Cheminformatics is a field that combines chemistry and computer science to address challenges in chemistry. Machine learning is a key aspect of cheminformatics, allowing for the processing of large amounts of data and predictions based on patterns in the data. Research in cheminformatics includes predicting metabolic pathways, predicting toxicity, and analyzing environmental data.
It is an interdisciplinary field that heavily relies on machine learning to address challenges in chemistry. The use of machine learning algorithms allows for the processing of large amounts of data and predictions based on patterns in the data. Cheminformatics has a wide range of applications, including drug discovery, toxicology prediction, and environmental analysis.
2024
Long, Derek; Eade, Liam; Dost, Katharina; Meier-Menches, Samuel M; Goldstone, David C; Sullivan, Matthew P; Hartinger, Christian; Wicker, Jörg; Taskova, Katerina
AdductHunter: Identifying Protein-Metal Complex Adducts in Mass Spectra Journal Article
In: Journal of Cheminformatics, vol. 16, iss. 1, 2024, ISSN: 1758-2946.
@article{Long2023adducthunter,
title = {AdductHunter: Identifying Protein-Metal Complex Adducts in Mass Spectra},
author = {Derek Long and Liam Eade and Katharina Dost and Samuel M Meier-Menches and David C Goldstone and Matthew P Sullivan and Christian Hartinger and J\"{o}rg Wicker and Katerina Taskova},
url = {https://adducthunter.wickerlab.org
https://doi.org/10.21203/rs.3.rs-3322854/v1},
doi = {10.1186/s13321-023-00797-7},
issn = {1758-2946},
year = {2024},
date = {2024-02-06},
urldate = {2023-05-29},
journal = {Journal of Cheminformatics},
volume = {16},
issue = {1},
abstract = {Mass spectrometry (MS) is an analytical technique for molecule identification that can be used for investigating protein-metal complex interactions. Once the MS data is collected, the mass spectra are usually interpreted manually to identify the adducts formed as a result of the interactions between proteins and metal-based species. However, with increasing resolution, dataset size, and species complexity, the time required to identify adducts and the error-prone nature of manual assignment have become limiting factors in MS analysis. AdductHunter is a open-source web-based analysis tool that automates the peak identification process using constraint integer optimization to find feasible combinations of protein and fragments, and dynamic time warping to calculate the dissimilarity between the theoretical isotope pattern of a species and its experimental isotope peak distribution. Empirical evaluation on a collection of 22 unique MS datasetsshows fast and accurate identification of protein-metal complex adducts in deconvoluted mass spectra.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mass spectrometry (MS) is an analytical technique for molecule identification that can be used for investigating protein-metal complex interactions. Once the MS data is collected, the mass spectra are usually interpreted manually to identify the adducts formed as a result of the interactions between proteins and metal-based species. However, with increasing resolution, dataset size, and species complexity, the time required to identify adducts and the error-prone nature of manual assignment have become limiting factors in MS analysis. AdductHunter is a open-source web-based analysis tool that automates the peak identification process using constraint integer optimization to find feasible combinations of protein and fragments, and dynamic time warping to calculate the dissimilarity between the theoretical isotope pattern of a species and its experimental isotope peak distribution. Empirical evaluation on a collection of 22 unique MS datasetsshows fast and accurate identification of protein-metal complex adducts in deconvoluted mass spectra.
2023
Dost, Katharina; Tam, Jason; Lorsbach, Tim; Schmidt, Sebastian; Wicker, Jörg
Defining Applicability Domain in Biodegradation Pathway Prediction Unpublished Forthcoming
Forthcoming.
@unpublished{dost2023defining,
title = {Defining Applicability Domain in Biodegradation Pathway Prediction},
author = {Katharina Dost and Jason Tam and Tim Lorsbach and Sebastian Schmidt and J\"{o}rg Wicker},
doi = {https://doi.org/10.21203/rs.3.rs-3587632/v1},
year = {2023},
date = {2023-11-10},
urldate = {2023-11-10},
abstract = {When developing a new chemical, investigating its long-term influences on the environment is crucial to prevent harm. Unfortunately, these experiments are time-consuming. In silico methods can learn from already obtained data to predict biotransformation pathways, and thereby help focus all development efforts on only the most promising chemicals. As all data-based models, these predictors will output pathway predictions for all input compounds in a suitable format, however, these predictions will be faulty unless the model has seen similar compounds during the training process. A common approach to prevent this for other types of models is to define an Applicability Domain for the model that makes predictions only for in-domain compounds and rejects out-of-domain ones. Nonetheless, although exploration of the compound space is particularly interesting in the development of new chemicals, no Applicability Domain method has been tailored to the specific data structure of pathway predictions yet. In this paper, we are the first to define Applicability Domain specialized in biodegradation pathway prediction. Assessing a model’s reliability from different angles, we suggest a three-stage approach that checks for applicability, reliability, and decidability of the model for a queried compound and only allows it to output a prediction if all three stages are passed. Experiments confirm that our proposed technique reliably rejects unsuitable compounds and therefore improves the safety of the biotransformation pathway predictor. },
keywords = {},
pubstate = {forthcoming},
tppubtype = {unpublished}
}
When developing a new chemical, investigating its long-term influences on the environment is crucial to prevent harm. Unfortunately, these experiments are time-consuming. In silico methods can learn from already obtained data to predict biotransformation pathways, and thereby help focus all development efforts on only the most promising chemicals. As all data-based models, these predictors will output pathway predictions for all input compounds in a suitable format, however, these predictions will be faulty unless the model has seen similar compounds during the training process. A common approach to prevent this for other types of models is to define an Applicability Domain for the model that makes predictions only for in-domain compounds and rejects out-of-domain ones. Nonetheless, although exploration of the compound space is particularly interesting in the development of new chemicals, no Applicability Domain method has been tailored to the specific data structure of pathway predictions yet. In this paper, we are the first to define Applicability Domain specialized in biodegradation pathway prediction. Assessing a model’s reliability from different angles, we suggest a three-stage approach that checks for applicability, reliability, and decidability of the model for a queried compound and only allows it to output a prediction if all three stages are passed. Experiments confirm that our proposed technique reliably rejects unsuitable compounds and therefore improves the safety of the biotransformation pathway predictor.
