publications | Ben Viggiano

2026

DrugTargetWorld: A Synthetic Biobank for Training and Benchmarking AI Scientists

Samuel Margolis, Paul Schmiedmayer, Alan Huang, and 12 more authors

Oct 2026

@article{Margolis2026-dtw,
  title = {{DrugTargetWorld}: A Synthetic Biobank for Training and
                   Benchmarking {AI} Scientists},
  author = {Margolis, Samuel and Schmiedmayer, Paul and Huang, Alan and Chen, Ethan and Bhattacharjee, Ishan and Shah, Atman and Viggiano, Ben and Cao, Fang and Reddy, Shriya and Xia, Roger and O'Sullivan, Jack and Katz, Daniel and Wheeler, Matthew and Ashley, Euan and Gomes, Bruna},
  journal = {arXiv},
  pages = {2610.09558},
  month = oct,
  year = {2026},
  url = {https://arxiv.org/abs/2610.09558},
}

Generative steering to adapt proteins beyond native biological contexts

Xiaowei Zhang^*, Wenhui Sophia Lu^*, Ben Viggiano^*, and 13 more authors

Oct 2026

^* These authors contributed equally.

bioRxiv DOI GitHub Cite

@article{Zhang2026-provada,
  title = {Generative steering to adapt proteins beyond native biological
                   contexts},
  author = {Zhang, Xiaowei and Lu, Wenhui Sophia and Viggiano, Ben and Reynolds, Kevin and Burick, Sophia and Sotillo, Elena and Dai, Haoyu and Lee, Geonhu and Liu, Zixuan and Yang, Nuoya and Mille-Fragoso, Luis S and Ashley, Euan and Yu, Bingfei and Mackall, Crystal L and Wong, Wing Hung and Gao, Xiaojing J},
  journal = {bioRxiv},
  pages = {2025.07.11.664238},
  month = oct,
  year = {2026},
  doi = {10.1101/2025.07.11.664238},
  url = {https://www.biorxiv.org/content/10.1101/2025.07.11.664238v2},
  note = {<sup>*</sup> These authors contributed equally.}
}

A high-level programming language for generative biology with Proto

Aditi T Merchant^*, Daniel Guo^*, Ben Viggiano^*, and 7 more authors

Jun 2026

^* These authors contributed equally.

bioRxiv GitHub Website Cite

@article{Merchant2026-hi,
  title = {A high-level programming language for generative biology with Proto},
  author = {Merchant, Aditi T and Guo, Daniel and Viggiano, Ben and Brennan-Almaraz, Lucas Emmanuel and Hurr, Evelyn and Mai, Tina and Yin, Peter and King, Samuel H and Ashley, Euan and Hie, Brian L},
  journal = {bioRxiv},
  pages = {2026.06.22.733870},
  month = jun,
  year = {2026},
  language = {en},
  url = {https://www.biorxiv.org/content/10.1101/2026.06.22.733870v1},
  note = {<sup>*</sup> These authors contributed equally.}
}

Steering Protein Generative Models at Test-Time for Guided AAV2 Capsid Design

Ben Viggiano^*, Wenhui Sophia Lu^*, Xiaowei Zhang^*, and 4 more authors

Jan 2026

^* These authors contributed equally.

PSB 2026 GitHub PubMed Cite Oral Presentation

true

@inproceedings{Viggiano2026-psb,
  author = {Viggiano, Ben and Lu, Wenhui Sophia and Zhang, Xiaowei and Mille-Fragoso, Luis S. and Gao, Xiaojing J. and Ashley, Euan and Wong, Wing Hung},
  title = {Steering Protein Generative Models at Test-Time for Guided AAV2 Capsid Design},
  booktitle = {Pacific Symposium on Biocomputing (PSB)},
  journal = {PSB 2026},
  month = jan,
  year = {2026},
  url = {https://psb.stanford.edu/psb-online/proceedings/psb26/#:%C2%A0:text=Steering%20Protein%20Generative%20Models%20at%20Test%2DTime%20for%20Guided%20AAV2%20Capsid%20Design:~:text=Ben%20Viggiano%2C%20Wenhui%20Sophia%20Lu%2C%20Xiaowei%20Zhang%2C%20Luis%20S.%20Mille%2DFragoso%2C%20Xiaojing%20J.%20Gao%2C%20Euan%20Ashley%2C%20Wing%20Hung%20Wong%3B%20Pacific%20Symposium%20on%20Biocomputing},
  pubmed = {https://pubmed.ncbi.nlm.nih.gov/41758159/},
  note = {<sup>*</sup> These authors contributed equally.}
}

