scholarly journals GRAPH WAVELET ALIGNMENT KERNELS FOR DRUG VIRTUAL SCREENING

2009 ◽  
Vol 07 (03) ◽  
pp. 473-497 ◽  
Author(s):  
AARON SMALTER ◽  
JUN HUAN ◽  
GERALD LUSHINGTON
Keyword(s):  
Virtual Screening ◽  
Kernel Function ◽  
Support Vector Machine Classifier ◽  
Support Vector ◽  
Activity Prediction ◽  
Graph Kernel ◽  
Computational Costs ◽  
Chemical Structures ◽  
Structure Activity ◽  
Local Topology

In this paper, we introduce a novel statistical modeling technique for target property prediction, with applications to virtual screening and drug design. In our method, we use graphs to model chemical structures and apply a wavelet analysis of graphs to summarize features capturing graph local topology. We design a novel graph kernel function to utilize the topology features to build predictive models for chemicals via Support Vector Machine classifier. We call the new graph kernel a graph wavelet-alignment kernel. We have evaluated the efficacy of the wavelet-alignment kernel using a set of chemical structure–activity prediction benchmarks. Our results indicate that the use of the kernel function yields performance profiles comparable to, and sometimes exceeding that of the existing state-of-the-art chemical classification approaches. In addition, our results also show that the use of wavelet functions significantly decreases the computational costs for graph kernel computation with more than ten fold speedup.

OFFLINE YORÙBÁ HANDWRITTEN WORD RECOGNITION USING GEOMETRIC FEATURE EXTRACTION AND SUPPORT VECTOR MACHINE CLASSIFIER

2020 ◽  
Vol 5 (2) ◽  
pp. 504
Author(s):  
Matthias Omotayo Oladele ◽  
Temilola Morufat Adepoju ◽  
Olaide ` Abiodun Olatoke ◽  
Oluwaseun Adewale Ojo
Keyword(s):  
Support Vector Machine ◽  
Feature Extraction ◽  
Word Recognition ◽  
Support Vector Machine Classifier ◽  
Recognition Accuracy ◽  
Recognition System ◽  
Support Vector ◽  
Geometric Features ◽  
Total Length ◽  
Yoruba Language

Yorùbá language is one of the three main languages that is been spoken in Nigeria. It is a tonal language that carries an accent on the vowel alphabets. There are twenty-five (25) alphabets in Yorùbá language with one of the alphabets a digraph (GB). Due to the difficulty in typing handwritten Yorùbá documents, there is a need to develop a handwritten recognition system that can convert the handwritten texts to digital format. This study discusses the offline Yorùbá handwritten word recognition system (OYHWR) that recognizes Yorùbá uppercase alphabets. Handwritten characters and words were obtained from different writers using the paint application and M708 graphics tablets. The characters were used for training and the words were used for testing. Pre-processing was done on the images and the geometric features of the images were extracted using zoning and gradient-based feature extraction. Geometric features are the different line types that form a particular character such as the vertical, horizontal, and diagonal lines. The geometric features used are the number of horizontal lines, number of vertical lines, number of right diagonal lines, number of left diagonal lines, total length of all horizontal lines, total length of all vertical lines, total length of all right slanting lines, total length of all left-slanting lines and the area of the skeleton. The characters are divided into 9 zones and gradient feature extraction was used to extract the horizontal and vertical components and geometric features in each zone. The words were fed into the support vector machine classifier and the performance was evaluated based on recognition accuracy. Support vector machine is a two-class classifier, hence a multiclass SVM classifier least square support vector machine (LSSVM) was used for word recognition. The one vs one strategy and RBF kernel were used and the recognition accuracy obtained from the tested words ranges between 66.7%, 83.3%, 85.7%, 87.5%, and 100%. The low recognition rate for some of the words could be as a result of the similarity in the extracted features.

Application of Machine Learning Approaches for the Design and Study of Anticancer Drugs

2019 ◽  
Vol 20 (5) ◽  
pp. 488-500 ◽  
Author(s):  
Yan Hu ◽  
Yi Lu ◽  
Shuo Wang ◽  
Mengying Zhang ◽  
Xiaosheng Qu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Design ◽  
Anticancer Drugs ◽  
Nearest Neighbor ◽  
Cost Effective ◽  
Support Vector ◽  
Learning Approaches ◽  
K Nearest Neighbor ◽  
Activity Prediction ◽  
Linear Discriminant

Background: Globally the number of cancer patients and deaths are continuing to increase yearly, and cancer has, therefore, become one of the world&#039;s highest causes of morbidity and mortality. In recent years, the study of anticancer drugs has become one of the most popular medical topics. </P><P> Objective: In this review, in order to study the application of machine learning in predicting anticancer drugs activity, some machine learning approaches such as Linear Discriminant Analysis (LDA), Principal components analysis (PCA), Support Vector Machine (SVM), Random forest (RF), k-Nearest Neighbor (kNN), and Naïve Bayes (NB) were selected, and the examples of their applications in anticancer drugs design are listed. </P><P> Results: Machine learning contributes a lot to anticancer drugs design and helps researchers by saving time and is cost effective. However, it can only be an assisting tool for drug design. </P><P> Conclusion: This paper introduces the application of machine learning approaches in anticancer drug design. Many examples of success in identification and prediction in the area of anticancer drugs activity prediction are discussed, and the anticancer drugs research is still in active progress. Moreover, the merits of some web servers related to anticancer drugs are mentioned.

Applications of Quantitative Structure-Activity Relationships (QSAR) based Virtual Screening in Drug Design: A Review

2020 ◽  
Vol 20 (14) ◽  
pp. 1375-1388 ◽  
Author(s):  
Patnala Ganga Raju Achary
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Virtual Screening ◽  
Model Building ◽  
Chemical Space ◽  
Qsar Model ◽  
Quantitative Structure ◽  
Efficient Manner ◽  
Qsar Analysis ◽  
Structure Activity

The scientists, and the researchers around the globe generate tremendous amount of information everyday; for instance, so far more than 74 million molecules are registered in Chemical Abstract Services. According to a recent study, at present we have around 1060 molecules, which are classified as new drug-like molecules. The library of such molecules is now considered as ‘dark chemical space’ or ‘dark chemistry.’ Now, in order to explore such hidden molecules scientifically, a good number of live and updated databases (protein, cell, tissues, structure, drugs, etc.) are available today. The synchronization of the three different sciences: ‘genomics’, proteomics and ‘in-silico simulation’ will revolutionize the process of drug discovery. The screening of a sizable number of drugs like molecules is a challenge and it must be treated in an efficient manner. Virtual screening (VS) is an important computational tool in the drug discovery process; however, experimental verification of the drugs also equally important for the drug development process. The quantitative structure-activity relationship (QSAR) analysis is one of the machine learning technique, which is extensively used in VS techniques. QSAR is well-known for its high and fast throughput screening with a satisfactory hit rate. The QSAR model building involves (i) chemo-genomics data collection from a database or literature (ii) Calculation of right descriptors from molecular representation (iii) establishing a relationship (model) between biological activity and the selected descriptors (iv) application of QSAR model to predict the biological property for the molecules. All the hits obtained by the VS technique needs to be experimentally verified. The present mini-review highlights: the web-based machine learning tools, the role of QSAR in VS techniques, successful applications of QSAR based VS leading to the drug discovery and advantages and challenges of QSAR.

Sign in / Sign up

Export Citation Format

Share Document