2024
8.
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.
2023
7.
Dost, Katharina; Pullar-Strecker, Zac; Brydon, Liam; Zhang, Kunyang; Hafner, Jasmin; Riddle, Pat; Wicker, Jörg
Combatting over-specialization bias in growing chemical databases Journal Article
In: Journal of Cheminformatics, vol. 15, iss. 1, pp. 53, 2023, ISSN: 1758-2946.
Abstract | Links | BibTeX | Altmetric | PlumX | Tags: bias, biodegradation, cheminformatics, computational sustainability, data mining, enviPath, machine learning, metabolic pathways, multi-label classification, reliable machine learning
@article{Dost2023Combatting,
title = {Combatting over-specialization bias in growing chemical databases},
author = {Katharina Dost and Zac Pullar-Strecker and Liam Brydon and Kunyang Zhang and Jasmin Hafner and Pat Riddle and J\"{o}rg Wicker},
url = {https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00716-w
},
doi = {10.1186/s13321-023-00716-w},
issn = {1758-2946},
year = {2023},
date = {2023-05-19},
urldate = {2023-05-19},
journal = {Journal of Cheminformatics},
volume = {15},
issue = {1},
pages = {53},
abstract = {Background
Predicting in advance the behavior of new chemical compounds can support the design process of new products by directing the research toward the most promising candidates and ruling out others. Such predictive models can be data-driven using Machine Learning or based on researchers’ experience and depend on the collection of past results. In either case: models (or researchers) can only make reliable assumptions about compounds that are similar to what they have seen before. Therefore, consequent usage of these predictive models shapes the dataset and causes a continuous specialization shrinking the applicability domain of all trained models on this dataset in the future, and increasingly harming model-based exploration of the space.
Proposed solution
In this paper, we propose cancels (CounterActiNg Compound spEciaLization biaS), a technique that helps to break the dataset specialization spiral. Aiming for a smooth distribution of the compounds in the dataset, we identify areas in the space that fall short and suggest additional experiments that help bridge the gap. Thereby, we generally improve the dataset quality in an entirely unsupervised manner and create awareness of potential flaws in the data. cancels does not aim to cover the entire compound space and hence retains a desirable degree of specialization to a specified research domain.
Results
An extensive set of experiments on the use-case of biodegradation pathway prediction not only reveals that the bias spiral can indeed be observed but also that cancels produces meaningful results. Additionally, we demonstrate that mitigating the observed bias is crucial as it cannot only intervene with the continuous specialization process, but also significantly improves a predictor’s performance while reducing the number of required experiments. Overall, we believe that cancels can support researchers in their experimentation process to not only better understand their data and potential flaws, but also to grow the dataset in a sustainable way. All code is available under github.com/KatDost/Cancels.},
keywords = {bias, biodegradation, cheminformatics, computational sustainability, data mining, enviPath, machine learning, metabolic pathways, multi-label classification, reliable machine learning},
pubstate = {published},
tppubtype = {article}
}
Background
Predicting in advance the behavior of new chemical compounds can support the design process of new products by directing the research toward the most promising candidates and ruling out others. Such predictive models can be data-driven using Machine Learning or based on researchers’ experience and depend on the collection of past results. In either case: models (or researchers) can only make reliable assumptions about compounds that are similar to what they have seen before. Therefore, consequent usage of these predictive models shapes the dataset and causes a continuous specialization shrinking the applicability domain of all trained models on this dataset in the future, and increasingly harming model-based exploration of the space.
Proposed solution
In this paper, we propose cancels (CounterActiNg Compound spEciaLization biaS), a technique that helps to break the dataset specialization spiral. Aiming for a smooth distribution of the compounds in the dataset, we identify areas in the space that fall short and suggest additional experiments that help bridge the gap. Thereby, we generally improve the dataset quality in an entirely unsupervised manner and create awareness of potential flaws in the data. cancels does not aim to cover the entire compound space and hence retains a desirable degree of specialization to a specified research domain.