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 Unpublished Forthcoming
Forthcoming.
@unpublished{nokey,
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},
doi = {10.21203/rs.3.rs-3607847/v1},
year = {2023},
date = {2023-11-03},
urldate = {2023-11-03},
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, that 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. Overall, enviPath has developed into a reliable database and prediction system with a unique use case in research in microbial biotransformations. },
keywords = {},
pubstate = {forthcoming},
tppubtype = {unpublished}
}
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, that 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. Overall, enviPath has developed into a reliable database and prediction system with a unique use case in research in microbial biotransformations.
Chang, Luke; Dost, Katharina; Zhai, Kaiqi; Demontis, Ambra; Roli, Fabio; Dobbie, Gillian; Wicker, Jörg
BAARD: Blocking Adversarial Examples by Testing for Applicability, Reliability and Decidability Proceedings Article
In: Kashima, Hisashi; Ide, Tsuyoshi; Peng, Wen-Chih (Ed.): The 27th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), pp. 3-14, Springer Nature Switzerland, Cham, 2023, ISSN: 978-3-031-33374-3.
@inproceedings{chang2021baard,
title = {BAARD: Blocking Adversarial Examples by Testing for Applicability, Reliability and Decidability},
author = {Luke Chang and Katharina Dost and Kaiqi Zhai and Ambra Demontis and Fabio Roli and Gillian Dobbie and J\"{o}rg Wicker},
editor = {Hisashi Kashima and Tsuyoshi Ide and Wen-Chih Peng},
url = {https://arxiv.org/abs/2105.00495
https://github.com/wickerlab/baard},
doi = {10.1007/978-3-031-33374-3_1},
issn = {978-3-031-33374-3},
year = {2023},
date = {2023-05-27},
urldate = {2023-05-27},
booktitle = {The 27th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD)},
journal = {The 27th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD)},
pages = {3-14},
publisher = {Springer Nature Switzerland},
address = {Cham},
abstract = {Adversarial defenses protect machine learning models from adversarial attacks, but are often tailored to one type of model or attack. The lack of information on unknown potential attacks makes detecting adversarial examples challenging. Additionally, attackers do not need to follow the rules made by the defender. To address this problem, we take inspiration from the concept of Applicability Domain in cheminformatics. Cheminformatics models struggle to make accurate predictions because only a limited number of compounds are known and available for training. Applicability Domain defines a domain based on the known compounds and rejects any unknown compound that falls outside the domain. Similarly, adversarial examples start as harmless inputs, but can be manipulated to evade reliable classification by moving outside the domain of the classifier. We are the first to identify the similarity between Applicability Domain and adversarial detection. Instead of focusing on unknown attacks, we focus on what is known, the training data. We propose a simple yet robust triple-stage data-driven framework that checks the input globally and locally, and confirms that they are coherent with the model’s output. This framework can be applied to any classification model and is not limited to specific attacks. We demonstrate these three stages work as one unit, effectively detecting various attacks, even for a white-box scenario.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Adversarial defenses protect machine learning models from adversarial attacks, but are often tailored to one type of model or attack. The lack of information on unknown potential attacks makes detecting adversarial examples challenging. Additionally, attackers do not need to follow the rules made by the defender. To address this problem, we take inspiration from the concept of Applicability Domain in cheminformatics. Cheminformatics models struggle to make accurate predictions because only a limited number of compounds are known and available for training. Applicability Domain defines a domain based on the known compounds and rejects any unknown compound that falls outside the domain. Similarly, adversarial examples start as harmless inputs, but can be manipulated to evade reliable classification by moving outside the domain of the classifier. We are the first to identify the similarity between Applicability Domain and adversarial detection. Instead of focusing on unknown attacks, we focus on what is known, the training data. We propose a simple yet robust triple-stage data-driven framework that checks the input globally and locally, and confirms that they are coherent with the model’s output. This framework can be applied to any classification model and is not limited to specific attacks. We demonstrate these three stages work as one unit, effectively detecting various attacks, even for a white-box scenario.
