Publications by Year

@misc{pal_improving_2026, title = {Improving RCT-Based CATE Estimation Under Covariate Mismatch via Double Calibration}, author = {Samhita Pal and Jared D. Huling and Amir Asiaee}, year = {2026}, eprint = {2603.17066}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2603.17066}, }

@misc{mallal_keystone_2026-1, title = {Keystone Epitope Theory in Deep Time: How Viral Endogenization and Sexual Dimorphism Wrote the Genomic Syllabus of Immunity.}, author = {Simon Mallal and Amir Asiaee and Elizabeth Phillips}, year = {2026}, publisher = {Zenodo}, doi = {10.5281/zenodo.18520426}, url = {https://zenodo.org/records/18520426}, }

@article{mallal_keystone_2026, title = {Keystone Epitope Theory: Implications for the Investigation of Multiple Sclerosis}, author = {Simon Mallal and Amir Asiaee and Natalie Mallal and Elizabeth Phillips}, year = {2026}, publisher = {Zenodo}, doi = {10.5281/zenodo.18520804}, url = {https://zenodo.org/records/18520804}, }

@article{asiaee_widespread_2026, title = {Widespread data leakage inflates accuracy and corrupts biomarker discovery in cancer drug response prediction}, author = {Amir Asiaee and Jared Strauch and Leila Azinfar and Samhita Pal and Heather H. Pua and James P. Long and Kevin R. Coombes}, year = {2026}, journal = {bioRxiv}, doi = {10.64898/2026.02.05.704016}, url = {https://doi.org/10.64898/2026.02.05.704016}, }

@inproceedings{asiaee_sharp_2026, title = {Sharp Bounds for Treatment Effect Generalization under Outcome Distribution Shift}, author = {Amir Asiaee and Samhita Pal and Cole Beck and Jared D. Huling}, year = {2026}, booktitle = {5th Conference on Causal Learning and Reasoning (CLeaR)}, eprint = {2602.09595}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2602.09595}, }

@article{asiaee_shape-constrained_2026, title = {A shape-constrained regression and wild bootstrap framework for reproducible drug synergy testing}, author = {Amir Asiaee and James P. Long and Samhita Pal and Heather H. Pua and Kevin R. Coombes}, year = {2026}, journal = {bioRxiv}, doi = {10.64898/2026.02.05.704019}, url = {https://doi.org/10.64898/2026.02.05.704019}, }

@misc{asiaee_risk-equalized_2026, title = {Risk-Equalized Differentially Private Synthetic Data: Protecting Outliers by Controlling Record-Level Influence}, author = {Amir Asiaee and Chao Yan and Zachary B. Abrams and Bradley A. Malin}, year = {2026}, publisher = {arXiv}, doi = {10.48550/arXiv.2602.10232}, eprint = {2602.10232}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2602.10232}, }

@misc{asiaee_prism_2026, title = {PRISM: Differentially Private Synthetic Data with Structure-Aware Budget Allocation for Prediction}, author = {Amir Asiaee and Chao Yan and Zachary B. Abrams and Bradley A. Malin}, year = {2026}, publisher = {arXiv}, doi = {10.48550/arXiv.2602.10228}, eprint = {2602.10228}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2602.10228}, }

@misc{asiaee_partial_2026, title = {Partial Causal Structure Learning for Valid Selective Conformal Inference under Interventions}, author = {Amir Asiaee and Kavey Aryan and James P. Long}, year = {2026}, eprint = {2603.02204}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2603.02204}, }

@misc{asiaee_omittedvariable_2026, title = {Omitted-Variable Sensitivity Analysis for Generalizing Randomized Trials}, author = {Amir Asiaee and Samhita Pal and Jared D. Huling}, year = {2026}, eprint = {2603.27788}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2603.27788}, }

@misc{asiaee_noisecalibrated_2026, title = {Noise-Calibrated Inference from Differentially Private Sufficient Statistics in Exponential Families}, author = {Amir Asiaee and Samhita Pal}, year = {2026}, eprint = {2603.02010}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2603.02010}, }

