Representation learning applications in biological sequence analysis

H Iuchi, T Matsutani, K Yamada, N Iwano… - Computational and …, 2021 - Elsevier
Although remarkable advances have been reported in high-throughput sequencing, the
ability to aptly analyze a substantial amount of rapidly generated biological …

[HTML][HTML] Omics data and data representations for deep learning-based predictive modeling

S Tsimenidis, E Vrochidou, GA Papakostas - International Journal of …, 2022 - mdpi.com
Medical discoveries mainly depend on the capability to process and analyze biological
datasets, which inundate the scientific community and are still expanding as the cost of next …

Development and validation of an explainable machine learning-based prediction model for drug–food interactions from chemical structures

QH Kha, VH Le, TNK Hung, NTK Nguyen, NQK Le - Sensors, 2023 - mdpi.com
Possible drug–food constituent interactions (DFIs) could change the intended efficiency of
particular therapeutics in medical practice. The increasing number of multiple-drug …

DLpTCR: an ensemble deep learning framework for predicting immunogenic peptide recognized by T cell receptor

Z Xu, M Luo, W Lin, G Xue, P Wang, X **… - Briefings in …, 2021 - academic.oup.com
Accurate prediction of immunogenic peptide recognized by T cell receptor (TCR) can greatly
benefit vaccine development and cancer immunotherapy. However, identifying …

DNN-DTIs: Improved drug-target interactions prediction using XGBoost feature selection and deep neural network

C Chen, H Shi, Z Jiang, A Salhi, R Chen, X Cui… - Computers in Biology …, 2021 - Elsevier
Abstract Analysis and prediction of drug-target interactions (DTIs) play an important role in
understanding drug mechanisms, as well as drug repositioning and design. Machine …

[HTML][HTML] Brain asymmetry detection and machine learning classification for diagnosis of early dementia

NJ Herzog, GD Magoulas - Sensors, 2021 - mdpi.com
Early identification of degenerative processes in the human brain is considered essential for
providing proper care and treatment. This may involve detecting structural and functional …

An integrated neural network and SEIR model to predict Covid-19

SN Zisad, MS Hossain, MS Hossain, K Andersson - Algorithms, 2021 - mdpi.com
A novel coronavirus (COVID-19), which has become a great concern for the world, was
identified first in Wuhan city in China. The rapid spread throughout the world was …

A general hybrid modeling framework for systems biology applications: Combining mechanistic knowledge with deep neural networks under the SBML standard

J Pinto, JRC Ramos, RS Costa, R Oliveira - AI, 2023 - mdpi.com
In this paper, a computational framework is proposed that merges mechanistic modeling
with deep neural networks obeying the Systems Biology Markup Language (SBML) …

Ssnet: A deep learning approach for protein-ligand interaction prediction

N Verma, X Qu, F Trozzi, M Elsaied, N Karki… - International journal of …, 2021 - mdpi.com
Computational prediction of Protein-Ligand Interaction (PLI) is an important step in the
modern drug discovery pipeline as it mitigates the cost, time, and resources required to …

Prediction of protein–ATP binding residues based on ensemble of deep convolutional neural networks and LightGBM algorithm

J Song, G Liu, J Jiang, P Zhang, Y Liang - International Journal of …, 2021 - mdpi.com
Accurately identifying protein–ATP binding residues is important for protein function
annotation and drug design. Previous studies have used classic machine-learning …