Giulia Bernardini

Current position 

Assistant professor at the University of Trieste (RTDA)

Previous positions 

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

Habilitations

• 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

Teaching and professional activities

• I am currently teaching the Algorithmic Design and the Algorithmic Data Mining courses in the Master’s Degree Programmes "Data Science and Artificial Intelligence" and "Scientific and Data Intensive Computing" at the University of Trieste

• I was part of the program committee 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)

• 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 (to me) 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