papers.bib

---
---

@article{tsui2026protein,
  title={Protein Circuit Tracing via Cross-layer Transcoders},
  author={Darin Tsui and Kunal Talreja and Daniel Saeedi and Amirali Aghazadeh},
  journal={arXiv:2602.12026},
  year={2026},
  website={https://protmech.github.io},
  code={https://github.com/amirgroup-codes/ProtoMech/tree/main},
  html={https://arxiv.org/pdf/2602.12026},
  preview={protomech.png},
    selected={true}
}

@article{jamali2026microscope,
  title={Thinking microscopes: agentic AI and the future of electron microscopy},
  author={Vida Jamali and Amirali Aghazadeh and Josh Kacher},
  journal={npj Computational Materials},
      volume = {12},
    number = {149},
  year={2026},
  html={https://www.nature.com/articles/s41524-026-02077-y},
  preview={microscope.png},
    selected={true}
}


@article{saeedi2025cryosense,
  title={cryoSENSE: Compressive Sensing Enables High-throughput Microscopy with Sparse and Generative Priors on the Protein Cryo-EM Image Manifold},
  author={Zain Shabeeb and Daniel Saeedi and  Darin Tsui and Vida Jamali and Amirali Aghazadeh},
  journal={Conference on Computer Vision and Pattern Recognition (CVPR)},
  year={2026},
  code={https://github.com/amirgroup-codes/cryoSENSE},
  website={https://cryosense.github.io},
  html={https://arxiv.org/abs/2511.12931},
  preview={ddpm.gif},
    selected={true}
}

@article{saeedi2025cryosense,
  title={Can scientists detect life without knowing what it looks like? Research using machine learning offers a new way},
  author={Amirali Aghazadeh},
  journal={The Conversation},
  year={2025},
  html={https://doi.org/10.64628/AAI.3c9dewyju},
  preview={rock.png}
}


@article{10.1093/pnasnexus/pgaf334,
    author = {Saeedi, Daniel and Buckner, Denise and Walton, Thomas A and Aponte, José C and Aghazadeh, Amirali},
    title = {Discriminating abiotic and biotic organics in meteorite and terrestrial samples using machine learning on mass spectrometry data},
    journal = {PNAS Nexus},
    volume = {4},
    number = {11},
    pages = {pgaf334},
    year = {2025},
    html = {https://doi.org/10.1093/pnasnexus/pgaf334},
    website={https://life-tracer.github.io/},
    media={https://www.eurekalert.org/news-releases/1105981},
    preview={pnasnexus.png},
      selected={false}
}


@article{walton2025specmer,
  title={SpecMER: Fast Protein Generation with K-mer Guided Speculative Decoding},
  author={Walton, Thomas and  Tsui, Darin and Musharaf, Aryan and  Aghazadeh, Amirali},
  journal={Conference on Neural Information Processing Systems (NeurIPS) Spotlight (top 3\% of 21,575 submissions)},
  year={2025},
  code={https://github.com/amirgroup-codes/SpecMER},
  html={https://arxiv.org/abs/2509.21689},
  preview={specme.png},
  selected={true}
}

@article{tsui2024shap,
  title={SHAP zero Explains Biological Sequence Models with Near-zero Marginal Cost for Future Queries},
  author={Tsui, Darin and Musharaf, Aryan and Erginbas, Yigit Efe and Kang, Justin Singh and  Aghazadeh, Amirali},
  journal={Conference on Neural Information Processing Systems (NeurIPS)},
  code={https://github.com/amirgroup-codes/shapzero},
  html={https://arxiv.org/abs/2410.19236},
  year={2025},
  preview={SHAPzero.jpg},
     selected={true}
}

@article{tsui2025sparse,
  title={Sparse Autoencoders for Low-$N$ Protein Function Prediction and Design},
  author={Tsui, Darin and Talreja, Kunal and Aghazadeh, Amirali},
  journal={NeurIPS 2025 Workshop AI4Science},
  year={2025},
  code={https://github.com/amirgroup-codes/LowNSAE},
  html={https://arxiv.org/abs/2508.18567},
preview={sae1.png}
}


@article{tsui2025efficient,
  title={Efficient Algorithm for Sparse Fourier Transform of Generalized q-ary Functions},
  author={Tsui, Darin and Talreja, Kunal and Aghazadeh, Amirali},
  journal={IEEE Information Theory Workshop (ITW)},
   code={https://github.com/amirgroup-codes/GFast},
   html={https://arxiv.org/abs/2501.12365},
  preview={fourier.jpg},
  year={2025}
}