Results
An extensive set of experiments on the use-case of biodegradation pathway prediction not only reveals that the bias spiral can indeed be observed but also that cancels produces meaningful results. Additionally, we demonstrate that mitigating the observed bias is crucial as it cannot only intervene with the continuous specialization process, but also significantly improves a predictor’s performance while reducing the number of required experiments. Overall, we believe that cancels can support researchers in their experimentation process to not only better understand their data and potential flaws, but also to grow the dataset in a sustainable way. All code is available under github.com/KatDost/Cancels.
Predicting in advance the behavior of new chemical compounds can support the design process of new products by directing the research toward the most promising candidates and ruling out others. Such predictive models can be data-driven using Machine Learning or based on researchers’ experience and depend on the collection of past results. In either case: models (or researchers) can only make reliable assumptions about compounds that are similar to what they have seen before. Therefore, consequent usage of these predictive models shapes the dataset and causes a continuous specialization shrinking the applicability domain of all trained models on this dataset in the future, and increasingly harming model-based exploration of the space.
Proposed solution
In this paper, we propose cancels (CounterActiNg Compound spEciaLization biaS), a technique that helps to break the dataset specialization spiral. Aiming for a smooth distribution of the compounds in the dataset, we identify areas in the space that fall short and suggest additional experiments that help bridge the gap. Thereby, we generally improve the dataset quality in an entirely unsupervised manner and create awareness of potential flaws in the data. cancels does not aim to cover the entire compound space and hence retains a desirable degree of specialization to a specified research domain.
Results
An extensive set of experiments on the use-case of biodegradation pathway prediction not only reveals that the bias spiral can indeed be observed but also that cancels produces meaningful results. Additionally, we demonstrate that mitigating the observed bias is crucial as it cannot only intervene with the continuous specialization process, but also significantly improves a predictor’s performance while reducing the number of required experiments. Overall, we believe that cancels can support researchers in their experimentation process to not only better understand their data and potential flaws, but also to grow the dataset in a sustainable way. All code is available under github.com/KatDost/Cancels.
2017
6.
Latino, Diogo; Wicker, Jörg; Gütlein, Martin; Schmid, Emanuel; Kramer, Stefan; Fenner, Kathrin
Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data Journal Article
In: Environmental Science: Process & Impact, 2017.
Abstract | Links | BibTeX | Altmetric | PlumX | Tags: biodegradation, cheminformatics, computational sustainability, data mining, enviPath, multi-label classification, REST, web services
@article{latino2017eawag,
title = {Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data},
author = {Diogo Latino and J\"{o}rg Wicker and Martin G\"{u}tlein and Emanuel Schmid and Stefan Kramer and Kathrin Fenner},
doi = {10.1039/C6EM00697C},
year = {2017},
date = {2017-01-01},
journal = {Environmental Science: Process \& Impact},
publisher = {The Royal Society of Chemistry},
abstract = {Developing models for the prediction of microbial biotransformation pathways and half-lives of trace organic contaminants in different environments requires as training data easily accessible and sufficiently large collections of respective biotransformation data that are annotated with metadata on study conditions. Here, we present the Eawag-Soil package, a public database that has been developed to contain all freely accessible regulatory data on pesticide degradation in laboratory soil simulation studies
for pesticides registered in the EU (282 degradation pathways, 1535 reactions, 1619 compounds and 4716 biotransformation half-life values with corresponding metadata on study conditions). We provide a thorough description of this novel data resource, and discuss important features of the pesticide soil degradation data that are relevant for model development. Most notably, the variability of half-life values for individual compounds is large and only about one order of magnitude lower than the entire range of median half-life values spanned by all compounds, demonstrating the need to consider study conditions in the development of more accurate models for biotransformation prediction. We further show how the data can be used to find missing rules relevant for predicting soil biotransformation pathways. From this analysis, eight examples of reaction types were presented that should trigger the formulation of new biotransformation rules, e.g., Ar-OH methylation, or the extension of existing rules e.g., hydroxylation in aliphatic rings. The data were also used to exemplarily explore the dependence of half-lives of different amide pesticides on chemical class and experimental parameters. This analysis highlighted the value of considering initial transformation reactions for the development of meaningful quantitative-structure biotransformation relationships (QSBR), which is a novel opportunity of f ered by the simultaneous encoding of transformation reactions and corresponding half-lives in Eawag-Soil. Overall, Eawag-Soil provides an unprecedentedly rich collection of manually extracted and curated biotransformation data, which should be useful in a great variety of applications.},
