Flavia Esposito

Flavia Esposito is a Research Fellow at the Department of Mathematics at University of Bari "Aldo Moro" (RTD-A in Numerical Analysis).

My research interests focus on mathematics for data science. I work in the MIDAS group since 2014 and our research topics range from dimensionality reduction techniques and matrix decompositions to optimization with the study of hyperparameter tuning in machine learning problems. Our main goal is to understand the mathematics behind data analysing it in different application domains such as bioinformatics and enviromental field.

She has been recently awarded as local PI for the project: "Repurposing marine products for the development of functional foods and bioactives to improve human health and coastal community sustainability" in collaboration with Prof. Raymond Thomas https://mbiproject.ca/.

Academic e-mail: flavia.esposito at uniba dot it 

Academic address: Room 24, Department of Mathematics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy

Journals

1. 1. Nicoletta Del Buono, Flavia Esposito, and Laura Selicato. “Penalizing Low-Rank Matrix Factorization:From theoretical connections to practical applications”. In: Journal of Computational Mathematics and Data Science 14 (Mar. 2025), p. 100111. issn: 2772-4158. doi: 10.1016/j.jcmds.2025.100111.url: http://dx.doi.org/10.1016/j.jcmds.2025.100111.

   2. Nicoletta Del Buono, Flavia Esposito, Laura Selicato, and Rafał Zdunek. “Penalty hyperparameter optimization with diversity measure for nonnegative low-rank approximation”. In: Applied Numerical Mathematics 208 (Feb. 2025), pp. 189–204. issn: 0168-9274. doi:10.1016/j.apnum.2024.10.002.url:http://dx.doi.org/10.1016/j.apnum.2024.10.002.

   3. Flavia Esposito and Andersen Ang. “Chordal-NMF with Riemannian Multiplicative Update”. In: to appear on Journal of Global Optimization (2025). arXiv: 2405.12823 [math.OC]. url: https://arxiv.org/abs/2405.12823.

   4. Flavia Esposito and Andersen Ang. “Riemannian Optimization on the Oblique Manifold for Sparse Simplex Constraints via Multiplicative Updates”. In: submitted (2025). url: https://arxiv.org/abs/2503.24075.

   5. Laura Selicato and Flavia Esposito. “Assess Optimal Penalty Hyperparameters in Nonnegative Matrix Factorization Within Hilbert Spaces Perspective”. In: Mediterranean Journal of Mathematics 22.5 (June 2025). issn: 1660-5454. doi: 10.1007/s00009-025-02875-6. url: http://dx.doi.org/10.1007/s00009-025-02875-6.

   6. Laura Selicato, Flavia Esposito, Andersen Ang, Nicoletta Del Buono, and Rafal Zdunek. “Sparse Hyperparametric Itakura-Saito NMF via Bi-Level Optimization”. In: arXiv preprint arXiv:2502.17123(2025). url: https://arxiv.org/abs/2502.17123.

   7. Laura Selicato, Alessandro Pagano, Flavia Esposito, and Matteo Icardi. “Topological data analysis for resilience assessment of water distribution networks”. In: Mathematics and Computers in Simulation 231 (May 2025), pp. 62–70. issn: 0378-4754. doi: 10.1016/j.matcom.2024.12.001. url:http://dx.doi.org/10.1016/j.matcom.2024.12.001.

   8. Gaetano Settembre, Flavia Esposito, and Nicoletta Del Buono. “Advancing blind hyperspectral unmixing in remote sensing: comparing deep-inspired subspace learning methods”. In: Advanced Modeling and Simulation in Engineering Sciences, in press (2025).

   9. Gaetano Settembre et al. “A land cover change framework analyzing wildfire-affected areas in bitemporal PRISMA hyperspectral images”. In: Mathematics and Computers in Simulation 229 (Mar. 2025), pp. 855–866. issn: 0378-4754. doi: 10 . 1016 / j . matcom . 2024 . 10 . 034. url:http://dx.doi.org/10.1016/j.matcom.2024.10.034.

