Publications by Topic

37.

Projected Boosting with Fairness Constraints: Quantifying the Cost of Fair Training Distributions Amir Asiaee, Kaveh Aryan. arXiv, 2026. PDF DOI BIB

31.

Fix Representation (Optimally) Before Fairness: Finite-Sample Shrinkage Population Correction and the True Price of Fairness Under Subpopulation Shift Amir Asiaee, Kaveh Aryan. arXiv, 2026. PDF DOI BIB

30.

Fairness Under Group-Conditional Prior Probability Shift: Invariance, Drift, and Target-Aware Post-Processing Amir Asiaee, Kaveh Aryan. arXiv, 2026. PDF DOI BIB

12.

SITH : An R package for visualizing and analyzing a spatial model of intratumor heterogeneity Phillip B. Nicol, Dániel L. Barabási, Kevin R. Coombes, Amir Asiaee. Computational and Systems Oncology, 2(2), e1033, 2022. PDF DOI BIB

11.

Oncogenetic network estimation with disjunctive Bayesian networks Phillip B. Nicol, Kevin R. Coombes, Courtney Deaver, Oksana Chkrebtii, Subhadeep Paul, Amanda E. Toland, Amir Asiaee. Computational and Systems Oncology, 1(2), e1027, 2021. PDF DOI BIB

9.

Learning Cancer Progression Network from Mutation Allele Frequencies Mohammad Sadegh Akhondzadeh, Alireza Omidi, Zeinab Maleki, Kevin Coombes, Amanda E. Toland, Amir Asiaee. Workshop on Computational Biology (WCB) at ICML, 2020. PDF DOI BIB

53.

Tissue-aware elastic net decomposition reveals shared and lineage-specific drug response biomarkers Jared Strauch, Leila Azinfar, Heather H. Pua, James P. Long, Kevin R. Coombes, Amir Asiaee. bioRxiv, 2026. PDF DOI BIB

41.

Widespread data leakage inflates accuracy and corrupts biomarker discovery in cancer drug response prediction Amir Asiaee, Jared Strauch, Leila Azinfar, Samhita Pal, Heather H. Pua, James P. Long, Kevin R. Coombes. bioRxiv, 2026. PDF DOI BIB

39.

A shape-constrained regression and wild bootstrap framework for reproducible drug synergy testing Amir Asiaee, James P. Long, Samhita Pal, Heather H. Pua, Kevin R. Coombes. bioRxiv, 2026. PDF DOI BIB

5.

Thirty biologically interpretable clusters of transcription factors distinguish cancer type Zachary B. Abrams, Mark Zucker, Min Wang, Amir Asiaee Taheri, Lynne V. Abruzzo, Kevin R. Coombes. BMC Genomics, 19(1), 738, 2018. PDF DOI BIB

23.

DAG DECORation: Continuous Optimization for Structure Learning under Hidden Confounding Samhita Pal, James O'quinn, Kaveh Aryan, Heather Pua, James P. Long, Amir Asiaee. arXiv, 2025. PDF DOI BIB

16.

Causal Discovery with Mixed Latent Confounding via Precision Decomposition Amir Asiaee, Samhita Pal, James O'quinn, James P. Long. arXiv, 2025. PDF DOI BIB

51.

Improving RCT-Based CATE Estimation Under Covariate Mismatch via Double Calibration Samhita Pal, Jared D. Huling, Amir Asiaee. , 2026. PDF DOI BIB

42.

Workload-Preserving Differentially Private Synthetic Data for Causal Inference via Maximum-Entropy Calibration Amir Asiaee, Kaveh Aryan. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 133--160, 2026. PDF DOI BIB

40.

Sharp Bounds for Treatment Effect Generalization under Outcome Distribution Shift Amir Asiaee, Samhita Pal, Cole Beck, Jared D. Huling. Proceedings of the 5th Conference on Causal Learning and Reasoning (CLeaR), 323, 1572--1603, 2026. PDF DOI BIB

35.