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.
@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 = {},
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.
Bensemann, Joshua; Cheena, Hasnain; Huang, David Tse Jung; Broadbent, Elizabeth; Williams, Jonathan; Wicker, Jörg
From What You See to What We Smell: Linking Human Emotions to Bio-markers in Breath Journal Article
In: IEEE Transactions on Affective Computing, pp. 1-13, 2023, ISSN: 1949-3045.
@article{bensemann2023from,
title = {From What You See to What We Smell: Linking Human Emotions to Bio-markers in Breath},
author = {Joshua Bensemann and Hasnain Cheena and David Tse Jung Huang and Elizabeth Broadbent and Jonathan Williams and J\"{o}rg Wicker},
url = {https://ieeexplore.ieee.org/document/10123109
https://doi.org/10.17608/k6.auckland.22777364
https://doi.org/10.17608/k6.auckland.22777352 },
doi = {10.1109/TAFFC.2023.3275216},
issn = {1949-3045},
year = {2023},
date = {2023-05-11},
urldate = {2023-05-11},
journal = {IEEE Transactions on Affective Computing},
pages = {1-13},
abstract = {Research has shown that the composition of breath can differ based on the human’s behavioral patterns and mental and physical states immediately before being collected. These breath-collection techniques have also been extended to observe the general processes occurring in groups of humans and can link them to what those groups are collectively experiencing. In this research, we applied machine learning techniques to the breath data collected from cinema audiences. These techniques included XGBOOST Regression, Hierarchical Clustering, and Item Basket analyses created using the Apriori algorithm. They were conducted to find associations between the biomarkers in the crowd’s breath and the movie’s audio-visual stimuli and thematic events. This analysis enabled us to directly link what the group was experiencing and their biological response to that experience. We first extracted visual and auditory features from a movie to achieve this. We compared it to the biomarkers in the crowd’s breath using regression and pattern mining techniques. Our results supported the theory that a crowd’s collective experience directly correlates to the biomarkers in the crowd’s breath. Consequently, these findings suggest that visual and auditory experiences have predictable effects on the human
body that can be monitored without requiring expensive or invasive neuroimaging techniques.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Research has shown that the composition of breath can differ based on the human’s behavioral patterns and mental and physical states immediately before being collected. These breath-collection techniques have also been extended to observe the general processes occurring in groups of humans and can link them to what those groups are collectively experiencing. In this research, we applied machine learning techniques to the breath data collected from cinema audiences. These techniques included XGBOOST Regression, Hierarchical Clustering, and Item Basket analyses created using the Apriori algorithm. They were conducted to find associations between the biomarkers in the crowd’s breath and the movie’s audio-visual stimuli and thematic events. This analysis enabled us to directly link what the group was experiencing and their biological response to that experience. We first extracted visual and auditory features from a movie to achieve this. We compared it to the biomarkers in the crowd’s breath using regression and pattern mining techniques. Our results supported the theory that a crowd’s collective experience directly correlates to the biomarkers in the crowd’s breath. Consequently, these findings suggest that visual and auditory experiences have predictable effects on the human
body that can be monitored without requiring expensive or invasive neuroimaging techniques.
body that can be monitored without requiring expensive or invasive neuroimaging techniques.
2021
Tam, Jason; Lorsbach, Tim; Schmidt, Sebastian; Wicker, Jörg
Holistic Evaluation of Biodegradation Pathway Prediction: Assessing Multi-Step Reactions and Intermediate Products Journal Article
In: Journal of Cheminformatics, vol. 13, no. 1, pp. 63, 2021.
