Complex Networks, Bio-Molecular Systems, and Machine Learning 2.0

Dear Colleagues,

Both, artificial intelligence and/or machine learning (AI/ML) and complex networks algorithms are important tools in the computational study of molecular systems. Some of these methods are artificial neural networks (ANNs), deep learning networks, support vector machines (SVMs), random forests (RFs), genetic algorithms (GAs), deep neural networks (DNNs), deep belief networks (DBNs), recurrent neural networks (RNNs), convolutional neural networks (CNNs), etc. We can use structural parameters, molecular descriptors, experimental conditions, chemometrics measurements, etc., as inputs to train these AI/ML algorithms. As a result, we can obtain predictive models for drug discovery, vaccine design, nanotechnology, etc.

On the other hand, complex networks are particularly useful in the study of complex bio-molecular systems. We can use complex networks to represent complex structural–function patterns in complex molecular bio-systems. This includes, but is not limited to, the structures of chemical compounds, synthetic chemical reaction routes, proteins, polymers, viral structures, RNA secondary structures, etc. This method is highly flexible; therefore, we can also represent larger bio-systems such as metabolic pathways, protein interaction networks (PINs), gene regulatory networks, brain cortexes, ecosystems, the internet, markets, social networks, etc. Within this approach, parts of a system (atoms, amino acids, monomers, proteins, reactions, neurons, organisms, etc.) are commonly represented as nodes, and the structure–function relationships among them (chemical bonds, hydrogen bonds, reactions, activation, co-expression, etc.) are represented as edges or links. This paves the way for the study of complex bio-molecular systems with graphs and the complex network theory. As a consequence, we can calculate multiple graph invariants (numeric parameters), which are useful to quantify the complex structure of these systems. This includes software/algorithms for the representation and study of distributions, emergent properties, transport phenomena, multiplex networks, dynamic systems properties, etc. In addition, although not mandatory, we can also train AI/ML algorithms using the numerical parameters of complex networks and bio-molecular systems as input in order to predict structure–function relationships and, as a consequence, the properties of these systems.

This framework opens the door to the development of new methods, algorithms, databases, and software for the study of complex bio-molecular systems using AI/ML and/or complex network algorithms. Consequently, the title of this issue is: “Complex Networks, Bio-Molecular Systems, and Machine Learning.” Authors are welcome to submit papers that utilize AI/ML algorithms alone, and we also welcome papers that utilize complex network algorithms alone. Overall, we especially welcome papers that combine both AI/ML and complex networks.

Prof. Dr. Humberto González-Díaz
Guest Editor

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