Partial Causal Structure Learning for Valid Selective Conformal Inference under Interventions Amir Asiaee, Kaveh Aryan, James P. Long. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 161--184, 2026. PDF DOI BIB

34.

Omitted-Variable Sensitivity Analysis for Generalizing Randomized Trials Amir Asiaee, Samhita Pal, Jared D. Huling. , 2026. PDF DOI BIB

32.

Improving RCT-Based Treatment Effect Estimation Under Covariate Mismatch via Calibrated Alignment Amir Asiaee, Samhita Pal. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 185--209, 2026. PDF DOI BIB

29.

Causal Mechanism Reduction: Mechanism Replacement for Neural Network Pruning and Abstraction Amir Asiaee. arXiv, 2026. PDF DOI BIB

27.

Certified Interventional Fidelity: Anytime-Valid, Adaptive Evaluation of Causal Claims in Mechanistic Interpretability Amir Asiaee. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 210--227, 2026. PDF DOI BIB

26.

CausalWrap: Model-Agnostic Causal Constraint Wrappers for Tabular Synthetic Data Amir Asiaee, Zhuohui J. Liang, Chao Yan. , 2026. PDF DOI BIB

25.

B-CALM: Bias-Limited Bayesian Borrowing for RCT-Anchored Treatment Effects under Covariate Mismatch Amir Asiaee, Samhita Pal. arXiv, 2026. PDF DOI BIB

18.

Improving Precision of RCT-Based CATE Estimation using Data Borrowing with Double Calibration Amir Asiaee, Chiara Di Gravio, Cole Beck, Yuting Mei, Samhita Pal, Jared D. Huling. arXiv, 2025. PDF DOI BIB

24.

AUPRC: a metric for evaluating the performance of in-silico perturbation methods in identifying differentially expressed genes Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P. Long. Briefings in bioinformatics, 26(5), bbaf426, 2025. PDF DOI BIB

3.

Revisiting non-progressive influence models: scalable influence maximization in social networks Golshan Golnari, Asiaee T. Amir, Arindam Banerjee, Zhi-Li Zhang. Proceedings of the Thirty-First Conference on Uncertainty in Artificial Intelligence, 316--325, 2015. PDF BIB

51.

Improving RCT-Based CATE Estimation Under Covariate Mismatch via Double Calibration Samhita Pal, Jared D. Huling, Amir Asiaee. , 2026. PDF DOI BIB

35.

Partial Causal Structure Learning for Valid Selective Conformal Inference under Interventions Amir Asiaee, Kaveh Aryan, James P. Long. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 161--184, 2026. PDF DOI BIB

34.

Omitted-Variable Sensitivity Analysis for Generalizing Randomized Trials Amir Asiaee, Samhita Pal, Jared D. Huling. , 2026. PDF DOI BIB

33.

Noise-Calibrated Inference from Differentially Private Sufficient Statistics in Exponential Families Amir Asiaee, Samhita Pal. , 2026. PDF DOI BIB

32.

Improving RCT-Based Treatment Effect Estimation Under Covariate Mismatch via Calibrated Alignment Amir Asiaee, Samhita Pal. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 185--209, 2026. PDF DOI BIB

28.

Context-dependent correlations mislead transcriptomic network inference in bulk and single-cell data Amir Asiaee, Polina Bombina, Reginald L. McGee, Jake Reed, Zachary B. Abrams, Lynne V. Abruzzo, Kevin R. Coombes. bioRxiv, 2026. PDF DOI BIB

26.

CausalWrap: Model-Agnostic Causal Constraint Wrappers for Tabular Synthetic Data Amir Asiaee, Zhuohui J. Liang, Chao Yan. , 2026. PDF DOI BIB

19.

Transcriptome Complexity Disentangled: A Regulatory Molecules Approach Amir Asiaee, Zachary B. Abrams, Heather H. Pua, Kevin R. Coombes. International journal of molecular sciences, 26(6), 2510, 2025. PDF DOI BIB

14.

Quantifying Differential Rhythmicity based on Effect Sizes with LimoRhyde2 Dora Obodo, Amir Asiaee. bioRxiv, 2024. PDF DOI BIB

10.