@article{tam2021holisticb,
title = {Holistic Evaluation of Biodegradation Pathway Prediction: Assessing Multi-Step Reactions and Intermediate Products},
author = {Jason Tam and Tim Lorsbach and Sebastian Schmidt and J\"{o}rg Wicker},
url = {https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00543-x
https://chemrxiv.org/articles/preprint/Holistic_Evaluation_of_Biodegradation_Pathway_Prediction_Assessing_Multi-Step_Reactions_and_Intermediate_Products/14315963
https://dx.doi.org/10.26434/chemrxiv.14315963},
doi = {10.1186/s13321-021-00543-x},
year = {2021},
date = {2021-09-03},
urldate = {2021-09-03},
journal = {Journal of Cheminformatics},
volume = {13},
number = {1},
pages = {63},
abstract = {The prediction of metabolism and biotransformation pathways of xenobiotics is a highly desired tool in environmental sciences, drug discovery, and (eco)toxicology. Several systems predict single transformation steps or complete pathways as series of parallel and subsequent steps. Their performance is commonly evaluated on the level of a single transformation step. Such an approach cannot account for some specific challenges that are caused by specific properties of biotransformation experiments. That is, missing transformation products in the reference data that occur only in low concentrations, e.g. transient intermediates or higher-generation metabolites. Furthermore, some rule-based prediction systems evaluate the performance only based on the defined set of transformation rules. Therefore, the performance of these models cannot be directly compared. In this paper, we introduce a new evaluation framework that extends the evaluation of biotransformation prediction from single transformations to whole pathways, taking into account multiple generations of metabolites. We introduce a procedure to address transient intermediates and propose a weighted scoring system that acknowledges the uncertainty of higher-generation metabolites. We implemented this framework in enviPath and demonstrate its strict performance metrics on predictions of in vitro biotransformation and degradation of xenobiotics in soil. Our approach is model-agnostic and can be transferred to other prediction systems. It is also capable of revealing knowledge gaps in terms of incompletely defined sets of transformation rules.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The prediction of metabolism and biotransformation pathways of xenobiotics is a highly desired tool in environmental sciences, drug discovery, and (eco)toxicology. Several systems predict single transformation steps or complete pathways as series of parallel and subsequent steps. Their performance is commonly evaluated on the level of a single transformation step. Such an approach cannot account for some specific challenges that are caused by specific properties of biotransformation experiments. That is, missing transformation products in the reference data that occur only in low concentrations, e.g. transient intermediates or higher-generation metabolites. Furthermore, some rule-based prediction systems evaluate the performance only based on the defined set of transformation rules. Therefore, the performance of these models cannot be directly compared. In this paper, we introduce a new evaluation framework that extends the evaluation of biotransformation prediction from single transformations to whole pathways, taking into account multiple generations of metabolites. We introduce a procedure to address transient intermediates and propose a weighted scoring system that acknowledges the uncertainty of higher-generation metabolites. We implemented this framework in enviPath and demonstrate its strict performance metrics on predictions of in vitro biotransformation and degradation of xenobiotics in soil. Our approach is model-agnostic and can be transferred to other prediction systems. It is also capable of revealing knowledge gaps in terms of incompletely defined sets of transformation rules.
Stepišnik, Tomaž; Škrlj, Blaž; Wicker, Jörg; Kocev, Dragi
A comprehensive comparison of molecular feature representations for use in predictive modeling Journal Article
In: Computers in Biology and Medicine, vol. 130, pp. 104197, 2021, ISSN: 0010-4825.
@article{stepisnik2021comprehensive,
title = {A comprehensive comparison of molecular feature representations for use in predictive modeling},
author = {Toma\v{z} Stepi\v{s}nik and Bla\v{z} \v{S}krlj and J\"{o}rg Wicker and Dragi Kocev},
url = {http://www.sciencedirect.com/science/article/pii/S001048252030528X},
doi = {10.1016/j.compbiomed.2020.104197},
issn = {0010-4825},
year = {2021},
date = {2021-03-01},
journal = {Computers in Biology and Medicine},
volume = {130},
pages = {104197},
abstract = {Machine learning methods are commonly used for predicting molecular properties to accelerate material and drug design. An important part of this process is deciding how to represent the molecules. Typically, machine learning methods expect examples represented by vectors of values, and many methods for calculating molecular feature representations have been proposed. In this paper, we perform a comprehensive comparison of different molecular features, including traditional methods such as fingerprints and molecular descriptors, and recently proposed learnable representations based on neural networks. Feature representations are evaluated on 11 benchmark datasets, used for predicting properties and measures such as mutagenicity, melting points, activity, solubility, and IC50. Our experiments show that several molecular features work similarly well over all benchmark datasets. The ones that stand out most are Spectrophores, which give significantly worse performance than other features on most datasets. Molecular descriptors from the PaDEL library seem very well suited for predicting physical properties of molecules. Despite their simplicity, MACCS fingerprints performed very well overall. The results show that learnable representations achieve competitive performance compared to expert based representations. However, task-specific representations (graph convolutions and Weave methods) rarely offer any benefits, even though they are computationally more demanding. Lastly, combining different molecular feature representations typically does not give a noticeable improvement in performance compared to individual feature representations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Machine learning methods are commonly used for predicting molecular properties to accelerate material and drug design. An important part of this process is deciding how to represent the molecules. Typically, machine learning methods expect examples represented by vectors of values, and many methods for calculating molecular feature representations have been proposed. In this paper, we perform a comprehensive comparison of different molecular features, including traditional methods such as fingerprints and molecular descriptors, and recently proposed learnable representations based on neural networks. Feature representations are evaluated on 11 benchmark datasets, used for predicting properties and measures such as mutagenicity, melting points, activity, solubility, and IC50. Our experiments show that several molecular features work similarly well over all benchmark datasets. The ones that stand out most are Spectrophores, which give significantly worse performance than other features on most datasets. Molecular descriptors from the PaDEL library seem very well suited for predicting physical properties of molecules. Despite their simplicity, MACCS fingerprints performed very well overall. The results show that learnable representations achieve competitive performance compared to expert based representations. However, task-specific representations (graph convolutions and Weave methods) rarely offer any benefits, even though they are computationally more demanding. Lastly, combining different molecular feature representations typically does not give a noticeable improvement in performance compared to individual feature representations.
