2024
2.
Hafner, Jasmin; Lorsbach, Tim; Schmidt, Sebastian; Brydon, Liam; Dost, Katharina; Zhang, Kunyang; Fenner, Kathrin; Wicker, Jörg
Advancements in Biotransformation Pathway Prediction: Enhancements, Datasets, and Novel Functionalities in enviPath Journal Article
In: Journal of Cheminformatics, vol. 16, no. 1, pp. 93, 2024, ISSN: 1758-2946.
Abstract | Links | BibTeX | Altmetric | PlumX | Tags: applicability domain, biodegradation, bioinformatics, cheminformatics, computational sustainability, enviPath, linked data, machine learning, multi-label classification, Process-based modeling
@article{hafner2023advancements,
title = {Advancements in Biotransformation Pathway Prediction: Enhancements, Datasets, and Novel Functionalities in enviPath},
author = {Jasmin Hafner and Tim Lorsbach and Sebastian Schmidt and Liam Brydon and Katharina Dost and Kunyang Zhang and Kathrin Fenner and J\"{o}rg Wicker},
url = {https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00881-6
https://envipath.org},
doi = {10.1186/s13321-024-00881-6},
issn = {1758-2946},
year = {2024},
date = {2024-08-06},
urldate = {2024-08-06},
journal = {Journal of Cheminformatics},
volume = {16},
number = {1},
pages = {93},
abstract = {enviPath is a widely used database and prediction system for microbial biotransformation pathways of primarily xenobiotic compounds. Data and prediction system are freely available both via a web interface and a public REST API. Since its initial release in 2016, we extended the data available in enviPath and improved the performance of the prediction system and usability of the overall system. We now provide three diverse data sets, covering microbial biotransformation in different environments and under different experimental conditions. This also enabled developing a pathway prediction model that is applicable to a more diverse set of chemicals. In the prediction engine, we implemented a new evaluation tailored towards pathway prediction, which returns a more honest and holistic view on the performance. We also implemented a novel applicability domain algorithm, which allows the user to estimate how well the model will perform on their data. Finally, we improved the implementation to speed up the overall system and provide new functionality via a plugin system.
},
keywords = {applicability domain, biodegradation, bioinformatics, cheminformatics, computational sustainability, enviPath, linked data, machine learning, multi-label classification, Process-based modeling},
pubstate = {published},
tppubtype = {article}
}
enviPath is a widely used database and prediction system for microbial biotransformation pathways of primarily xenobiotic compounds. Data and prediction system are freely available both via a web interface and a public REST API. Since its initial release in 2016, we extended the data available in enviPath and improved the performance of the prediction system and usability of the overall system. We now provide three diverse data sets, covering microbial biotransformation in different environments and under different experimental conditions. This also enabled developing a pathway prediction model that is applicable to a more diverse set of chemicals. In the prediction engine, we implemented a new evaluation tailored towards pathway prediction, which returns a more honest and holistic view on the performance. We also implemented a novel applicability domain algorithm, which allows the user to estimate how well the model will perform on their data. Finally, we improved the implementation to speed up the overall system and provide new functionality via a plugin system.
2012
1.
Čerepnalkoski, Darko; Taškova, Katerina; Todorovski, Ljupčo; Atanasova, Nataša; Džeroski, Sašo
The influence of parameter fitting methods on model structure selection in automated modeling of aquatic ecosystems Journal Article
In: Ecological Modelling, vol. 245, pp. 136-165, 2012, ISSN: 0304-3800, (7th European Conference on Ecological Modelling (ECEM)).
Abstract | Links | BibTeX | Altmetric | PlumX | Tags: Aquatic ecosystems, Dynamical systems, Equation discovery, Meta-heuristic optimization, Parameter estimation, Process-based modeling
@article{CEREPNALKOSKI2012136,
title = {The influence of parameter fitting methods on model structure selection in automated modeling of aquatic ecosystems},
author = {Darko \v{C}erepnalkoski and Katerina Ta\v{s}kova and Ljup\v{c}o Todorovski and Nata\v{s}a Atanasova and Sa\v{s}o D\v{z}eroski},
url = {https://www.sciencedirect.com/science/article/pii/S0304380012002724},
doi = {https://doi.org/10.1016/j.ecolmodel.2012.06.001},
issn = {0304-3800},
year = {2012},
date = {2012-01-01},
journal = {Ecological Modelling},
volume = {245},
pages = {136-165},
abstract = {Modeling dynamical systems involves two subtasks: structure identification and parameter estimation. ProBMoT is a tool for automated modeling of dynamical systems that addresses both tasks simultaneously. It takes into account domain knowledge formalized as templates for components of the process-based models: entities and processes. Taking a conceptual model of the system, the library of domain knowledge, and measurements of a particular dynamical system, it identifies both the structure and numerical parameters of the appropriate process-based model. ProBMoT has two main components corresponding to the two subtasks of modeling. The first component is concerned with generating candidate model structures that adhere to the conceptual model specified as input. The second subsystem uses the measured data to find suitable values for the constant parameters of a given model by using parameter estimation methods. ProBMoT uses model error to rank model structures and select the one that fits measured data best. In this paper, we investigate the influence of the selection of the parameter estimation methods on the structure identification. We consider one local (derivative-based) and one global (meta-heuristic) parameter estimation method. As opposed to other comparative studies of parameter estimation methods that focus on identifying parameters of a single model structure, we compare the parameter estimation methods in the context of repetitive parameter estimation for a number of candidate model structures. The results confirm the superiority of the global optimization methods over the local ones in the context of structure identification.},
note = {7th European Conference on Ecological Modelling (ECEM)},
keywords = {Aquatic ecosystems, Dynamical systems, Equation discovery, Meta-heuristic optimization, Parameter estimation, Process-based modeling},
pubstate = {published},
tppubtype = {article}
}
Modeling dynamical systems involves two subtasks: structure identification and parameter estimation. ProBMoT is a tool for automated modeling of dynamical systems that addresses both tasks simultaneously. It takes into account domain knowledge formalized as templates for components of the process-based models: entities and processes. Taking a conceptual model of the system, the library of domain knowledge, and measurements of a particular dynamical system, it identifies both the structure and numerical parameters of the appropriate process-based model. ProBMoT has two main components corresponding to the two subtasks of modeling. The first component is concerned with generating candidate model structures that adhere to the conceptual model specified as input. The second subsystem uses the measured data to find suitable values for the constant parameters of a given model by using parameter estimation methods. ProBMoT uses model error to rank model structures and select the one that fits measured data best. In this paper, we investigate the influence of the selection of the parameter estimation methods on the structure identification. We consider one local (derivative-based) and one global (meta-heuristic) parameter estimation method. As opposed to other comparative studies of parameter estimation methods that focus on identifying parameters of a single model structure, we compare the parameter estimation methods in the context of repetitive parameter estimation for a number of candidate model structures. The results confirm the superiority of the global optimization methods over the local ones in the context of structure identification.