   10. Angelina Boccarelli, Nicoletta Del Buono, and Flavia Esposito. “Review of Patient Gene Profiles Obtained through a Non-Negative Matrix Factorization-Based Framework to Determine the Role Inflammation Plays in Neuroblastoma Pathogenesis”. In: International Journal of Molecular Sciences 25.8 (Apr. 2024), p. 4406. issn: 1422-0067. doi: 10.3390/ijms25084406. url: http://dx.doi.org/10.3390/ijms25084406.

   11. Ciro Castiello, Nicoletta Del Buono, and Flavia Esposito. “Novel color space representation extracted by NMF to segment a color image”. In: Journal of Computational Mathematics and Data Science13 (Dec. 2024), p. 100104. issn: 2772-4158. doi: 10.1016/j.jcmds.2024.100104. url: http://dx.doi.org/10.1016/j.jcmds.2024.100104

   12. Flavia Esposito, Syed Muhammad Atif, and Nicolas Gillis. “Accelerated SVD-based initialization for nonnegative matrix factorization”. In: Computational and Applied Mathematics 43.6 (Sept. 2024).issn: 1807-0302. doi: 10.1007/s40314-024-02905-1. url: http://dx.doi.org/10.1007/s40314-024-02905-1.

   13. Grazia Gargano et al. “A targeted gene signature stratifying mediastinal gray zone lymphoma into classical HL-like or PMBL-like subtypes”. In: Haematologica 109.11 (July 2024), p. 3771. issn: 0390-6078. doi: 10.3324/haematol.2024.285266. url: http://dx.doi.org/10.3324/haematol.2024.285266.

   14. Angelina Boccarelli, Nicoletta Del Buono, and Flavia Esposito. “Cluster of resistance-inducing genes in MCF-7 cells by estrogen, insulin, methotrexate and tamoxifen extracted via NMF”. In: Pathology Research and Practice 242 (Feb. 2023), p. 154347. issn: 0344-0338. doi: 10.1016/j.prp.2023.154347. url: http://dx.doi.org/10.1016/j.prp.2023.154347.

   15. Nicoletta Del Buono, Flavia Esposito, Laura Selicato, and Rafał Zdunek. “Bi-level algorithm for optimizing hyperparameters in penalized nonnegative matrix factorization”. In: Applied Mathematics and Computation 457 (Nov. 2023), p. 128184. issn: 0096-3003. doi: 10.1016/j.amc.2023.128184. url: http://dx.doi.org/10.1016/j.amc.2023.128184.

   16. Flavia Esposito, Laura Selicato, and Caterina Sportelli. “Theoretical Aspects in Penalty Hyperparameters Optimization”. In: Mediterranean Journal of Mathematics 20.6 (Sept. 2023). issn: 1660-5454. doi: 10.1007/s00009-023-02497-w. url: http://dx.doi.org/10.1007/s00009-023-02497-w.

   17. Filippo Giordano et al. “Effect of music therapy intervention on anxiety and pain during percutaneous renal biopsy: a randomized controlled trial”. In: Clinical Kidney Journal 16.12 (2023), pp. 2721–2727.doi: 10.1093/ckj/sfad246. url: https://doi.org/10.1093/ckj/sfad246.

   18. Gian Maria Zaccaria et al. “A Decision-tree Approach to Stratify DLBCL Risk Based on Stromal and Immune Microenvironment Determinants”. In: HemaSphere 7.4 (Apr. 2023), e862. issn: 2572-9241. doi: 10.1097/hs9.0000000000000862. url: http://dx.doi.org/10.1097/HS9.0000000000000862.

   19. Angelina Boccarelli, Nicoletta Del Buono, and Flavia Esposito. “Colorectal cancer in Crohn’s disease evaluated with genes belonging to fibroblasts of the intestinal mucosa selected by NMF”. In: Pathology- Research and Practice 229 (Jan. 2022), p. 153728. issn: 0344-0338. doi: 10.1016/j.prp.2021.153728. url: http://dx.doi.org/10.1016/j.prp.2021.153728.

