You can also find my articles on my Google Scholar profile.

Algorithmic Fairness

27.
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. PDFDOI BIB
26.
Fairness Under Group-Conditional Prior Probability Shift: Invariance, Drift, and Target-Aware Post-Processing Amir Asiaee, Kaveh Aryan. arXiv, 2026. PDFDOI BIB

Cancer Progression

9.
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. PDFDOI BIB
8.
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. PDFDOI BIB

Cancer Research

36.
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. PDFDOI BIB
34.
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. PDFDOI BIB
4.
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. PDFDOI BIB

Causal Discovery

22.
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. PDFDOI BIB
13.
Causal Discovery with Mixed Latent Confounding via Precision Decomposition Amir Asiaee, Samhita Pal, James O'quinn, James P. Long. arXiv, 2025. PDFDOI BIB

Causal Inference

39.
Improving RCT-Based CATE Estimation Under Covariate Mismatch via Double Calibration Samhita Pal, Jared D. Huling, Amir Asiaee. , 2026. PDFDOI BIB
35.
Sharp Bounds for Treatment Effect Generalization under Outcome Distribution Shift Amir Asiaee, Samhita Pal, Cole Beck, Jared D. Huling. 5th Conference on Causal Learning and Reasoning (CLeaR), 2026. PDFDOI BIB
31.
Partial Causal Structure Learning for Valid Selective Conformal Inference under Interventions Amir Asiaee, Kavey Aryan, James P. Long. , 2026. PDFDOI BIB
30.
Omitted-Variable Sensitivity Analysis for Generalizing Randomized Trials Amir Asiaee, Samhita Pal, Jared D. Huling. , 2026. PDFDOI BIB
28.
Improving RCT-Based CATE Estimation Under Covariate Mismatch via Calibrated Alignment Amir Asiaee, Samhita Pal. , 2026. PDFDOI BIB
25.
Efficient Discovery of Approximate Causal Abstractions via Neural Mechanism Sparsification Amir Asiaee. , 2026. PDFDOI BIB
24.
CausalWrap: Model-Agnostic Causal Constraint Wrappers for Tabular Synthetic Data Amir Asiaee, Zhuohui J. Liang, Chao Yan. , 2026. PDFDOI BIB
15.
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. PDFDOI BIB

Cell Perturbation Experiments

23.
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. PDFDOI BIB

Complex Networks

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

Computational Biology

39.
Improving RCT-Based CATE Estimation Under Covariate Mismatch via Double Calibration Samhita Pal, Jared D. Huling, Amir Asiaee. , 2026. PDFDOI BIB
31.
Partial Causal Structure Learning for Valid Selective Conformal Inference under Interventions Amir Asiaee, Kavey Aryan, James P. Long. , 2026. PDFDOI BIB
30.
Omitted-Variable Sensitivity Analysis for Generalizing Randomized Trials Amir Asiaee, Samhita Pal, Jared D. Huling. , 2026. PDFDOI BIB
29.
Noise-Calibrated Inference from Differentially Private Sufficient Statistics in Exponential Families Amir Asiaee, Samhita Pal. , 2026. PDFDOI BIB
28.
Improving RCT-Based CATE Estimation Under Covariate Mismatch via Calibrated Alignment Amir Asiaee, Samhita Pal. , 2026. PDFDOI BIB
24.
CausalWrap: Model-Agnostic Causal Constraint Wrappers for Tabular Synthetic Data Amir Asiaee, Zhuohui J. Liang, Chao Yan. , 2026. PDFDOI BIB
16.
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. PDFDOI BIB
11.
Quantifying Differential Rhythmicity based on Effect Sizes with LimoRhyde2 Dora Obodo, Amir Asiaee. bioRxiv, 2024. PDFDOI BIB
7.
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. PDFDOI BIB
4.
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. PDFDOI BIB

Computational Oncology

9.
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. PDFDOI BIB
8.
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. PDFDOI BIB

Conditional Average Treatment Effect

35.
Sharp Bounds for Treatment Effect Generalization under Outcome Distribution Shift Amir Asiaee, Samhita Pal, Cole Beck, Jared D. Huling. 5th Conference on Causal Learning and Reasoning (CLeaR), 2026. PDFDOI BIB
15.
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. PDFDOI BIB

Deconfounding

22.
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. PDFDOI BIB
13.
Causal Discovery with Mixed Latent Confounding via Precision Decomposition Amir Asiaee, Samhita Pal, James O'quinn, James P. Long. arXiv, 2025. PDFDOI BIB

Differential Privacy

33.
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. PDFDOI BIB
32.
PRISM: Differentially Private Synthetic Data with Structure-Aware Budget Allocation for Prediction Amir Asiaee, Chao Yan, Zachary B. Abrams, Bradley A. Malin. arXiv, 2026. PDFDOI BIB

Drug Discovery

12.
Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning Jared Strauch, Amir Asiaee. bioRxiv, 2024. PDFDOI BIB

Drug Hypersensitivity

21.
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. PDFDOI BIB
20.
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. PDFDOI BIB

Evaluation Metrics

23.
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. PDFDOI BIB

Heterogeneous Treatment Effect

35.
Sharp Bounds for Treatment Effect Generalization under Outcome Distribution Shift Amir Asiaee, Samhita Pal, Cole Beck, Jared D. Huling. 5th Conference on Causal Learning and Reasoning (CLeaR), 2026. PDFDOI BIB
15.
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. PDFDOI BIB