@misc{asiaee_improving_2026, title = {Improving RCT-Based CATE Estimation Under Covariate Mismatch via Calibrated Alignment}, author = {Amir Asiaee and Samhita Pal}, year = {2026}, eprint = {2603.19186}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2603.19186}, }

@misc{asiaee_fix_2026, title = {Fix Representation (Optimally) Before Fairness: Finite-Sample Shrinkage Population Correction and the True Price of Fairness Under Subpopulation Shift}, author = {Amir Asiaee and Kaveh Aryan}, year = {2026}, journal = {arXiv}, eprint = {2602.05707}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2602.05707}, }

@misc{asiaee_fairness_2026, title = {Fairness Under Group-Conditional Prior Probability Shift: Invariance, Drift, and Target-Aware Post-Processing}, author = {Amir Asiaee and Kaveh Aryan}, year = {2026}, journal = {arXiv}, eprint = {2602.05144}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2602.05144}, }

@misc{asiaee_efficient_2026, title = {Efficient Discovery of Approximate Causal Abstractions via Neural Mechanism Sparsification}, author = {Amir Asiaee}, year = {2026}, eprint = {2602.24266}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2602.24266}, }

@misc{asiaee_causalwrap_2026, title = {CausalWrap: Model-Agnostic Causal Constraint Wrappers for Tabular Synthetic Data}, author = {Amir Asiaee and Zhuohui J. Liang and Chao Yan}, year = {2026}, eprint = {2603.02015}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2603.02015}, }

@article{zhu_auprc_2025, title = {AUPRC: a metric for evaluating the performance of in-silico perturbation methods in identifying differentially expressed genes}, author = {Hongxu Zhu and Amir Asiaee and Leila Azinfar and Jun Li and Han Liang and Ehsan Irajizad and Kim-Anh Do and James P. Long}, year = {2025}, journal = {Briefings in bioinformatics}, volume = {26}, number = {5}, pages = {bbaf426}, url = {https://academic.oup.com/bib/article-abstract/26/5/bbaf426/8245187}, }

@misc{pal_dag_2025, title = {DAG DECORation: Continuous Optimization for Structure Learning under Hidden Confounding}, author = {Samhita Pal and James O'quinn and Kaveh Aryan and Heather Pua and James P. Long and Amir Asiaee}, year = {2025}, publisher = {arXiv}, doi = {10.48550/arXiv.2510.02117}, eprint = {2510.02117}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2510.02117}, }

@article{mukherjee_immune_2025, title = {Immune checkpoint inhibitors as independent and synergistic drivers of SJS/TEN}, author = {Eric Milan Mukherjee and Dodie Park and Amir Asiaee and Matthew S. Krantz and Cosby A. Stone Jr and Michelle Martin-Pozo and Elizabeth Phillips}, year = {2025}, journal = {JAMA oncology}, volume = {11}, number = {12}, pages = {1542--1545}, url = {https://jamanetwork.com/journals/jamaoncology/article-abstract/2840512}, }

@misc{mukherjee_demographics_2025, title = {Demographics, Overlap, and Latency of Severe Cutaneous Adverse Reactions in an FDA Database}, author = {Eric M. Mukherjee and Dodie Park and Amir Asiaee and Matthew S. Krantz and Cosby A. Stone and Michelle Martin-Pozo and Elizabeth Jane Phillips}, year = {2025}, journal = {medRxiv}, doi = {10.1101/2025.03.05.25323441}, url = {https://www.medrxiv.org/content/10.1101/2025.03.05.25323441v4}, }

@article{mallal_keystone_2025-1, title = {Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability}, author = {Simon Mallal and Amir Asiaee}, year = {2025}, journal = {Zenodo}, doi = {10.5281/zenodo.17087093}, url = {https://www.amirasiaee.com/publications/mallal_keystone_2025-1.pdf}, }

