Publications

@article{strauch_tissue-aware_2026, title = {Tissue-aware elastic net decomposition reveals shared and lineage-specific drug response biomarkers}, author = {Jared Strauch and Leila Azinfar and Heather H. Pua and James P. Long and Kevin R. Coombes and Amir Asiaee}, year = {2026}, journal = {bioRxiv}, doi = {10.64898/2026.06.21.733619}, url = {https://www.biorxiv.org/content/10.64898/2026.06.21.733619v1}, }

@article{ratchataswan_multiple_2026, title = {Multiple Antibiotic Allergy Evaluation Strategy (MAAES): A Comparative Effectiveness Study}, author = {Thanaporn Ratchataswan and Rebecca Lee and Amir Asiaee and Matthew S. Krantz and Grace Koo and Cosby A. Stone and Elizabeth J. Phillips}, year = {2026}, journal = {The Journal of Allergy and Clinical Immunology: In Practice}, doi = {10.1016/j.jaip.2026.07.005}, url = {https://doi.org/10.1016/j.jaip.2026.07.005}, }

@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}, }

@article{mukherjee_immune_2026, title = {Immune checkpoint blockade reshapes drug-associated toxicity: a pharmacovigilance atlas of drug-ICI interactions}, author = {Eric M. Mukherjee and Amir Asiaee and Dodi Park and Matthew S. Krantz and Cosby A. Stone and Michelle Martin-Pozo and Elizabeth J. Phillips}, year = {2026}, journal = {medRxiv}, doi = {10.64898/2026.08.31.26361880}, url = {https://www.medrxiv.org/content/10.64898/2026.08.31.26361880v3}, }

@article{mukherjee_host_2026, title = {HIV as a Host Susceptibility State for Severe Drug Hypersensitivity: Disentangling Biological Susceptibility from Drug Exposure in the FAERS Database}, author = {Eric M. Mukherjee and Dodi Park and Amir Asiaee and Matthew S. Krantz and Cosby A. Stone and Michelle Martin-Pozo and Elizabeth J. Phillips}, year = {2026}, journal = {medRxiv}, doi = {10.64898/2026.07.07.26356279}, url = {https://www.medrxiv.org/content/10.64898/2026.07.07.26356279v1}, }

@article{mallal_keystone_2026-2, title = {Keystone Epitope Theory: Implications for Hypersensitivity, Autoimmunity, and Transplantation}, author = {Simon Mallal and Amir Asiaee and Elizabeth Phillips}, year = {2026}, journal = {Pathogens and Immunity}, volume = {11}, number = {2}, pages = {16--38}, doi = {10.20411/pai.v11i2.1016}, url = {https://doi.org/10.20411/pai.v11i2.1016}, }

@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.18520425}, url = {https://zenodo.org/records/18520426}, }

@misc{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.18520803}, url = {https://zenodo.org/records/21971415}, }

@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 = {2026}, journal = {Pathogens and Immunity}, volume = {11}, number = {2}, pages = {39--65}, doi = {10.20411/pai.v11i1.1011}, url = {https://doi.org/10.20411/pai.v11i1.1011}, }

@misc{mallal_association_2026, title = {From HLA Association to Tissue Injury: Lessons from Drug Hypersensitivity and Multiple Sclerosis}, author = {Simon Mallal and Amir Asiaee and Elizabeth Phillips}, year = {2026}, publisher = {Zenodo}, doi = {10.5281/zenodo.21940980}, url = {https://zenodo.org/records/21940981}, }

@article{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 Kevin H. Guo 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 = {2026}, journal = {Nature Communications}, volume = {17}, number = {1}, pages = {7857}, doi = {10.1038/s41467-026-74492-0}, url = {https://www.nature.com/articles/s41467-026-74492-0}, }

@inproceedings{asiaee_workload-preserving_2026, title = {Workload-Preserving Differentially Private Synthetic Data for Causal Inference via Maximum-Entropy Calibration}, author = {Amir Asiaee and Kaveh Aryan}, year = {2026}, booktitle = {Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI)}, volume = {337}, pages = {133--160}, eprint = {2607.08122}, archivePrefix = {arXiv}, url = {https://proceedings.mlr.press/v337/asiaee26a.html}, }

@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 = {Proceedings of the 5th Conference on Causal Learning and Reasoning (CLeaR)}, volume = {323}, pages = {1572--1603}, eprint = {2602.09595}, archivePrefix = {arXiv}, url = {https://proceedings.mlr.press/v323/asiaee26a.html}, }

