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Self-supervised pretraining (SSP) has been recognized as a method to enhance prediction accuracy in various downstream tasks. However, its efficacy for DNA sequences remains somewhat constrained. This limitation stems primarily from the…

Compact photonic elements that control both the diffraction and interference of light offer superior performance at ultra-compact dimensions. Unlike conventional optical structures, these diffractive optical elements can provide…

Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA…

Automated and accurate 3D medical image segmentation plays an essential role in assisting medical professionals to evaluate disease progresses and make fast therapeutic schedules. Although deep convolutional neural networks (DCNNs) have…

Based on the predictive coding theory in neuroscience, we designed a bi-directional and recurrent neural net, namely deep predictive coding networks (PCN). It has feedforward, feedback, and recurrent connections. Feedback connections from a…

Computational prediction of origin of replication (ORI) has been of great interest in bioinformatics and several methods including GC-skew, auto-correlation etc. have been explored in the past. In this paper, we have extended the…

We propose doubly nested network(DNNet) where all neurons represent their own sub-models that solve the same task. Every sub-model is nested both layer-wise and channel-wise. While nesting sub-models layer-wise is straight-forward with…

Motivation: Deep learning architectures have recently demonstrated their power in predicting DNA- and RNA-binding specificities. Existing methods fall into three classes: Some are based on Convolutional Neural Networks (CNNs), others use…

Detection of cell nuclei in microscopic images is a challenging research topic, because of limitations in cellular image quality and diversity of nuclear morphology, i.e. varying nuclei shapes, sizes, and overlaps between multiple cell…

Despite the significant advances in iris segmentation, accomplishing accurate iris segmentation in non-cooperative environment remains a grand challenge. In this paper, we present a deep learning framework, referred to as Iris R-CNN, to…

Feature engineering has been the key to the success of many prediction models. However, the process is non-trivial and often requires manual feature engineering or exhaustive searching. DNNs are able to automatically learn feature…

Predicting DNA-protein binding is an important and classic problem in bioinformatics. Convolutional neural networks have outperformed conventional methods in modeling the sequence specificity of DNA-protein binding. However, none of the…

Inter-and intra-observer variation in delineating regions of interest (ROIs) occurs because of differences in expertise level and preferences of the radiation oncologists. We evaluated the accuracy of a segmentation model using the U-Net…

In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…

Time-frequency analysis is an important and challenging task in many applications. Fourier and wavelet analysis are two classic methods that have achieved remarkable success in many fields. However, they also exhibit limitations when…

Deep neural networks (DNN) are increasingly being used to perform algorithm-selection in combinatorial optimisation domains, particularly as they accommodate input representations which avoid designing and calculating features. Mounting…

Explainable Artificial Intelligence (xAI) has the potential to enhance the transparency and trust of AI-based systems. Although accurate predictions can be made using Deep Neural Networks (DNNs), the process used to arrive at such…

Fully convolutional neural networks have made promising progress in joint liver and liver tumor segmentation. Instead of following the debates over 2D versus 3D networks (for example, pursuing the balance between large-scale 2D pretraining…

Prostate segmentation from Magnetic Resonance (MR) images plays an important role in image guided interven- tion. However, the lack of clear boundary specifically at the apex and base, and huge variation of shape and texture between the…

Ubiquitous artificial intelligence (AI) is considered one of the key services in 6G systems. AI services typically rely on deep neural network (DNN) requiring heavy computation. Hence, in order to support ubiquitous AI, it is crucial to…