2019
Williams, Jonathan; Stönner, Christof; Edtbauer, Achim; Derstorff, Bettina; Bourtsoukidis, Efstratios; Klüpfel, Thomas; Krauter, Nicolas; Wicker, Jörg; Kramer, Stefan
What can we learn from the air chemistry of crowds? Proceedings Article
In: Hansel, Armin; Dunkl, Jürgen (Ed.): 8th International Conference on Proton Transfer Reaction Mass Spectrometry and its Applications, pp. 121-123, Innsbruck University Press, Innsbruck, 2019.
@inproceedings{williams2019what,
title = {What can we learn from the air chemistry of crowds?},
author = {Jonathan Williams and Christof St\"{o}nner and Achim Edtbauer and Bettina Derstorff and Efstratios Bourtsoukidis and Thomas Kl\"{u}pfel and Nicolas Krauter and J\"{o}rg Wicker and Stefan Kramer},
editor = {Armin Hansel and J\"{u}rgen Dunkl},
url = {https://www.ionicon.com/sites/default/files/uploads/doc/Contributions_8th-PTR-MS-Conference-2019_web.pdf#page=122},
year = {2019},
date = {2019-05-10},
booktitle = {8th International Conference on Proton Transfer Reaction Mass Spectrometry and its Applications},
pages = {121-123},
publisher = {Innsbruck University Press},
address = {Innsbruck},
abstract = {Current PTR-MS technology allows hundreds of volatile trace gases in air to be measured every second at extremely low levels (parts per trillion). These instruments are often used in atmospheric research on planes and ships and even in the Amazon rainforest. Recently, we have used this technology to examine air composition changes caused by large groups of people (10,000-30,000) under real world conditions at a football match and in a movie theater. In both cases the trace gas signatures measured in ambient air are shown to reflect crowd behavior. By applying advanced data mining techniques we have shown that groups of people reproducibly respond to certain emotional stimuli (e.g. suspense and comedy) by exhaling specific trace gases. Furthermore, we explore whether this information can be used to determine the age classification of films.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Current PTR-MS technology allows hundreds of volatile trace gases in air to be measured every second at extremely low levels (parts per trillion). These instruments are often used in atmospheric research on planes and ships and even in the Amazon rainforest. Recently, we have used this technology to examine air composition changes caused by large groups of people (10,000-30,000) under real world conditions at a football match and in a movie theater. In both cases the trace gas signatures measured in ambient air are shown to reflect crowd behavior. By applying advanced data mining techniques we have shown that groups of people reproducibly respond to certain emotional stimuli (e.g. suspense and comedy) by exhaling specific trace gases. Furthermore, we explore whether this information can be used to determine the age classification of films.
2018
Stönner, Christof; Edtbauer, Achim; Derstorff, Bettina; Bourtsoukidis, Efstratios; Klüpfel, Thomas; Wicker, Jörg; Williams, Jonathan
Proof of concept study: Testing human volatile organic compounds as tools for age classification of films Journal Article
In: PLOS One, vol. 13, no. 10, pp. 1-14, 2018.
@article{Stonner2018,
title = {Proof of concept study: Testing human volatile organic compounds as tools for age classification of films},
author = {Christof St\"{o}nner and Achim Edtbauer and Bettina Derstorff and Efstratios Bourtsoukidis and Thomas Kl\"{u}pfel and J\"{o}rg Wicker and Jonathan Williams},
doi = {10.1371/journal.pone.0203044},
year = {2018},
date = {2018-10-11},
journal = {PLOS One},
volume = {13},
number = {10},
pages = {1-14},
publisher = {Public Library of Science},
abstract = {Humans emit numerous volatile organic compounds (VOCs) through breath and skin. The nature and rate of these emissions are affected by various factors including emotional state. Previous measurements of VOCs and CO2 in a cinema have shown that certain chemicals are reproducibly emitted by audiences reacting to events in a particular film. Using data from films with various age classifications, we have studied the relationship between the emission of multiple VOCs and CO2 and the age classifier (0, 6, 12, and 16) with a view to developing a new chemically based and objective film classification method. We apply a random forest model built with time independent features extracted from the time series of every measured compound, and test predictive capability on subsets of all data. It was found that most compounds were not able to predict all age classifiers reliably, likely reflecting the fact that current classification is based on perceived sensibilities to many factors (e.g. incidences of violence, sex, antisocial behaviour, drug use, and bad language) rather than the visceral biological responses expressed in the data. However, promising results were found for isoprene which reliably predicted 0, 6 and 12 age classifiers for a variety of film genres and audience age groups. Therefore, isoprene emission per person might in future be a valuable aid to national classification boards, or even offer an alternative, objective, metric for rating films based on the reactions of large groups of people.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Humans emit numerous volatile organic compounds (VOCs) through breath and skin. The nature and rate of these emissions are affected by various factors including emotional state. Previous measurements of VOCs and CO2 in a cinema have shown that certain chemicals are reproducibly emitted by audiences reacting to events in a particular film. Using data from films with various age classifications, we have studied the relationship between the emission of multiple VOCs and CO2 and the age classifier (0, 6, 12, and 16) with a view to developing a new chemically based and objective film classification method. We apply a random forest model built with time independent features extracted from the time series of every measured compound, and test predictive capability on subsets of all data. It was found that most compounds were not able to predict all age classifiers reliably, likely reflecting the fact that current classification is based on perceived sensibilities to many factors (e.g. incidences of violence, sex, antisocial behaviour, drug use, and bad language) rather than the visceral biological responses expressed in the data. However, promising results were found for isoprene which reliably predicted 0, 6 and 12 age classifiers for a variety of film genres and audience age groups. Therefore, isoprene emission per person might in future be a valuable aid to national classification boards, or even offer an alternative, objective, metric for rating films based on the reactions of large groups of people.