Genome modelling and design across all domains of life with Evo 2

Garyk Brixi, Matthew G Durrant, Jerome Ku, and 59 more authors

Mar 2026

Nature GitHub Cite

@article{Brixi2026-ae,
  title = {Genome modelling and design across all domains of life with Evo 2},
  author = {Brixi, Garyk and Durrant, Matthew G and Ku, Jerome and Naghipourfar, Mohsen and Poli, Michael and Sun, Gwanggyu and Brockman, Greg and Chang, Daniel and Fanton, Alison and Gonzalez, Gabriel A and King, Samuel H and Li, David B and Merchant, Aditi T and Nguyen, Eric and Ricci-Tam, Chiara and Romero, David W and Schmok, Jonathan C and Taghibakhshi, Ali and Vorontsov, Anton and Yang, Brandon and Deng, Myra and Gorton, Liv and Nguyen, Nam and Wang, Nicholas K and Pearce, Michael T and Simon, Elana and Adams, Etowah and Amador, Zachary J and Ashley, Euan A and Baccus, Stephen A and Dai, Haoyu and Dillmann, Steven and Ermon, Stefano and Guo, Daniel and Herschl, Michael H and Ilango, Rajesh and Janik, Ken and Lu, Amy X and Mehta, Reshma and Mofrad, Mohammad R K and Ng, Madelena Y and Pannu, Jaspreet and Ré, Christopher and St. John, John and Sullivan, Jeremy and Tey, Joseph and Viggiano, Ben and Zhu, Kevin and Zynda, Greg and Balsam, Daniel and Collison, Patrick and Costa, Anthony B and Hernandez-Boussard, Tina and Ho, Eric and Liu, Ming-Yu and McGrath, Thomas and Powell, Kimberly and Pinglay, Sudarshan and Burke, Dave P and Goodarzi, Hani and Hsu, Patrick D and Hie, Brian L},
  journal = {Nature},
  publisher = {Nature Publishing Group},
  volume = {652},
  number = {8112},
  pages = {1349--1361},
  month = mar,
  year = {2026},
  language = {en},
  url = {https://www.nature.com/articles/s41586-026-10176-5},
}

2025

Approach to the postmarket evaluation of consumer wearable technologies

Krishna Pundi, Sanjeev Bhavnani, Clark Seninger, and 22 more authors

Oct 2025

JAMA Cardiol. Cite

@article{Pundi2025-eu,
  title = {Approach to the postmarket evaluation of consumer wearable
                 technologies},
  author = {Pundi, Krishna and Bhavnani, Sanjeev and Seninger, Clark and Zuckerman, Bram and Paulsen, Jessica and Aguel, Felipe and Din, Natasha and Viggiano, Ben and Yoo, Richard M and Dalal, Nirav and Go, Alan S and Granger, Christopher and Krumholz, Harlan and Lacar, Kathleen and Li, Ron and Lin, Steven and Mahaffey, Kenneth W and Mahoney, Megan and McCall, Debbe and Hills, Mellanie True and Harrington, Robert A and Hernandez-Boussard, Tina and Saha, Anindita and Shah, Nigam and Turakhia, Mintu P},
  journal = {JAMA Cardiol.},
  publisher = {American Medical Association (AMA)},
  volume = {10},
  number = {10},
  pages = {1061--1068},
  month = oct,
  year = {2025},
  language = {en},
  url = {https://jamanetwork.com/journals/jamacardiology/fullarticle/2838852},
}

Diagnostic Yield and Healthcare Utilization of Wearable Notifications for Atrial Fibrillation

Krishna Pundi, Ben Viggiano, Natasha Din, and 4 more authors

Sep 2025

Heart Rhythm O2 DOI Cite

@article{Pundi2025-hro2,
  title = {Diagnostic Yield and Healthcare Utilization of Wearable
                 Notifications for Atrial Fibrillation},
  author = {Pundi, Krishna and Viggiano, Ben and Din, Natasha and Yoo, Richard and Fan, Jun and Turakhia, Mintu P and Shah, Nigam},
  journal = {Heart Rhythm O2},
  publisher = {Elsevier},
  volume = {6},
  number = {9},
  pages = {S43},
  month = sep,
  year = {2025},
  doi = {10.1016/j.hroo.2025.07.099},
  url = {https://www.heartrhythmopen.com/article/S2666-5018(25)00364-2/fulltext},
}

