Brain-computer interface design for asynchronous control applications: improvements to the LF-ASD asynchronous brain switch. - Jaimie F. Borisoff; Steven G. Mason; Ali Bashashati; Gary E. Birch (IEEE Trans. Biomed. Eng., 2004)

A hybrid genetic algorithm approach for improving the performance of the LF-ASD brain computer interface. - Mehrdad Fatourechi; Ali Bashashati; Rabab K. Ward; Gary E. Birch (ICASSP (5), 2005)

Detection of Hand Extension Movements in the Context of a 3-State Asynchronous Brain Interface. - Ali Bashashati; Rabab K. Ward; Gary E. Birch (ICASSP (5), 2006)

Automatic user customization for improving the performance of a self-paced brain interface system. - Mehrdad Fatourechi; Ali Bashashati; Gary E. Birch; Rabab K. Ward (Medical Biol. Eng. Comput., 2006)

An experimental study to investigate the effects of a motion tracking electromagnetic sensor during EEG data acquisition. - Ali Bashashati; Borna Noureddin; Rabab K. Ward; Peter D. Lawrence; Gary E. Birch (IEEE Trans. Biomed. Eng., 2006)

Towards Development of a 3-State Self-Paced Brain-Computer Interface. - Ali Bashashati; Rabab K. Ward; Gary E. Birch (Comput. Intell. Neurosci., 2007)

A Survey of Flow Cytometry Data Analysis Methods. - Ali Bashashati; Ryan Remy Brinkman (Adv. Bioinformatics, 2009)

Merging Mixture Components for Cell Population Identification in Flow Cytometry. - Greg Finak; Ali Bashashati; Ryan Remy Brinkman; Raphael Gottardo (Adv. Bioinformatics, 2009)

Random forests-based 2D-to-3D video conversion. - Mahsa T. Pourazad; Panos Nasiopoulos; Ali Bashashati (ICECS, 2010)

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. - Jiarui Ding; Ali Bashashati; Andrew Roth; Arusha Oloumi; Kane Tse; Thomas Zeng 002; Gholamreza Haffari; Martin Hirst; Marco A. Marra; Anne Condon; Sam Aparicio; Sohrab P. Shah (Bioinform., 2012)

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. - Andrew Roth; Jiarui Ding; Ryan D. Morin; Anamaria Crisan; Gavin Ha; Ryan Giuliany; Ali Bashashati; Martin Hirst; Gulisa Turashvili; Arusha Oloumi; Marco A. Marra; Sam Aparicio; et al. (Bioinform., 2012)

Hidden Markov Support Vector Machines for Self-Paced Brain Computer Interfaces. - Hossein Bashashati; Rabab K. Ward; Ali Bashashati (ICMLA, 2015)

Bayesian optimization of BCI parameters. - Hossein Bashashati; Rabab K. Ward; Ali Bashashati (CCECE, 2016)

Neural Network Conditional Random Fields for Self-Paced Brain Computer Interfaces. - Hossein Bashashati; Rabab K. Ward; Ali Bashashati; Amr M. Mohamed (ICMLA, 2016)

Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models. - Tyler Funnell; Allen W. Zhang; Diljot Grewal; Steven McKinney; Ali Bashashati; Yi Kan Wang; Sohrab P. Shah (PLoS Comput. Biol., 2019)

Classification of Epithelial Ovarian Carcinoma Whole-Slide Pathology Images Using Deep Transfer Learning. - Yiping Wang; David Farnell; Hossein Farahani; Mitchell Nursey; Basile Tessier-Cloutier; Steven J. M. Jones; David G. Huntsman; C. Blake Gilks; Ali Bashashati (CoRR, 2020)

CCRL: Contrastive Cell Representation Learning. - Ramin Nakhli; Amirali Darbandsari; Hossein Farahani; Ali Bashashati (ECCV Workshops (7), 2022)

Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images. - Ramin Nakhli; Puria Azadi Moghadam; Haoyang Mi; Hossein Farahani; Alexander Baras; C. Blake Gilks; Ali Bashashati (CVPR, 2023)

CO-PILOT: Dynamic Top-Down Point Cloud with Conditional Neighborhood Aggregation for Multi-Gigapixel Histopathology Image Representation. - Ramin Nakhli; Allen W. Zhang; Ali Khajegili Mirabadi; Katherine Rich; Maryam Asadi; C. Blake Gilks; Hossein Farahani; Ali Bashashati (ICCV, 2023)

