Bioactivity Prediction Using Convolutional Neural Network

  • Hentabli HamzaEmail author
  • Maged Nasser
  • Naomie Salim
  • Faisal Saeed
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 1073)


According to the similar property principle, structurally similar compounds exhibit very similar properties as well as similar biological activities. Many researchers have applied this principle to discover novel drugs, thereby leading to the emergence of the prediction of the activities of compounds based on their chemical structure, since the toxic or biological properties of compounds are determined by their chemical structure, particularly, their substructures. The concept of functional groups (FGs) of connected atoms (small molecules) determining the properties and reactivity of the parent molecule forms the cornerstone of organic chemistry, medicinal chemistry, toxicity assessments and QSAR. This study introduced a novel predictive system, i.e., a convolutional neural network that enables the prediction of molecular bioactivities using a novel molecular matrix representation. The number of atoms in small molecules were investigated to determine its accuracy during the prediction of the activities of the orphan compounds. This approach was applied to popular datasets and the performance of this system was compared with three other classical ML algorithms. All the experiments indicated that the proposed model was able to provide an interesting prediction rate (accuracy of 90.21).


Bioactive molecules Activity prediction model Convolutional neural network Deep learning Biological activities 



This work is supported by the Ministry of Higher Education (MOHE) and the Research Management Centre (RMC) at the Universiti Teknologi Malaysia (UTM) under the Research University Grant Category (VOT Q.J130000.2528.16H74 and R.J130000.7828.4F985).


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Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Hentabli Hamza
    • 1
    Email author
  • Maged Nasser
    • 1
  • Naomie Salim
    • 1
  • Faisal Saeed
    • 2
  1. 1.School of ComputingUniversiti Teknologi MalaysiaJohor BahruMalaysia
  2. 2.College of Computer Science and EngineeringTaibah UniversityMedinaSaudi Arabia

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