scholarly journals Using Domain-specific Fingerprints Generated Through Neural Networks to Enhance Ligand-based Virtual Screening.

2020 ◽  
Author(s):  
Janosch Menke ◽  
Oliver Koch
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Virtual Screening ◽  
Molecular Fingerprint ◽  
Molecular Fingerprints ◽  
Domain Specific ◽  
Trained Neural Network ◽  
Hidden Layer ◽  
Graph Neural Networks ◽  
Combine Information

Molecular fingerprints are essential for different cheminformatics approaches like similarity-based virtual screening. In this work, the concept of neural (network) fingerprints in the context of similarity search is introduced in which the activation of the last hidden layer of a trained neural network represents the molecular fingerprint. The neural fingerprint performance of five different neural network architectures was analyzed and compared to the well-established Extended Connectivity Fingerprint (ECFP) and an autoencoder-based fingerprint. This is done using a published compound dataset with known bioactivity on 160 different kinase targets. We expect neural networks to combine information about the molecular space of<br>already known bioactive compounds together with the information on the molecular structure of the query and by doing so enrich the fingerprint. The results show that indeed neural fingerprints can greatly improve the performance of similarity searches. Most importantly, it could be shown that the neural fingerprint performs well even for kinase targets that were not included in the training. Surprisingly, while Graph Neural Networks (GNNs) are thought to offer an advantageous alternative, the best performing neural fingerprints were based on traditional fully connected layers using the ECFP4 as input. The best performing kinase-specific neural fingerprint will be provided for public use.

scholarly journals Using Domain-specific Fingerprints Generated Through Neural Networks to Enhance Ligand-based Virtual Screening.

2020 ◽  
Author(s):  
Janosch Menke ◽  
Oliver Koch
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Virtual Screening ◽  
Molecular Fingerprint ◽  
Molecular Fingerprints ◽  
Domain Specific ◽  
Trained Neural Network ◽  
Hidden Layer ◽  
Graph Neural Networks ◽  
Combine Information

Molecular fingerprints are essential for different cheminformatics approaches like similarity-based virtual screening. In this work, the concept of neural (network) fingerprints in the context of similarity search is introduced in which the activation of the last hidden layer of a trained neural network represents the molecular fingerprint. The neural fingerprint performance of five different neural network architectures was analyzed and compared to the well-established Extended Connectivity Fingerprint (ECFP) and an autoencoder-based fingerprint. This is done using a published compound dataset with known bioactivity on 160 different kinase targets. We expect neural networks to combine information about the molecular space of<br>already known bioactive compounds together with the information on the molecular structure of the query and by doing so enrich the fingerprint. The results show that indeed neural fingerprints can greatly improve the performance of similarity searches. Most importantly, it could be shown that the neural fingerprint performs well even for kinase targets that were not included in the training. Surprisingly, while Graph Neural Networks (GNNs) are thought to offer an advantageous alternative, the best performing neural fingerprints were based on traditional fully connected layers using the ECFP4 as input. The best performing kinase-specific neural fingerprint will be provided for public use.

scholarly journals SketchGNN: Semantic Sketch Segmentation with Graph Neural Networks

2021 ◽  
Vol 40 (3) ◽  
pp. 1-13
Author(s):  
Lumin Yang ◽  
Jiajie Zhuang ◽  
Hongbo Fu ◽  
Xiangzhi Wei ◽  
Kun Zhou ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Network Architecture ◽  
Large Scale ◽  
State Of The Art ◽  
Semantic Segmentation ◽  
Structure Information ◽  
Graph Neural Networks ◽  
Node Labels ◽  
Point Level

We introduce SketchGNN , a convolutional graph neural network for semantic segmentation and labeling of freehand vector sketches. We treat an input stroke-based sketch as a graph with nodes representing the sampled points along input strokes and edges encoding the stroke structure information. To predict the per-node labels, our SketchGNN uses graph convolution and a static-dynamic branching network architecture to extract the features at three levels, i.e., point-level, stroke-level, and sketch-level. SketchGNN significantly improves the accuracy of the state-of-the-art methods for semantic sketch segmentation (by 11.2% in the pixel-based metric and 18.2% in the component-based metric over a large-scale challenging SPG dataset) and has magnitudes fewer parameters than both image-based and sequence-based methods.