keywords = {biodegradation, cheminformatics, computational sustainability, data mining, enviPath, multi-label classification, REST, web services},
pubstate = {published},
tppubtype = {article}
}
Developing models for the prediction of microbial biotransformation pathways and half-lives of trace organic contaminants in different environments requires as training data easily accessible and sufficiently large collections of respective biotransformation data that are annotated with metadata on study conditions. Here, we present the Eawag-Soil package, a public database that has been developed to contain all freely accessible regulatory data on pesticide degradation in laboratory soil simulation studies
for pesticides registered in the EU (282 degradation pathways, 1535 reactions, 1619 compounds and 4716 biotransformation half-life values with corresponding metadata on study conditions). We provide a thorough description of this novel data resource, and discuss important features of the pesticide soil degradation data that are relevant for model development. Most notably, the variability of half-life values for individual compounds is large and only about one order of magnitude lower than the entire range of median half-life values spanned by all compounds, demonstrating the need to consider study conditions in the development of more accurate models for biotransformation prediction. We further show how the data can be used to find missing rules relevant for predicting soil biotransformation pathways. From this analysis, eight examples of reaction types were presented that should trigger the formulation of new biotransformation rules, e.g., Ar-OH methylation, or the extension of existing rules e.g., hydroxylation in aliphatic rings. The data were also used to exemplarily explore the dependence of half-lives of different amide pesticides on chemical class and experimental parameters. This analysis highlighted the value of considering initial transformation reactions for the development of meaningful quantitative-structure biotransformation relationships (QSBR), which is a novel opportunity of f ered by the simultaneous encoding of transformation reactions and corresponding half-lives in Eawag-Soil. Overall, Eawag-Soil provides an unprecedentedly rich collection of manually extracted and curated biotransformation data, which should be useful in a great variety of applications.
for pesticides registered in the EU (282 degradation pathways, 1535 reactions, 1619 compounds and 4716 biotransformation half-life values with corresponding metadata on study conditions). We provide a thorough description of this novel data resource, and discuss important features of the pesticide soil degradation data that are relevant for model development. Most notably, the variability of half-life values for individual compounds is large and only about one order of magnitude lower than the entire range of median half-life values spanned by all compounds, demonstrating the need to consider study conditions in the development of more accurate models for biotransformation prediction. We further show how the data can be used to find missing rules relevant for predicting soil biotransformation pathways. From this analysis, eight examples of reaction types were presented that should trigger the formulation of new biotransformation rules, e.g., Ar-OH methylation, or the extension of existing rules e.g., hydroxylation in aliphatic rings. The data were also used to exemplarily explore the dependence of half-lives of different amide pesticides on chemical class and experimental parameters. This analysis highlighted the value of considering initial transformation reactions for the development of meaningful quantitative-structure biotransformation relationships (QSBR), which is a novel opportunity of f ered by the simultaneous encoding of transformation reactions and corresponding half-lives in Eawag-Soil. Overall, Eawag-Soil provides an unprecedentedly rich collection of manually extracted and curated biotransformation data, which should be useful in a great variety of applications.
2016
5.
Wicker, Jörg; Fenner, Kathrin; Kramer, Stefan
A Hybrid Machine Learning and Knowledge Based Approach to Limit Combinatorial Explosion in Biodegradation Prediction Book Section
In: Lässig, Jörg; Kersting, Kristian; Morik, Katharina (Ed.): Computational Sustainability, pp. 75-97, Springer International Publishing, Cham, 2016, ISBN: 978-3-319-31858-5.