   20. Moganatharsa Ganeshalingam et al. “Role of lipidomics in assessing the functional lipid composition in breast milk”. In: Frontiers in Nutrition 9 (Sept. 2022). issn: 2296-861X. doi: 10.3389/fnut.2022.899401. url: http://dx.doi.org/10.3389/fnut.2022.899401.

   21. Maria Carmela Vegliante et al. “A Digital Gene-Expression Signature Supports Mediastinal Gray Zone Lymphoma Stratification within Classical Hodgkin or Primary Mediastinal B-Cell Lymphoma”. In:Blood 140.Supplement 1 (Nov. 2022), pp. 9312–9313. issn: 1528-0020. doi: 10.1182/blood-2022-159478. url: http://dx.doi.org/10.1182/blood-2022-159478.

   22. Maria Carmela Vegliante et al. “NR1H3 (LXR) is associated with pro-inflammatory macrophages,predicts survival and suggests potential therapeutic rationales in diffuse large b-cell lymphoma”. In:Hematological Oncology 40.5 (Aug. 2022), pp. 864–875. issn: 1099-1069. doi: 10.1002/hon.3050.url: http://dx.doi.org/10.1002/hon.3050.

   23. Angelina Boccarelli, Nicoletta Del Buono, and Flavia Esposito. “Analysis of fibroblast genes selected by NMF to reveal the potential crosstalk between ulcerative colitis and colorectal cancer”. In:Experimental and Molecular Pathology 123 (Dec. 2021), p. 104713. issn: 0014-4800. doi: 10.1016/j.yexmp.2021.104713. url:http://dx.doi.org/10.1016/j.yexmp.2021.104713.

   24. Flavia Esposito. “A Review on Initialization Methods for Nonnegative Matrix Factorization: TowardsOmics Data Experiments”. In: Mathematics 9.9 (Apr. 2021), p. 1006. issn: 2227-7390. doi: 10.3390/math9091006. url: http://dx.doi.org/10.3390/math9091006

   25. Flavia Esposito, Nicoletta Del Buono, and Laura Selicato. “Nonnegative Matrix Factorization models for knowledge extraction from biomedical and other real world data”. In: PAMM 20.1 (Jan. 2021),e202000032. issn: 1617-7061. doi: 10.1002/pamm.202000032. url: http://dx.doi.org/10.1002/pamm.202000032.

   26. Laura Selicato et al. “A New Ensemble Method for Detecting Anomalies in Gene Expression Matrices”.In: Mathematics 9.8 (Apr. 2021), p. 882. issn: 2227-7390. doi: 10.3390/math9080882. url:http://dx.doi.org/10.3390/math9080882.

   27. Gian Maria Zaccaria et al. “Electronic case report forms generation from pathology reports by ARGO,automatic record generator for onco-hematology”. In: Scientific Reports 11.1 (Dec. 2021). issn:2045-2322. doi: 10.1038/s41598-021-03204-z. url: http://dx.doi.org/10.1038/s41598-021-03204-z.

   28. Flavia Esposito, Angelina Boccarelli, and Nicoletta Del Buono. “An NMF-Based Methodology for Selecting Biomarkers in the Landscape of Genes of Heterogeneous Cancer-Associated Fibroblast Populations”.In: Bioinformatics and Biology Insights 14 (Jan. 2020), p. 117793222090682. issn: 1177-9322.doi: 10.1177/1177932220906827. url: http://dx.doi.org/10.1177/1177932220906827.

   29. Filippo Giordano et al. “The influence of music therapy on preoperative anxiety in pediatric oncology patients undergoing invasive procedures”. In: The Arts in Psychotherapy 68 (Mar. 2020), p. 101649.issn: 0197-4556. doi: 10.1016/j.aip.2020.101649. url: http://dx.doi.org/10.1016/j.aip.2020.101649.

