publications

for more recent publications please check my google scholar.

2025

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    SpecMER: Fast Protein Generation with K-mer Guided Speculative Decoding
    Thomas Walton, Darin Tsui, Aryan Musharaf, and 1 more author
    Conference on Neural Information Processing Systems (NeurIPS) Spotlight (top 3% of 21,575 submissions), 2025
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    SHAP zero Explains Biological Sequence Models with Near-zero Marginal Cost for Future Queries
    Darin Tsui, Aryan Musharaf, Yigit Efe Erginbas, and 2 more authors
    Conference on Neural Information Processing Systems (NeurIPS), 2025
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    Sparse Autoencoders for Low-N Protein Function Prediction and Design
    Darin Tsui, Kunal Talreja, and Amirali Aghazadeh
    NeurIPS 2025 Workshop AI4Science, 2025
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    Efficient Algorithm for Sparse Fourier Transform of Generalized q-ary Functions
    Darin Tsui, Kunal Talreja, and Amirali Aghazadeh
    IEEE Information Theory Workshop (ITW), 2025
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    GOLF: A Generative AI Framework for Pathogenicity Prediction of Myocilin OLF Variants
    Thomas Alan Walton, Darin Tsui, Lauren Fogel, and 4 more authors
    Machine Learning in Computational Biology (MLCB), 2025
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    Challenges and Opportunities in Using Amino Acids to Decode Carbonaceous Chondrite and Asteroid Parent Body Processes
    José C Aponte, Hannah L McLain, Daniel Saeedi, and 4 more authors
    Astrobiology, 2025
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    AI scientist ’team’ joins the search for extraterrestrial life
    Celeste Biever
    Nature, 2025
    This article covers a story about our AstroAgents paper.
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    AstroAgents: A Multi-Agent AI for Hypothesis Generation from Mass Spectrometry Data
    Daniel Saeedi, Denise Buckner, José Aponte, and 1 more author
    International Conference on Learning Representation (ICLR) Workshop on Towards Agentic AI for Science: Hypothesis Generation, Comprehension, Quantification, and Validation, 2025
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2024

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    On Recovering Higher-order Interactions from Protein Language Models
    Darin Tsui, and Amirali Aghazadeh
    International Conference on Learning Representation (ICLR) Workshop on Generative and Experimental perspectives in bioMolecular design (GEM), 2024
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2023

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    ProtiGeno: a prokaryotic short gene finder using protein language models
    Tony Tu, Gautham Krishna, and Amirali Aghazadeh
    International Conference on Machine Learning (ICML) Workshop on Computational Biology, 2023
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    Efficiently Computing Sparse Fourier Transforms of q -ary Functions
    Yigit Efe Erginbas, Justin Singh Kang, Amirali Aghazadeh, and 1 more author
    International Symposium on Information Theory (ISIT), 2023
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    Spectral Regularization Allows Data-frugal Learning over Combinatorial Spaces
    Amirali Aghazadeh, Nived Rajaraman, Tony Tu, and 1 more author
    Transactions on Machine Learning Research (TMLR), 2023
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2022

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    Current progress and open challenges for applying deep learning across the biosciences
    Nicolae Sapoval, Amirali Aghazadeh, Michael G Nute, and 8 more authors
    Nature Communications, 2022
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    On the sparsity of fitness functions and implications for learning
    David H Brookes, Amirali Aghazadeh, and Jennifer Listgarten
    Proceedings of the National Academy of Sciences (PNAS), 2022
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    BEAR: Sketching BFGS Algorithm for Ultra-High Dimensional Feature Selection in Sublinear Memory
    Amirali Aghazadeh, Vipul Gupta, Alex DeWeese, and 2 more authors
    In Mathematical and Scientific Machine Learning (MSML), 2022
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2021

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    Epistatic Net allows the sparse spectral regularization of deep neural networks for inferring fitness functions
    Amirali Aghazadeh, Hunter Nisonoff, Orhan Ocal, and 5 more authors
    Nature Communications, 2021
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    Group-Structured Adversarial Training
    Farzan Farnia, Amirali Aghazadeh, James Zou, and 1 more author
    arXiv:2106.10324, 2021
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    Anomalous nanoparticle surface diffusion in LCTEM is revealed by deep learning-assisted analysis
    Vida Jamali, Cory Hargus, Assaf Ben-Moshe, and 4 more authors
    Proceedings of the National Academy of Sciences, 2021
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2020

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    CRISPRLand: Interpretable large-scale inference of DNA repair landscape based on a spectral approach
    Amirali Aghazadeh, Orhan Ocal, and Kannan Ramchandran
    Bioinformatics, 2020
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2019

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    Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells
    Ryan T Leenay, Amirali Aghazadeh, Joseph Hiatt, and 8 more authors
    Nature Biotechnology, 2019
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    Data-driven semi-supervised and supervised learning algorithms for health monitoring of pipes
    Debarshi Sen, Amirali Aghazadeh, Ali Mousavi, and 3 more authors
    Mechanical Systems and Signal Processing, 2019
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    Sparsity-based approaches for damage detection in plates
    Debarshi Sen, Amirali Aghazadeh, Ali Mousavi, and 2 more authors
    Mechanical Systems and Signal Processing, 2019
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2018

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    MISSION: Ultra large-scale feature selection using Count Sketches
    Amirali Aghazadeh, Ryan Spring, Daniel LeJeune, and 3 more authors
    In International Conference on Machine Learning (ICML), 2018
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    Insense: Incoherent sensor selection for sparse signals
    Amirali Aghazadeh, Mohammad Golbabaee, Andrew Lan, and 1 more author
    Signal Processing, 2018
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2017

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    Rhash: Robust hashing via l∞-norm distortion
    Amirali Aghazadeh, Andrew Lan, Anshumali Shrivastava, and 1 more author
    In International Joint Conference on Artificial Intelligence (IJCAI), 2017
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    Machine Learning in Large-scale Genomics: Sensing, Processing, and Analysis
    Amirali Aghazadeh
    Rice University, 2017
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2016

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    Universal microbial diagnostics using random DNA probes
    Amirali Aghazadeh, Adam Y Lin, Mona A Sheikh, and 6 more authors
    Science Advances, 2016
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2013

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    Adaptive step size selection for optimization via the ski rental problem
    Amirali Aghazadeh, Ali Ayremlou, Daniel D Calderón, and 4 more authors
    In International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2013
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