Optimization Artificial Neural Network Using Artificial Bee Colony in Letter Recognition Classification

2020 ◽  
Vol 8 (4) ◽  
pp. 469
Author(s):  
I Gusti Ngurah Alit Indrawan ◽  
I Made Widiartha
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Artificial Neural Networks ◽  
Classification Accuracy ◽  
Artificial Bee Colony Algorithm ◽  
Artificial Bee Colony ◽  
Letter Recognition ◽  
Bee Colony ◽  
Artificial Neural ◽  
Hidden Layer

Artificial Neural Networks or commonly abbreviated as ANN is one branch of science from the field of artificial intelligence which is often used to solve various problems in fields that involve grouping and pattern recognition. This research aims to classify Letter Recognition datasets using Artificial Neural Networks which are weighted optimally using the Artificial Bee Colony algorithm. The best classification accuracy results from this study were 92.85% using a combination of 4 hidden layers with each hidden layer containing 10 neurons.

Fourier Neural Networks and Generalized Single Hidden Layer Networks in Aircraft Engine Fault Diagnostics

2005 ◽  
Vol 128 (4) ◽  
pp. 773-782 ◽  
Author(s):  
H. S. Tan
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Network Architecture ◽  
Fourier Transforms ◽  
Aircraft Engine ◽  
Fault Classification ◽  
Noise Robustness ◽  
Fault Diagnostics ◽  
Multiple Faults ◽  
Hidden Layer

The conventional approach to neural network-based aircraft engine fault diagnostics has been mainly via multilayer feed-forward systems with sigmoidal hidden neurons trained by back propagation as well as radial basis function networks. In this paper, we explore two novel approaches to the fault-classification problem using (i) Fourier neural networks, which synthesizes the approximation capability of multidimensional Fourier transforms and gradient-descent learning, and (ii) a class of generalized single hidden layer networks (GSLN), which self-structures via Gram-Schmidt orthonormalization. Using a simulation program for the F404 engine, we generate steady-state engine parameters corresponding to a set of combined two-module deficiencies and require various neural networks to classify the multiple faults. We show that, compared to the conventional network architecture, the Fourier neural network exhibits stronger noise robustness and the GSLNs converge at a much superior speed.

scholarly journals Towards Heterogeneous Multi-Agent Reinforcement Learning with Graph Neural Networks

2020 ◽  
Author(s):  
Douglas Meneghetti ◽  
Reinaldo Bianchi
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Network Architecture ◽  
Communication Channels ◽  
Neural Network Architecture ◽  
Graph Representations ◽  
Labeled Graph ◽  
Multiple Agent ◽  
Multi Agent ◽  
Graph Neural Networks

This work proposes a neural network architecture that learns policies for multiple agent classes in a heterogeneous multi-agent reinforcement setting. The proposed network uses directed labeled graph representations for states, encodes feature vectors of different sizes for different entity classes, uses relational graph convolution layers to model different communication channels between entity types and learns distinct policies for different agent classes, sharing parameters wherever possible. Results have shown that specializing the communication channels between entity classes is a promising step to achieve higher performance in environments composed of heterogeneous entities.

Simultaneous Approximations of Polynomials and Derivatives and Their Applications to Neural Networks

2008 ◽  
Vol 20 (11) ◽  
pp. 2757-2791 ◽  
Author(s):  
Yoshifusa Ito
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Uniform Norm ◽  
Degree Of Approximation ◽  
Probability Measures ◽  
Compact Sets ◽  
Network Parameters ◽  
Whole Space ◽  
Hidden Layer ◽  
Approximating Polynomials

We have constructed one-hidden-layer neural networks capable of approximating polynomials and their derivatives simultaneously. Generally, optimizing neural network parameters to be trained at later steps of the BP training is more difficult than optimizing those to be trained at the first step. Taking into account this fact, we suppressed the number of parameters of the former type. We measure degree of approximation in both the uniform norm on compact sets and the Lp-norm on the whole space with respect to probability measures.