Abstract | Links | BibTeX | Altmetric | PlumX | Tags: biodegradation, cheminformatics, computational sustainability, enviPath, machine learning, metabolic pathways, multi-label classification
@incollection{wicker2016ahybrid,
title = {A Hybrid Machine Learning and Knowledge Based Approach to Limit Combinatorial Explosion in Biodegradation Prediction},
author = {J\"{o}rg Wicker and Kathrin Fenner and Stefan Kramer},
editor = {J\"{o}rg L\"{a}ssig and Kristian Kersting and Katharina Morik},
url = {http://dx.doi.org/10.1007/978-3-319-31858-5_5},
doi = {10.1007/978-3-319-31858-5_5},
isbn = {978-3-319-31858-5},
year = {2016},
date = {2016-04-21},
booktitle = {Computational Sustainability},
pages = {75-97},
publisher = {Springer International Publishing},
address = {Cham},
abstract = {One of the main tasks in chemical industry regarding the sustainability of a product is the prediction of its environmental fate, i.e., its degradation products and pathways. Current methods for the prediction of biodegradation products and pathways of organic environmental pollutants either do not take into account domain knowledge or do not provide probability estimates. In this chapter, we propose a hybrid knowledge-based and machine learning-based approach to overcome these limitations in the context of the University of Minnesota Pathway Prediction System (UM-PPS). The proposed solution performs relative reasoning in a machine learning framework, and obtains one probability estimate for each biotransformation rule of the system. Since the application of a rule then depends on a threshold for the probability estimate, the trade-off between recall (sensitivity) and precision (selectivity) can be addressed and leveraged in practice. Results from leave-one-out cross-validation show that a recall and precision of approximately 0.8 can be achieved for a subset of 13 transformation rules. The set of used rules is further extended using multi-label classification, where dependencies among the transformation rules are exploited to improve the predictions. While the results regarding recall and precision vary, the area under the ROC curve can be improved using multi-label classification. Therefore, it is possible to optimize precision without compromising recall. Recently, we integrated the presented approach into enviPath, a complete redesign and re-implementation of UM-PPS.},
keywords = {biodegradation, cheminformatics, computational sustainability, enviPath, machine learning, metabolic pathways, multi-label classification},
pubstate = {published},
tppubtype = {incollection}
}
One of the main tasks in chemical industry regarding the sustainability of a product is the prediction of its environmental fate, i.e., its degradation products and pathways. Current methods for the prediction of biodegradation products and pathways of organic environmental pollutants either do not take into account domain knowledge or do not provide probability estimates. In this chapter, we propose a hybrid knowledge-based and machine learning-based approach to overcome these limitations in the context of the University of Minnesota Pathway Prediction System (UM-PPS). The proposed solution performs relative reasoning in a machine learning framework, and obtains one probability estimate for each biotransformation rule of the system. Since the application of a rule then depends on a threshold for the probability estimate, the trade-off between recall (sensitivity) and precision (selectivity) can be addressed and leveraged in practice. Results from leave-one-out cross-validation show that a recall and precision of approximately 0.8 can be achieved for a subset of 13 transformation rules. The set of used rules is further extended using multi-label classification, where dependencies among the transformation rules are exploited to improve the predictions. While the results regarding recall and precision vary, the area under the ROC curve can be improved using multi-label classification. Therefore, it is possible to optimize precision without compromising recall. Recently, we integrated the presented approach into enviPath, a complete redesign and re-implementation of UM-PPS.
4.
Wicker, Jörg; Tyukin, Andrey; Kramer, Stefan
A Nonlinear Label Compression and Transformation Method for Multi-Label Classification using Autoencoders Proceedings Article
In: Bailey, James; Khan, Latifur; Washio, Takashi; Dobbie, Gill; Huang, Zhexue Joshua; Wang, Ruili (Ed.): The 20th Pacific Asia Conference on Knowledge Discovery and Data Mining (PAKDD), pp. 328-340, Springer International Publishing, Switzerland, 2016, ISBN: 978-3-319-31753-3.