Explaining Gene Expression Using Twenty-One MicroRNAs Amir Asiaee, Zachary B. Abrams, Samantha Nakayiza, Deepa Sampath, Kevin R. Coombes. Journal of Computational Biology, 27(7), 1157--1170, 2020. PDF DOI BIB

5.

Thirty biologically interpretable clusters of transcription factors distinguish cancer type Zachary B. Abrams, Mark Zucker, Min Wang, Amir Asiaee Taheri, Lynne V. Abruzzo, Kevin R. Coombes. BMC Genomics, 19(1), 738, 2018. PDF DOI BIB

12.

SITH : An R package for visualizing and analyzing a spatial model of intratumor heterogeneity Phillip B. Nicol, Dániel L. Barabási, Kevin R. Coombes, Amir Asiaee. Computational and Systems Oncology, 2(2), e1033, 2022. PDF DOI BIB

11.

Oncogenetic network estimation with disjunctive Bayesian networks Phillip B. Nicol, Kevin R. Coombes, Courtney Deaver, Oksana Chkrebtii, Subhadeep Paul, Amanda E. Toland, Amir Asiaee. Computational and Systems Oncology, 1(2), e1027, 2021. PDF DOI BIB

9.

Learning Cancer Progression Network from Mutation Allele Frequencies Mohammad Sadegh Akhondzadeh, Alireza Omidi, Zeinab Maleki, Kevin Coombes, Amanda E. Toland, Amir Asiaee. Workshop on Computational Biology (WCB) at ICML, 2020. PDF DOI BIB

40.

Sharp Bounds for Treatment Effect Generalization under Outcome Distribution Shift Amir Asiaee, Samhita Pal, Cole Beck, Jared D. Huling. Proceedings of the 5th Conference on Causal Learning and Reasoning (CLeaR), 323, 1572--1603, 2026. PDF DOI BIB

18.

Improving Precision of RCT-Based CATE Estimation using Data Borrowing with Double Calibration Amir Asiaee, Chiara Di Gravio, Cole Beck, Yuting Mei, Samhita Pal, Jared D. Huling. arXiv, 2025. PDF DOI BIB

23.

DAG DECORation: Continuous Optimization for Structure Learning under Hidden Confounding Samhita Pal, James O'quinn, Kaveh Aryan, Heather Pua, James P. Long, Amir Asiaee. arXiv, 2025. PDF DOI BIB

16.

Causal Discovery with Mixed Latent Confounding via Precision Decomposition Amir Asiaee, Samhita Pal, James O'quinn, James P. Long. arXiv, 2025. PDF DOI BIB

42.

Workload-Preserving Differentially Private Synthetic Data for Causal Inference via Maximum-Entropy Calibration Amir Asiaee, Kaveh Aryan. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 133--160, 2026. PDF DOI BIB

38.

Risk-Equalized Differentially Private Synthetic Data: Protecting Outliers by Controlling Record-Level Influence Amir Asiaee, Chao Yan, Zachary B. Abrams, Bradley A. Malin. arXiv, 2026. PDF DOI BIB

36.

PRISM: Differentially Private Synthetic Data with Structure-Aware Budget Allocation for Prediction Amir Asiaee, Chao Yan, Zachary B. Abrams, Bradley A. Malin. arXiv, 2026. PDF DOI BIB

53.

Tissue-aware elastic net decomposition reveals shared and lineage-specific drug response biomarkers Jared Strauch, Leila Azinfar, Heather H. Pua, James P. Long, Kevin R. Coombes, Amir Asiaee. bioRxiv, 2026. PDF DOI BIB

15.

Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning Jared Strauch, Amir Asiaee. bioRxiv, 2024. PDF DOI BIB

52.

Multiple Antibiotic Allergy Evaluation Strategy (MAAES): A Comparative Effectiveness Study Thanaporn Ratchataswan, Rebecca Lee, Amir Asiaee, Matthew S. Krantz, Grace Koo, Cosby A. Stone, Elizabeth J. Phillips. The Journal of Allergy and Clinical Immunology: In Practice, 2026. PDF DOI BIB

50.

