Literature DB >> 30310652

Big-data and machine learning to revamp computational toxicology and its use in risk assessment.

Thomas Luechtefeld1, Craig Rowlands2, Thomas Hartung1.   

Abstract

The creation of large toxicological databases and advances in machine-learning techniques have empowered computational approaches in toxicology. Work with these large databases based on regulatory data has allowed reproducibility assessment of animal models, which highlight weaknesses in traditional in vivo methods. This should lower the bars for the introduction of new approaches and represents a benchmark that is achievable for any alternative method validated against these methods. Quantitative Structure Activity Relationships (QSAR) models for skin sensitization, eye irritation, and other human health hazards based on these big databases, however, also have made apparent some of the challenges facing computational modeling, including validation challenges, model interpretation issues, and model selection issues. A first implementation of machine learning-based predictions termed REACHacross achieved unprecedented sensitivities of >80% with specificities >70% in predicting the six most common acute and topical hazards covering about two thirds of the chemical universe. While this is awaiting formal validation, it demonstrates the new quality introduced by big data and modern data-mining technologies. The rapid increase in the diversity and number of computational models, as well as the data they are based on, create challenges and opportunities for the use of computational methods.

Entities:  

Year:  2018        PMID: 30310652      PMCID: PMC6116175          DOI: 10.1039/c8tx00051d

Source DB:  PubMed          Journal:  Toxicol Res (Camb)        ISSN: 2045-452X            Impact factor:   3.524


  56 in total

1.  Opinion versus evidence for the need to move away from animal testing.

Authors:  Thomas Hartung
Journal:  ALTEX       Date:  2017       Impact factor: 6.043

2.  Chemical regulators have overreached.

Authors:  Thomas Hartung; Costanza Rovida
Journal:  Nature       Date:  2009-08-27       Impact factor: 49.962

3.  Food for thought ... on in silico methods in toxicology.

Authors:  Thomas Hartung; Sebastian Hoffmann
Journal:  ALTEX       Date:  2009       Impact factor: 6.043

4.  The need for strategic development of safety sciences.

Authors:  Francois Busquet; Thomas Hartung
Journal:  ALTEX       Date:  2017       Impact factor: 6.043

5.  The added value of the 90-day repeated dose oral toxicity test for industrial chemicals with a low (sub)acute toxicity profile in a high quality dataset.

Authors:  Katy Taylor; David J Andrew; Laura Rego
Journal:  Regul Toxicol Pharmacol       Date:  2014-04-23       Impact factor: 3.271

6.  Predictive Modeling of Estrogen Receptor Binding Agents Using Advanced Cheminformatics Tools and Massive Public Data.

Authors:  Kathryn Ribay; Marlene T Kim; Wenyi Wang; Daniel Pinolini; Hao Zhu
Journal:  Front Environ Sci       Date:  2016-03-08

7.  The Threshold of Toxicological Concern for prenatal developmental toxicity in rats and rabbits.

Authors:  B van Ravenzwaay; X Jiang; T Luechtefeld; T Hartung
Journal:  Regul Toxicol Pharmacol       Date:  2017-06-20       Impact factor: 3.271

Review 8.  Use of QSARs in international decision-making frameworks to predict health effects of chemical substances.

Authors:  Mark T D Cronin; Joanna S Jaworska; John D Walker; Michael H I Comber; Christopher D Watts; Andrew P Worth
Journal:  Environ Health Perspect       Date:  2003-08       Impact factor: 9.031

9.  Analysis of public oral toxicity data from REACH registrations 2008-2014.

Authors:  Thomas Luechtefeld; Alexandra Maertens; Daniel P Russo; Costanza Rovida; Hao Zhu; Thomas Hartung
Journal:  ALTEX       Date:  2016-02-11       Impact factor: 6.043

10.  From "weight of evidence" to quantitative data integration using multicriteria decision analysis and Bayesian methods.