High Dimensional Statistics

10.
High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. arXiv, 2023. PDFDOI BIB
5.
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. PDFDOI BIB

Immune Checkpoint Inhibitors

21.
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. PDFDOI BIB

Immunology

38.
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. PDFDOI BIB
37.
Keystone Epitope Theory: Implications for the Investigation of Multiple Sclerosis Simon Mallal, Amir Asiaee, Natalie Mallal, Elizabeth Phillips. Zenodo, 2026. PDFDOI BIB
19.
Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI BIB
18.
Keystone Epitope Theory: An Ecological Perspective on RNA Viruses, Tumor Immunoediting, and Vaccine Design Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI BIB
14.
Co-evolved Partners of Immunity: A Trait-Based Map of Human Keystone Organisms Amir Asiaee, Natalie Mallal, Elizabeth Phillips, Simon Mallal. bioRxiv, 2025. PDFDOI BIB

In silico Cell Models

23.
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. PDFDOI BIB

Infectious Disease

14.
Co-evolved Partners of Immunity: A Trait-Based Map of Human Keystone Organisms Amir Asiaee, Natalie Mallal, Elizabeth Phillips, Simon Mallal. bioRxiv, 2025. PDFDOI BIB

Keystone Theory

38.
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. PDFDOI BIB
37.
Keystone Epitope Theory: Implications for the Investigation of Multiple Sclerosis Simon Mallal, Amir Asiaee, Natalie Mallal, Elizabeth Phillips. Zenodo, 2026. PDFDOI BIB
19.
Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI BIB
18.
Keystone Epitope Theory: An Ecological Perspective on RNA Viruses, Tumor Immunoediting, and Vaccine Design Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI BIB

Machine Learning

39.
Improving RCT-Based CATE Estimation Under Covariate Mismatch via Double Calibration Samhita Pal, Jared D. Huling, Amir Asiaee. , 2026. PDFDOI BIB
36.
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. PDFDOI BIB
31.
Partial Causal Structure Learning for Valid Selective Conformal Inference under Interventions Amir Asiaee, Kavey Aryan, James P. Long. , 2026. PDFDOI BIB
30.
Omitted-Variable Sensitivity Analysis for Generalizing Randomized Trials Amir Asiaee, Samhita Pal, Jared D. Huling. , 2026. PDFDOI BIB
28.
Improving RCT-Based CATE Estimation Under Covariate Mismatch via Calibrated Alignment Amir Asiaee, Samhita Pal. , 2026. PDFDOI BIB
27.
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. PDFDOI BIB
26.
Fairness Under Group-Conditional Prior Probability Shift: Invariance, Drift, and Target-Aware Post-Processing Amir Asiaee, Kaveh Aryan. arXiv, 2026. PDFDOI BIB
25.
Efficient Discovery of Approximate Causal Abstractions via Neural Mechanism Sparsification Amir Asiaee. , 2026. PDFDOI BIB
24.
CausalWrap: Model-Agnostic Causal Constraint Wrappers for Tabular Synthetic Data Amir Asiaee, Zhuohui J. Liang, Chao Yan. , 2026. PDFDOI BIB
12.
Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning Jared Strauch, Amir Asiaee. bioRxiv, 2024. PDFDOI BIB
10.
High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. arXiv, 2023. PDFDOI BIB
5.
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. PDFDOI 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. PDFDOI BIB

MicroRNA

16.
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. PDFDOI BIB
7.
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. PDFDOI BIB

Multi-task Learning

10.
High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. arXiv, 2023. PDFDOI BIB
5.
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. PDFDOI BIB

Natural Language Processing

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. PDFDOI BIB

NK Cell

19.
Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI BIB

Probabilistic Graphical Models

8.
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. PDFDOI BIB

Randomized Controlled Trial

15.
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. PDFDOI BIB

SCAR

21.
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. PDFDOI BIB
20.
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. PDFDOI BIB

Sentiment Analysis

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. PDFDOI BIB

SJS/TEN

21.
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. PDFDOI BIB
20.
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. PDFDOI BIB

Social Networks

25.
Efficient Discovery of Approximate Causal Abstractions via Neural Mechanism Sparsification Amir Asiaee. , 2026. PDFDOI 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

Social Networks Analysis

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

Statistical Methods

34.
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. PDFDOI BIB
29.
Noise-Calibrated Inference from Differentially Private Sufficient Statistics in Exponential Families Amir Asiaee, Samhita Pal. , 2026. PDFDOI BIB
12.
Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning Jared Strauch, Amir Asiaee. bioRxiv, 2024. PDFDOI BIB

Statistical Shape Analysis

6.
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. PDFDOI BIB

Structur Learning

22.
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. PDFDOI BIB

Structure Learning

13.
Causal Discovery with Mixed Latent Confounding via Precision Decomposition Amir Asiaee, Samhita Pal, James O'quinn, James P. Long. arXiv, 2025. PDFDOI BIB

Synthetic Data

33.
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. PDFDOI BIB
32.
PRISM: Differentially Private Synthetic Data with Structure-Aware Budget Allocation for Prediction Amir Asiaee, Chao Yan, Zachary B. Abrams, Bradley A. Malin. arXiv, 2026. PDFDOI BIB
17.
Generating Synthetic Multi-national Longitudinal Cohorts for Clinically Grounded HIV Research Zhuohui J. Liang, Zhuohang Li, Nicholas J. Jackson, 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. medRxiv, 2025. PDFDOI BIB

T Cell

19.
Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI BIB

Transcription Factor

16.
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. PDFDOI BIB