Stönner, Christof; Edtbauer, Achim; Derstorff, Bettina; Bourtsoukidis, Efstratios; Klüpfel, Thomas; Wicker, Jörg; Williams, Jonathan
Investigating human emissions of volatile organic compounds in a cinema, flux rates, links to scene content, and possible applications Conference
15th Conference of the International Society of Indoor Air Quality and Climate, INDOOR AIR 2018, International Society of Indoor Air Quality and Climate, 2018, ISBN: 978-171382651-4.
@conference{St\"{o}nner2018investigating,
title = {Investigating human emissions of volatile organic compounds in a cinema, flux rates, links to scene content, and possible applications},
author = {Christof St\"{o}nner and Achim Edtbauer and Bettina Derstorff and Efstratios Bourtsoukidis and Thomas Kl\"{u}pfel and J\"{o}rg Wicker and Jonathan Williams},
isbn = {978-171382651-4},
year = {2018},
date = {2018-07-22},
booktitle = {15th Conference of the International Society of Indoor Air Quality and Climate, INDOOR AIR 2018},
publisher = {International Society of Indoor Air Quality and Climate},
abstract = {Humans emit numerous volatile organic compounds (VOCs) into the air via skin and breath. These emissions can depend on various factors such as nutrition, sporting activity and also the emotional state. It is shown that the emission rates of the main endogenous breath gases like CO2, acetone and isoprene are generally lower for children than for adults. In contrast, VOCs from exogenous sources strongly vary over the course of day. Interestingly, small scale variances in emission rates were found to occur reproducibly over multiple screenings of the same film. The peaks occurring in the time series of a compound during the screening of the film were induced by the physiological response of the audience to audio-visual stimuli. Additionally, the question whether this chemical reaction of the audience can be used for the prediction of age classification of films is addressed.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
Humans emit numerous volatile organic compounds (VOCs) into the air via skin and breath. These emissions can depend on various factors such as nutrition, sporting activity and also the emotional state. It is shown that the emission rates of the main endogenous breath gases like CO2, acetone and isoprene are generally lower for children than for adults. In contrast, VOCs from exogenous sources strongly vary over the course of day. Interestingly, small scale variances in emission rates were found to occur reproducibly over multiple screenings of the same film. The peaks occurring in the time series of a compound during the screening of the film were induced by the physiological response of the audience to audio-visual stimuli. Additionally, the question whether this chemical reaction of the audience can be used for the prediction of age classification of films is addressed.
2017
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.
@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 = {},
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
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.
@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 = {},
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.
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.
@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 = {},
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.
Williams, Jonathan; Stönner, Christof; Wicker, Jörg; Krauter, Nicolas; Derstorff, Bettina; Bourtsoukidis, Efstratios; Klüpfel, Thomas; Kramer, Stefan
Cinema audiences reproducibly vary the chemical composition of air during films, by broadcasting scene specific emissions on breath Journal Article
In: Scientific Reports, vol. 6, 2016.
@article{williams2015element,
title = {Cinema audiences reproducibly vary the chemical composition of air during films, by broadcasting scene specific emissions on breath},
author = {Jonathan Williams and Christof St\"{o}nner and J\"{o}rg Wicker and Nicolas Krauter and Bettina Derstorff and Efstratios Bourtsoukidis and Thomas Kl\"{u}pfel and Stefan Kramer},
url = {http://www.nature.com/articles/srep25464},
doi = {10.1038/srep25464},
year = {2016},
date = {2016-01-01},
urldate = {2016-01-01},
journal = {Scientific Reports},
volume = {6},
publisher = {Nature Publishing Group},
abstract = {Human beings continuously emit chemicals into the air by breath and through the skin. In order to determine whether these emissions vary predictably in response to audiovisual stimuli, we have continuously monitored carbon dioxide and over one hundred volatile organic compounds in a cinema. It was found that many airborne chemicals in cinema air varied distinctively and reproducibly with time for a particular film, even in different screenings to different audiences. Application of scene labels and advanced data mining methods revealed that specific film events, namely "suspense" or "comedy" caused audiences to change their emission of specific chemicals. These event-type synchronous, broadcasted human chemosignals open the possibility for objective and non-invasive assessment of a human group response to stimuli by continuous measurement of chemicals in air. Such methods can be applied to research fields such as psychology and biology, and be valuable to industries such as film making and advertising.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Human beings continuously emit chemicals into the air by breath and through the skin. In order to determine whether these emissions vary predictably in response to audiovisual stimuli, we have continuously monitored carbon dioxide and over one hundred volatile organic compounds in a cinema. It was found that many airborne chemicals in cinema air varied distinctively and reproducibly with time for a particular film, even in different screenings to different audiences. Application of scene labels and advanced data mining methods revealed that specific film events, namely "suspense" or "comedy" caused audiences to change their emission of specific chemicals. These event-type synchronous, broadcasted human chemosignals open the possibility for objective and non-invasive assessment of a human group response to stimuli by continuous measurement of chemicals in air. Such methods can be applied to research fields such as psychology and biology, and be valuable to industries such as film making and advertising.
