Sökning: L773:1758 2946 >
CPSign :
CPSign : Conformal Prediction for Cheminformatics Modeling
-
- Arvidsson McShane, Staffan, 1990- (författare)
- Uppsala universitet,Institutionen för farmaceutisk biovetenskap,Science for Life Laboratory, SciLifeLab,Pharmaceutical Bioinformatics,Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, 75124, Sweden
-
- Norinder, Ulf, 1956- (författare)
- Örebro universitet,Uppsala universitet,Institutionen för farmaceutisk biovetenskap,Science for Life Laboratory, SciLifeLab,Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Sweden; Department of Computer and Systems Sciences, Stockholm University, Sweden; MTM Research Centre, School of Science and Technology, Örebro University, Sweden,Institutionen för naturvetenskap och teknik,Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, 75124, Sweden; Department of Computer and Systems Sciences, Stockholm University, Stockholm, 10587, Sweden
-
- Alvarsson, Jonathan, 1981- (författare)
- Uppsala universitet,Institutionen för farmaceutisk biovetenskap,Science for Life Laboratory, SciLifeLab,Pharmaceutical Bioinformatics,Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, 75124, Sweden
-
visa fler...
-
- Ahlberg, Ernst (författare)
- Uppsala universitet,Institutionen för farmaceutisk biovetenskap,Science for Life Laboratory, SciLifeLab,Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, 75124, Sweden; Department of Computer Science, Royal Holloway University of London, Egham, TW20 0EX, UK
-
- Carlsson, Lars (författare)
- Jönköping University,JTH, Avdelningen för datavetenskap,Department of Computer Science, Royal Holloway University of London, Egham, TW20 0EX, UK; Department of Computing, Jönköping University, Jönköping, 55111, Sweden
-
- Spjuth, Ola, Professor, 1977- (författare)
- Uppsala universitet,Institutionen för farmaceutisk biovetenskap,Science for Life Laboratory, SciLifeLab,Pharmaceutical Bioinformatics,Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, 75124, Sweden
-
visa färre...
-
(creator_code:org_t)
- BioMed Central (BMC), 2024
- 2024
- Engelska.
-
Ingår i: Journal of Cheminformatics. - : BioMed Central (BMC). - 1758-2946. ; 16
- Relaterad länk:
-
https://doi.org/10.1...
-
visa fler...
-
https://uu.diva-port... (primary) (Raw object)
-
https://doi.org/10.1...
-
https://urn.kb.se/re...
-
https://doi.org/10.1...
-
https://urn.kb.se/re...
-
https://urn.kb.se/re...
-
visa färre...
Abstract
Ämnesord
Stäng
- Conformal prediction has seen many applications in pharmaceutical science, being able to calibrate outputs of machine learning models and producing valid prediction intervals. We here present the open source software CPSign that is a complete implementation of conformal prediction for cheminformatics modeling. CPSign implements inductive and transductive conformal prediction for classification and regression, and probabilistic prediction with the Venn-ABERS methodology. The main chemical representation is signatures but other types of descriptors are also supported. The main modeling methodology is support vector machines (SVMs), but additional modeling methods are supported via an extension mechanism, e.g. DeepLearning4J models. We also describe features for visualizing results from conformal models including calibration and efficiency plots, as well as features to publish predictive models as REST services. We compare CPSign against other common cheminformatics modeling approaches including random forest, and a directed message-passing neural network. The results show that CPSign produces robust predictive performance with comparative predictive efficiency, with superior runtime and lower hardware requirements compared to neural network based models. CPSign has been used in several studies and is in production-use in multiple organizations. The ability to work directly with chemical input files, perform descriptor calculation and modeling with SVM in the conformal prediction framework, with a single software package having a low footprint and fast execution time makes CPSign a convenient and yet flexible package for training, deploying, and predicting on chemical data. CPSign can be downloaded from GitHub at https://github.com/arosbio/cpsign.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Farmaceutiska vetenskaper (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Pharmaceutical Sciences (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Datavetenskap (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Computer Sciences (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Nyckelord
- machine learning
- QSAR
- Conformal prediction
- Venn-ABERS
- Bioinformatics
- Bioinformatik
- Farmaceutisk vetenskap
- Pharmaceutical Science
- Machine learning
- Maskininlärning
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
Hitta via bibliotek
Till lärosätets databas