scholarly journals A Chemoinformatic Exploration of the Chemical Space of Natural Steroids.

Author(s):  
Marcelo Otero ◽  
Silvina Sarno ◽  
Sofía Acebedo ◽  
Javier Alberto Ramirez

Chemoinformatic tools have been widely used to analyze the properties of large sets of natural compounds, mostly in the context of drug discovery. Nevertheless, fewer reports have aimed to answer basic biological questions. In this work, we have applied unsupervised machine learning techniques to assess the diversity and complexity of a set of natural steroids by characterizing them through simple topological and physicochemical molecular descriptors. As a most noteworthy result, these properties, derived from the molecular graphs of the compounds, are closely related to their biological functions and to their biosynthetic origins. Moreover, a trend paralleling diversification of the properties and metabolic evolution can be established, demonstrating the potential contribution of these computational approaches to better understanding the vast wealth of natural products.

Author(s):  
Christine A. Toh ◽  
Elizabeth M. Starkey ◽  
Conrad S. Tucker ◽  
Scarlett R. Miller

The emergence of ideation methods that generate large volumes of early-phase ideas has led to a need for reliable and efficient metrics for measuring the creativity of these ideas. However, existing methods of human judgment-based creativity assessments, as well as numeric model-based creativity assessment approaches suffer from low reliability and prohibitive computational burdens on human raters due to the high level of human input needed to calculate creativity scores. In addition, there is a need for an efficient method of computing the creativity of large sets of design ideas typically generated during the design process. This paper focuses on developing and empirically testing a machine learning approach for computing design creativity of large sets of design ideas to increase the efficiency and reliability of creativity evaluation methods in design research. The results of this study show that machine learning techniques can predict creativity of ideas with relatively high accuracy and sensitivity. These findings show that machine learning has the potential to be used for rating the creativity of ideas generated based on their descriptions.


2020 ◽  
Vol 16 (4) ◽  
pp. 407-419
Author(s):  
Aytun Onay ◽  
Melih Onay

Background: Virtual screening of candidate drug molecules using machine learning techniques plays a key role in pharmaceutical industry to design and discovery of new drugs. Computational classification methods can determine drug types according to the disease groups and distinguish approved drugs from withdrawn ones. Introduction: Classification models developed in this study can be used as a simple filter in drug modelling to eliminate potentially inappropriate molecules in the early stages. In this work, we developed a Drug Decision Support System (DDSS) to classify each drug candidate molecule as potentially drug or non-drug and to predict its disease group. Methods: Molecular descriptors were identified for the determination of a number of rules in drug molecules. They were derived using ADRIANA.Code program and Lipinski's rule of five. We used Artificial Neural Network (ANN) to classify drug molecules correctly according to the types of diseases. Closed frequent molecular structures in the form of subgraph fragments were also obtained with Gaston algorithm included in ParMol Package to find common molecular fragments for withdrawn drugs. Results: We observed that TPSA, XlogP Natoms, HDon_O and TPSA are the most distinctive features in the pool of the molecular descriptors and evaluated the performances of classifiers on all datasets and found that classification accuracies are very high on all the datasets. Neural network models achieved 84.6% and 83.3% accuracies on test sets including cardiac therapy, anti-epileptics and anti-parkinson drugs with approved and withdrawn drugs for drug classification problems. Conclusion: The experimental evaluation shows that the system is promising at determination of potential drug molecules to classify drug molecules correctly according to the types of diseases.


Nanoscale ◽  
2021 ◽  
Author(s):  
Susana I. L. Gomes ◽  
Mónica J. B. Amorim ◽  
Suman Pokhrel ◽  
Lutz Mädler ◽  
Matteo Fasano ◽  
...  

Based on a highly detailed materials characterisation database (including atomistic and multiscale modelling), single and univariate statistical methods, combined with machine learning techniques, revealed key descriptors of biological functions.


2018 ◽  
Vol 7 (5) ◽  
pp. 732-744 ◽  
Author(s):  
Thomas Luechtefeld ◽  
Craig Rowlands ◽  
Thomas Hartung

The creation of large toxicological databases and advances in machine-learning techniques have empowered computational approaches in toxicology.


Author(s):  
Kemal Oflazer

Morphology is the study of the structure of words and how words are forme3d by combining smaller units of linguistic information called morphemes. Any natural language processing application will need to computationally process the words in a language before any of the more complex processing is done. This is especially a must for morphologically complex languages. After a compact overview of the basic concepts in morphology, this chapter presents the state-of-the-art computational approaches to morphology, concentrating on two-level morphology and cascaded-rules and describing how morphographemics and morphotactics are handled in a finite-state setting. The chapter then summarizes recent approaches to how machine learning techniques are applied in morphological processing.


