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

By Year By Topic

Algorithmic Fairness

27.
Projected Boosting with Fairness Constraints: Quantifying the Cost of Fair Training Distributions Amir Asiaee, Kaveh Aryan. arXiv preprint arXiv:2602.05713, 2026. PDFLink
25.
Fix Representation (Optimally) Before Fairness: Finite-Sample Shrinkage Population Correction and the True Price of Fairness Under Subpopulation Shift Amir Asiaee, Kaveh Aryan. arXiv preprint arXiv:2602.05707, 2026. PDFLink
24.
Fairness Under Group-Conditional Prior Probability Shift: Invariance, Drift, and Target-Aware Post-Processing Amir Asiaee, Kaveh Aryan. arXiv preprint arXiv:2602.05144, 2026. PDFLink

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
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

Cancer Research

31.
Widespread data leakage inflates performance estimates in cancer drug response prediction Amir Asiaee, Jared Strauch, Leila Azinfar, Samhita Pal, Heather H. Pua, James P. Long, Kevin R. Coombes. bioRxiv, 2026--02, 2026. PDFLink
29.
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--02, 2026. PDFLink
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

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
13.
Causal Discovery with Mixed Latent Confounding via Precision Decomposition Amir Asiaee, Samhita Pal, James O'quinn, James P. Long. arXiv preprint arXiv:2512.24696, 2025. PDFLink

Causal Inference

30.
Sharp Bounds for Treatment Effect Generalization under Outcome Distribution Shift Amir Asiaee, Samhita Pal, Cole Beck, Jared D. Huling. arXiv preprint arXiv:2602.09595, 2026. PDFLink
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

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. PDFLink

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

Computational Biology

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. PDFLink
11.
Quantifying Differential Rhythmicity based on Effect Sizes with LimoRhyde2 Dora Obodo, Amir Asiaee. bioRxiv, 2024--05, 2024. PDFLink
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
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

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
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

Conditional Average Treatment Effect

30.
Sharp Bounds for Treatment Effect Generalization under Outcome Distribution Shift Amir Asiaee, Samhita Pal, Cole Beck, Jared D. Huling. arXiv preprint arXiv:2602.09595, 2026. PDFLink
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

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
13.
Causal Discovery with Mixed Latent Confounding via Precision Decomposition Amir Asiaee, Samhita Pal, James O'quinn, James P. Long. arXiv preprint arXiv:2512.24696, 2025. PDFLink

Differential Privacy

28.
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
26.
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

Drug Discovery

12.
Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning Jared Strauch, Amir Asiaee. bioRxiv, 2024--05, 2024. PDFLink

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. PDFLink
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

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. PDFLink

Heterogeneous Treatment Effect

30.
Sharp Bounds for Treatment Effect Generalization under Outcome Distribution Shift Amir Asiaee, Samhita Pal, Cole Beck, Jared D. Huling. arXiv preprint arXiv:2602.09595, 2026. PDFLink
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

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
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. PDFLink

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. PDFLink

Immunology

33.
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
32.
Keystone Epitope Theory: Implications for the Investigation of Multiple Sclerosis Simon Mallal, Amir Asiaee, Natalie Mallal, Elizabeth Phillips. Zenodo, 2026. PDFDOI
19.
Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI
18.
Keystone Epitope Theory: An Ecological Perspective on RNA Viruses, Tumor Immunoediting, and Vaccine Design Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI
14.
Co-evolved Partners of Immunity: A Trait-Based Map of Human Keystone Organisms Amir Asiaee, Natalie Mallal, Elizabeth Phillips, Simon Mallal. bioRxiv, 2025--08, 2025. PDFLink

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. PDFLink

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--08, 2025. PDFLink

Keystone Theory

33.
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
32.
Keystone Epitope Theory: Implications for the Investigation of Multiple Sclerosis Simon Mallal, Amir Asiaee, Natalie Mallal, Elizabeth Phillips. Zenodo, 2026. PDFDOI
19.
Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI
18.
Keystone Epitope Theory: An Ecological Perspective on RNA Viruses, Tumor Immunoediting, and Vaccine Design Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI

Machine Learning

31.
Widespread data leakage inflates performance estimates in cancer drug response prediction Amir Asiaee, Jared Strauch, Leila Azinfar, Samhita Pal, Heather H. Pua, James P. Long, Kevin R. Coombes. bioRxiv, 2026--02, 2026. PDFLink
27.
Projected Boosting with Fairness Constraints: Quantifying the Cost of Fair Training Distributions Amir Asiaee, Kaveh Aryan. arXiv preprint arXiv:2602.05713, 2026. PDFLink
25.
Fix Representation (Optimally) Before Fairness: Finite-Sample Shrinkage Population Correction and the True Price of Fairness Under Subpopulation Shift Amir Asiaee, Kaveh Aryan. arXiv preprint arXiv:2602.05707, 2026. PDFLink
24.
Fairness Under Group-Conditional Prior Probability Shift: Invariance, Drift, and Target-Aware Post-Processing Amir Asiaee, Kaveh Aryan. arXiv preprint arXiv:2602.05144, 2026. PDFLink
12.
Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning Jared Strauch, Amir Asiaee. bioRxiv, 2024--05, 2024. PDFLink
10.
High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. arXiv, 2023. PDFDOI
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. PDFLink
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

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. PDFLink
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

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
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. PDFLink

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

NK Cell

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

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

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

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. PDFLink
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

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

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. PDFLink
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

Social Networks

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

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

Statistical Methods

29.
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--02, 2026. PDFLink
12.
Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning Jared Strauch, Amir Asiaee. bioRxiv, 2024--05, 2024. PDFLink

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

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

Structure Learning

13.
Causal Discovery with Mixed Latent Confounding via Precision Decomposition Amir Asiaee, Samhita Pal, James O'quinn, James P. Long. arXiv preprint arXiv:2512.24696, 2025. PDFLink

Synthetic Data

28.
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
26.
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
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

T Cell

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

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. PDFLink