2024

Scalable approach to consumer wearable postmarket surveillance: Development and validation study

Richard M Yoo, Ben Viggiano, Krishna N Pundi, and 5 more authors

Apr 2024

JMIR Med. Inform. Cite

@article{Yoo2024-ke,
  title = {Scalable approach to consumer wearable postmarket surveillance:
                Development and validation study},
  author = {Yoo, Richard M and Viggiano, Ben and Pundi, Krishna N and Fries, Jason A and Zahedivash, Aydin and Podchiyska, Tanya and Din, Natasha and Shah, Nigam H},
  journal = {JMIR Med. Inform.},
  volume = {12},
  pages = {e51171},
  month = apr,
  year = {2024},
  language = {en},
  url = {https://pubmed.ncbi.nlm.nih.gov/38596848/},
}

WONDERBREAD: A benchmark for evaluating multimodal foundation models on business process management tasks

Michael Wornow, Avanika Narayan, Ben Viggiano, and 15 more authors

Dec 2024

NeurIPS 2024 GitHub Website Cite

@inproceedings{Wornow2024-neurips,
  title = {{WONDERBREAD}: A benchmark for evaluating multimodal foundation
                    models on business process management tasks},
  author = {Wornow, Michael and Narayan, Avanika and Viggiano, Ben and Khare, Ishan S and Verma, Tathagat and Thompson, Tibor and Hernandez, Miguel Angel Fuentes and Sundar, Sudharsan and Trujillo, Chloe and Chawla, Krrish and Lu, Rongfei and Shen, Justin and Nagaraj, Divya and Martinez, Joshua and Agrawal, Vardhan and Hudson, Althea and Shah, Nigam H and Ré, Christopher},
  booktitle = {NeurIPS Datasets and Benchmarks Track 2024},
  journal = {NeurIPS 2024},
  volume = {37},
  pages = {115963--116021},
  month = dec,
  year = {2024},
  url = {https://neurips.cc/virtual/2024/poster/97485},
}

2023

Harnessing artificial intelligence for risk stratification in acute myeloid leukemia (AML): Evaluating the utility of longitudinal electronic health record (EHR) data via graph neural networks

Riya Sinha, Matthew Schwede, Ben Viggiano, and 7 more authors

Nov 2023

ASH 2023 Cite

@inproceedings{Sinha2023-ash,
  title = {Harnessing artificial intelligence for risk stratification in
                    acute myeloid leukemia ({AML}): Evaluating the utility of
                    longitudinal electronic health record ({EHR}) data via graph
                    neural networks},
  author = {Sinha, Riya and Schwede, Matthew and Viggiano, Ben and Kuo, David and Henry, Solomon and Wood, Douglas and Mannis, Gabriel and Majeti, Ravindra and Chen, Jonathan and Zhang, Tian Y},
  booktitle = {ASH Annual Meeting 2023},
  journal = {ASH 2023},
  volume = {142},
  number = {Supplement 1},
  pages = {960--960},
  month = nov,
  year = {2023},
  language = {en},
  url = {https://ashpublications.org/blood/article/142/Supplement%201/960/503720/},
}

Assessing the impact of upstream reconstruction models on downstream image analysis: A workflow-centric evaluation

Ben Viggiano, Aashna Desai, Elka Rubin, and 7 more authors

2023

ISMRM 2023 Cite

@inproceedings{Viggiano2023-ismrm,
  title = {Assessing the impact of upstream reconstruction models on
                    downstream image analysis: A workflow-centric evaluation},
  author = {Viggiano, Ben and Desai, Aashna and Rubin, Elka and Schmidt, Andrew and Boutin, Robert and Stevens, Kathryn and Gold, Garry and Ré, Christopher and Chaudhari, Akshay and Desai, Arjun},
  booktitle = {ISMRM Annual Meeting 2023},
  journal = {ISMRM 2023},
  year = {2023},
  url = {https://cds.ismrm.org/protected/23MProceedings/PDFfiles/3772_GGetWARFS.html},
}

2021

A metric for quantification of iodine contrast enhancement (Q-ICE) in computed tomography