@article{mallal_keystone_2025, title = {Keystone Epitope Theory: An Ecological Perspective on RNA Viruses, Tumor Immunoediting, and Vaccine Design}, author = {Simon Mallal and Amir Asiaee}, year = {2025}, journal = {Zenodo}, doi = {10.5281/zenodo.17915417}, url = {https://www.amirasiaee.com/publications/mallal_keystone_2025.pdf}, }

@misc{liang_generating_2025, title = {Generating Synthetic Multi-national Longitudinal Cohorts for Clinically Grounded HIV Research}, author = {Zhuohui J. Liang and Zhuohang Li and Nicholas J. Jackson and Yanink Caro-Vega and Ronaldo I. Moreira and Fabio Paredes and Jordany Bernadin and Diana Varela and Carina Cesar and Alessandro Blasimme and Jessica M. Perkins and Amir Asiaee and Stephany N. Duda and Bradley A. Malin and Bryan E. Shepherd and Chao Yan}, year = {2025}, journal = {medRxiv}, doi = {10.1101/2025.11.14.25340245}, url = {https://www.medrxiv.org/content/10.1101/2025.11.14.25340245v1}, }

@article{asiaee_transcriptome_2025, title = {Transcriptome Complexity Disentangled: A Regulatory Molecules Approach}, author = {Amir Asiaee and Zachary B. Abrams and Heather H. Pua and Kevin R. Coombes}, year = {2025}, journal = {International journal of molecular sciences}, volume = {26}, number = {6}, pages = {2510}, url = {https://www.mdpi.com/1422-0067/26/6/2510}, }

@misc{asiaee_improving_2025, title = {Improving Precision of RCT-Based CATE Estimation using Data Borrowing with Double Calibration}, author = {Amir Asiaee and Chiara Di Gravio and Cole Beck and Yuting Mei and Samhita Pal and Jared D. Huling}, year = {2025}, publisher = {arXiv}, doi = {10.48550/arXiv.2306.17478}, eprint = {2306.17478}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2306.17478}, }

@article{asiaee_co-evolved_2025, title = {Co-evolved Partners of Immunity: A Trait-Based Map of Human Keystone Organisms}, author = {Amir Asiaee and Natalie Mallal and Elizabeth Phillips and Simon Mallal}, year = {2025}, journal = {bioRxiv}, doi = {10.1101/2025.08.19.671142}, url = {https://doi.org/10.1101/2025.08.19.671142}, }

@misc{asiaee_causal_2025, title = {Causal Discovery with Mixed Latent Confounding via Precision Decomposition}, author = {Amir Asiaee and Samhita Pal and James O'quinn and James P. Long}, year = {2025}, journal = {arXiv}, eprint = {2512.24696}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2512.24696}, }

@article{strauch_improving_2024, title = {Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning}, author = {Jared Strauch and Amir Asiaee}, year = {2024}, journal = {bioRxiv}, doi = {10.1101/2024.05.09.593186}, url = {https://doi.org/10.1101/2024.05.09.593186}, }

@article{obodo_quantifying_2024, title = {Quantifying Differential Rhythmicity based on Effect Sizes with LimoRhyde2}, author = {Dora Obodo and Amir Asiaee}, year = {2024}, journal = {bioRxiv}, doi = {10.1101/2024.05.09.593377}, url = {https://doi.org/10.1101/2024.05.09.593377}, }

@misc{asiaee_high_2023, title = {High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient}, author = {Amir Asiaee and Samet Oymak and Kevin R. Coombes and Arindam Banerjee}, year = {2023}, publisher = {arXiv}, doi = {10.48550/arXiv.1806.04047}, url = {http://arxiv.org/abs/1806.04047}, }