Abstract | Links | BibTeX | Altmetric | PlumX | Tags: autoencoders, label compression, machine learning, multi-label classification
@inproceedings{wicker2016nonlinear,
title = {A Nonlinear Label Compression and Transformation Method for Multi-Label Classification using Autoencoders},
author = {J\"{o}rg Wicker and Andrey Tyukin and Stefan Kramer},
editor = {James Bailey and Latifur Khan and Takashi Washio and Gill Dobbie and Zhexue Joshua Huang and Ruili Wang},
url = {http://dx.doi.org/10.1007/978-3-319-31753-3_27},
doi = {10.1007/978-3-319-31753-3_27},
isbn = {978-3-319-31753-3},
year = {2016},
date = {2016-04-16},
booktitle = {The 20th Pacific Asia Conference on Knowledge Discovery and Data Mining (PAKDD)},
volume = {9651},
pages = {328-340},
publisher = {Springer International Publishing},
address = {Switzerland},
series = {Lecture Notes in Computer Science},
abstract = {Multi-label classification targets the prediction of multiple interdependent and non-exclusive binary target variables. Transformation-based algorithms transform the data set such that regular single-label algorithms can be applied to the problem. A special type of transformation-based classifiers are label compression methods, that compress the labels and then mostly use single label classifiers to predict the compressed labels. So far, there are no compression-based algorithms follow a problem transformation approach and address non-linear dependencies in the labels. In this paper, we propose a new algorithm, called Maniac (Multi-lAbel classificatioN usIng AutoenCoders), which extracts the non-linear dependencies by compressing the labels using autoencoders. We adapt the training process of autoencoders in a way to make them more suitable for a parameter optimization in the context of this algorithm. The method is evaluated on eight standard multi-label data sets. Experiments show that despite not producing a good ranking, Maniac generates a particularly good bipartition of the labels into positives and negatives. This is caused by rather strong predictions with either really high or low probability. Additionally, the algorithm seems to perform better given more labels and a higher label cardinality in the data set.},
keywords = {autoencoders, label compression, machine learning, multi-label classification},
pubstate = {published},
tppubtype = {inproceedings}
}
Multi-label classification targets the prediction of multiple interdependent and non-exclusive binary target variables. Transformation-based algorithms transform the data set such that regular single-label algorithms can be applied to the problem. A special type of transformation-based classifiers are label compression methods, that compress the labels and then mostly use single label classifiers to predict the compressed labels. So far, there are no compression-based algorithms follow a problem transformation approach and address non-linear dependencies in the labels. In this paper, we propose a new algorithm, called Maniac (Multi-lAbel classificatioN usIng AutoenCoders), which extracts the non-linear dependencies by compressing the labels using autoencoders. We adapt the training process of autoencoders in a way to make them more suitable for a parameter optimization in the context of this algorithm. The method is evaluated on eight standard multi-label data sets. Experiments show that despite not producing a good ranking, Maniac generates a particularly good bipartition of the labels into positives and negatives. This is caused by rather strong predictions with either really high or low probability. Additionally, the algorithm seems to perform better given more labels and a higher label cardinality in the data set.
3.
Wicker, Jörg; Lorsbach, Tim; Gütlein, Martin; Schmid, Emanuel; Latino, Diogo; Kramer, Stefan; Fenner, Kathrin
enviPath – The Environmental Contaminant Biotransformation Pathway Resource Journal Article
In: Nucleic Acid Research, vol. 44, no. D1, pp. D502-D508, 2016.