@article{walton2025golf,
  title={GOLF: A Generative AI Framework for Pathogenicity Prediction of Myocilin OLF Variants},
  author={Walton, Thomas Alan and Tsui, Darin and Fogel, Lauren and Huard, Dustin and Chagas, Rafael and Lieberman, Raquel L and Aghazadeh, Amirali},
  journal={Machine Learning in Computational Biology (MLCB)},
   html={https://www.biorxiv.org/content/10.1101/2025.06.17.660210v1.abstract},
  year={2025},
  code={https://github.com/amirgroup-codes/GOLF.git},
  publisher={Cold Spring Harbor Laboratory},
    preview={OLF.png}
}


@article{aponte2025challenges,
  title={Challenges and Opportunities in Using Amino Acids to Decode Carbonaceous Chondrite and Asteroid Parent Body Processes},
  author={Aponte, Jos{\'e} C and McLain, Hannah L and Saeedi, Daniel and Aghazadeh, Amirali and Elsila, Jamie E and Glavin, Daniel P and Dworkin, Jason P},
  journal={Astrobiology},
  year={2025},
  html={https://liebertpub.com/doi/10.1089/ast.2025.0017},
  preview={MeteoriteAmino.png}
}

@article{bieverai,
  title={AI scientist 'team' joins the search for extraterrestrial life},
  author={Biever, Celeste},
     html={https://www.nature.com/articles/d41586-025-01364-w},
    year={2025},
    note = {This article covers a story about our AstroAgents paper.},
    preview={nature.png},
  journal={Nature}
}


@article{saeedi2025,
  title={AstroAgents: A Multi-Agent AI for Hypothesis Generation from Mass Spectrometry Data},
  author={Saeedi, Daniel and Buckner, Denise, and Aponte,  Jos{\'e} and Aghazadeh, Amirali},
  journal={International Conference on Learning Representation (ICLR) Workshop on Towards Agentic AI for Science: Hypothesis Generation, Comprehension, Quantification, and Validation},
  year={2025},
  code={https://github.com/amirgroup-codes/AstroAgents},
  html={https://openreview.net/pdf?id=1WUCSNAjjB},
 website={https://astroagents.github.io},
preview={AstroAgents.png},
 selected={false}
}



@article{aghazadeh2021epistatic,
  title={Epistatic Net allows the sparse spectral regularization of deep neural networks for inferring fitness functions},
  author={Aghazadeh, Amirali and Nisonoff, Hunter and Ocal, Orhan and Brookes, David H and Huang, Yijie and Koyluoglu, O Ozan and Listgarten, Jennifer and Ramchandran, Kannan},
  journal={Nature Communications},
  volume={12},
  number={1},
  pages={1--10},
  year={2021},
  publisher={Nature Publishing Group},
  code={https://github.com/amirmohan/epistatic-net},
  html={https://www.nature.com/articles/s41467-021-25371-3},
  preview={order.jpeg}
}

@article{tsuilangmodel2024,
  title={On Recovering Higher-order Interactions from Protein Language Models},
  author={Tsui, Darin and Aghazadeh, Amirali},
  journal={International Conference on Learning Representation (ICLR) Workshop on Generative and Experimental perspectives in bioMolecular design (GEM)},
  year={2024},
  code={https://github.com/amirgroup-codes/InteractionRecovery},
  html={https://arxiv.org/abs/2405.06645},
  preview={align.jpeg}
}

@article{tu2023protigeno,
  title={ProtiGeno: a prokaryotic short gene finder using protein language models},
  author={Tu, Tony and Krishna, Gautham and Aghazadeh, Amirali},
  journal={International Conference on Machine Learning (ICML) Workshop on Computational Biology},
  year={2023},
  code={https://github.com/tonytu16/protigeno},
  html={https://icml-compbio.github.io/2023/papers/WCBICML2023_paper161.pdf},
  preview={gene.jpeg}
}


@article{erginbas2023efficiently,
  title={Efficiently Computing Sparse Fourier Transforms of $ q $-ary Functions},
  author={Erginbas, Yigit Efe and Kang, Justin Singh and Aghazadeh, Amirali and Ramchandran, Kannan},
  journal={International Symposium on Information Theory (ISIT)},
  year={2023},
  code={https://github.com/basics-lab/qsft},
  html={https://arxiv.org/abs/2301.06200},
  preview={ring.jpg}
}

