Contact Information:
Ali Ghodsi
Research interests
Machine learning, deep learning, large language models, and AI for scientific and mathematical discovery.
Professor Ghodsi's research focuses on developing machine learning and AI methods, with particular interests in deep learning, large language models, and the use of AI to tackle open problems in science, mathematics, and statistics.
Selected publications
Karami M, Ghodsi A (2026). Auto-Regressive Masked Diffusion Models. International Conference on Artificial Intelligence and Statistics (AISTATS).
Ghodsi A (2025). How Many Heads Make an SSM? A Unified Framework for Attention and State Space Models. arXiv preprint.
Podina L, Ghodsi A, Kohandel M (2025). Learning Chemotherapy Drug Action via Universal Physics-Informed Neural Networks. Pharmaceutical Research, 42, 593–612.
Karami M, Ghodsi A (2024). Orchid: Flexible and Data-Dependent Convolution for Sequence Modeling. Neural Information Processing Systems (NeurIPS).
Ma Z, Chen J, Xin L, Ghodsi A (2024). GraphPI: Efficient Protein Inference with Graph Neural Networks. Journal of Proteome Research, 23 (11), 4821–4834.
Valipour M, Rezagholizadeh M, Kobyzev I, Ghodsi A (2023). DyLoRA: Parameter-Efficient Tuning of Pre-trained Models Using Dynamic Search-Free Low-Rank Adaptation. European Chapter of the Association for Computational Linguistics (EACL).
Tahaei M, Charlaix E, Nia V, Ghodsi A, Rezagholizadeh M (2022). KroneckerBERT: Significant Compression of Pre-trained Language Models Through Kronecker Decomposition and Knowledge Distillation. North American Chapter of the Association for Computational Linguistics (NAACL).
Qiao R, Tran NH, Xin L, Chen X, Li M, Shan B, Ghodsi A (2021). Computationally Instrument-Resolution-Independent de Novo Peptide Sequencing for High-Resolution Devices. Nature Machine Intelligence, 3 (5), 420–425.
Riasatian A, Babaie M, Maleki D, Kalra S, Valipour M, Hemati S, Zaveri M, Safarpoor A, Shafiei S, Afshari M, Rasoolijaberi M, Sikaroudi M, Adnan M, Shah S, Choi C, Damaskinos S, Campbell CJV, Diamandis P, Pantanowitz L, Kashani H, Ghodsi A, Tizhoosh HR (2021). Fine-Tuning and Training of DenseNet for Histopathology Image Representation Using TCGA Diagnostic Slides. Medical Image Analysis.
Tran NH, Qiao R, Xin L, Chen X, Liu C, Zhang X, Shan B, Ghodsi A, Li M (2020). Deep Learning Enables de Novo Peptide Sequencing from Data-Independent-Acquisition Mass Spectrometry. Nature Methods, 16 (1), 63–66.
Rezaeinia SM, Rahmani R, Ghodsi A, Veisi H (2019). Sentiment Analysis Based on Improved Pre-trained Word Embeddings. Expert Systems with Applications.
Barshan E, Ghodsi A, Azimifar Z, Jahromi MZ (2011). Supervised Principal Component Analysis: Visualization, Classification and Regression on Subspaces and Submanifolds. Pattern Recognition.
Biggs M, Ghodsi A, Vavasis S (2008). Nonnegative Matrix Factorization via Rank-One Downdate. International Conference on Machine Learning (ICML).
Zhu M, Ghodsi A (2006). Automatic Dimensionality Selection from the Scree Plot via the Use of Profile Likelihood. Computational Statistics and Data Analysis.