Abstract | Links | BibTeX | Altmetric | PlumX | Tags: biodegradation, cheminformatics, computational sustainability, data mining, enviPath, linked data, machine learning, metabolic pathways, multi-label classification
@article{wicker2016envipath,
title = {enviPath - The Environmental Contaminant Biotransformation Pathway Resource},
author = {J\"{o}rg Wicker and Tim Lorsbach and Martin G\"{u}tlein and Emanuel Schmid and Diogo Latino and Stefan Kramer and Kathrin Fenner},
editor = {Michael Galperin},
url = {http://nar.oxfordjournals.org/content/44/D1/D502.abstract},
doi = {10.1093/nar/gkv1229},
year = {2016},
date = {2016-01-01},
journal = {Nucleic Acid Research},
volume = {44},
number = {D1},
pages = {D502-D508},
abstract = {The University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System (UM-BBD/PPS) has been a unique resource covering microbial biotransformation pathways of primarily xenobiotic chemicals for over 15 years. This paper introduces the successor system, enviPath (The Environmental Contaminant Biotransformation Pathway Resource), which is a complete redesign and reimplementation of UM-BBD/PPS. enviPath uses the database from the UM-BBD/PPS as a basis, extends the use of this database, and allows users to include their own data to support multiple use cases. Relative reasoning is supported for the refinement of predictions and to allow its extensions in terms of previously published, but not implemented machine learning models. User access is simplified by providing a REST API that simplifies the inclusion of enviPath into existing workflows. An RDF database is used to enable simple integration with other databases. enviPath is publicly available at https://envipath.org with free and open access to its core data.},
keywords = {biodegradation, cheminformatics, computational sustainability, data mining, enviPath, linked data, machine learning, metabolic pathways, multi-label classification},
pubstate = {published},
tppubtype = {article}
}
The University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System (UM-BBD/PPS) has been a unique resource covering microbial biotransformation pathways of primarily xenobiotic chemicals for over 15 years. This paper introduces the successor system, enviPath (The Environmental Contaminant Biotransformation Pathway Resource), which is a complete redesign and reimplementation of UM-BBD/PPS. enviPath uses the database from the UM-BBD/PPS as a basis, extends the use of this database, and allows users to include their own data to support multiple use cases. Relative reasoning is supported for the refinement of predictions and to allow its extensions in terms of previously published, but not implemented machine learning models. User access is simplified by providing a REST API that simplifies the inclusion of enviPath into existing workflows. An RDF database is used to enable simple integration with other databases. enviPath is publicly available at https://envipath.org with free and open access to its core data.
2013
2.
Wicker, Jörg
Large Classifier Systems in Bio- and Cheminformatics PhD Thesis
Technische Universität München, 2013.
Abstract | Links | BibTeX | Tags: biodegradation, bioinformatics, cheminformatics, computational sustainability, data mining, enviPath, machine learning, multi-label classification, multi-relational learning, toxicity
@phdthesis{wicker2013large,
title = {Large Classifier Systems in Bio- and Cheminformatics},
author = {J\"{o}rg Wicker},
url = {http://mediatum.ub.tum.de/node?id=1165858},
year = {2013},
date = {2013-01-01},
school = {Technische Universit\"{a}t M\"{u}nchen},
abstract = {Large classifier systems are machine learning algorithms that use multiple
classifiers to improve the prediction of target values in advanced
classification tasks. Although learning problems in bio- and
cheminformatics commonly provide data in schemes suitable for large
classifier systems, they are rarely used in these domains. This thesis
introduces two new classifiers incorporating systems of classifiers
using Boolean matrix decomposition to handle data in a schema that
often occurs in bio- and cheminformatics.
The first approach, called MLC-BMaD (multi-label classification using
Boolean matrix decomposition), uses Boolean matrix decomposition to
decompose the labels in a multi-label classification task. The
decomposed matrices are a compact representation of the information
in the labels (first matrix) and the dependencies among the labels
(second matrix). The first matrix is used in a further multi-label
classification while the second matrix is used to generate the final
matrix from the predicted values of the first matrix.
MLC-BMaD was evaluated on six standard multi-label data sets, the
experiments showed that MLC-BMaD can perform particularly well on data
sets with a high number of labels and a small number of instances and
can outperform standard multi-label algorithms.
Subsequently, MLC-BMaD is extended to a special case of
multi-relational learning, by considering the labels not as simple
labels, but instances. The algorithm, called ClassFact
(Classification factorization), uses both matrices in a multi-label
classification. Each label represents a mapping between two
instances.
Experiments on three data sets from the domain of bioinformatics show
that ClassFact can outperform the baseline method, which merges the
relations into one, on hard classification tasks.
Furthermore, large classifier systems are used on two cheminformatics
data sets, the first one is used to predict the environmental fate of
chemicals by predicting biodegradation pathways. The second is a data
set from the domain of predictive toxicology. In biodegradation
pathway prediction, I extend a knowledge-based system and incorporate
a machine learning approach to predict a probability for
biotransformation products based on the structure- and knowledge-based
predictions of products, which are based on transformation rules. The
use of multi-label classification improves the performance of the
classifiers and extends the number of transformation rules that can be
covered.
