Machine learning models for drug–target interactions: current knowledge and future directions

2020 ◽  
Vol 25 (4) ◽  
pp. 748-756 ◽  
Author(s):  
Sofia D’Souza ◽  
K.V. Prema ◽  
Seetharaman Balaji
2020 ◽  
Vol 10 (4) ◽  
pp. 247
Author(s):  
Christina Vasilopoulou ◽  
Andrew P. Morris ◽  
George Giannakopoulos ◽  
Stephanie Duguez ◽  
William Duddy

Amyotrophic Lateral Sclerosis (ALS) is the most common late-onset motor neuron disorder, but our current knowledge of the molecular mechanisms and pathways underlying this disease remain elusive. This review (1) systematically identifies machine learning studies aimed at the understanding of the genetic architecture of ALS, (2) outlines the main challenges faced and compares the different approaches that have been used to confront them, and (3) compares the experimental designs and results produced by those approaches and describes their reproducibility in terms of biological results and the performances of the machine learning models. The majority of the collected studies incorporated prior knowledge of ALS into their feature selection approaches, and trained their machine learning models using genomic data combined with other types of mined knowledge including functional associations, protein-protein interactions, disease/tissue-specific information, epigenetic data, and known ALS phenotype-genotype associations. The importance of incorporating gene-gene interactions and cis-regulatory elements into the experimental design of future ALS machine learning studies is highlighted. Lastly, it is suggested that future advances in the genomic and machine learning fields will bring about a better understanding of ALS genetic architecture, and enable improved personalized approaches to this and other devastating and complex diseases.


Electronics ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1289 ◽  
Author(s):  
Sérgio Branco ◽  
André G. Ferreira ◽  
Jorge Cabral

The number of devices connected to the Internet is increasing, exchanging large amounts of data, and turning the Internet into the 21st-century silk road for data. This road has taken machine learning to new areas of applications. However, machine learning models are not yet seen as complex systems that must run in powerful computers (i.e., Cloud). As technology, techniques, and algorithms advance, these models are implemented into more computational constrained devices. The following paper presents a study about the optimizations, algorithms, and platforms used to implement such models into the network’s end, where highly resource-scarce microcontroller units (MCUs) are found. The paper aims to provide guidelines, taxonomies, concepts, and future directions to help decentralize the network’s intelligence.


2021 ◽  
Vol 23 (1) ◽  
pp. 86-99
Author(s):  
Ninghao Liu ◽  
Mengnan Du ◽  
Ruocheng Guo ◽  
Huan Liu ◽  
Xia Hu

Despite the recent advances in a wide spectrum of applications, machine learning models, especially deep neural networks, have been shown to be vulnerable to adversarial attacks. Attackers add carefully-crafted perturbations to input, where the perturbations are almost imperceptible to humans, but can cause models to make wrong predictions. Techniques to protect models against adversarial input are called adversarial defense methods. Although many approaches have been proposed to study adversarial attacks and defenses in different scenarios, an intriguing and crucial challenge remains that how to really understand model vulnerability? Inspired by the saying that "if you know yourself and your enemy, you need not fear the battles", we may tackle the challenge above after interpreting machine learning models to open the black-boxes. The goal of model interpretation, or interpretable machine learning, is to extract human-understandable terms for the working mechanism of models. Recently, some approaches start incorporating interpretation into the exploration of adversarial attacks and defenses. Meanwhile, we also observe that many existing methods of adversarial attacks and defenses, although not explicitly claimed, can be understood from the perspective of interpretation. In this paper, we review recent work on adversarial attacks and defenses, particularly from the perspective of machine learning interpretation. We categorize interpretation into two types, feature-level interpretation, and model-level interpretation. For each type of interpretation, we elaborate on how it could be used for adversarial attacks and defenses. We then briefly illustrate additional correlations between interpretation and adversaries. Finally, we discuss the challenges and future directions for tackling adversary issues with interpretation.


2020 ◽  
Vol 2 (1) ◽  
pp. 3-6
Author(s):  
Eric Holloway

Imagination Sampling is the usage of a person as an oracle for generating or improving machine learning models. Previous work demonstrated a general system for using Imagination Sampling for obtaining multibox models. Here, the possibility of importing such models as the starting point for further automatic enhancement is explored.


2021 ◽  
Author(s):  
Norberto Sánchez-Cruz ◽  
Jose L. Medina-Franco

<p>Epigenetic targets are a significant focus for drug discovery research, as demonstrated by the eight approved epigenetic drugs for treatment of cancer and the increasing availability of chemogenomic data related to epigenetics. This data represents a large amount of structure-activity relationships that has not been exploited thus far for the development of predictive models to support medicinal chemistry efforts. Herein, we report the first large-scale study of 26318 compounds with a quantitative measure of biological activity for 55 protein targets with epigenetic activity. Through a systematic comparison of machine learning models trained on molecular fingerprints of different design, we built predictive models with high accuracy for the epigenetic target profiling of small molecules. The models were thoroughly validated showing mean precisions up to 0.952 for the epigenetic target prediction task. Our results indicate that the herein reported models have considerable potential to identify small molecules with epigenetic activity. Therefore, our results were implemented as freely accessible and easy-to-use web application.</p>


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