Alberto Zeni, PhD

NECSTLab

Via Ponzio 34-5

Milan, Milan 20133

I am currently a Post-Doc at Politecnico di Milano at NECSTLab working on Genome Analysis and High Performance Computing.

My research concentrates on the development and acceleration of genome analysis algorithms. I focus on analyzing current bottlenecks in various genome pipelines and developing new solutions that can reduce the time required for the analysis. To this end, I am developing solutions on FPGA or GPU architectures, depending on which is most suited for the task, and providing drop-in replacements for state-of-the-art software solutions.

A recent CV.

The best way to contact me is by email: alberto.zeni@polimi.it

selected publications

Logan: High-performance gpu-based x-drop long-read alignment

Alberto Zeni, Giulia Guidi, Marquita Ellis, and 6 more authors

In 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2020

Bib

@inproceedings{zeni2020logan,
  title = {Logan: High-performance gpu-based x-drop long-read alignment},
  author = {Zeni, Alberto and Guidi, Giulia and Ellis, Marquita and Ding, Nan and Santambrogio, Marco D and Hofmeyr, Steven and Bulu{\c{c}}, Ayd{\i}n and Oliker, Leonid and Yelick, Katherine},
  booktitle = {2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS)},
  pages = {462--471},
  year = {2020},
  organization = {IEEE}
}

The importance of being x-drop: High performance genome alignment on reconfigurable hardware

Alberto Zeni, Guido Walter Di Donato, Lorenzo Di Tucci, and 2 more authors

In 2021 IEEE 29th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM), 2021

Bib

@inproceedings{zeni2021importance,
  title = {The importance of being x-drop: High performance genome alignment on reconfigurable hardware},
  author = {Zeni, Alberto and Di Donato, Guido Walter and Di Tucci, Lorenzo and Rabozzi, Marco and Santambrogio, Marco D},
  booktitle = {2021 IEEE 29th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM)},
  pages = {133--141},
  year = {2021},
  organization = {IEEE}
}

Optimized implementation of the hpcg benchmark on reconfigurable hardware

Alberto Zeni, Kenneth O’Brien, Michaela Blott, and 1 more author

In Euro-Par 2021: Parallel Processing: 27th International Conference on Parallel and Distributed Computing, Lisbon, Portugal, September 1–3, 2021, Proceedings 27, 2021

Bib

@inproceedings{zeni2021optimized,
  title = {Optimized implementation of the hpcg benchmark on reconfigurable hardware},
  author = {Zeni, Alberto and O’Brien, Kenneth and Blott, Michaela and Santambrogio, Marco D},
  booktitle = {Euro-Par 2021: Parallel Processing: 27th International Conference on Parallel and Distributed Computing, Lisbon, Portugal, September 1--3, 2021, Proceedings 27},
  pages = {616--630},
  year = {2021},
  organization = {Springer International Publishing}
}

On the Genome Sequence Alignment FPGA Acceleration via KSW2z

Alberto Zeni, Guido Walter Di Donato, Alessia Della Valle, and 2 more authors

In 2023 IEEE International Symposium on Circuits and Systems (ISCAS), 2023

Bib

@inproceedings{zeni2023genome,
  title = {On the Genome Sequence Alignment FPGA Acceleration via KSW2z},
  author = {Zeni, Alberto and Di Donato, Guido Walter and Della Valle, Alessia and Carloni, Filippo and Santambrogio, Marco D},
  booktitle = {2023 IEEE International Symposium on Circuits and Systems (ISCAS)},
  pages = {1--5},
  year = {2023},
  organization = {IEEE}
}

TSUNAMI: a GPU implementation of the WFA algorithm

Giulia Gerometta, Alberto Zeni, and Marco D Santambrogio

In 2023 32nd International Conference on Parallel Architectures and Compilation Techniques (PACT), 2023

Bib

@inproceedings{gerometta2023tsunami,
  title = {TSUNAMI: a GPU implementation of the WFA algorithm},
  author = {Gerometta, Giulia and Zeni, Alberto and Santambrogio, Marco D},
  booktitle = {2023 32nd International Conference on Parallel Architectures and Compilation Techniques (PACT)},
  pages = {150--161},
  year = {2023},
  organization = {IEEE}
}

Starlight: A kernel optimizer for GPU processing

Alberto Zeni, Emanuele Del Sozzo, Eleonora D’Arnese, and 2 more authors

Journal of Parallel and Distributed Computing, 2024

Bib

@article{zeni2024starlight,
  title = {Starlight: A kernel optimizer for GPU processing},
  author = {Zeni, Alberto and Del Sozzo, Emanuele and D'Arnese, Eleonora and Conficconi, Davide and Santambrogio, Marco D},
  journal = {Journal of Parallel and Distributed Computing},
  pages = {104832},
  year = {2024},
  publisher = {Elsevier}
}