For the prediction of toxic effects of chemicals, I applied large
classifier systems to the ToxCasttexttrademark data set, which maps
toxic effects to chemicals. As the given toxic effects are not easy to
predict due to missing information and a skewed class
distribution, I introduce a filtering step in the multi-label
classification, which finds labels that are usable in multi-label
prediction and does not take the others in the
prediction into account. Experiments show
that this approach can improve upon the baseline method using binary
classification, as well as multi-label approaches using no filtering.
The presented results show that large classifier systems can play a
role in future research challenges, especially in bio- and
cheminformatics, where data sets frequently consist of more complex
structures and data can be rather small in terms of the number of
instances compared to other domains.},
keywords = {biodegradation, bioinformatics, cheminformatics, computational sustainability, data mining, enviPath, machine learning, multi-label classification, multi-relational learning, toxicity},
pubstate = {published},
tppubtype = {phdthesis}
}
Large classifier systems are machine learning algorithms that use multiple
classifiers to improve the prediction of target values in advanced
classification tasks. Although learning problems in bio- and
cheminformatics commonly provide data in schemes suitable for large
classifier systems, they are rarely used in these domains. This thesis
introduces two new classifiers incorporating systems of classifiers
using Boolean matrix decomposition to handle data in a schema that
often occurs in bio- and cheminformatics.
The first approach, called MLC-BMaD (multi-label classification using
Boolean matrix decomposition), uses Boolean matrix decomposition to
decompose the labels in a multi-label classification task. The
decomposed matrices are a compact representation of the information
in the labels (first matrix) and the dependencies among the labels
(second matrix). The first matrix is used in a further multi-label
classification while the second matrix is used to generate the final
matrix from the predicted values of the first matrix.
MLC-BMaD was evaluated on six standard multi-label data sets, the
experiments showed that MLC-BMaD can perform particularly well on data
sets with a high number of labels and a small number of instances and
can outperform standard multi-label algorithms.
Subsequently, MLC-BMaD is extended to a special case of
multi-relational learning, by considering the labels not as simple
labels, but instances. The algorithm, called ClassFact
(Classification factorization), uses both matrices in a multi-label
classification. Each label represents a mapping between two
instances.
Experiments on three data sets from the domain of bioinformatics show
that ClassFact can outperform the baseline method, which merges the
relations into one, on hard classification tasks.
Furthermore, large classifier systems are used on two cheminformatics
data sets, the first one is used to predict the environmental fate of
chemicals by predicting biodegradation pathways. The second is a data
set from the domain of predictive toxicology. In biodegradation
pathway prediction, I extend a knowledge-based system and incorporate
a machine learning approach to predict a probability for
biotransformation products based on the structure- and knowledge-based
predictions of products, which are based on transformation rules. The
use of multi-label classification improves the performance of the
classifiers and extends the number of transformation rules that can be
covered.
For the prediction of toxic effects of chemicals, I applied large
classifier systems to the ToxCasttexttrademark data set, which maps
toxic effects to chemicals. As the given toxic effects are not easy to
predict due to missing information and a skewed class
distribution, I introduce a filtering step in the multi-label
classification, which finds labels that are usable in multi-label
prediction and does not take the others in the
prediction into account. Experiments show
that this approach can improve upon the baseline method using binary
classification, as well as multi-label approaches using no filtering.
The presented results show that large classifier systems can play a
role in future research challenges, especially in bio- and
cheminformatics, where data sets frequently consist of more complex
structures and data can be rather small in terms of the number of
instances compared to other domains.
classifiers to improve the prediction of target values in advanced
classification tasks. Although learning problems in bio- and
cheminformatics commonly provide data in schemes suitable for large
classifier systems, they are rarely used in these domains. This thesis
introduces two new classifiers incorporating systems of classifiers
using Boolean matrix decomposition to handle data in a schema that
often occurs in bio- and cheminformatics.
The first approach, called MLC-BMaD (multi-label classification using
Boolean matrix decomposition), uses Boolean matrix decomposition to
decompose the labels in a multi-label classification task. The
decomposed matrices are a compact representation of the information
in the labels (first matrix) and the dependencies among the labels
(second matrix). The first matrix is used in a further multi-label
classification while the second matrix is used to generate the final
matrix from the predicted values of the first matrix.