@article{nicol_sith_2022, title = {SITH : An R package for visualizing and analyzing a spatial model of intratumor heterogeneity}, author = {Phillip B. Nicol and Dániel L. Barabási and Kevin R. Coombes and Amir Asiaee}, year = {2022}, journal = {Computational and Systems Oncology}, volume = {2}, number = {2}, pages = {e1033}, doi = {10.1002/cso2.1033}, url = {https://onlinelibrary.wiley.com/doi/10.1002/cso2.1033}, }

@article{nicol_oncogenetic_2021, title = {Oncogenetic network estimation with disjunctive Bayesian networks}, author = {Phillip B. Nicol and Kevin R. Coombes and Courtney Deaver and Oksana Chkrebtii and Subhadeep Paul and Amanda E. Toland and Amir Asiaee}, year = {2021}, journal = {Computational and Systems Oncology}, volume = {1}, number = {2}, pages = {e1027}, doi = {10.1002/cso2.1027}, url = {https://onlinelibrary.wiley.com/doi/10.1002/cso2.1027}, }

@article{asiaee_explaining_2020, title = {Explaining Gene Expression Using Twenty-One MicroRNAs}, author = {Amir Asiaee and Zachary B. Abrams and Samantha Nakayiza and Deepa Sampath and Kevin R. Coombes}, year = {2020}, journal = {Journal of Computational Biology}, volume = {27}, number = {7}, pages = {1157--1170}, doi = {10.1089/cmb.2019.0321}, url = {https://www.liebertpub.com/doi/10.1089/cmb.2019.0321}, }

@article{cho_elastic_2019, title = {Elastic Statistical Shape Analysis of Biological Structures with Case Studies: A Tutorial}, author = {Min Ho Cho and Amir Asiaee and Sebastian Kurtek}, year = {2019}, journal = {Bulletin of Mathematical Biology}, volume = {81}, number = {7}, pages = {2052--2073}, doi = {10.1007/s11538-019-00609-w}, url = {http://link.springer.com/10.1007/s11538-019-00609-w}, }

@inproceedings{asiaee_data_2019, title = {Data enrichment: Multi-task learning in high dimension with theoretical guarantees}, author = {Amir Asiaee and Samet Oymak and Kevin R. Coombes and Arindam Banerjee}, year = {2019}, booktitle = {Adaptive and Multitask Learning Workshop at the ICML. IMLS, Long Beach, CA}, url = {https://openreview.net/forum?id=Byx1S9Bj3N}, }

@article{abrams_thirty_2018, title = {Thirty biologically interpretable clusters of transcription factors distinguish cancer type}, author = {Zachary B. Abrams and Mark Zucker and Min Wang and Amir Asiaee Taheri and Lynne V. Abruzzo and Kevin R. Coombes}, year = {2018}, journal = {BMC Genomics}, volume = {19}, number = {1}, pages = {738}, doi = {10.1186/s12864-018-5093-z}, url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5093-z}, }

@inproceedings{golnari_revisiting_2015, title = {Revisiting non-progressive influence models: scalable influence maximization in social networks}, author = {Golshan Golnari and Asiaee T. Amir and Arindam Banerjee and Zhi-Li Zhang}, year = {2015}, booktitle = {Proceedings of the Thirty-First Conference on Uncertainty in Artificial Intelligence}, pages = {316--325}, }

@inproceedings{asiaee_taheri_influence_2013, title = {Influence maximization for informed agents in collective behavior}, author = {Amir Asiaee Taheri and Mohammad Afshar and Masoud Asadpour}, year = {2013}, booktitle = {Distributed Autonomous Robotic Systems: The 10th International Symposium}, pages = {389--402}, }

@inproceedings{asiaee_t_if_2012, title = {If you are happy and you know it... tweet}, author = {Amir Asiaee T. and Mariano Tepper and Arindam Banerjee and Guillermo Sapiro}, year = {2012}, booktitle = {Proceedings of the 21st ACM international conference on Information and knowledge management}, pages = {1602--1606}, doi = {10.1145/2396761.2398481}, url = {https://dl.acm.org/doi/10.1145/2396761.2398481}, }