2020 ◽  
Author(s):  
Phyo Phyo Zin ◽  
Xinhao Li ◽  
Dhoha TRIKI ◽  
Denis Fourches

This study presents CryptoChem, a new method and associated software to securely store and transfer information using chemicals. Relying on the concept of Big Chemical Data, molecular descriptors and machine learning techniques, CryptoChem offers a highly complex and robust system with multiple layers of security for transmitting confidential information. This revolutionary technology adds fully untapped layers of complexity and is thus of relevance for different types of applications and users. The algorithm directly uses chemical structures and their properties as the central element of the secured storage. QSDR (Quantitative Structure-Data Relationship) models are used as private keys to encode and decode the data. Herein, we validate the software with a series of five datasets consisting of numerical and textual information with increasing size and complexity. We discuss <i>(i)</i> the initial concept and current features of CryptoChem, <i>(ii)</i> the associated Molread and Molwrite programs which encode messages as series of molecules and decodes them with an ensemble of QSDR machine learning models, <i>(iii)</i> the Analogue Retriever and Label Swapper methods, which enforce additional layers of security, <i>(iv)</i> the results of encoding and decoding the five datasets using CryptoChem, and (v) the comparison of CryptoChem to contemporary encryption methods. CryptoChem is freely available for testing at <a href="https://github.com/XinhaoLi74/CryptoChem">https://github.com/XinhaoLi74/CryptoChem</a>


2021 ◽  
Vol 15 (3) ◽  
pp. 1-37
Author(s):  
Omid Gheibi ◽  
Danny Weyns ◽  
Federico Quin

Recently, we have been witnessing a rapid increase in the use of machine learning techniques in self-adaptive systems. Machine learning has been used for a variety of reasons, ranging from learning a model of the environment of a system during operation to filtering large sets of possible configurations before analyzing them. While a body of work on the use of machine learning in self-adaptive systems exists, there is currently no systematic overview of this area. Such an overview is important for researchers to understand the state of the art and direct future research efforts. This article reports the results of a systematic literature review that aims at providing such an overview. We focus on self-adaptive systems that are based on a traditional Monitor-Analyze-Plan-Execute (MAPE)-based feedback loop. The research questions are centered on the problems that motivate the use of machine learning in self-adaptive systems, the key engineering aspects of learning in self-adaptation, and open challenges in this area. The search resulted in 6,709 papers, of which 109 were retained for data collection. Analysis of the collected data shows that machine learning is mostly used for updating adaptation rules and policies to improve system qualities, and managing resources to better balance qualities and resources. These problems are primarily solved using supervised and interactive learning with classification, regression, and reinforcement learning as the dominant methods. Surprisingly, unsupervised learning that naturally fits automation is only applied in a small number of studies. Key open challenges in this area include the performance of learning, managing the effects of learning, and dealing with more complex types of goals. From the insights derived from this systematic literature review, we outline an initial design process for applying machine learning in self-adaptive systems that are based on MAPE feedback loops.


2020 ◽  
Author(s):  
Phyo Phyo Zin ◽  
Xinhao Li ◽  
Dhoha TRIKI ◽  
Denis Fourches

This study presents CryptoChem, a new method and associated software to securely store and transfer information using chemicals. Relying on the concept of Big Chemical Data, molecular descriptors and machine learning techniques, CryptoChem offers a highly complex and robust system with multiple layers of security for transmitting confidential information. This revolutionary technology adds fully untapped layers of complexity and is thus of relevance for different types of applications and users. The algorithm directly uses chemical structures and their properties as the central element of the secured storage. QSDR (Quantitative Structure-Data Relationship) models are used as private keys to encode and decode the data. Herein, we validate the software with a series of five datasets consisting of numerical and textual information with increasing size and complexity. We discuss <i>(i)</i> the initial concept and current features of CryptoChem, <i>(ii)</i> the associated Molread and Molwrite programs which encode messages as series of molecules and decodes them with an ensemble of QSDR machine learning models, <i>(iii)</i> the Analogue Retriever and Label Swapper methods, which enforce additional layers of security, <i>(iv)</i> the results of encoding and decoding the five datasets using CryptoChem, and (v) the comparison of CryptoChem to contemporary encryption methods. CryptoChem is freely available for testing at <a href="https://github.com/XinhaoLi74/CryptoChem">https://github.com/XinhaoLi74/CryptoChem</a>


2006 ◽  
Author(s):  
Christopher Schreiner ◽  
Kari Torkkola ◽  
Mike Gardner ◽  
Keshu Zhang

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