World of Empowered IoT Users. - Sayed Hadi Hashemi; Faraz Faghri; Paul Rausch; Roy H. Campbell (IoTDI, 2016)

Decentralized User-Centric Access Control using PubSub over Blockchain. - Sayed Hadi Hashemi; Faraz Faghri; Roy H. Campbell (CoRR, 2017)

Toward Scalable Machine Learning and Data Mining: the Bioinformatics Case. - Faraz Faghri; Sayed Hadi Hashemi; Mohammad Babaeizadeh; Mike A. Nalls; Saurabh Sinha; Roy H. Campbell (CoRR, 2017)

Learning the progression and clinical subtypes of Alzheimer's disease from longitudinal clinical data. - Vipul Satone; Rachneet Kaur; Faraz Faghri; Mike A. Nalls; Andrew B. Singleton; Roy H. Campbell (CoRR, 2018)

Learning a long healthy aging - Faraz Faghri (2019)

GenoML: Automated Machine Learning for Genomics. - Mary B. Makarious; Hampton L. Leonard; Dan Vitale; Hirotaka Iwaki; David Saffo; Lana Sargent; Anant Dadu; Eduardo Salmerón Castaño; John F. Carter; Melina Maleknia; Juan A. Botía; Cornelis Blauwendraat; et al. (CoRR, 2021)

Uncovering the complexities of biological structures with network-based learning: An application in SARS-CoV-2. - Faraz Faghri; Mike A. Nalls (Patterns, 2021)

PhenoExam: gene set analyses through integration of different phenotype databases. - Alejandro Cisterna; Aurora González-Vidal; Daniel Ruiz; Jordi Ortiz; Alicia Gómez-Pascual; Zhongbo Chen; Mike A. Nalls; Faraz Faghri; John Hardy; Irene Díez; Paolo Maietta; Sara Álvarez; et al. (BMC Bioinform., 2022)

Application of Aligned-UMAP to longitudinal biomedical studies. - Anant Dadu; Vipul Satone; Rachneet Kaur; Mathew J. Koretsky; Hirotaka Iwaki; Yue A. Qi; Daniel M. Ramos; Brian B. Avants; Jacob Hesterman; Roger Gunn; Mark R. Cookson; Michael E. Ward; et al. (Patterns, 2023)

Multimodal Patient Representation Learning with Missing Modalities and Labels. - Zhenbang Wu; Anant Dadu; Nicholas J. Tustison; Brian B. Avants; Mike A. Nalls; Jimeng Sun 001; Faraz Faghri (ICLR, 2024)

Instruction Tuning Large Language Models to Understand Electronic Health Records. - Zhenbang Wu; Anant Dadu; Mike A. Nalls; Faraz Faghri; Jimeng Sun 001 (NeurIPS, 2024)

Federated learning for multi-omics: A performance evaluation in Parkinson's disease. - Benjamin P. Danek; Mary B. Makarious; Anant Dadu; Dan Vitale; Paul Suhwan Lee; Andrew B. Singleton; Mike A. Nalls; Jimeng Sun 001; Faraz Faghri (Patterns, 2024)

SECONDGRAM: Self-conditioned diffusion with gradient manipulation for longitudinal MRI imputation. - Brandon Theodorou; Anant Dadu; Mike A. Nalls; Faraz Faghri; Jimeng Sun 001 (Patterns, 2025)

Lost in the Haystack: Smaller Needles are More Difficult for LLMs to Find. - Owen Bianchi; Mathew J. Koretsky; Maya Willey; Chelsea X. Alvarado; Tanay Nayak; Adi Asija; Nicole Kuznetsov; Mike A. Nalls; Faraz Faghri; Daniel Khashabi (CoRR, 2025)

BiomedSQL: Text-to-SQL for Scientific Reasoning on Biomedical Knowledge Bases. - Mathew J. Koretsky; Maya Willey; Adi Asija; Owen Bianchi; Chelsea X. Alvarado; Tanay Nayak; Nicole Kuznetsov; Sungwon Kim; Mike A. Nalls; Daniel Khashabi; Faraz Faghri (CoRR, 2025)