Ali Bashashati

36 papers A* 4A 1C 2Journal 22Unranked 7

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	KAFSTExp: Kernel Adaptive Filtering With Nyström Approximation for Predicting Spatial Gene Expression From Histology Images. IEEE J. Biomed. Health Informatics Haoran Liu, Hossein Farahani, Xifeng Li, Yongle Xie, Ali Bashashati
2025	J	`jnl`	AI-driven 3D Spatial Transcriptomics. CoRR 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, Sizun Jiang, Ali Bashashati, Jonathan T. C. Liu, Faisal Mahmood
2025	J	`jnl`	ATEC23 Challenge: Automated prediction of treatment effectiveness in ovarian cancer using histopathological images. Medical Image Anal. 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, Yong Xia, Tai-Kuang Chao
2025	A*	`conf`	Boltzmann Semantic Score: A Semantic Metric for Evaluating Large Vision Models Using Large Language Models. ICLR Ali Khajegili Mirabadi, Katherine Rich, Hossein Farahani, Ali Bashashati
2024	J	`jnl`	Benchmarking Histopathology Foundation Models for Ovarian Cancer Bevacizumab Treatment Response Prediction from Whole Slide Images. CoRR Mayur Mallya, Ali Khajegili Mirabadi, Hossein Farahani, Ali Bashashati
2024	J	`jnl`	GRASP: GRAph-Structured Pyramidal Whole Slide Image Representation. CoRR Ali Khajegili Mirabadi, Graham Archibald, Amirali Darbandsari, Alberto Contreras-Sanz, Ramin Ebrahim Nakhli, Maryam Asadi, Allen Zhang, C. Blake Gilks, Peter Black, Gang Wang, Hossein Farahani, Ali Bashashati
2024	A*	`conf`	How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval. NeurIPS Philip Fradkin, Puria Azadi Moghadam, Karush Suri, Frederik Wenkel, Ali Bashashati, Maciej Sypetkowski, Dominique Beaini
2024	J	`jnl`	How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval. CoRR Philip Fradkin, Puria Azadi, Karush Suri, Frederik Wenkel, Ali Bashashati, Maciej Sypetkowski, Dominique Beaini
2024	J	`jnl`	Multi-scale relational graph convolutional network for multiple instance learning in histopathology images. Medical Image Anal. Roozbeh Bazargani, Ladan Fazli, Martin E. Gleave, Larry Goldenberg, Ali Bashashati, Septimiu E. Salcudean
2023	A	`conf`	A Morphology Focused Diffusion Probabilistic Model for Synthesis of Histopathology Images. WACV Puria Azadi Moghadam, Sanne Van Dalen, Karina C. Martin, Jochen K. Lennerz, Stephen Yip, Hossein Farahani, Ali Bashashati
2023	—	`conf`	A novel H&E color augmentation for domain invariance classification of unannotated histopathology prostate cancer images. Digital and Computational Pathology Roozbeh Bazargani, Wanwen Chen, Sadaf Sadeghian, Maryam Asadi, Jeffrey Boschman, Amirali Darbandsari, Ali Bashashati, Septimiu E. Salcudean
2023	—	`conf`	ALL-IN: ALocal GLobal Graph-Based DIstillatioN Model for Representation Learning of Gigapixel Histopathology Images With Application In Cancer Risk Assessment. MICCAI (6) Puria Azadi, Jonathan Suderman, Ramin Nakhli, Katherine Rich, Maryam Asadi, Sonia Kung, Htoo Oo, Mira Keyes, Hossein Farahani, Calum MacAulay, Larry Goldenberg, Peter Black, Ali Bashashati
2023	J	`jnl`	AMIGO: Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images. CoRR Ramin Nakhli, Puria Azadi Moghadam, Haoyang Mi, Hossein Farahani, Alexander Baras, C. Blake Gilks, Ali Bashashati
2023	A*	`conf`	CO-PILOT: Dynamic Top-Down Point Cloud with Conditional Neighborhood Aggregation for Multi-Gigapixel Histopathology Image Representation. ICCV Ramin Nakhli, Allen W. Zhang, Ali Khajegili Mirabadi, Katherine Rich, Maryam Asadi, C. Blake Gilks, Hossein Farahani, Ali Bashashati
2023	A*	`conf`	Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images. CVPR Ramin Nakhli, Puria Azadi Moghadam, Haoyang Mi, Hossein Farahani, Alexander Baras, C. Blake Gilks, Ali Bashashati