MLC-BMaD was evaluated on six standard multi-label data sets, the
experiments showed that MLC-BMaD can perform particularly well on data
sets with a high number of labels and a small number of instances and
can outperform standard multi-label algorithms.
Subsequently, MLC-BMaD is extended to a special case of
multi-relational learning, by considering the labels not as simple
labels, but instances. The algorithm, called ClassFact
(Classification factorization), uses both matrices in a multi-label
classification. Each label represents a mapping between two
instances.
Experiments on three data sets from the domain of bioinformatics show
that ClassFact can outperform the baseline method, which merges the
relations into one, on hard classification tasks.
Furthermore, large classifier systems are used on two cheminformatics
data sets, the first one is used to predict the environmental fate of
chemicals by predicting biodegradation pathways. The second is a data
set from the domain of predictive toxicology. In biodegradation
pathway prediction, I extend a knowledge-based system and incorporate
a machine learning approach to predict a probability for
biotransformation products based on the structure- and knowledge-based
predictions of products, which are based on transformation rules. The
use of multi-label classification improves the performance of the
classifiers and extends the number of transformation rules that can be
covered.
For the prediction of toxic effects of chemicals, I applied large
classifier systems to the ToxCasttexttrademark data set, which maps
toxic effects to chemicals. As the given toxic effects are not easy to
predict due to missing information and a skewed class
distribution, I introduce a filtering step in the multi-label
classification, which finds labels that are usable in multi-label
prediction and does not take the others in the
prediction into account. Experiments show
that this approach can improve upon the baseline method using binary
classification, as well as multi-label approaches using no filtering.
The presented results show that large classifier systems can play a
role in future research challenges, especially in bio- and
cheminformatics, where data sets frequently consist of more complex
structures and data can be rather small in terms of the number of
instances compared to other domains.
2012
1.
Wicker, Jörg; Pfahringer, Bernhard; Kramer, Stefan
Multi-label Classification Using Boolean Matrix Decomposition Proceedings Article
In: Proceedings of the 27th Annual ACM Symposium on Applied Computing, pp. 179–186, ACM, 2012, ISBN: 978-1-4503-0857-1.
Abstract | Links | BibTeX | Altmetric | PlumX | Tags: associations, Boolean matrix decomposition, machine learning, multi-label classification
@inproceedings{wicker2012multi,
title = {Multi-label Classification Using Boolean Matrix Decomposition},
author = {J\"{o}rg Wicker and Bernhard Pfahringer and Stefan Kramer},
url = {https://wicker.nz/nwp-acm/authorize.php?id=N10032
http://doi.acm.org/10.1145/2245276.2245311},
doi = {10.1145/2245276.2245311},
isbn = {978-1-4503-0857-1},
year = {2012},
date = {2012-01-01},
booktitle = {Proceedings of the 27th Annual ACM Symposium on Applied Computing},
pages = {179--186},
publisher = {ACM},
series = {SAC '12},
abstract = {This paper introduces a new multi-label classifier based on Boolean matrix decomposition. Boolean matrix decomposition is used to extract, from the full label matrix, latent labels representing useful Boolean combinations of the original labels. Base level models predict latent labels, which are subsequently transformed into the actual labels by Boolean matrix multiplication with the second matrix from the decomposition. The new method is tested on six publicly available datasets with varying numbers of labels. The experimental evaluation shows that the new method works particularly well on datasets with a large number of labels and strong dependencies among them.},
keywords = {associations, Boolean matrix decomposition, machine learning, multi-label classification},
pubstate = {published},
tppubtype = {inproceedings}
}
This paper introduces a new multi-label classifier based on Boolean matrix decomposition. Boolean matrix decomposition is used to extract, from the full label matrix, latent labels representing useful Boolean combinations of the original labels. Base level models predict latent labels, which are subsequently transformed into the actual labels by Boolean matrix multiplication with the second matrix from the decomposition. The new method is tested on six publicly available datasets with varying numbers of labels. The experimental evaluation shows that the new method works particularly well on datasets with a large number of labels and strong dependencies among them.