3 Search Results for "Utro, Filippo"

Document
DOI: 10.4230/LIPIcs.SoCG.2025.58
Tracking the Persistence of Harmonic Chains: Barcode and Stability

Authors: Tao Hou, Salman Parsa, and Bei Wang

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
The persistence barcode is a topological descriptor of data that plays a fundamental role in topological data analysis. Given a filtration of data, the persistence barcode tracks the evolution of its homology groups. In this paper, we introduce a new type of barcode, called the harmonic chain barcode, which tracks the evolution of harmonic chains. In addition, we show that the harmonic chain barcode is stable. Given a filtration of a simplicial complex of size m, we present an algorithm to compute its harmonic chain barcode in O(m³) time. Consequently, the harmonic chain barcode can enrich the family of topological descriptors in applications where a persistence barcode is applicable, such as feature vectorization and machine learning.
Cite as

Tao Hou, Salman Parsa, and Bei Wang. Tracking the Persistence of Harmonic Chains: Barcode and Stability. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 58:1-58:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{hou_et_al:LIPIcs.SoCG.2025.58,
  author =	{Hou, Tao and Parsa, Salman and Wang, Bei},
  title =	{{Tracking the Persistence of Harmonic Chains: Barcode and Stability}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{58:1--58:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.58},
  URN =		{urn:nbn:de:0030-drops-232100},
  doi =		{10.4230/LIPIcs.SoCG.2025.58},
  annote =	{Keywords: Persistent homology, harmonic chains, topological data analysis}
}
Document
DOI: 10.4230/LIPIcs.WABI.2018.14
Essential Simplices in Persistent Homology and Subtle Admixture Detection

Authors: Saugata Basu, Filippo Utro, and Laxmi Parida

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
We introduce a robust mathematical definition of the notion of essential elements in a basis of the homology space and prove that these elements are unique. Next we give a novel visualization of the essential elements of the basis of the homology space through a rainfall-like plot (RFL). This plot is data-centric, i.e., is associated with the individual samples of the data, as opposed to the structure-centric barcodes of persistent homology. The proof-of-concept was tested on data generated by SimRA that simulates different admixture scenarios. We show that the barcode analysis can be used not just to detect the presence of admixture but also estimate the number of admixed populations. We also demonstrate that data-centric RFL plots have the potential to further disentangle the common history into admixture events and relative timing of the events, even in very complex scenarios.
Cite as

Saugata Basu, Filippo Utro, and Laxmi Parida. Essential Simplices in Persistent Homology and Subtle Admixture Detection. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 14:1-14:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

Copy BibTex To Clipboard

@InProceedings{basu_et_al:LIPIcs.WABI.2018.14,
  author =	{Basu, Saugata and Utro, Filippo and Parida, Laxmi},
  title =	{{Essential Simplices in Persistent Homology and Subtle Admixture Detection}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{14:1--14:10},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.14},
  URN =		{urn:nbn:de:0030-drops-93166},
  doi =		{10.4230/LIPIcs.WABI.2018.14},
  annote =	{Keywords: population admixture, topological data analysis, persistent homology, population evolution}
}
Document
DOI: 10.4230/DagSemProc.10231.6
Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures

Authors: Raffaele Giancarlo, Davide Corona, Valeria Di Benedetto, Alessandra Gabriele, and Filippo Utro

Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)

Abstract
In the quest for a mathematical measure able to capture and shed light on the dual notions of information and complexity in biosequences, Hazen et al. have introduced the notion of Functional Information (FI for short). It is also the result of earlier considerations and findings by Szostak and Carothers et al. Based on the experiments by Charoters et al., regarding FI in RNA binding activities, we decided to study the relation existing between FI and classic measures of complexity applied on protein-DNA interactions on a genome-wide scale. Using classic complexity measures, i.e, Shannon entropy and Kolmogorov Complexity as both estimated by data compression, we found that FI applied to protein-DNA interactions is genuinely different from them. Such a fact, together with the non-triviality of the biological function considered, contributes to the establishment of FI as a novel and useful measure of biocomplexity. Remarkably, we also found a relationship, on a genome-wide scale, between the redundancy of a genomic region and its ability to interact with a protein. This latter finding justifies even more some principles for the design of motif discovery algorithms. Finally, our experiments bring to light methodological limitations of Linguistic Complexity measures, i.e., a class of measures that is a function of the vocabulary richness of a sequence. Indeed, due to the technology and associated statistical preprocessing procedures used to conduct our studies, i.e., genome-wide ChIP-chip experiments, that class of measures cannot give any statistically significant indication about complexity and function. A serious limitation due to the widespread use of the technology. References J.M. Carothers, S.C. Oestreich, J.H. Davis, and J.W. Szostack. Informational complexity and functional activity of RNA structures. J. AM. CHEM. SOC., 126 (2004), pp. 5130-5137. R.M. Hazen, P.L. Griffin, J.M. Carothers, and J.W. Szostak. Functional Information and the emergence of biocomplexity. Proc. of Nat. Acad. Sci, 104 (2007), pp. 8574-8581. J.W. Szostak. Functional Information: molecular messages, Nature, 423 (2003).
Cite as

Raffaele Giancarlo, Davide Corona, Valeria Di Benedetto, Alessandra Gabriele, and Filippo Utro. Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

Copy BibTex To Clipboard

@InProceedings{giancarlo_et_al:DagSemProc.10231.6,
  author =	{Giancarlo, Raffaele and Corona, Davide and Di Benedetto, Valeria and Gabriele, Alessandra and Utro, Filippo},
  title =	{{Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures}},
  booktitle =	{Structure Discovery in Biology: Motifs, Networks \& Phylogenies},
  pages =	{1--13},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{10231},
  editor =	{Alberto Apostolico and Andreas Dress and Laxmi Parida},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.6},
  URN =		{urn:nbn:de:0030-drops-26884},
  doi =		{10.4230/DagSemProc.10231.6},
  annote =	{Keywords: Functional activity, sequence complexity, combinatorics on words, protein-DNA interaction.}
}
  • Refine by Type
  • 3 Document/PDF
  • 1 Document/HTML

  • Refine by Publication Year
  • 1 2025
  • 1 2018
  • 1 2010

  • Refine by Author
  • 2 Utro, Filippo
  • 1 Basu, Saugata
  • 1 Corona, Davide
  • 1 Di Benedetto, Valeria
  • 1 Gabriele, Alessandra
  • Show More...

  • Refine by Series/Journal
  • 2 LIPIcs
  • 1 DagSemProc

  • Refine by Classification
  • 1 Applied computing → Life and medical sciences
  • 1 Mathematics of computing → Topology
  • 1 Theory of computation → Design and analysis of algorithms

  • Refine by Keyword
  • 2 topological data analysis
  • 1 Functional activity
  • 1 Persistent homology
  • 1 combinatorics on words
  • 1 harmonic chains
  • Show More...

Any Issues?
X

Feedback on the Current Page

CAPTCHA

Thanks for your feedback!

Feedback submitted to Dagstuhl Publishing

Could not send message

Please try again later or send an E-mail
© 2023-2026 Schloss Dagstuhl – LZI GmbH Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact