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José Pinto 0007

dblp:330/6553 · DBLP profile ↗
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1ranked-venue papers
1as first author
1since 2021 · last 2023
0000-0002-2196-9756ORCID · verified

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 1 heaviest of 2, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › systems biology › computational systems biology
systems biology modeling
0.712023
SBML2HYB: a Python interface for SBML compatible hybrid modeling · Bioinform. 2023

Methods — techniques the papers use, named apart from their topics

semi-parametric modeling · 0.7machine learning · 0.7SBML · 0.7
YearPublicationVenuePosition
2023 SBML2HYB: a Python interface for SBML compatible hybrid modeling
abstract
SUMMARY: Here, we present sbml2hyb, an easy-to-use standalone Python tool that facilitates the conversion of existing mechanistic models of biological systems in Systems Biology Markup Language (SBML) into hybrid semiparametric models that combine mechanistic functions with machine learning (ML). The so-formed hybrid models can be trained and stored back in databases in SBML format. The tool supports a user-friendly export interface with an internal format validator. Two case studies illustrate the use of the sbml2hyb tool. Additionally, we describe HMOD, a new model format designed to support and facilitate hybrid models building. It aggregates the mechanistic model information with the ML information and follows as close as possible the SBML rules. We expect the sbml2hyb tool and HMOD to greatly facilitate the widespread usage of hybrid modeling techniques for biological systems analysis. AVAILABILITY AND IMPLEMENTATION: The Python interface, source code and the example models used for the case studies are accessible at: https://github.com/r-costa/sbml2hyb. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
José Pinto 0007, Rafael S. Costa, Leonardo Alexandre, Rui Oliveira 0002
Bioinform.1