   30. Flavia Esposito, Nicolas Gillis, and Nicoletta Del Buono. “Orthogonal joint sparse NMF for microarray data analysis”. In: Journal of Mathematical Biology 79.1 (Apr. 2019), pp. 223–247. issn: 1432-1416.doi: 10.1007/s00285-019-01355-2. url: http://dx.doi.org/10.1007/s00285-019-01355-2.

   31. Angelina Boccarelli et al. “Improving knowledge on the activation of bone marrow fibroblasts in MGUS and MM disease through the automatic extraction of genes via a nonnegative matrix factorization approach on gene expression profiles”. In: Journal of Translational Medicine 16.1 (Aug. 2018). issn:1479-5876. doi: 10.1186/s12967-018-1589-1. url: http://dx.doi.org/10.1186/s12967-018-1589-1.

Book Chapter

1. Ciro Castiello, Nicoletta Del Buono, and Flavia Esposito. “Improving Color Image Binary Segmentation Using Nonnegative Matrix Factorization”. In: Computational Science and Its Applications – ICCSA 2023 Workshops. Springer Nature Switzerland, 2023, pp. 623–640. isbn: 9783031371172. doi:10.1007/978-3-031-37117-2_42. url: http://dx.doi.org/10.1007/978-3-031-37117-2_42.

2. Nicoletta Del Buono et al. “Detecting Anomalies in Marine Data: A Framework for Time Series Analysis”. In: Machine Learning, Optimization, and Data Science. Springer Nature Switzerland, 2023,pp. 485–500. isbn: 9783031255991. doi: 10 . 1007 / 978 - 3 - 031 - 25599 - 1 _ 36. url: http ://dx.doi.org/10.1007/978-3-031-25599-1_36.

3. Gaetano Settembre, Nicola Corriero, Nicoletta Del Buono, Flavia Esposito, and Rosanna Rizzi.“Machine Learning Approaches for Predicting Crystal Systems: A Brief Review and a Case Study”. In:Machine Learning, Optimization, and Data Science. Springer Nature Switzerland, 2023, pp. 93–107.isbn: 9783031255991. doi: 10.1007/978-3-031-25599-1_8. url: http://dx.doi.org/10.1007/978-3-031-25599-1_8.

4. Nicoletta Del Buono, Flavia Esposito, and Laura Selicato. “Toward a New Approach for Tuning Regularization Hyperparameter in NMF”. In: Machine Learning, Optimization, and Data Science. Springer International Publishing, 2022, pp. 500–511. isbn: 9783030954673. doi: 10.1007/978-3-030-95467-3_36. url: http://dx.doi.org/10.1007/978-3-030-95467-3_36.

5. Nicoletta Del Buono, Flavia Esposito, and Laura Selicato. “Methods for Hyperparameters Optimization in Learning Approaches: An Overview”. In: Machine Learning, Optimization, and Data Science.Springer International Publishing, 2020, pp. 100–112. isbn: 9783030645830. doi: 10.1007/978-3-030-64583-0_11. url: http://dx.doi.org/10.1007/978-3-030-64583-0_11.

6. Nicoletta Del Buono and Flavia Esposito. “Investigating NMF Initializations: A survey and a microarray case study.” In: Universitas Studiorum, 2019. Chap. Series in Applied Sciences.

7. Nicoletta Del Buono and Flavia Esposito. “On some practical issues related to Nonnegative Matrix Factorization in Microarray Data Analysis context”. In: Universitas Studiorum, 2018. Chap. Series in Applied Sciences.

8. Gabriella Casalino, Ciro Castiello, Nicoletta Del Buono, Flavia Esposito, and Corrado Mencar. “Q-matrix Extraction from Real Response Data Using Nonnegative Matrix Factorizations”. In: Computational Science and Its Applications – ICCSA 2017. Springer International Publishing, 2017, pp. 203–216. isbn: 9783319623924. doi: 10.1007/978-3-319-62392-4_15. url: http://dx.doi.org/10.1007/978-3-319-62392-4_15.

