Giulio Ermanno Pibiri

As of June 2022, I am Assistant Professor of Computer Science at Ca’ Foscari University of Venice, Department of Environmental Sciences, Informatics and Statistics. Before that, I have been a Research Fellow in Computer Science at the CNR in Pisa, HPC-Lab, from November 2018 to May 2022 (3 times Young Researcher Award, for the years 2019, 2020, and 2021).

I obtained a PhD in Computer Science in March 2019, and a Master Degree in Computer Science in March 2015 (Best Master Thesis Award in Theoretical Computer Science from EATCS; Master Degree Award from Scuola Superiore Sant’Anna) from the University of Pisa.

I keep an updated copy of my CV here.

My research activity focuses on the design and implementation of compressed data structures for indexing large quantities of data coming from different fields of Computing, such as Bioinformatics, Information Retrieval, and Natural Language Processing. The main objective is to improve the efficiency of complex tasks in these fields by providing efficient (i.e., “fast”) and effective (i.e., “small”) indexes to maintain/query data. In fact, a compressed index uses less storage space than the original data, thus permitting:

for a fixed memory budget, to handle larger datasets;
for the same dataset, to maintain its compressed representation in faster memory levels (e.g., RAM instead of disk), hence granting faster access.

I am committed to efficient software production: my software is available on GitHub.

Some selected research problems I have worked on include: Colored and compacted de Bruijn Graph Indexes, Compressed and Weighted Dictionaries for K-Mers, Minimal Perfect Hashing, Rank/Select and Prefix-Sum Queries, Bitmap Compression, Indexing and Estimation of Language Models, Inverted Index Compression.

If you are interested in problems of this kind, feel free to drop me a line! (giulioermanno.pibiri@unive.it)

Selected Publications

RECOMB2024

Meta-colored compacted de Bruijn graphs

Giulio Ermanno Pibiri, Jason Fan, and Rob Patro

In 28-th International Conference on Research in Computational Molecular Biology, 2024

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TKDE2023

Parallel and External-Memory Construction of Minimal Perfect Hash Functions with PTHash

Giulio Ermanno Pibiri, and Roberto Trani

IEEE Transactions on Knowledge and Data Engineering, 2023

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ISMB2023

Locality-Preserving Minimal Perfect Hashing of k-mers

Giulio Ermanno Pibiri, Yoshihiro Shibuya, and Antoine Limasset

Bioinformatics, 2023

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ISMB2022

Sparse and Skew Hashing of k-mers

Giulio Ermanno Pibiri

Bioinformatics, 2022

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CSUR2021

Techniques for Inverted Index Compression

Giulio Ermanno Pibiri, and Rossano Venturini

ACM Computing Surveys, 2021

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SPE2021

Practical trade-offs for the prefix-sum problem

Giulio Ermanno Pibiri, and Rossano Venturini

Software: Practice and Experience, 2021

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