Efficient Dimensionality Reduction for High-Dimensional Network Estimation. - Safiye Celik; Benjamin A. Logsdon; Su-In Lee (ICML, 2014)

High-dimensional machine learning for drug target discovery and precision medicine. - Safiye Celik (2018)

Masked autoencoders are scalable learners of cellular morphology. - Oren Kraus; Kian Kenyon-Dean; Saber Saberian; Maryam Fallah; Peter McLean; Jess Leung; Vasudev Sharma; Ayla Khan; Jia Balakrishnan; Safiye Celik; Maciej Sypetkowski; Chi Vicky Cheng; et al. (CoRR, 2023)

Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology. - Oren Kraus; Kian Kenyon-Dean; Saber Saberian; Maryam Fallah; Peter McLean; Jess Leung; Vasudev Sharma; Ayla Khan; Jia Balakrishnan; Safiye Celik; Dominique Beaini; Maciej Sypetkowski; et al. (CVPR, 2024)

ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy. - Kian Kenyon-Dean; Zitong Jerry Wang; John Urbanik; Konstantin Donhauser; Jason S. Hartford; Saber Saberian; Nil Sahin; Ihab Bendidi; Safiye Celik; Marta M. Fay; Juan Sebastian Rodriguez Vera; Imran S. Haque; et al. (CoRR, 2024)

Building, benchmarking, and exploring perturbative maps of transcriptional and morphological data. - Safiye Celik; Jan-Christian Hütter; Sandra Melo Carlos; Nathan H. Lazar; Rahul Mohan; Conor Tillinghast; Tommaso Biancalani; Marta M. Fay; Berton Earnshaw; Imran S. Haque (PLoS Comput. Biol., 2024)

RxRx3-core: Benchmarking drug-target interactions in High-Content Microscopy. - Oren Kraus; Federico Comitani; John Urbanik; Kian Kenyon-Dean; Lakshmanan Arumugam; Saber Saberian; Cas Wognum; Safiye Celik; Imran S. Haque (CoRR, 2025)