T Szczykutowicz, Ben Viggiano, Sean D Rose, and 2 more authors

Aug 2021

J. Comput. Assist. Tomogr. Cite

@article{Szczykutowicz2021-ow,
  title = {A metric for quantification of iodine contrast enhancement
                 ({Q}-{ICE}) in computed tomography},
  author = {Szczykutowicz, T and Viggiano, Ben and Rose, Sean D and Pickhardt, P and Lubner, M},
  journal = {J. Comput. Assist. Tomogr.},
  publisher = {LWW},
  volume = {45},
  number = {6},
  pages = {870--876},
  month = aug,
  year = {2021},
  url = {https://pubmed.ncbi.nlm.nih.gov/34469906/},
}

Applying a new CT quality metric in radiology: How CT pulmonary angiography repeat rates compare across institutions

Sean Rose, Ben Viggiano, Robert Bour, and 3 more authors

Jul 2021

J. Am. Coll. Radiol. Cite

@article{Rose2021-ur,
  title = {Applying a new {CT} quality metric in radiology: How {CT}
                 pulmonary angiography repeat rates compare across institutions},
  author = {Rose, Sean and Viggiano, Ben and Bour, Robert and Bartels, Carrie and Kanne, Jeffery P and Szczykutowicz, Timothy P},
  journal = {J. Am. Coll. Radiol.},
  publisher = {Elsevier BV},
  volume = {18},
  number = {7},
  pages = {962--968},
  month = jul,
  year = {2021},
  language = {en},
  url = {https://pubmed.ncbi.nlm.nih.gov/33741373/},
}

Effect of contrast agent administration on water equivalent diameter in CT

Ben Viggiano, Sean Rose, and Timothy P Szczykutowicz

Mar 2021

Med. Phys. Cite

@article{Viggiano2021-tk,
  title = {Effect of contrast agent administration on water equivalent
                 diameter in {CT}},
  author = {Viggiano, Ben and Rose, Sean and Szczykutowicz, Timothy P},
  journal = {Med. Phys.},
  publisher = {Wiley},
  volume = {48},
  number = {3},
  pages = {1117--1124},
  month = mar,
  year = {2021},
  language = {en},
  url = {https://pubmed.ncbi.nlm.nih.gov/33440020/},
}

Apparatus for tomography repeat rate/reject rate capture

Timothy P Szczykutowicz, Ben Viggiano, and Sean Rose

Mar 2021

US Patent: 10957444 Cite

@misc{Szczykutowicz2021-de,
  title = {Apparatus for tomography repeat rate/reject rate capture},
  author = {Szczykutowicz, Timothy P and Viggiano, Ben and Rose, Sean},
  journal = {US Patent: 10957444},
  month = mar,
  year = {2021},
  url = {https://patents.google.com/patent/US10957444B2/},
}

2020

A multiinstitutional study on wasted CT scans for over 60,000 patients

Sean Rose, Ben Viggiano, Robert Bour, and 2 more authors

Nov 2020

AJR Am. J. Roentgenol. Cite

@article{Rose2020-ap,
  title = {A multiinstitutional study on wasted {CT} scans for over 60,000
                 patients},
  author = {Rose, Sean and Viggiano, Ben and Bour, Robert and Bartels, Carrie and Szczykutowicz, Timothy},
  journal = {AJR Am. J. Roentgenol.},
  publisher = {American Roentgen Ray Society},
  volume = {215},
  number = {5},
  pages = {1123--1129},
  month = nov,
  year = {2020},
  language = {en},
  url = {https://pubmed.ncbi.nlm.nih.gov/32960668/},
}

2019

A Method for Automated Repeat/Reject Rate Analysis in CT

Sean Rose, Ben Viggiano, and Timothy P Szczykutowicz

Jun 2019

AAPM 2019 Cite

@inproceedings{Rose2019-aapm,
  title = {A Method for Automated Repeat/Reject Rate Analysis in {CT}},
  author = {Rose, Sean and Viggiano, Ben and Szczykutowicz, Timothy P},
  booktitle = {AAPM Annual Meeting 2019},
  journal = {AAPM 2019},
  volume = {46},
  number = {6},
  pages = {E506},
  month = jun,
  year = {2019},
  url = {https://w3.aapm.org/meetings/2019AM/programInfo/programAbs.php?sid=8010&aid=45304},
}