Multilevel characterization of unknown protein sequences using hierarchical long short term memory model

Multilevel characterization of the recently developed Unknown Protein Sequence (UPS) is significant for the drug-designing, disease-diagnosis, and treatment plans. UPS can demonstrate harmful as well as useful characters. Long Short Term Memory (LSTM) based Multilevel Protein Characterization (ML_PC) model using Neuro-Fuzzy Classifier (NFC) and transfer learning has been proposed in this paper for characteristics, species, and function prediction of the UPS. Gram Negative (GN) dataset with known 2286 protein sequences, is used for formation and validation of the ML_PC model. Thereafter NFC is applied at initial stage of the validated ML_PC model to filter the 518 independent protein sequences of the UPS dataset as GN or Non-GN in context with known GN dataset. However, NFC is competent to handle likelihood classification complications of supervised learning. Characteristics, species, and functions of the filtered GN UPS have been predicted in succeeding levels of the ML_PC framework through Protein Characterization (PC) model. LSTM and transfer learning based PC model has been trained and validated using augmented feature of the known GN protein sequence samples, while tested with UPS and filtered GN protein sequences. Transfer learning has been applied as requisite postprocessing to overcome overfitting in the prediction of bacterial protein species with insufficient protein sequence samples. Performance of the multilevel model is improved by 7.52% after combining with transfer learning and NFC. ML_PC model has been compatible to extract relevant biological information of the UPS in context to various categories of bacterial proteins.