% Key papers for Brain and biological graph learning (scime atlas, https://atlas.scime.ai). Authors are not included: add them from the paper pages.

@inproceedings{aaai2020_learning_100227,
  title = {{Learning the Graphical Structure of Electronic Health Records with Graph Convolutional Transformer}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2020},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/5400},
}

@inproceedings{cvpr2020_predicting_16057,
  title = {{Predicting Lymph Node Metastasis Using Histopathological Images Based on Multiple Instance Learning With Deep Graph Convolution}},
  booktitle = {IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  year = {2020},
}

@inproceedings{cvpr2018_deep_12972,
  title = {{Deep Lesion Graphs in the Wild: Relationship Learning and Organization of Significant Radiology Image Findings in a Diverse Large-Scale Lesion Database}},
  booktitle = {IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  year = {2018},
  url = {https://openaccess.thecvf.com/content_cvpr_2018/html/Yan_Deep_Lesion_Graphs_CVPR_2018_paper.html},
}

@inproceedings{aaai2022_zinb_2963,
  title = {{ZINB-Based Graph Embedding Autoencoder for Single-Cell RNA-Seq Interpretations}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2022},
  url = {https://aaai.org/papers/04671-zinb-based-graph-embedding-autoencoder-for-single-cell-rna-seq-interpretations/},
}

@inproceedings{cvpr2021_quantifying_17683,
  title = {{Quantifying Explainers of Graph Neural Networks in Computational Pathology}},
  booktitle = {IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  year = {2021},
}

@inproceedings{cvpr2019_adaptively_13830,
  title = {{Adaptively Connected Neural Networks}},
  booktitle = {IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  year = {2019},
}

@inproceedings{iclr2022_self_31608,
  title = {{Self-Supervised Graph Neural Networks for Improved Electroencephalographic Seizure Analysis}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2022},
  url = {https://iclr.cc/virtual/2022/poster/7027},
}

@inproceedings{aaai2019_affinitynet_100190,
  title = {{AffinityNet: Semi-Supervised Few-Shot Learning for Disease Type Prediction}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2019},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/3898},
}

@inproceedings{neurips2022_brain_63751,
  title = {{Brain Network Transformer}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2022},
  url = {https://nips.cc/virtual/2022/poster/54219},
}

@inproceedings{aaai2018_multi_100324,
  title = {{Multi-View Multi-Graph Embedding for Brain Network Clustering Analysis}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2018},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/11288},
}

@inproceedings{aaai2023_self_4650,
  title = {{Self-Supervised Graph Learning for Long-Tailed Cognitive Diagnosis}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2023},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/25082},
}

@inproceedings{cvpr2020_sequential_16229,
  title = {{Sequential Motif Profiles and Topological Plots for Offline Signature Verification}},
  booktitle = {IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)},
  year = {2020},
}

@inproceedings{aaai2021_gaining_652,
  title = {{Gaining Insight into SARS-CoV-2 Infection and COVID-19 Severity Using Self-supervised Edge Features and Graph Neural Networks}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2021},
  url = {https://aaai.org/papers/04864-gaining-insight-into-sars-cov-2-infection-and-covid-19-severity-using-self-supervised-edge-features-and-graph-neural-networks/},
}

@inproceedings{aaai2021_a_55,
  title = {{A Theory of Independent Mechanisms for Extrapolation in Generative Models}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2021},
  url = {https://aaai.org/papers/06741-a-theory-of-independent-mechanisms-for-extrapolation-in-generative-models/},
}

@inproceedings{neurips2023_muse_66781,
  title = {{MuSe-GNN: Learning Unified Gene Representation From Multimodal Biological Graph Data}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2023},
  url = {https://nips.cc/virtual/2023/poster/72853},
}

@inproceedings{aaai2024_cell_5391,
  title = {{Cell Graph Transformer for Nuclei Classification}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2024},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/28179},
}

@inproceedings{neurips2021_learning_63164,
  title = {{Learning Semantic Representations to Verify Hardware Designs}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2021},
  url = {https://nips.cc/virtual/2021/poster/28488},
}

@inproceedings{aaai2021_rna_1227,
  title = {{RNA Secondary Structure Representation Network for RNA-proteins Binding Prediction}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2021},
  url = {https://aaai.org/papers/00362-rna-secondary-structure-representation-network-for-rna-proteins-binding-prediction/},
}

