% Key papers for Generative latent models for single-cell data (scime atlas, https://atlas.scime.ai). Authors are not included: add them from the paper pages.

@inproceedings{iclr2018_syntax_28647,
  title = {{Syntax-Directed Variational Autoencoder for Structured Data}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2018},
  url = {https://iclr.cc/virtual/2018/poster/32},
}

@inproceedings{icml2016_dirichlet_35796,
  title = {{Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2016},
  url = {https://proceedings.mlr.press/v48/prabhakaran16.html},
}

@inproceedings{neurips2018_constrained_56964,
  title = {{Constrained Generation of Semantically Valid Graphs via Regularizing Variational Autoencoders}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2018},
  url = {https://nips.cc/virtual/2018/poster/11685},
}

@inproceedings{iclr2020_rna_29576,
  title = {{RNA Secondary Structure Prediction By Learning Unrolled Algorithms}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2020},
  url = {https://openreview.net/forum?id=S1eALyrYDH},
}

@inproceedings{aaai2021_panther_1134,
  title = {{PANTHER: Pathway Augmented Nonnegative Tensor Factorization for HighER-order Feature Learning}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2021},
  url = {https://aaai.org/papers/00371-panther-pathway-augmented-nonnegative-tensor-factorization-for-higher-order-feature-learning/},
}

@inproceedings{neurips2023_modelling_67389,
  title = {{Modelling Cellular Perturbations with the Sparse Additive Mechanism Shift Variational Autoencoder}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2023},
  url = {https://nips.cc/virtual/2023/poster/72340},
}

@inproceedings{aaai2024_constraint_5479,
  title = {{Constraint Latent Space Matters: An Anti-anomalous Waveform Transformation Solution from Photoplethysmography to Arterial Blood Pressure}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2024},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/28985},
}

@inproceedings{neurips2022_probabilistic_64932,
  title = {{Probabilistic Transformer: Modelling Ambiguities and Distributions for RNA Folding and Molecule Design}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2022},
  url = {https://nips.cc/virtual/2022/poster/53270},
}

@inproceedings{neurips2024_contrastive_73376,
  title = {{Contrastive losses as generalized models of global epistasis}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/94075},
}

@inproceedings{icml2021_ace_38998,
  title = {{ACE: Explaining cluster from an adversarial perspective}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2021},
  url = {https://icml.cc/virtual/2021/poster/10155},
}

@inproceedings{aaai2024_scalable_7260,
  title = {{Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2024},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/28943},
}

@inproceedings{neurips2024_phylogen_71387,
  title = {{PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/95863},
}

@inproceedings{icml2025_suica_47640,
  title = {{SUICA: Learning Super-high Dimensional Sparse Implicit Neural Representations for Spatial Transcriptomics}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/44957},
}

@inproceedings{neurips2021_amortized_63486,
  title = {{Amortized Synthesis of Constrained Configurations Using a Differentiable Surrogate}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2021},
  url = {https://nips.cc/virtual/2021/poster/26809},
}

@inproceedings{neurips2023_datasets_68255,
  title = {{Datasets and Benchmarks for Nanophotonic Structure and Parametric Design Simulations}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2023},
  url = {https://nips.cc/virtual/2023/poster/73583},
}

@inproceedings{iclr2024_automatic_34953,
  title = {{Automatic Functional Differentiation in JAX}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/18121},
}

@inproceedings{icml2023_beam_42021,
  title = {{Beam Tree Recursive Cells}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2023},
  url = {https://icml.cc/virtual/2023/poster/23660},
}

@inproceedings{icml2025_return_47450,
  title = {{Return of the Latent Space COWBOYS: Re-thinking the use of VAEs for Bayesian Optimisation of Structured Spaces}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/45143},
}

@inproceedings{icml2026_what_49775,
  title = {{What Makes a Representation Good for Single-Cell Perturbation Prediction?}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=5cLRC1hrTP},
}

@inproceedings{icml2026_modeling_50038,
  title = {{Modeling Temporal scRNA-seq Data with Latent Gaussian Process and Optimal Transport}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=8RE5i7g4uB},
}

@inproceedings{icml2026_efficient_50247,
  title = {{Efficient Synthetic Network Generation via Latent Embedding Reconstruction}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=AW0sphpLo7},
}

@inproceedings{icml2026_pepcompass_50947,
  title = {{PepCompass: Navigating Peptide Embedding Spaces Using Riemannian Geometry}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=HENUU9VR8F},
}

@inproceedings{icml2026_hdtree_54158,
  title = {{HDTree: Generative Modeling of Cellular Hierarchies for Robust Lineage Inference}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=mURSJDd7hU},
}

@inproceedings{icml2026_tree_54544,
  title = {{Tree-Structured Orthonormal Decomposition of the Aitchison Simplex}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=pws8t4kBP4},
}

@inproceedings{icml2026_exact_54567,
  title = {{Exact Functional ANOVA Decomposition for Categorical Inputs Models}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=qC9FEfYjai},
}

@inproceedings{icml2026_perturbdiff_55353,
  title = {{PerturbDiff: Functional Diffusion for Single-Cell Perturbation Modeling}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2026},
  url = {https://openreview.net/forum?id=yBAqonxCdp},
}

@inproceedings{neurips2025_equi_80265,
  title = {{Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=xs5aoDH3HX},
}

@inproceedings{neurips2026_discovering_91906,
  title = {{Discovering Mechanistic Models of Neural Activity: System Identification in an in Silico Zebrafish}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2026},
  url = {https://neurips.cc/virtual/2026/poster/149717},
}

@inproceedings{icml2025_feature_46328,
  title = {{Feature-Mapping Topology Optimization with Neural Heaviside Signed Distance Functions}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/46233},
}

@inproceedings{icml2025_reconstructing_46902,
  title = {{Reconstructing Cell Lineage Trees from Phenotypic Features with Metric Learning}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/45677},
}

@inproceedings{icml2025_wyckoff_48010,
  title = {{Wyckoff Transformer: Generation of Symmetric Crystals}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/44595},
}