9. Nicoletta Del Buono, Flavia Esposito, Fabio Fumarola, Angelina Boccarelli, and Mauro Coluccia.“Breast Cancer’s Microarray Data: Pattern Discovery Using Nonnegative Matrix Factorizations”. In:Machine Learning, Optimization, and Big Data. Springer International Publishing, 2016, pp. 281–292.isbn: 9783319514697. doi: 10.1007/978-3-319-51469-7_24. url: http://dx.doi.org/10.1007/978-3-319-51469-7_24.

Conference Proceedings

1. Gaetano Settembre, Nicoló Taggio, Nicoletta Del Buono, Antonello Aiello, and Flavia Esposito.“Low-Rank Hierarchical Clustering of PRISMA Hyperspectral Images to Identify Burned Areas”. In:Machine Learning and Principles and Practice of Knowledge Discovery in Databases. Springer Nature Switzerland, 2025, pp. 412–423. isbn: 9783031746338. doi: 10.1007/978-3-031-74633-8_30.url: http://dx.doi.org/10.1007/978-3-031-74633-8_30.

2. Gaetano Settembre, Nicoletta Del Buono, Flavia Esposito, and Nicolò Taggio. “Deep NMF and Autoencoder: A Comparative Analysis for Hyperspectral Unmixing Using Prisma Real Images”. In:IGARSS 2024 - 2024 IEEE International Geoscience and Remote Sensing Symposium. IEEE, July 2024, pp. 3708–3712. doi: 10.1109/igarss53475.2024.10642930. url: http://dx.doi.org/10.1109/IGARSS53475.2024.10642930.

3. Nicoletta Del Buono, Flavia Esposito, Laura Selicato, and Maria Carmela Vegliante. “Anomalies Detection in Gene Expression Matrices: Towards a New Approach.” In: BIOINFORMATICS. SCITEPRESS- Science and Technology Publications, 2021, pp. 162–169. doi: 10.5220/0010342300002865. url:http://dx.doi.org/10.5220/0010342300002865.

4. Alessandra Scarcelli et al. “RADON Project: From Children’s Game To Intelligent Personal Dosimeter”.In: 2020 IEEE International Workshop on Metrology for Industry 4.0 & IoT. IEEE, June 2020, pp. 146–151. doi: 10.1109/metroind4.0iot48571.2020.9138190. url: http://dx.doi.org/10.1109/MetroInd4.0IoT48571.2020.9138190.

Thesis

• Nonnegative Matrix Factorizations for Knowledge Extraction from Biomedical and other real world data. F. Esposito, Department of Computer Science, University of Bari Aldo Moro, Italy PhD thesis, 2019

• Mathematical Models and Numerical Methods for Omics Data Analysis, Dottorato di ricerca in Informatica e Matematica, UniBa (AY 2024-2025);

• Low-rank Approaches for Data Analysis: Models, Numerical Methods and Applications, Remagen University, Germany(AY 2022-2023);

• Low-rank Approaches for Data Analysis: Models, Numerical Methods and Applications, Dottorato di ricerca Computer Science and Engineering , University of Bologna (AY 2022-2023);

• Metodi Numerici per la Bioinformatica, CdL Magistrale Bioinformatica, UniBa (AYs 2023-2024);

• Fondamenti di Matematica per l'Analisi dei Dati, CdL Magistrale Bioinformatica, UniBa (AYs 2022-2023, 2023-2024, 2024-2025, 2025-2026);

• Laboratorio di Programmazione e Calcolo CdL Triennale in Chimica, UniBa (AYs 2021-2022, 2022-2023);

• Metodi Numerici per la Data Science CdL Triennale in Matematica,UniBa (AYs 2020-2021, 2021-2022, 2022-2023, 2023-2024, 2024-2025, 2025-2026), Materials;

• OFA CdL Triennale in Matematica, UniBa (AY 2020-2021);