@article{leenay2019large,
  title={Large dataset enables prediction of repair after CRISPR--Cas9 editing in primary T cells},
  author={Leenay, Ryan T and Aghazadeh, Amirali and Hiatt, Joseph and Tse, David and Roth, Theodore L and Apathy, Ryan and Shifrut, Eric and Hultquist, Judd F and Krogan, Nevan and Wu, Zhenqin and others},
  journal={Nature Biotechnology},
  volume={37},
  number={9},
  pages={1034--1037},
  year={2019},
  publisher={Nature Publishing Group},
  code={https://github.com/amirmohan/SPROUT},
  html={https://doi.org/10.1038/s41587-019-0203-2},
  preview={crispr.jpeg}
}

@inproceedings{aghazadeh2018mission,
  title={{MISSION}: Ultra large-scale feature selection using Count Sketches},
  author={Aghazadeh, Amirali and Spring, Ryan and LeJeune, Daniel and Dasarathy, Gautam and Shrivastava, Anshumali and others},
  booktitle={International Conference on Machine Learning (ICML)},
  pages={80--88},
  year={2018},
  organization={PMLR},
  preview={pattern.png},
  code={https://github.com/rdspring1/MISSION},
  html={https://proceedings.mlr.press/v80/aghazadeh18a.html}
}

@article{aghazadeh2016universal,
  title={Universal microbial diagnostics using random DNA probes},
  author={Aghazadeh, Amirali and Lin, Adam Y and Sheikh, Mona A and Chen, Allen L and Atkins, Lisa M and Johnson, Coreen L and Petrosino, Joseph F and Drezek, Rebekah A and Baraniuk, Richard G},
  journal={Science Advances},
  volume={2},
  number={9},
  pages={e1600025},
  year={2016},
  publisher={American Association for the Advancement of Science},
  html={https://www.science.org/doi/10.1126/sciadv.1600025},
  preview={umd.png}
}

@article{sapoval2022current,
  title={Current progress and open challenges for applying deep learning across the biosciences},
  author={Sapoval, Nicolae and Aghazadeh, Amirali and Nute, Michael G and Antunes, Dinler A and Balaji, Advait and Baraniuk, Richard and Barberan, CJ and Dannenfelser, Ruth and Dun, Chen and Edrisi, Mohammadamin and others},
  journal={Nature Communications},
  volume={13},
  number={1},
  pages={1--12},
  year={2022},
  publisher={Nature Publishing Group},
  html={https://www.nature.com/articles/s41467-022-29268-7},
  preview={fold2.jpeg}
}

@article{sen2019data,
  title={Data-driven semi-supervised and supervised learning algorithms for health monitoring of pipes},
  author={Sen, Debarshi and Aghazadeh, Amirali and Mousavi, Ali and Nagarajaiah, Satish and Baraniuk, Richard and Dabak, Anand},
  journal={Mechanical Systems and Signal Processing},
  volume={131},
  pages={524--537},
  year={2019},
  publisher={Elsevier},
  html={https://www.sciencedirect.com/science/article/pii/S0888327019303784},
  preview={pipe.jpg}
}

@article{sen2019sparsity,
  title={Sparsity-based approaches for damage detection in plates},
  author={Sen, Debarshi and Aghazadeh, Amirali and Mousavi, Ali and Nagarajaiah, Satish and Baraniuk, Richard},
  journal={Mechanical Systems and Signal Processing},
  volume={117},
  pages={333--346},
  year={2019},
  publisher={Elsevier},
  html={https://www.sciencedirect.com/science/article/abs/pii/S0888327018304898},
  preview={plate.jpeg}
}

@article{brookes2022sparsity,
  title={On the sparsity of fitness functions and implications for learning},
  author={Brookes, David H and Aghazadeh, Amirali and Listgarten, Jennifer},
  journal={Proceedings of the National Academy of Sciences (PNAS)},
  volume={119},
  number={1},
  pages={e2109649118},
  year={2022},
  publisher={National Acad Sciences},
  code={https://github.com/dhbrookes/FitnessSparsity},
  html={https://www.pnas.org/doi/10.1073/pnas.2109649118},
  preview={gnk.png}
}


@article{aghazadeh2018insense,
  title={Insense: Incoherent sensor selection for sparse signals},
  author={Aghazadeh, Amirali and Golbabaee, Mohammad and Lan, Andrew and Baraniuk, Richard},
  journal={Signal Processing},
  volume={150},
  pages={57--65},
  year={2018},
  publisher={Elsevier},
  code={https://github.com/amirmohan/Insense},
  html={https://www.sciencedirect.com/science/article/abs/pii/S016516841830121X},
  preview={sensors.png}
}