ALL-IN: ALocal GLobal Graph-Based DIstillatioN Model for Representation Learning of Gigapixel Histopathology Images With Application In Cancer Risk Assessment. - Puria Azadi; Jonathan Suderman; Ramin Nakhli; Katherine Rich; Maryam Asadi; Sonia Kung; Htoo Oo; Mira Keyes; Hossein Farahani; Calum MacAulay; Larry Goldenberg; Peter Black; et al. (MICCAI (6), 2023)

A novel H&E color augmentation for domain invariance classification of unannotated histopathology prostate cancer images. - Roozbeh Bazargani; Wanwen Chen; Sadaf Sadeghian; Maryam Asadi; Jeffrey Boschman; Amirali Darbandsari; Ali Bashashati; Septimiu E. Salcudean (Digital and Computational Pathology, 2023)

A Morphology Focused Diffusion Probabilistic Model for Synthesis of Histopathology Images. - Puria Azadi Moghadam; Sanne Van Dalen; Karina C. Martin; Jochen K. Lennerz; Stephen Yip; Hossein Farahani; Ali Bashashati (WACV, 2023)

AMIGO: Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images. - Ramin Nakhli; Puria Azadi Moghadam; Haoyang Mi; Hossein Farahani; Alexander Baras; C. Blake Gilks; Ali Bashashati (CoRR, 2023)

VOLTA: an Environment-Aware Contrastive Cell Representation Learning for Histopathology. - Ramin Nakhli; Allen Zhang 002; Hossein Farahani; Amirali Darbandsari; Elahe Shenasa; Sidney Thiessen; Katy Milne; Jessica McAlpine; Brad Nelson; C. Blake Gilks; Ali Bashashati (CoRR, 2023)

How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval. - Philip Fradkin; Puria Azadi Moghadam; Karush Suri; Frederik Wenkel; Ali Bashashati; Maciej Sypetkowski; Dominique Beaini (NeurIPS, 2024)

GRASP: GRAph-Structured Pyramidal Whole Slide Image Representation. - Ali Khajegili Mirabadi; Graham Archibald; Amirali Darbandsari; Alberto Contreras-Sanz; Ramin Ebrahim Nakhli; Maryam Asadi; Allen Zhang 002; C. Blake Gilks; Peter Black; Gang Wang; Hossein Farahani; Ali Bashashati (CoRR, 2024)

Benchmarking Histopathology Foundation Models for Ovarian Cancer Bevacizumab Treatment Response Prediction from Whole Slide Images. - Mayur Mallya; Ali Khajegili Mirabadi; Hossein Farahani; Ali Bashashati (CoRR, 2024)

How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval. - Philip Fradkin; Puria Azadi; Karush Suri; Frederik Wenkel; Ali Bashashati; Maciej Sypetkowski; Dominique Beaini (CoRR, 2024)

Multi-scale relational graph convolutional network for multiple instance learning in histopathology images. - Roozbeh Bazargani; Ladan Fazli; Martin E. Gleave; Larry Goldenberg; Ali Bashashati; Septimiu E. Salcudean (Medical Image Anal., 2024)

Boltzmann Semantic Score: A Semantic Metric for Evaluating Large Vision Models Using Large Language Models. - Ali Khajegili Mirabadi; Katherine Rich; Hossein Farahani; Ali Bashashati (ICLR, 2025)

ATEC23 Challenge: Automated prediction of treatment effectiveness in ovarian cancer using histopathological images. - Ching-Wei Wang; Nabila Puspita Firdi; Tzu-Chiao Chu; Mohammad Faiz Iqbal Faiz; Mohammad Zafar Iqbal; Yifan Li; Bo Yang; Mayur Mallya; Ali Bashashati; Fei Li; Haipeng Wang; Mengkang Lu; et al. (Medical Image Anal., 2025)

AI-driven 3D Spatial Transcriptomics. - Cristina Almagro-Pérez; Andrew H. Song; Luca L. Weishaupt; Ahrong Kim; Guillaume Jaume; Drew F. K. Williamson; Konstantin Hemker; Ming Y. Lu; Kritika Singh; Bowen Chen; Long Phi Le; Alexander S. Baras; et al. (CoRR, 2025)