Evaluation of Parameter Settings for Training Neural Networks Using Backpropagation Algorithms

2022 ◽  
pp. 202-226
Author(s):  
Leema N. ◽  
Khanna H. Nehemiah ◽  
Elgin Christo V. R. ◽  
Kannan A.
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Activation Function ◽  
Neural Network Training ◽  
Network Parameter ◽  
Network Parameters ◽  
Network Training ◽  
Rate Minimum ◽  
Hidden Layer ◽  
Function Number

Artificial neural networks (ANN) are widely used for classification, and the training algorithm commonly used is the backpropagation (BP) algorithm. The major bottleneck faced in the backpropagation neural network training is in fixing the appropriate values for network parameters. The network parameters are initial weights, biases, activation function, number of hidden layers and the number of neurons per hidden layer, number of training epochs, learning rate, minimum error, and momentum term for the classification task. The objective of this work is to investigate the performance of 12 different BP algorithms with the impact of variations in network parameter values for the neural network training. The algorithms were evaluated with different training and testing samples taken from the three benchmark clinical datasets, namely, Pima Indian Diabetes (PID), Hepatitis, and Wisconsin Breast Cancer (WBC) dataset obtained from the University of California Irvine (UCI) machine learning repository.

scholarly journals Massive computational acceleration by using neural networks to emulate mechanism-based biological models

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Shangying Wang ◽  
Kai Fan ◽  
Nan Luo ◽  
Yangxiaolu Cao ◽  
Feilun Wu ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Mechanistic Model ◽  
Time Frame ◽  
Biological Applications ◽  
Biological Models ◽  
Parametric Space ◽  
Trained Neural Network ◽  
Short Time

Abstract For many biological applications, exploration of the massive parametric space of a mechanism-based model can impose a prohibitive computational demand. To overcome this limitation, we present a framework to improve computational efficiency by orders of magnitude. The key concept is to train a neural network using a limited number of simulations generated by a mechanistic model. This number is small enough such that the simulations can be completed in a short time frame but large enough to enable reliable training. The trained neural network can then be used to explore a much larger parametric space. We demonstrate this notion by training neural networks to predict pattern formation and stochastic gene expression. We further demonstrate that using an ensemble of neural networks enables the self-contained evaluation of the quality of each prediction. Our work can be a platform for fast parametric space screening of biological models with user defined objectives.

scholarly journals Fast and Deep Graph Neural Networks

2020 ◽  
Vol 34 (04) ◽  
pp. 3898-3905 ◽  
Author(s):  
Claudio Gallicchio ◽  
Alessio Micheli
Keyword(s):  
Neural Network ◽  
Dynamical System ◽  
Neural Networks ◽  
State Of The Art ◽  
Input Graph ◽  
Sparse Networks ◽  
Set Up ◽  
The Stability ◽  
Graph Neural Networks ◽  
Architectural Organization

We address the efficiency issue for the construction of a deep graph neural network (GNN). The approach exploits the idea of representing each input graph as a fixed point of a dynamical system (implemented through a recurrent neural network), and leverages a deep architectural organization of the recurrent units. Efficiency is gained by many aspects, including the use of small and very sparse networks, where the weights of the recurrent units are left untrained under the stability condition introduced in this work. This can be viewed as a way to study the intrinsic power of the architecture of a deep GNN, and also to provide insights for the set-up of more complex fully-trained models. Through experimental results, we show that even without training of the recurrent connections, the architecture of small deep GNN is surprisingly able to achieve or improve the state-of-the-art performance on a significant set of tasks in the field of graphs classification.

Sign in / Sign up

Export Citation Format

Share Document