2015
Wicker, Jörg; Krauter, Nicolas; Derstorff, Bettina; Stönner, Christof; Bourtsoukidis, Efstratios; Klüpfel, Thomas; Williams, Jonathan; Kramer, Stefan
Cinema Data Mining: The Smell of Fear Proceedings Article
In: Proceedings of the 21st ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 1235-1304, ACM ACM, New York, NY, USA, 2015, ISBN: 978-1-4503-3664-2.
@inproceedings{wicker2015cinema,
title = {Cinema Data Mining: The Smell of Fear},
author = {J\"{o}rg Wicker and Nicolas Krauter and Bettina Derstorff and Christof St\"{o}nner and Efstratios Bourtsoukidis and Thomas Kl\"{u}pfel and Jonathan Williams and Stefan Kramer},
url = {https://wicker.nz/nwp-acm/authorize.php?id=N10031
http://doi.acm.org/10.1145/2783258.2783404},
doi = {10.1145/2783258.2783404},
isbn = {978-1-4503-3664-2},
year = {2015},
date = {2015-01-01},
booktitle = {Proceedings of the 21st ACM SIGKDD International Conference on Knowledge Discovery and Data Mining},
pages = {1235-1304},
publisher = {ACM},
address = {New York, NY, USA},
organization = {ACM},
series = {KDD '15},
abstract = {While the physiological response of humans to emotional events or stimuli is well-investigated for many modalities (like EEG, skin resistance, ...), surprisingly little is known about the exhalation of so-called Volatile Organic Compounds (VOCs) at quite low concentrations in response to such stimuli. VOCs are molecules of relatively small mass that quickly evaporate or sublimate and can be detected in the air that surrounds us. The paper introduces a new field of application for data mining, where trace gas responses of people reacting on-line to films shown in cinemas (or movie theaters) are related to the semantic content of the films themselves. To do so, we measured the VOCs from a movie theatre over a whole month in intervals of thirty seconds, and annotated the screened films by a controlled vocabulary compiled from multiple sources. To gain a better understanding of the data and to reveal unknown relationships, we have built prediction models for so-called forward prediction (the prediction of future VOCs from the past), backward prediction (the prediction of past scene labels from future VOCs) and for some forms of abductive reasoning and Granger causality. Experimental results show that some VOCs and some labels can be predicted with relatively low error, and that hints for causality with low p-values can be detected in the data.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
While the physiological response of humans to emotional events or stimuli is well-investigated for many modalities (like EEG, skin resistance, …), surprisingly little is known about the exhalation of so-called Volatile Organic Compounds (VOCs) at quite low concentrations in response to such stimuli. VOCs are molecules of relatively small mass that quickly evaporate or sublimate and can be detected in the air that surrounds us. The paper introduces a new field of application for data mining, where trace gas responses of people reacting on-line to films shown in cinemas (or movie theaters) are related to the semantic content of the films themselves. To do so, we measured the VOCs from a movie theatre over a whole month in intervals of thirty seconds, and annotated the screened films by a controlled vocabulary compiled from multiple sources. To gain a better understanding of the data and to reveal unknown relationships, we have built prediction models for so-called forward prediction (the prediction of future VOCs from the past), backward prediction (the prediction of past scene labels from future VOCs) and for some forms of abductive reasoning and Granger causality. Experimental results show that some VOCs and some labels can be predicted with relatively low error, and that hints for causality with low p-values can be detected in the data.
2013
Wicker, Jörg
Large Classifier Systems in Bio- and Cheminformatics PhD Thesis
Technische Universität München, 2013.
@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 = {},
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.
2010
Hardy, Barry; Douglas, Nicki; Helma, Christoph; Rautenberg, Micha; Jeliazkova, Nina; Jeliazkov, Vedrin; Nikolova, Ivelina; Benigni, Romualdo; Tcheremenskaia, Olga; Kramer, Stefan; Girschick, Tobias; Buchwald, Fabian; Wicker, Jörg; Karwath, Andreas; Gütlein, Martin; Maunz, Andreas; Sarimveis, Haralambos; Melagraki, Georgia; Afantitis, Antreas; Sopasakis, Pantelis; Gallagher, David; Poroikov, Vladimir; Filimonov, Dmitry; Zakharov, Alexey; Lagunin, Alexey; Gloriozova, Tatyana; Novikov, Sergey; Skvortsova, Natalia; Druzhilovsky, Dmitry; Chawla, Sunil; Ghosh, Indira; Ray, Surajit; Patel, Hitesh; Escher, Sylvia
Collaborative development of predictive toxicology applications Journal Article
In: Journal of Cheminformatics, vol. 2, no. 1, pp. 7, 2010, ISSN: 1758-2946.
