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Most uses of machine learning today involve training a model from scratch for a particular task, or sometimes starting with a model pretrained on a related task and then fine-tuning on a downstream task. Both approaches offer limited…
Gene promoters are the key DNA regulatory elements positioned around the transcription start sites and are responsible for regulating gene transcription process. Various alignment-based, signal-based and content-based approaches are…
Automated ranking of pre-trained Deep Neural Networks (DNNs) reduces the required time for selecting optimal pre-trained DNN and boost the classification performance in transfer learning. In this paper, we introduce a novel algorithm to…
Background: Small interfering RNA (siRNA) is a promising therapeutic agent due to its ability to silence disease-related genes via RNA interference. While traditional machine learning and early deep learning methods have made progress in…
Wind energy forecasting helps to manage power production, and hence, reduces energy cost. Deep Neural Networks (DNN) mimics hierarchical learning in the human brain and thus possesses hierarchical, distributed, and multi-task learning…
Predicting user responses, such as click-through rate and conversion rate, are critical in many web applications including web search, personalised recommendation, and online advertising. Different from continuous raw features that we…
Recent technological advancements in data acquisition tools allowed life scientists to acquire multimodal data from different biological application domains. Broadly categorized in three types (i.e., sequences, images, and signals), these…
Deep Material Network (DMN) has recently emerged as a data-driven surrogate model for heterogeneous materials. Given a particular microstructural morphology, the effective linear and nonlinear behaviors can be successfully approximated by…
MicroRNAs (miRNAs) are endogenous 22-nucleotide RNAs, which suppress gene expression by selectively binding to the 3-noncoding region of specific message RNAs through base-pairing. Given the diversity and abundance of miRNA targets, miRNAs…
DNA microarray gene-expression data has been widely used to identify cancerous gene signatures. Microarray can increase the accuracy of cancer diagnosis and prognosis. However, analyzing the large amount of gene expression data from…
KNN is one of the most popular classification methods, but it often fails to work well with inappropriate choice of distance metric or due to the presence of numerous class-irrelevant features. Linear feature transformation methods have…
Predicting cross-immunity between viral strains is vital for public health surveillance and vaccine development. Traditional neural network methods, such as BiLSTM, could be ineffective due to the lack of lab data for model training and the…
MicroRNAs (miRNAs) play crucial roles in multifarious biological processes associated with human diseases. Identifying potential miRNA-disease associations contributes to understanding the molecular mechanisms of miRNA-related diseases.…
We derive a new margin-based regularization formulation, termed multi-margin regularization (MMR), for deep neural networks (DNNs). The MMR is inspired by principles that were applied in margin analysis of shallow linear classifiers, e.g.,…
Developing Intelligent Systems involves artificial intelligence approaches including artificial neural networks. Here, we present a tutorial of Deep Neural Networks (DNNs), and some insights about the origin of the term "deep"; references…
Neural networks have long strived to emulate the learning capabilities of the human brain. While deep neural networks (DNNs) draw inspiration from the brain in neuron design, their training methods diverge from biological foundations.…
Deep learning models are favored in many research and industry areas and have reached the accuracy of approximating or even surpassing human level. However they've long been considered by researchers as black-box models for their…
Understanding the results of deep neural networks is an essential step towards wider acceptance of deep learning algorithms. Many approaches address the issue of interpreting artificial neural networks, but often provide divergent…
Functional annotation of microbial genomes is often biased toward protein-coding genes, leaving a vast, unexplored landscape of non-coding RNAs (ncRNAs) that are critical for regulating bacterial and archaeal physiology, stress response and…
MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene expression. Identification of total number of miRNAs even in completely sequenced organisms is still an open problem. However, researchers have been using techniques that…