Authors:  Igor Linkov; Olivia Massey; Jeff Keisler; Ivan Rusyn; Thomas Hartung
Journal:  ALTEX       Date:  2015       Impact factor: 6.043

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  10 in total

1.  Internationalization of read-across as a validated new approach method (NAM) for regulatory toxicology.

Authors:  Costanza Rovida; Tara Barton-Maclaren; Emilio Benfenati; Francesca Caloni; P. Charukeshi Chandrasekera; Christophe Chesné; Mark T D Cronin; Joop De Knecht; Daniel R Dietrich; Sylvia E Escher; Suzanne Fitzpatrick; Brenna Flannery; Matthias Herzler; Susanne Hougaard Bennekou; Bruno Hubesch; Hennicke Kamp; Jaffar Kisitu; Nicole Kleinstreuer; Simona Kovarich; Marcel Leist; Alexandra Maertens; Kerry Nugent; Giorgia Pallocca; Manuel Pastor; Grace Patlewicz; Manuela Pavan; Octavio Presgrave; Lena Smirnova; Michael Schwarz; Takashi Yamada; Thomas Hartung
Journal:  ALTEX       Date:  2020-04-30       Impact factor: 6.250

2.  Recent efforts to elucidate the scientific validity of animal-based drug tests by the pharmaceutical industry, pro-testing lobby groups, and animal welfare organisations.

Authors:  Jarrod Bailey; Michael Balls
Journal:  BMC Med Ethics       Date:  2019-03-01       Impact factor: 2.652

3.  Skin Doctor: Machine Learning Models for Skin Sensitization Prediction that Provide Estimates and Indicators of Prediction Reliability.

Authors:  Anke Wilm; Conrad Stork; Christoph Bauer; Andreas Schepky; Jochen Kühnl; Johannes Kirchmair
Journal:  Int J Mol Sci       Date:  2019-09-28       Impact factor: 5.923

4.  Bringing Big Data to Bear in Environmental Public Health: Challenges and Recommendations.

Authors:  Saskia Comess; Alexia Akbay; Melpomene Vasiliou; Ronald N Hines; Lucas Joppa; Vasilis Vasiliou; Nicole Kleinstreuer
Journal:  Front Artif Intell       Date:  2020-05-15

Review 5.  Developments in high-resolution mass spectrometric analyses of new psychoactive substances.

Authors:  Joshua Klingberg; Bethany Keen; Adam Cawley; Daniel Pasin; Shanlin Fu
Journal:  Arch Toxicol       Date:  2022-02-09       Impact factor: 5.153

Review 6.  Probabilistic risk assessment - the keystone for the future of toxicology.

Authors:  Alexandra Maertens; Emily Golden; Thomas H Luechtefeld; Sebastian Hoffmann; Katya Tsaioun; Thomas Hartung
Journal:  ALTEX       Date:  2022       Impact factor: 6.250

7.  Revealing Adverse Outcome Pathways from Public High-Throughput Screening Data to Evaluate New Toxicants by a Knowledge-Based Deep Neural Network Approach.

Authors:  Heather L Ciallella; Daniel P Russo; Lauren M Aleksunes; Fabian A Grimm; Hao Zhu
Journal:  Environ Sci Technol       Date:  2021-07-25       Impact factor: 11.357

8.  Machine Learning of Toxicological Big Data Enables Read-Across Structure Activity Relationships (RASAR) Outperforming Animal Test Reproducibility.

Authors:  Thomas Luechtefeld; Dan Marsh; Craig Rowlands; Thomas Hartung
Journal:  Toxicol Sci       Date:  2018-09-01       Impact factor: 4.849

9.  Predictive modeling of estrogen receptor agonism, antagonism, and binding activities using machine- and deep-learning approaches.

Authors:  Heather L Ciallella; Daniel P Russo; Lauren M Aleksunes; Fabian A Grimm; Hao Zhu
Journal:  Lab Invest       Date:  2020-08-10       Impact factor: 5.662

10.  A framework for chemical safety assessment incorporating new approach methodologies within REACH.

Authors:  Nicholas Ball; Remi Bars; Philip A Botham; Andreea Cuciureanu; Mark T D Cronin; John E Doe; Tatsiana Dudzina; Timothy W Gant; Marcel Leist; Bennard van Ravenzwaay
Journal:  Arch Toxicol       Date:  2022-02-01       Impact factor: 5.153

  10 in total

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