Related papers: Next-Step Conditioned Deep Convolutional Neural Ne…
We propose a simple two-step approach for speeding up convolution layers within large convolutional neural networks based on tensor decomposition and discriminative fine-tuning. Given a layer, we use non-linear least squares to compute a…
In this work we set out to find a method to classify protein structures using a Deep Learning methodology. Our Artificial Intelligence has been trained to recognize complex biomolecule structures extrapolated from the Protein Data Bank…
Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foundational but accuracy-limited…
Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…
Evolutionary computation methods have been successfully applied to neural networks since two decades ago, while those methods cannot scale well to the modern deep neural networks due to the complicated architectures and large quantities of…
A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design.…
Deep networks are now able to achieve human-level performance on a broad spectrum of recognition tasks. Independently, neuromorphic computing has now demonstrated unprecedented energy-efficiency through a new chip architecture based on…
Computational biology and bioinformatics provide vast data gold-mines from protein sequences, ideal for Language Models taken from NLP. These LMs reach for new prediction frontiers at low inference costs. Here, we trained two…
We investigate in this paper the architecture of deep convolutional networks. Building on existing state of the art models, we propose a reconfiguration of the model parameters into several parallel branches at the global network level,…
We present a simple, modular graph-based convolutional neural network that takes structural information from protein-ligand complexes as input to generate models for activity and binding mode prediction. Complex structures are generated by…
Deep convolutional neural network has made huge revolution and shown its superior performance on computer vision tasks such as classification and segmentation. Recent years, researches devote much effort to scaling down size of network…
Figuring out small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many virtual and real drug-discovery scenarios. Since it is not always easy to find such binding sites based on…
Deep convolutional neural networks (CNNs) have shown excellent performance in object recognition tasks and dense classification problems such as semantic segmentation. However, training deep neural networks on large and sparse datasets is…
Deep neural networks have recently drawn considerable attention to build and evaluate artificial learning models for perceptual tasks. Here, we present a study on the performance of the deep learning models to deal with global optimization…
Compared to earlier multistage frameworks using CNN features, recent end-to-end deep approaches for fine-grained recognition essentially enhance the mid-level learning capability of CNNs. Previous approaches achieve this by introducing an…
Recent progress in deep learning has been driven by increasingly larger models. However, their computational and energy demands have grown proportionally, creating significant barriers to their deployment and to a wider adoption of deep…
In this study, we tackle the challenging task of predicting secondary structures from protein primary sequences, a pivotal initial stride towards predicting tertiary structures, while yielding crucial insights into protein activity,…
In this work, we build a generic architecture of Convolutional Neural Networks to discover empirical properties of neural networks. Our first contribution is to introduce a state-of-the-art framework that depends upon few hyper parameters…
Machine learning and the use of neural networks has increased precipitously over the past few years primarily due to the ever-increasing accessibility to data and the growth of computation power. It has become increasingly easy to harness…
Convolutional Neural Networks (CNNs) have shown strong promise for analyzing scientific data from many domains including particle imaging detectors. However, the challenge of choosing the appropriate network architecture (depth, kernel…