Immune checkpoint blockade reshapes drug-associated toxicity: a pharmacovigilance atlas of drug-ICI interactions Eric M. Mukherjee, Amir Asiaee, Dodi Park, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth J. Phillips. medRxiv, 2026. PDF DOI BIB

49.

HIV as a Host Susceptibility State for Severe Drug Hypersensitivity: Disentangling Biological Susceptibility from Drug Exposure in the FAERS Database Eric M. Mukherjee, Dodi Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth J. Phillips. medRxiv, 2026. PDF DOI BIB

48.

Keystone Epitope Theory: Implications for Hypersensitivity, Autoimmunity, and Transplantation Simon Mallal, Amir Asiaee, Elizabeth Phillips. Pathogens and Immunity, 11(2), 16--38, 2026. PDF Supp DOI BIB

44.

From HLA Association to Tissue Injury: Lessons from Drug Hypersensitivity and Multiple Sclerosis Simon Mallal, Amir Asiaee, Elizabeth Phillips. Zenodo, 2026. PDF DOI BIB

22.

Immune checkpoint inhibitors as independent and synergistic drivers of SJS/TEN Eric Milan Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone Jr, Michelle Martin-Pozo, Elizabeth Phillips. JAMA oncology, 11(12), 1542--1545, 2025. PDF DOI BIB

21.

Demographics, Overlap, and Latency of Severe Cutaneous Adverse Reactions in an FDA Database Eric M. Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth Jane Phillips. medRxiv, 2025. PDF DOI BIB

24.

AUPRC: a metric for evaluating the performance of in-silico perturbation methods in identifying differentially expressed genes Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P. Long. Briefings in bioinformatics, 26(5), bbaf426, 2025. PDF DOI BIB

40.

Sharp Bounds for Treatment Effect Generalization under Outcome Distribution Shift Amir Asiaee, Samhita Pal, Cole Beck, Jared D. Huling. Proceedings of the 5th Conference on Causal Learning and Reasoning (CLeaR), 323, 1572--1603, 2026. PDF DOI BIB

25.

B-CALM: Bias-Limited Bayesian Borrowing for RCT-Anchored Treatment Effects under Covariate Mismatch Amir Asiaee, Samhita Pal. arXiv, 2026. PDF DOI BIB

18.

Improving Precision of RCT-Based CATE Estimation using Data Borrowing with Double Calibration Amir Asiaee, Chiara Di Gravio, Cole Beck, Yuting Mei, Samhita Pal, Jared D. Huling. arXiv, 2025. PDF DOI BIB

13.

High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. arXiv, 2023. PDF DOI BIB

7.

Data enrichment: Multi-task learning in high dimension with theoretical guarantees Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. Adaptive and Multitask Learning Workshop at the ICML. IMLS, Long Beach, CA, 2019. PDF DOI BIB

4.

High Dimensional Structured Estimation with Noisy Designs Amir Asiaee T., Soumyadeep Chaterjee, Arindam Banerjee. Proceedings of the 2016 SIAM International Conference on Data Mining (SDM), 801--809, 2016. PDF DOI BIB

50.

Immune checkpoint blockade reshapes drug-associated toxicity: a pharmacovigilance atlas of drug-ICI interactions Eric M. Mukherjee, Amir Asiaee, Dodi Park, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth J. Phillips. medRxiv, 2026. PDF DOI BIB

22.

Immune checkpoint inhibitors as independent and synergistic drivers of SJS/TEN Eric Milan Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone Jr, Michelle Martin-Pozo, Elizabeth Phillips. JAMA oncology, 11(12), 1542--1545, 2025. PDF DOI BIB

48.

Keystone Epitope Theory: Implications for Hypersensitivity, Autoimmunity, and Transplantation Simon Mallal, Amir Asiaee, Elizabeth Phillips. Pathogens and Immunity, 11(2), 16--38, 2026. PDF Supp DOI BIB

47.