@article{hardy2010collaborative,
title = {Collaborative development of predictive toxicology applications},
author = {Barry Hardy and Nicki Douglas and Christoph Helma and Micha Rautenberg and Nina Jeliazkova and Vedrin Jeliazkov and Ivelina Nikolova and Romualdo Benigni and Olga Tcheremenskaia and Stefan Kramer and Tobias Girschick and Fabian Buchwald and J\"{o}rg Wicker and Andreas Karwath and Martin G\"{u}tlein and Andreas Maunz and Haralambos Sarimveis and Georgia Melagraki and Antreas Afantitis and Pantelis Sopasakis and David Gallagher and Vladimir Poroikov and Dmitry Filimonov and Alexey Zakharov and Alexey Lagunin and Tatyana Gloriozova and Sergey Novikov and Natalia Skvortsova and Dmitry Druzhilovsky and Sunil Chawla and Indira Ghosh and Surajit Ray and Hitesh Patel and Sylvia Escher},
url = {http://www.jcheminf.com/content/2/1/7},
doi = {10.1186/1758-2946-2-7},
issn = {1758-2946},
year = {2010},
date = {2010-01-01},
journal = {Journal of Cheminformatics},
volume = {2},
number = {1},
pages = {7},
abstract = {OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals.The OpenTox Framework includes APIs and services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The OpenTox approach to ontology allows for efficient mapping of complementary data coming from different datasets into a unifying structure having a shared terminology and representation.Two initial OpenTox applications are presented as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised Framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals.The OpenTox Framework includes APIs and services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The OpenTox approach to ontology allows for efficient mapping of complementary data coming from different datasets into a unifying structure having a shared terminology and representation.Two initial OpenTox applications are presented as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised Framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way.
Wicker, Jörg; Fenner, Kathrin; Ellis, Lynda; Wackett, Larry; Kramer, Stefan
Predicting biodegradation products and pathways: a hybrid knowledge- and machine learning-based approach Journal Article
In: Bioinformatics, vol. 26, no. 6, pp. 814-821, 2010.
@article{wicker2010predicting,
title = {Predicting biodegradation products and pathways: a hybrid knowledge- and machine learning-based approach},
author = {J\"{o}rg Wicker and Kathrin Fenner and Lynda Ellis and Larry Wackett and Stefan Kramer},
url = {http://bioinformatics.oxfordjournals.org/content/26/6/814.full},
doi = {10.1093/bioinformatics/btq024},
year = {2010},
date = {2010-01-01},
journal = {Bioinformatics},
volume = {26},
number = {6},
pages = {814-821},
publisher = {Oxford University Press},
abstract = {Motivation: 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 article, we propose a hybrid knowledge- 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. As 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: Results from leave-one-out cross-validation show that a recall and precision of ∼0.8 can be achieved for a subset of 13 transformation rules. Therefore, it is possible to optimize precision without compromising recall. We are currently integrating the results into an experimental version of the UM-PPS server.Availability: The program is freely available on the web at http://wwwkramer.in.tum.de/research/applications/biodegradation/data.Contact: kramer@in.tum.de},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Motivation: 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 article, we propose a hybrid knowledge- 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. As 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: Results from leave-one-out cross-validation show that a recall and precision of ∼0.8 can be achieved for a subset of 13 transformation rules. Therefore, it is possible to optimize precision without compromising recall. We are currently integrating the results into an experimental version of the UM-PPS server.Availability: The program is freely available on the web at http://wwwkramer.in.tum.de/research/applications/biodegradation/data.Contact: kramer@in.tum.de
2008
Wicker, Jörg; Fenner, Kathrin; Ellis, Lynda; Wackett, Larry; Kramer, Stefan
Machine Learning and Data Mining Approaches to Biodegradation Pathway Prediction Proceedings Article
In: Bridewell, Will; Calders, Toon; Medeiros, Ana Karla; Kramer, Stefan; Pechenizkiy, Mykola; Todorovski, Ljupco (Ed.): Proceedings of the Second International Workshop on the Induction of Process Models at ECML PKDD 2008, 2008.
@inproceedings{wicker2008machine,
title = {Machine Learning and Data Mining Approaches to Biodegradation Pathway Prediction},
author = {J\"{o}rg Wicker and Kathrin Fenner and Lynda Ellis and Larry Wackett and Stefan Kramer},
editor = {Will Bridewell and Toon Calders and Ana Karla Medeiros and Stefan Kramer and Mykola Pechenizkiy and Ljupco Todorovski},
url = {http://www.ecmlpkdd2008.org/files/pdf/workshops/ipm/9.pdf},
year = {2008},
date = {2008-01-01},
booktitle = {Proceedings of the Second International Workshop on the Induction of Process Models at ECML PKDD 2008},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}