Drug discovery with explainable artificial intelligence
TLDR
A review of the most prominent algorithmic concepts of explainable artificial intelligence, and forecasts future opportunities, potential applications as well as several remaining challenges is provided in this article. But, the review is limited to the use of deep learning for drug discovery.Abstract:
Deep learning bears promise for drug discovery, including advanced image analysis, prediction of molecular structure and function, and automated generation of innovative chemical entities with bespoke properties. Despite the growing number of successful prospective applications, the underlying mathematical models often remain elusive to interpretation by the human mind. There is a demand for ‘explainable’ deep learning methods to address the need for a new narrative of the machine language of the molecular sciences. This Review summarizes the most prominent algorithmic concepts of explainable artificial intelligence, and forecasts future opportunities, potential applications as well as several remaining challenges. We also hope it encourages additional efforts towards the development and acceptance of explainable artificial intelligence techniques. Drug discovery has recently profited greatly from the use of deep learning models. However, these models can be notoriously hard to interpret. In this Review, Jimenez-Luna and colleagues summarize recent approaches to use explainable artificial intelligence techniques in drug discovery.read more
Citations
More filters
Journal ArticleDOI
A guide to machine learning for biologists.
TL;DR: Machine learning is becoming a widely used tool for the analysis of biological data as mentioned in this paper, however, proper use of machine learning methods can be challenging for experimentalists, proper application of ML methods can also be challenging, and best practices and points to consider when embarking on experiments involving machine learning are discussed.
Journal ArticleDOI
Artificial intelligence to deep learning: machine intelligence approach for drug discovery.
TL;DR: In this article, Artificial Neural Networks and deep learning algorithms have been implemented in several drug discovery processes such as peptide synthesis, structure-based virtual screening, ligand-based screening, toxicity prediction, drug monitoring and release, pharmacophore modeling, quantitative structure-activity relationship, drug repositioning, polypharmacology, and physiochemical activity.
Journal ArticleDOI
Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems.
John A. Keith,Valentin Vassilev-Galindo,Bingqing Cheng,Stefan Chmiela,Michael Gastegger,Klaus-Robert Müller,Alexandre Tkatchenko +6 more
TL;DR: A critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design are reviewed.
Journal ArticleDOI
Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems.
John A. Keith,Valentin Vassilev-Galindo,Bingqing Cheng,Stefan Chmiela,Michael Gastegger,Klaus-Robert Müller,Alexandre Tkatchenko +6 more
TL;DR: In this paper, the authors provide a review of the applications of computational chemistry and machine learning in molecular and materials modeling, retrosyntheses, catalysis, and drug design.
Journal ArticleDOI
Why 90% of clinical drug development fails and how to improve it?
TL;DR: In this paper , the authors proposed structure-tissue exposure/selectivity-activity relationship (STAR) to improve drug optimization, which classifies drug candidates based on drug's potency, tissue exposure, and required dose for balancing clinical efficacy/toxicity.
References
More filters
Proceedings Article
ImageNet Classification with Deep Convolutional Neural Networks
TL;DR: The state-of-the-art performance of CNNs was achieved by Deep Convolutional Neural Networks (DCNNs) as discussed by the authors, which consists of five convolutional layers, some of which are followed by max-pooling layers, and three fully-connected layers with a final 1000-way softmax.
Journal ArticleDOI
Long short-term memory
TL;DR: A novel, efficient, gradient based method called long short-term memory (LSTM) is introduced, which can learn to bridge minimal time lags in excess of 1000 discrete-time steps by enforcing constant error flow through constant error carousels within special units.
Proceedings Article
Attention is All you Need
Ashish Vaswani,Noam Shazeer,Niki Parmar,Jakob Uszkoreit,Llion Jones,Aidan N. Gomez,Lukasz Kaiser,Illia Polosukhin +7 more
TL;DR: This paper proposed a simple network architecture based solely on an attention mechanism, dispensing with recurrence and convolutions entirely and achieved state-of-the-art performance on English-to-French translation.
Journal Article
Scikit-learn: Machine Learning in Python
Fabian Pedregosa,Gaël Varoquaux,Alexandre Gramfort,Vincent Michel,Bertrand Thirion,Olivier Grisel,Mathieu Blondel,Peter Prettenhofer,Ron Weiss,Vincent Dubourg,Jake Vanderplas,Alexandre Passos,David Cournapeau,Matthieu Brucher,Matthieu Perrot,Edouard Duchesnay +15 more
TL;DR: Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems, focusing on bringing machine learning to non-specialists using a general-purpose high-level language.
Journal ArticleDOI
Learning representations by back-propagating errors
TL;DR: Back-propagation repeatedly adjusts the weights of the connections in the network so as to minimize a measure of the difference between the actual output vector of the net and the desired output vector, which helps to represent important features of the task domain.