@inproceedings{aaai2024_unsupervised_7718,
  title = {{Unsupervised Gene-Cell Collective Representation Learning with Optimal Transport}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2024},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/27789},
}

@inproceedings{aaai2025_cg_8342,
  title = {{CG-TGAN: Conditional Generative Adversarial Networks with Graph Neural Networks for Tabular Data Synthesizing}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2025},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/33996},
}

@inproceedings{aaai2024_robust_7177,
  title = {{Robust Stochastic Graph Generator for Counterfactual Explanations}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2024},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/30149},
}

@inproceedings{aaai2024_dr_5575,
  title = {{DR-Label: Label Deconstruction and Reconstruction of GNN Models for Catalysis Systems}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2024},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/29471},
}

@inproceedings{aaai2025_dusted_8628,
  title = {{DUSTED: Dual-Attention Enhanced Spatial Transcriptomics Denoiser}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2025},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/32110},
}

@inproceedings{aaai2026_learning_99841,
  title = {{Learning Structurally Stabilized Representations for Lossless DNA Storage}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2026},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/36962},
}

@inproceedings{icml2025_modeling_48092,
  title = {{Modeling All-Atom Glycan Structures via Hierarchical Message Passing and Multi-Scale Pre-training}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/44516},
}

@inproceedings{neurips2024_deepite_71337,
  title = {{DeepITE: Designing Variational Graph Autoencoders for Intervention Target Estimation}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/95911},
}

@inproceedings{neurips2024_gene_73308,
  title = {{Gene-Gene Relationship Modeling Based on Genetic Evidence for Single-Cell RNA-Seq Data Imputation}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/94136},
}

@inproceedings{neurips2025_mihc_77851,
  title = {{MIHC: Multi-View Interpretable Hypergraph Neural Networks with Information Bottleneck for Chip Congestion Prediction}},
  booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
  year = {2025},
  url = {https://openreview.net/forum?id=YFQ0Xx5YlW},
}

@inproceedings{iclr2026_a_86424,
  title = {{A Brain Graph Foundation Model: Pre-Training and Prompt-Tuning across Broad Atlases and Disorders}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2026},
  url = {https://openreview.net/forum?id=PeGHkAaRxs},
}

@inproceedings{aaai2026_when_99926,
  title = {{When Genes Speak: A Semantic-Guided Framework for Spatially Resolved Transcriptomics Data Clustering}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2026},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/37047},
}

@inproceedings{aaai2026_kclnet_100058,
  title = {{KCLNet: Electrically Equivalence-Oriented Graph Representation Learning for Analog Circuits}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2026},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/37109},
}

@inproceedings{aaai2026_giim_104303,
  title = {{GIIM: Graph-based Learning of Inter- and Intra-view Dependencies for Multi-view Medical Image Diagnosis}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2026},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/37830},
}

@inproceedings{aaai2026_brainhgt_106510,
  title = {{BrainHGT: A Hierarchical Graph Transformer for Interpretable Brain Network Analysis}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2026},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/38817},
}

@inproceedings{aaai2025_disentangled_8763,
  title = {{Disentangled Table-Graph Representation for Interpretable Transmission Line Fault Location}},
  booktitle = {AAAI Conference on Artificial Intelligence (AAAI)},
  year = {2025},
  url = {https://ojs.aaai.org/index.php/AAAI/article/view/32083},
}

@inproceedings{iclr2024_neural_33482,
  title = {{Neural Architecture Retrieval}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/19593},
}

@inproceedings{iclr2024_encoding_35527,
  title = {{Encoding Unitig-level Assembly Graphs with Heterophilous Constraints for Metagenomic Contigs Binning}},
  booktitle = {International Conference on Learning Representations (ICLR)},
  year = {2024},
  url = {https://iclr.cc/virtual/2024/poster/17546},
}

@inproceedings{icml2025_neurotree_47933,
  title = {{NeuroTree: Hierarchical Functional Brain Pathway Decoding for Mental Health Disorders}},
  booktitle = {International Conference on Machine Learning (ICML)},
  year = {2025},
  url = {https://icml.cc/virtual/2025/poster/44671},
}