

@inproceedings{neurips2026_lemon_93751,
  title = {{LEMON-ZEST: Evolution-Informed Tokenization for Efficient Protein Language Modeling}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2026},
  url = {https://neurips.cc/virtual/2026/poster/153755},
}

@inproceedings{cvpr2026_autoregressive_98575,
  title = {{AutoRegressive Generation with B-rep Holistic Token Sequence Representation}},
  booktitle = {IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  year = {2026},
  url = {https://openaccess.thecvf.com/content/CVPR2026/html/Li_AutoRegressive_Generation_with_B-rep_Holistic_Token_Sequence_Representation_CVPR_2026_paper.html},
}