Keystone Epitope Theory in Deep Time: How Viral Endogenization and Sexual Dimorphism Wrote the Genomic Syllabus of Immunity Simon Mallal, Amir Asiaee, Elizabeth Phillips. Zenodo, 2026. PDF DOI BIB

46.

Keystone Epitope Theory: Implications for the Investigation of Multiple Sclerosis Simon Mallal, Amir Asiaee, Natalie Mallal, Elizabeth Phillips. Zenodo, 2026. PDF DOI BIB

45.

Keystone Epitope Theory: An Ecological Perspective on RNA Viruses, Tumor Immunoediting, and Vaccine Design Simon Mallal, Amir Asiaee. Pathogens and Immunity, 11(2), 39--65, 2026. PDF Supp DOI BIB

44.

From HLA Association to Tissue Injury: Lessons from Drug Hypersensitivity and Multiple Sclerosis Simon Mallal, Amir Asiaee, Elizabeth Phillips. Zenodo, 2026. PDF DOI BIB

20.

Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDF DOI BIB

17.

Co-evolved Partners of Immunity: A Trait-Based Map of Human Keystone Organisms Amir Asiaee, Natalie Mallal, Elizabeth Phillips, Simon Mallal. bioRxiv, 2025. PDF DOI BIB

24.

AUPRC: a metric for evaluating the performance of in-silico perturbation methods in identifying differentially expressed genes Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P. Long. Briefings in bioinformatics, 26(5), bbaf426, 2025. PDF DOI BIB

17.

Co-evolved Partners of Immunity: A Trait-Based Map of Human Keystone Organisms Amir Asiaee, Natalie Mallal, Elizabeth Phillips, Simon Mallal. bioRxiv, 2025. PDF DOI BIB

48.

Keystone Epitope Theory: Implications for Hypersensitivity, Autoimmunity, and Transplantation Simon Mallal, Amir Asiaee, Elizabeth Phillips. Pathogens and Immunity, 11(2), 16--38, 2026. PDF Supp DOI BIB

47.

Keystone Epitope Theory in Deep Time: How Viral Endogenization and Sexual Dimorphism Wrote the Genomic Syllabus of Immunity Simon Mallal, Amir Asiaee, Elizabeth Phillips. Zenodo, 2026. PDF DOI BIB

46.

Keystone Epitope Theory: Implications for the Investigation of Multiple Sclerosis Simon Mallal, Amir Asiaee, Natalie Mallal, Elizabeth Phillips. Zenodo, 2026. PDF DOI BIB

45.

Keystone Epitope Theory: An Ecological Perspective on RNA Viruses, Tumor Immunoediting, and Vaccine Design Simon Mallal, Amir Asiaee. Pathogens and Immunity, 11(2), 39--65, 2026. PDF Supp DOI BIB

44.

From HLA Association to Tissue Injury: Lessons from Drug Hypersensitivity and Multiple Sclerosis Simon Mallal, Amir Asiaee, Elizabeth Phillips. Zenodo, 2026. PDF DOI BIB

20.

Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDF DOI BIB

53.

Tissue-aware elastic net decomposition reveals shared and lineage-specific drug response biomarkers Jared Strauch, Leila Azinfar, Heather H. Pua, James P. Long, Kevin R. Coombes, Amir Asiaee. bioRxiv, 2026. PDF DOI BIB

51.

Improving RCT-Based CATE Estimation Under Covariate Mismatch via Double Calibration Samhita Pal, Jared D. Huling, Amir Asiaee. , 2026. PDF DOI BIB

41.

Widespread data leakage inflates accuracy and corrupts biomarker discovery in cancer drug response prediction Amir Asiaee, Jared Strauch, Leila Azinfar, Samhita Pal, Heather H. Pua, James P. Long, Kevin R. Coombes. bioRxiv, 2026. PDF DOI BIB

37.

Projected Boosting with Fairness Constraints: Quantifying the Cost of Fair Training Distributions Amir Asiaee, Kaveh Aryan. arXiv, 2026. PDF DOI BIB

35.

Partial Causal Structure Learning for Valid Selective Conformal Inference under Interventions Amir Asiaee, Kaveh Aryan, James P. Long. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 161--184, 2026. PDF DOI BIB

34.