2023	J	`jnl`	VOLTA: an Environment-Aware Contrastive Cell Representation Learning for Histopathology. CoRR Ramin Nakhli, Allen Zhang, Hossein Farahani, Amirali Darbandsari, Elahe Shenasa, Sidney Thiessen, Katy Milne, Jessica McAlpine, Brad Nelson, C. Blake Gilks, Ali Bashashati
2022	J	`jnl`	A Morphology Focused Diffusion Probabilistic Model for Synthesis of Histopathology Images. CoRR Puria Azadi Moghadam, Sanne Van Dalen, Karina C. Martin, Jochen K. Lennerz, Stephen Yip, Hossein Farahani, Ali Bashashati
2022	—	`conf`	CCRL: Contrastive Cell Representation Learning. ECCV Workshops (7) Ramin Nakhli, Amirali Darbandsari, Hossein Farahani, Ali Bashashati
2022	J	`jnl`	CCRL: Contrastive Cell Representation Learning. CoRR Ramin Nakhli, Amirali Darbandsari, Hossein Farahani, Ali Bashashati
2022	J	`jnl`	Multi-Scale Relational Graph Convolutional Network for Multiple Instance Learning in Histopathology Images. CoRR Roozbeh Bazargani, Ladan Fazli, Larry Goldenberg, Martin E. Gleave, Ali Bashashati, Septimiu E. Salcudean
2020	J	`jnl`	Classification of Epithelial Ovarian Carcinoma Whole-Slide Pathology Images Using Deep Transfer Learning. CoRR Yiping Wang, David Farnell, Hossein Farahani, Mitchell Nursey, Basile Tessier-Cloutier, Steven J. M. Jones, David G. Huntsman, C. Blake Gilks, Ali Bashashati
2019	J	`jnl`	Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models. PLoS Comput. Biol. Tyler Funnell, Allen W. Zhang, Diljot Grewal, Steven McKinney, Ali Bashashati, Yi Kan Wang, Sohrab P. Shah
2016	—	`conf`	Bayesian optimization of BCI parameters. CCECE Hossein Bashashati, Rabab K. Ward, Ali Bashashati
2016	C	`conf`	Neural Network Conditional Random Fields for Self-Paced Brain Computer Interfaces. ICMLA Hossein Bashashati, Rabab K. Ward, Ali Bashashati, Amr M. Mohamed
2015	C	`conf`	Hidden Markov Support Vector Machines for Self-Paced Brain Computer Interfaces. ICMLA Hossein Bashashati, Rabab K. Ward, Ali Bashashati
2012	J	`jnl`	Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinform. Jiarui Ding, Ali Bashashati, Andrew Roth, Arusha Oloumi, Kane Tse, Thomas Zeng, Gholamreza Haffari, Martin Hirst, Marco A. Marra, Anne Condon, Sam Aparicio, Sohrab P. Shah
2012	J	`jnl`	JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinform. 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, Sohrab P. Shah
2010	—	`conf`	Random forests-based 2D-to-3D video conversion. ICECS Mahsa T. Pourazad, Panos Nasiopoulos, Ali Bashashati
2009	J	`jnl`	A Survey of Flow Cytometry Data Analysis Methods. Adv. Bioinformatics Ali Bashashati, Ryan Remy Brinkman
2009	J	`jnl`	Merging Mixture Components for Cell Population Identification in Flow Cytometry. Adv. Bioinformatics Greg Finak, Ali Bashashati, Ryan Remy Brinkman, Raphael Gottardo
2007	J	`jnl`	Towards Development of a 3-State Self-Paced Brain-Computer Interface. Comput. Intell. Neurosci. Ali Bashashati, Rabab K. Ward, Gary E. Birch
2006	J	`jnl`	An experimental study to investigate the effects of a motion tracking electromagnetic sensor during EEG data acquisition. IEEE Trans. Biomed. Eng. Ali Bashashati, Borna Noureddin, Rabab K. Ward, Peter D. Lawrence, Gary E. Birch
2006	J	`jnl`	Automatic user customization for improving the performance of a self-paced brain interface system. Medical Biol. Eng. Comput. Mehrdad Fatourechi, Ali Bashashati, Gary E. Birch, Rabab K. Ward
2006	—	`conf`	Detection of Hand Extension Movements in the Context of a 3-State Asynchronous Brain Interface. ICASSP (5) Ali Bashashati, Rabab K. Ward, Gary E. Birch
2005	—	`conf`	A hybrid genetic algorithm approach for improving the performance of the LF-ASD brain computer interface. ICASSP (5) Mehrdad Fatourechi, Ali Bashashati, Rabab K. Ward, Gary E. Birch
2004	J	`jnl`	Brain-computer interface design for asynchronous control applications: improvements to the LF-ASD asynchronous brain switch. IEEE Trans. Biomed. Eng. Jaimie F. Borisoff, Steven G. Mason, Ali Bashashati, Gary E. Birch