| Title: |
How to measure the topological quality of protein parse trees? |
| Authors: |
Pyzik, Mateusz; Coste, François; Dyrka, Witold |
| Contributors: |
Wrocław University of Science and Technology = Politechnika Wroclawska Wrocław; Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss); Inria Rennes – Bretagne Atlantique; Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7); Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA); Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes); Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique); Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes); Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA); Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique); Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT) |
| Source: |
ICGI 2018 - 14th International Conference on Grammatical Inference ; https://inria.hal.science/hal-01938608 ; ICGI 2018 - 14th International Conference on Grammatical Inference, Sep 2018, Wroclaw, Poland. pp.118 - 138 |
| Publisher Information: |
HAL CCSD |
| Publication Year: |
2018 |
| Collection: |
Université de Rennes 1: Publications scientifiques (HAL) |
| Subject Terms: |
context-free grammar; parse tree; contact map; molecular language; [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]; [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG]; [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI] |
| Subject Geographic: |
Wroclaw; Poland |
| Description: |
International audience ; Human readability and, consequently, interpretability is often considered a key advantage of grammatical descriptors. Beyond the natural language, this is also true in analyzing biological sequences of RNA, typically modeled by grammars of at least context-free level of expressiveness. However, in protein sequence analysis, the explanatory power of grammatical descriptors beyond regular has never been thoroughly assessed. Since the biological meaning of a protein molecule is directly related to its spatial structure, it is justified to expect that the parse tree of a protein sequence reflects the spatial structure of the protein. In this piece of research, we propose and assess quantitative measures for comparing topology of the parse tree of a context-free grammar with topology of the protein structure succinctly represented by a contact map. Our results are potentially interesting beyond its bioinformatic context wherever a reference matrix of dependencies between sequence constituents is available. |
| Document Type: |
conference object |
| Language: |
English |
| Availability: |
https://inria.hal.science/hal-01938608; https://inria.hal.science/hal-01938608v1/document; https://inria.hal.science/hal-01938608v1/file/pyzik18.pdf |
| Rights: |
info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.13748493 |
| Database: |
BASE |