Giulia Bernardini

News

• I am organising a summer school with Gabriele Fici on 12-13 June -- the week before CPM. Registration is free but mandatory. We will have three outstanding speakers: Jonas Ellert, Hideo Bannai, and Giulia Punzi. 

• I am an invited speaker at SEA 2025

Current position 

Assistant Professor at the University of Milano (RTT - tenure track)

Previous positions 

Assistant Professor at the University of Trieste (RTDA)

Postdoc at CWI Amsterdam (2021). Advisor: Prof. Leen Stougie

Ph.D. candidate at the University of Milano - Bicocca (Biaslab) (2017-2021).  Thesis: Combinatorial Methods for the Analysis of Related Genomic Sequences

ASN

• National Scientific qualification as associate professor in the Italian higher education system for the 09/H1 disciplinary field - Information processing systems. Obtained on 10 July 2024

• National Scientific qualification as associate professor in the Italian higher education system for the 01/B1 disciplinary field - Informatics. Obtained on 15 July 2024

Awards

Best Italian PhD Thesis in Theoretical Computer Science 2021 (awarded by the Italian Chapter of EATCS) 

Research interests

• Algorithms and data structures on sequences and graphs with applications in Computational Biology (analysis of genomic sequences and phylogenies) and Data Mining (data sanitisation and pattern mining)

• Optimisation with machine learning: learning-augmented algorithms and learning-aided algorithmic design

Activities

• I was an invited speaker at WABI 2024 (slides) 

• I was a program co-chair (together with Yuto Nakashima) of WCTA 2024

• I am in the PC of CPM 2025 and NeurIPS 202;  I was in the PC of  SPIRE 2024, CPM 2024, ECAI 2024, WABI 2024, ESA (track B) 2023 , CPM 2023, SPIRE 2023, WORDS 2023, AAAI 2023, and CMC 2022

• I organised Automata 2023  and CMC 2022 at the University of Trieste

Publications  (dblp)

• Indexing Strings with Utilities. G.B., H. Chen, A. Conte, R. Grossi, V. Guerrini, G. Loukides, N. Pisanti, S. P. Pissis. (Accepted at ICDE 2025) (preprint)

• Differentially Private Substring and Document Counting. G. B., P. Bille, I. L. Gørtz, T. A. Steiner. (Accepted at PODS 2025) (preprint)

• Cycles and Global Attractors of Reactantless and Inhibitorless Reaction Systems. R. Ascone, G.B., L. Manzoni. (Theoretical Computer Science)

• Missing value replacement in strings and applications.  G.B., C. Liu, G. Loukides, A. Marchetti-Spaccamela, S.P. Pissis, L. Stougie, M. Sweering. (Data Mining and Knowledge Discovery) (preprint)

• Chemical pure reaction automata in maximally parallel manner. R. Ascone, G.B., F.Leiter, L.Manzoni (Journal of Membrane Computing) (preprint)

• Elastic-Degenerate String Matching with 1 Error or Mismatch. G.B., E.Gabory, S.P.Pissis, L.Stougie, M.Sweering, W.Zuba (Theory of Computing Systems) (preprint)

• A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs.  R.Ascone, G.B., A.Conte, M.Equi, E.Gabory, R.Grossi, N.Pisanti (WABI 2024)

• Inferring phylogenetic networks from multifurcating trees via cherry picking and machine learning. G.B., L. van Iersel,  E. Julien, L. Stougie (Molecular Phylogenetics and Evolution) (preprint)

• Utility-Oriented String Mining. G.B., H. Chen, A. Conte, R. Grossi, V. Guerrini, G. Loukides, N. Pisanti, S.P. Pissis (SDM 2024) (preprint)

• Connecting de Bruijn Graphs.  G.B., H. Chen, I. Li Gørtz, C. Krogh, G. Loukides, S.P. Pissis,  L. Stougie, M. Sweering (CPM 2024) (preprint)

• Pure Reaction Automata. R. Ascone, G.B., E.Formenti, F.Leiter, L.Manzoni (Natural Computing)

• Fixed Points and Attractors of Additive Reaction Systems. R.Ascone, G.B., L.Manzoni (Natural Computing)

• Fixed Points and Attractors of Reactantless and Inhibitorless Reaction Systems. R.Ascone, G.B., L.Manzoni (Theoretical Computer Science)

• Substring Complexity in Sublinear Space.  G.B., G. Fici, P. Gawrychowski, S. P. Pissis (ISAAC 2023) (full version)

• Constructing Phylogenetic Networks via Cherry Picking and Machine Learning. G.B., L.van Iersel, E.Julien, L.Stougie (Algorithms for Molecular Biology)

• A Universal Error Measure for Input Predictions Applied to Online Graph Problems. G.B.,  A. Lindermayr,  A. Marchetti-Spaccamela, N. Megow, L. Stougie, M. Sweering (NeurIPS 2022) (preprint)

• Reconstructing Phylogenetic Networks via Cherry Picking and Machine Learning. G.B., L.van Iersel, E.Julien, L.Stougie (WABI 2022) (preprint)

• Elastic-Degenerate String Matching with 1 Error. G.B., E.Gabory, S.P.Pissis, L.Stougie, M.Sweering, W.Zuba (LATIN 2022) (preprint)

• Elastic-Degenerate String Matching via Fast Matrix Multiplication.  G.B., P. Gawrychowski, N. Pisanti, S.P. Pissis, G. Rosone (SIAM Journal on Computing)

• On Strings Having the Same Length-k Substrings.  G.B., A. Conte, E. Gabory, R. Grossi, G. Loukides, S.P. Pissis, G. Punzi,  M. Sweering (CPM 2022)  (preprint)

• Making de Bruijn Graphs Eulerian.  G.B., H. Chen, G. Loukides, S.P. Pissis,  L. Stougie, M. Sweering (CPM 2022) (preprint)

• Hide and Mine in Strings: Hardness, Algorithms and Experiments.  G.B., A. Conte, G. Gourdel, R. Grossi, G. Loukides, N. Pisanti, S.P. Pissis, G. Punzi,  L. Stougie, M. Sweering. (IEEE Transactions on Knowledge and Data Engineering)   (preprint)

• Alignment-Free Genotyping of Known Variations with MALVA. L. Denti, M. Previtali, G.B. (Methods in Molecular Biology)

• Incomplete Directed Perfect Phylogeny in Linear Time.  G.B., P. Bonizzoni, P. Gawrychowski (WADS 2021)   (preprint)   (slides)   (video)

• Reverse-Safe Text Indexing.  G.B., H. Chen, G. Fici, G. Loukides, S.P. Pissis (ACM Journal of Experimental Algorithmics)   (preprint)

• Constructing Strings Avoiding Forbidden Substrings.  G.B., A. Marchetti-Spaccamela, S.P. Pissis, L. Stougie, M. Sweering. (CPM 2021)  (slides)   (preprint)

• Hide and Mine in Strings: Hardness and Algorithms.  G.B., A. Conte, G. Gourdel, R. Grossi, G. Loukides, N. Pisanti, S.P. Pissis, G. Punzi,  L. Stougie, M. Sweering. (20th ICDM)   (preprint)

• Combinatorial Algorithms for String Sanitization.  G.B., H. Chen, A. Conte, R. Grossi, G. Loukides, N. Pisanti, S.P. Pissis, G. Rosone, M. Sweering. (ACM Transactions on Knowledge Discovery from Data)  (preprint) 

• Triplet-Based Similarity Score for Fully Multi-Labeled Trees with Poly-Occurring Labels.  S. Ciccolella, G.B., L. Denti, P. Bonizzoni, M. Previtali, G. Della Vedova  (Bioinformatics)

• On Two Measures of Distance Between Fully-Labelled Trees.  G.B., P. Bonizzoni, P. Gawrychowski  (31th CPM)  (video)  (slides)  (preprint)

• String Sanitization Under Edit Distance.  G.B., H. Chen, A. Conte, R. Grossi, G. Loukides, N. Pisanti, S.P. Pissis, G. Rosone, M. Sweering (31th CPM)   (preprint)

• Longest Property-Preserved Common Factor: A New String-Processing Framework.  L. Ayad, G.B., R. Grossi, C. S. Iliopoulos, N. Pisanti, S. P. Pissis, G. Rosone (Theoretical Computer Science)

• Reverse-Safe Data Structures for Text Indexing.  G.B., H. Chen, G. Fici, G. Loukides, S.P. Pissis (22nd ALENEX)  (slides)

• Comparing Degenerate Strings.  M. Alzamel, L. Ayad, G.B., R. Grossi, C.S. Iliopoulos, N. Pisanti, S.P. Pissis, G. Rosone (Fundamenta Informaticae)  

• String Sanitization: A Combinatorial Approach.  G.B., H. Chen, A. Conte, R. Grossi, G. Loukides, N. Pisanti, S.P. Pissis, G. Rosone (ECML/PKDD 2019)  (preprint)

• Approximate Pattern Matching on Elastic-Degenerate Text.  G.B., N. Pisanti, S.P. Pissis, G. Rosone (Theoretical Computer Science)

• MALVA: genotyping by Mapping-free ALlele detection of known VAriants.  L. Denti, M. Previtali, G.B.,  A. Schönhuth, P. Bonizzoni (iScience) 

• Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication.  G.B., P. Gawrychowski, N. Pisanti, S.P. Pissis, G. Rosone (46th ICALP)  (slides)  (preprint)

• A Rearrangement Distance for Fully-Labelled Trees.  G.B., P. Bonizzoni, G. Della Vedova, M. Patterson (30th CPM)

• Longest Property-Preserved Common Factor.  L. Ayad, G.B., R. Grossi, C.S. Iliopoulos, N. Pisanti, S.P. Pissis, G. Rosone (25th SPIRE)  (preprint)

• Degenerate String Comparison and Applications.  M. Alzamel, L. Ayad, G.B., R. Grossi, C.S. Iliopoulos, N. Pisanti, S.P. Pissis, G. Rosone (18th WABI)  

• Pattern matching on Elastic-Degenerate Text with Errors.  G.B., N. Pisanti, S.P. Pissis, G. Rosone (24th SPIRE)  (preprint)

Interesting links

Zooniverse - an amazing platform for people-powered research, with dozens of wonderful projects to participate in

Giò&Giulia - a live  cam on the nest of two peregrine falcons on top of the Pirellone building in Milan

The Cornell Lab - live cams on red-tailed hawks and other birds