Omitted-Variable Sensitivity Analysis for Generalizing Randomized Trials Amir Asiaee, Samhita Pal, Jared D. Huling. , 2026. PDF DOI BIB

32.

Improving RCT-Based Treatment Effect Estimation Under Covariate Mismatch via Calibrated Alignment Amir Asiaee, Samhita Pal. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 185--209, 2026. PDF DOI BIB

31.

Fix Representation (Optimally) Before Fairness: Finite-Sample Shrinkage Population Correction and the True Price of Fairness Under Subpopulation Shift Amir Asiaee, Kaveh Aryan. arXiv, 2026. PDF DOI BIB

30.

Fairness Under Group-Conditional Prior Probability Shift: Invariance, Drift, and Target-Aware Post-Processing Amir Asiaee, Kaveh Aryan. arXiv, 2026. PDF DOI BIB

29.

Causal Mechanism Reduction: Mechanism Replacement for Neural Network Pruning and Abstraction Amir Asiaee. arXiv, 2026. PDF DOI BIB

27.

Certified Interventional Fidelity: Anytime-Valid, Adaptive Evaluation of Causal Claims in Mechanistic Interpretability Amir Asiaee. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 210--227, 2026. PDF DOI BIB

26.

CausalWrap: Model-Agnostic Causal Constraint Wrappers for Tabular Synthetic Data Amir Asiaee, Zhuohui J. Liang, Chao Yan. , 2026. PDF DOI BIB

15.

Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning Jared Strauch, Amir Asiaee. bioRxiv, 2024. PDF DOI BIB

13.

High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. arXiv, 2023. PDF DOI BIB

7.

Data enrichment: Multi-task learning in high dimension with theoretical guarantees Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. Adaptive and Multitask Learning Workshop at the ICML. IMLS, Long Beach, CA, 2019. PDF DOI BIB

6.

Time Series Deinterleaving of DNS Traffic Amir Asiaee, Hardik Goel, Shalini Ghosh, Vinod Yegneswaran, Arindam Banerjee. 1st Deep Learning and Security Workshop (DLS), IEEE Security and Privacy Workshops, 2018. PDF DOI BIB

4.

High Dimensional Structured Estimation with Noisy Designs Amir Asiaee T., Soumyadeep Chaterjee, Arindam Banerjee. Proceedings of the 2016 SIAM International Conference on Data Mining (SDM), 801--809, 2016. PDF DOI BIB

1.

If you are happy and you know it... tweet Amir Asiaee T., Mariano Tepper, Arindam Banerjee, Guillermo Sapiro. Proceedings of the 21st ACM international conference on Information and knowledge management, 1602--1606, 2012. PDF DOI BIB

27.

Certified Interventional Fidelity: Anytime-Valid, Adaptive Evaluation of Causal Claims in Mechanistic Interpretability Amir Asiaee. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 210--227, 2026. PDF DOI BIB

19.

Transcriptome Complexity Disentangled: A Regulatory Molecules Approach Amir Asiaee, Zachary B. Abrams, Heather H. Pua, Kevin R. Coombes. International journal of molecular sciences, 26(6), 2510, 2025. PDF DOI BIB

10.

Explaining Gene Expression Using Twenty-One MicroRNAs Amir Asiaee, Zachary B. Abrams, Samantha Nakayiza, Deepa Sampath, Kevin R. Coombes. Journal of Computational Biology, 27(7), 1157--1170, 2020. PDF DOI BIB

13.

High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. arXiv, 2023. PDF DOI BIB

7.

Data enrichment: Multi-task learning in high dimension with theoretical guarantees Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. Adaptive and Multitask Learning Workshop at the ICML. IMLS, Long Beach, CA, 2019. PDF DOI BIB

1.

If you are happy and you know it... tweet Amir Asiaee T., Mariano Tepper, Arindam Banerjee, Guillermo Sapiro. Proceedings of the 21st ACM international conference on Information and knowledge management, 1602--1606, 2012. PDF DOI BIB

20.

Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDF DOI BIB

11.

Oncogenetic network estimation with disjunctive Bayesian networks Phillip B. Nicol, Kevin R. Coombes, Courtney Deaver, Oksana Chkrebtii, Subhadeep Paul, Amanda E. Toland, Amir Asiaee. Computational and Systems Oncology, 1(2), e1027, 2021. PDF DOI BIB

25.

B-CALM: Bias-Limited Bayesian Borrowing for RCT-Anchored Treatment Effects under Covariate Mismatch Amir Asiaee, Samhita Pal. arXiv, 2026. PDF DOI BIB

18.

Improving Precision of RCT-Based CATE Estimation using Data Borrowing with Double Calibration Amir Asiaee, Chiara Di Gravio, Cole Beck, Yuting Mei, Samhita Pal, Jared D. Huling. arXiv, 2025. PDF DOI BIB

50.

Immune checkpoint blockade reshapes drug-associated toxicity: a pharmacovigilance atlas of drug-ICI interactions Eric M. Mukherjee, Amir Asiaee, Dodi Park, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth J. Phillips. medRxiv, 2026. PDF DOI BIB

49.

HIV as a Host Susceptibility State for Severe Drug Hypersensitivity: Disentangling Biological Susceptibility from Drug Exposure in the FAERS Database Eric M. Mukherjee, Dodi Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth J. Phillips. medRxiv, 2026. PDF DOI BIB

22.

Immune checkpoint inhibitors as independent and synergistic drivers of SJS/TEN Eric Milan Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone Jr, Michelle Martin-Pozo, Elizabeth Phillips. JAMA oncology, 11(12), 1542--1545, 2025. PDF DOI BIB

21.

Demographics, Overlap, and Latency of Severe Cutaneous Adverse Reactions in an FDA Database Eric M. Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth Jane Phillips. medRxiv, 2025. PDF DOI BIB

1.

If you are happy and you know it... tweet Amir Asiaee T., Mariano Tepper, Arindam Banerjee, Guillermo Sapiro. Proceedings of the 21st ACM international conference on Information and knowledge management, 1602--1606, 2012. PDF DOI BIB

50.

Immune checkpoint blockade reshapes drug-associated toxicity: a pharmacovigilance atlas of drug-ICI interactions Eric M. Mukherjee, Amir Asiaee, Dodi Park, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth J. Phillips. medRxiv, 2026. PDF DOI BIB

22.

Immune checkpoint inhibitors as independent and synergistic drivers of SJS/TEN Eric Milan Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone Jr, Michelle Martin-Pozo, Elizabeth Phillips. JAMA oncology, 11(12), 1542--1545, 2025. PDF DOI BIB

21.

Demographics, Overlap, and Latency of Severe Cutaneous Adverse Reactions in an FDA Database Eric M. Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth Jane Phillips. medRxiv, 2025. PDF DOI BIB

29.

Causal Mechanism Reduction: Mechanism Replacement for Neural Network Pruning and Abstraction Amir Asiaee. arXiv, 2026. PDF DOI BIB

2.

Influence maximization for informed agents in collective behavior Amir Asiaee Taheri, Mohammad Afshar, Masoud Asadpour. Distributed Autonomous Robotic Systems: The 10th International Symposium, 389--402, 2013. PDF BIB

3.

Revisiting non-progressive influence models: scalable influence maximization in social networks Golshan Golnari, Asiaee T. Amir, Arindam Banerjee, Zhi-Li Zhang. Proceedings of the Thirty-First Conference on Uncertainty in Artificial Intelligence, 316--325, 2015. PDF BIB

39.

A shape-constrained regression and wild bootstrap framework for reproducible drug synergy testing Amir Asiaee, James P. Long, Samhita Pal, Heather H. Pua, Kevin R. Coombes. bioRxiv, 2026. PDF DOI BIB

33.

Noise-Calibrated Inference from Differentially Private Sufficient Statistics in Exponential Families Amir Asiaee, Samhita Pal. , 2026. PDF DOI BIB

28.