@article{aghazadeh2020crisprl,
  title={CRISPRLand: Interpretable large-scale inference of DNA repair landscape based on a spectral approach},
  author={Aghazadeh, Amirali and Ocal, Orhan and Ramchandran, Kannan},
  journal={Bioinformatics},
  volume={36},
  number={Supplement\_1},
  pages={i560--i568},
  year={2020},
  publisher={Oxford University Press},
  code={https://github.com/UCBASiCS/CRISPRLand},
  html={https://pubmed.ncbi.nlm.nih.gov/32657417/},
  website={https://www.youtube.com/watch?v=IQ9PDs1nqe8&t=500s},
  preview={sparseg.png}
}

@inproceedings{aghazadeh2017rhash,
  title={Rhash: Robust hashing via l∞-norm distortion},
  author={Aghazadeh, Amirali and Lan, Andrew and Shrivastava, Anshumali and Baraniuk, Richard},
  booktitle={International Joint Conference on Artificial Intelligence (IJCAI)},
  pages={1386--1394},
  year={2017},
  html={https://www.ijcai.org/proceedings/2017/192},
  preview={infinity.jpg}
}

@inproceedings{aghazadeh2022bear,
  title={BEAR: Sketching BFGS Algorithm for Ultra-High Dimensional Feature Selection in Sublinear Memory},
  author={Aghazadeh, Amirali and Gupta, Vipul and DeWeese, Alex and Koyluoglu, Ozan and Ramchandran, Kannan},
  booktitle={Mathematical and Scientific Machine Learning (MSML)},
  pages={75--92},
  year={2022},
  organization={PMLR},
  code={https://github.com/BEAR-algorithm/BEAR},
  html={https://proceedings.mlr.press/v145/aghazadeh22a.html},
  website={https://www.youtube.com/watch?v=CPP4c2G2fBk&ab_channel=MSML21},
  preview={bear.png}
}

@article{aghazadeh2022spectral,
  title={Spectral Regularization Allows Data-frugal Learning over Combinatorial Spaces},
  author={Aghazadeh, Amirali and Rajaraman, Nived and Tu, Tony and Ramchandran, Kannan},
  journal={Transactions on Machine Learning Research (TMLR)},
  year={2023},
  preview={wh.png},
  html={https://openreview.net/forum?id=mySiFHCeAl&referrer=%5BTMLR%5D(%2Fgroup%3Fid%3DTMLR)},
  website={https://www.youtube.com/watch?v=ER12pwvxTSU}
}

@article{farnia2021group,
  title={Group-Structured Adversarial Training},
  author={Farnia, Farzan and Aghazadeh, Amirali and Zou, James and Tse, David},
  journal={arXiv:2106.10324},
  year={2021},
  html={https://arxiv.org/abs/2106.10324},
  preview={distance.png}
}

@article{jamali2021anomalous,
  title={Anomalous nanoparticle surface diffusion in LCTEM is revealed by deep learning-assisted analysis},
  author={Jamali, Vida and Hargus, Cory and Ben-Moshe, Assaf and Aghazadeh, Amirali and Ha, Hyun Dong and Mandadapu, Kranthi K and Alivisatos, A Paul},
  journal={Proceedings of the National Academy of Sciences},
  volume={118},
  number={10},
  pages={e2017616118},
  year={2021},
  publisher={National Acad Sciences},
  code={https://github.com/AliviGitHub/MoNet},
  html={https://www.pnas.org/doi/10.1073/pnas.2017616118},
  website={https://www.youtube.com/watch?v=qyXFbH-gu94&ab_channel=vidajamali},
  preview={brownian-motion.gif}
}


@inproceedings{aghazadeh2013adaptive,
  title={Adaptive step size selection for optimization via the ski rental problem},
  author={Aghazadeh, Amirali and Ayremlou, Ali and Calder{\'o}n, Daniel D and Goldstein, Tom and Patel, Raajen and Vats, Divyanshu and Baraniuk, Richard G},
  booktitle={International Conference on Acoustics, Speech and Signal Processing (ICASSP)},
  pages={5383--5387},
  year={2013},
  organization={IEEE},
  html={https://ieeexplore.ieee.org/document/6638691},
  preview={ski.png}
}

@phdthesis{aghazadeh2017machine,
  title={Machine Learning in Large-scale Genomics: Sensing, Processing, and Analysis},
  author={Aghazadeh, Amirali},
  year={2017},
  school={Rice University},
  html={https://scholarship.rice.edu/handle/1911/96111},
  preview={genome.jpeg}
}