@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_projected_2026, title = {Projected Boosting with Fairness Constraints: Quantifying the Cost of Fair Training Distributions}, author = {Amir Asiaee and Kaveh Aryan}, year = {2026}, journal = {arXiv}, eprint = {2602.05713}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2602.05713}, }

@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}, }

@inproceedings{asiaee_partial_2026, title = {Partial Causal Structure Learning for Valid Selective Conformal Inference under Interventions}, author = {Amir Asiaee and Kaveh Aryan and James P. Long}, year = {2026}, booktitle = {Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI)}, volume = {337}, pages = {161--184}, eprint = {2603.02204}, archivePrefix = {arXiv}, url = {https://proceedings.mlr.press/v337/asiaee26b.html}, }

@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}, }

@inproceedings{asiaee_improving_2026, title = {Improving RCT-Based Treatment Effect Estimation Under Covariate Mismatch via Calibrated Alignment}, author = {Amir Asiaee and Samhita Pal}, year = {2026}, booktitle = {Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI)}, volume = {337}, pages = {185--209}, eprint = {2603.19186}, archivePrefix = {arXiv}, url = {https://proceedings.mlr.press/v337/asiaee26c.html}, }

@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 = {Causal Mechanism Reduction: Mechanism Replacement for Neural Network Pruning and Abstraction}, author = {Amir Asiaee}, year = {2026}, journal = {arXiv}, eprint = {2602.24266}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2602.24266}, }

@article{asiaee_context-dependent_2026, title = {Context-dependent correlations mislead transcriptomic network inference in bulk and single-cell data}, author = {Amir Asiaee and Polina Bombina and Reginald L. McGee and Jake Reed and Zachary B. Abrams and Lynne V. Abruzzo and Kevin R. Coombes}, year = {2026}, journal = {bioRxiv}, doi = {10.64898/2026.06.23.733936}, url = {https://www.biorxiv.org/content/10.64898/2026.06.23.733936v1}, }

@inproceedings{asiaee_certified_2026, title = {Certified Interventional Fidelity: Anytime-Valid, Adaptive Evaluation of Causal Claims in Mechanistic Interpretability}, author = {Amir Asiaee}, year = {2026}, booktitle = {Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI)}, volume = {337}, pages = {210--227}, eprint = {2607.08349}, archivePrefix = {arXiv}, url = {https://proceedings.mlr.press/v337/asiaee26d.html}, }

@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}, }

@misc{asiaee_bcalm_2026, title = {B-CALM: Bias-Limited Bayesian Borrowing for RCT-Anchored Treatment Effects under Covariate Mismatch}, author = {Amir Asiaee and Samhita Pal}, year = {2026}, journal = {arXiv}, eprint = {2607.04036}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/2607.04036}, }

@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}, }

@misc{mallal_keystone_2025-1, title = {Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability}, author = {Simon Mallal and Amir Asiaee}, year = {2025}, publisher = {Zenodo}, doi = {10.5281/zenodo.17087092}, url = {https://zenodo.org/records/17087093}, }

@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}, }

@inproceedings{akhondzadeh_learning_2020, title = {Learning Cancer Progression Network from Mutation Allele Frequencies}, author = {Mohammad Sadegh Akhondzadeh and Alireza Omidi and Zeinab Maleki and Kevin Coombes and Amanda E. Toland and Amir Asiaee}, year = {2020}, booktitle = {Workshop on Computational Biology (WCB) at ICML}, url = {https://icml-compbio.github.io/icml-website-2020/2020/papers/WCBICML2020_paper_36.pdf}, }

@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}, }

@inproceedings{asiaee_time_2018, title = {Time Series Deinterleaving of DNS Traffic}, author = {Amir Asiaee and Hardik Goel and Shalini Ghosh and Vinod Yegneswaran and Arindam Banerjee}, year = {2018}, booktitle = {1st Deep Learning and Security Workshop (DLS), IEEE Security and Privacy Workshops}, eprint = {1807.05650}, archivePrefix = {arXiv}, url = {https://arxiv.org/abs/1807.05650}, }

@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{asiaee_high_2016, title = {High Dimensional Structured Estimation with Noisy Designs}, author = {Amir Asiaee T. and Soumyadeep Chaterjee and Arindam Banerjee}, year = {2016}, booktitle = {Proceedings of the 2016 SIAM International Conference on Data Mining (SDM)}, pages = {801--809}, doi = {10.1137/1.9781611974348.90}, url = {https://doi.org/10.1137/1.9781611974348.90}, }

@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}, }