Context-dependent correlations mislead transcriptomic network inference in bulk and single-cell data Amir Asiaee, Polina Bombina, Reginald L. McGee, Jake Reed, Zachary B. Abrams, Lynne V. Abruzzo, Kevin R. Coombes. bioRxiv, 2026. PDF DOI BIB

15.

Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning Jared Strauch, Amir Asiaee. bioRxiv, 2024. PDF DOI BIB

8.

Elastic Statistical Shape Analysis of Biological Structures with Case Studies: A Tutorial Min Ho Cho, Amir Asiaee, Sebastian Kurtek. Bulletin of Mathematical Biology, 81(7), 2052--2073, 2019. PDF DOI BIB

23.

DAG DECORation: Continuous Optimization for Structure Learning under Hidden Confounding Samhita Pal, James O'quinn, Kaveh Aryan, Heather Pua, James P. Long, Amir Asiaee. arXiv, 2025. PDF DOI BIB

16.

Causal Discovery with Mixed Latent Confounding via Precision Decomposition Amir Asiaee, Samhita Pal, James O'quinn, James P. Long. arXiv, 2025. PDF DOI BIB

43.

Generating synthetic multi-national longitudinal cohorts for clinically grounded HIV research Zhuohui J. Liang, Zhuohang Li, Nicholas J. Jackson, Kevin H. Guo, Yanink Caro-Vega, Ronaldo I. Moreira, Fabio Paredes, Jordany Bernadin, Diana Varela, Carina Cesar, Alessandro Blasimme, Jessica M. Perkins, Amir Asiaee, Stephany N. Duda, Bradley A. Malin, Bryan E. Shepherd, Chao Yan. Nature Communications, 17(1), 7857, 2026. PDF DOI BIB

42.

Workload-Preserving Differentially Private Synthetic Data for Causal Inference via Maximum-Entropy Calibration Amir Asiaee, Kaveh Aryan. Proceedings of the 42nd Conference on Uncertainty in Artificial Intelligence (UAI), 337, 133--160, 2026. PDF DOI BIB

38.

Risk-Equalized Differentially Private Synthetic Data: Protecting Outliers by Controlling Record-Level Influence Amir Asiaee, Chao Yan, Zachary B. Abrams, Bradley A. Malin. arXiv, 2026. PDF DOI BIB

36.

PRISM: Differentially Private Synthetic Data with Structure-Aware Budget Allocation for Prediction Amir Asiaee, Chao Yan, Zachary B. Abrams, Bradley A. Malin. arXiv, 2026. PDF DOI BIB

20.

Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDF DOI BIB

28.

Context-dependent correlations mislead transcriptomic network inference in bulk and single-cell data Amir Asiaee, Polina Bombina, Reginald L. McGee, Jake Reed, Zachary B. Abrams, Lynne V. Abruzzo, Kevin R. Coombes. bioRxiv, 2026. PDF DOI BIB

19.

Transcriptome Complexity Disentangled: A Regulatory Molecules Approach Amir Asiaee, Zachary B. Abrams, Heather H. Pua, Kevin R. Coombes. International journal of molecular sciences, 26(6), 2510, 2025. PDF DOI BIB

Algorithmic Fairness

Cancer Progression

Cancer Research

Causal Discovery

Causal Inference

Cell Perturbation Experiments

Complex Networks

Computational Biology

Computational Oncology

Conditional Average Treatment Effect

Deconfounding

Differential Privacy

Drug Discovery

Drug Hypersensitivity

Evaluation Metrics

Heterogeneous Treatment Effect

High Dimensional Statistics

Immune Checkpoint Inhibitors

Immunology

In silico Cell Models

Infectious Disease

Keystone Theory

Machine Learning

Mechanistic Interpretability

MicroRNA

Multi-task Learning

Natural Language Processing

NK Cell

Probabilistic Graphical Models

Randomized Controlled Trial

SCAR

Sentiment Analysis

SJS/TEN

Social Networks

Social Networks Analysis

Statistical Methods

Statistical Shape Analysis

Structur Learning

Structure Learning

Synthetic Data

T Cell

Transcription Factor