scholarly journals Optical Biopsy Using a Neural Network to Predict Gene Expression From Photos of Wounds

2022 ◽  
Vol 270 ◽  
pp. 547-554
Author(s):  
Grant Schumaker ◽  
Andrew Becker ◽  
Gary An ◽  
Stephen Badylak ◽  
Scott Johnson ◽  
...  
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Optical Biopsy ◽  
Predict Gene Expression

scholarly journals Predicting Gene Expression from DNA Sequence using Residual Neural Network

2020 ◽  
Author(s):  
Yilun Zhang ◽  
Xin Zhou ◽  
Xiaodong Cai
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Dna Sequence ◽  
Mrna Level ◽  
Network Models ◽  
Transcription Start ◽  
Neural Network Models ◽  
Expression Of Genes ◽  
A Cell ◽  
Predict Gene Expression

AbstractIt is known that cis-acting DNA motifs play an important role in regulating gene expression. The genome in a cell thus contains the information that not only encodes for the synthesis of proteins but also is necessary for regulating expression of genes. Therefore, the mRNA level of a gene may be predictable from the DNA sequence. Indeed, three deep neural network models were developed recently to predict the mRNA level of a gene directly or indirectly from the DNA sequence around the transcription start side of the gene. In this work, we develop a deep residual network model, named ExpResNet, to predict gene expression directly from DNA sequence. Applying ExpResNet to the GTEx data, we demonstrate that ExpResNet outperforms the three existing models across four tissues tested. Our model may be useful in the investigation of gene regulation.

scholarly journals Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network

2019 ◽  
Author(s):  
Wanwen Zeng ◽  
Yong Wang ◽  
Rui Jiang
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Convolutional Neural Network ◽  
Driving Forces ◽  
Wide Spectrum ◽  
Regulatory Elements ◽  
Proximal Promoter ◽  
Supplementary Information ◽  
Promoter Sequences ◽  
Predict Gene Expression

Abstract Motivation Interactions among cis-regulatory elements such as enhancers and promoters are main driving forces shaping context-specific chromatin structure and gene expression. Although there have been computational methods for predicting gene expression from genomic and epigenomic information, most of them neglect long-range enhancer–promoter interactions, due to the difficulty in precisely linking regulatory enhancers to target genes. Recently, HiChIP, a novel high-throughput experimental approach, has generated comprehensive data on high-resolution interactions between promoters and distal enhancers. Moreover, plenty of studies suggest that deep learning achieves state-of-the-art performance in epigenomic signal prediction, and thus promoting the understanding of regulatory elements. In consideration of these two factors, we integrate proximal promoter sequences and HiChIP distal enhancer–promoter interactions to accurately predict gene expression. Results We propose DeepExpression, a densely connected convolutional neural network, to predict gene expression using both promoter sequences and enhancer–promoter interactions. We demonstrate that our model consistently outperforms baseline methods, not only in the classification of binary gene expression status but also in regression of continuous gene expression levels, in both cross-validation experiments and cross-cell line predictions. We show that the sequential promoter information is more informative than the experimental enhancer information; meanwhile, the enhancer–promoter interactions within ±100 kbp around the TSS of a gene are most beneficial. We finally visualize motifs in both promoter and enhancer regions and show the match of identified sequence signatures with known motifs. We expect to see a wide spectrum of applications using HiChIP data in deciphering the mechanism of gene regulation. Availability and implementation DeepExpression is freely available at https://github.com/wanwenzeng/DeepExpression. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network

2018 ◽  
Author(s):  
Wanwen Zeng ◽  
Yong Wang ◽  
Rui Jiang
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Convolutional Neural Network ◽  
Driving Forces ◽  
Wide Spectrum ◽  
Regulatory Elements ◽  
Proximal Promoter ◽  
Supplementary Information ◽  
Promoter Sequences ◽  
Predict Gene Expression

AbstractMotivationInteractions among such cis-regulatory elements as enhancers and promoters are main driving forces shaping context-specific chromatin structure and gene expression. Although there have been computational methods for predicting gene expression from genomic and epigenomic information, most of them overlook long-range enhancer-promoter interactions, due to the difficulty in precisely linking regulatory enhancers to target genes. Recently, a novel high-throughput experimental approach named HiChIP has been developed and generating comprehensive data on high-resolution interactions between promoters and distal enhancers. On the other hand, plenty of studies have suggested that deep learning achieves state-of-the-art performance in epigenomic signal prediction, and thus promoting the understanding of regulatory elements. In consideration of these two factors, we integrate proximal promoter sequences and HiChIP distal enhancer-promoter interactions to accurately model gene expression.ResultsWe propose DeepExpression, a densely connected convolutional neural network to predict gene expression using both promoter sequences and enhancer-promoter interactions. We demonstrate that our model consistently outperforms baseline methods not only in the classification of binary gene expression status but also in the regression of continuous gene expression levels, in both cross-validation experiments and cross-cell lines predictions. We show that sequential promoter information is more informative than experimental enhancer information while enhancer-promoter interactions are most beneficial from those within ±100 kbp around the TSS of a gene. We finally visualize motifs in both promoter and enhancer regions and show the match of identified sequence signatures and known motifs. We expect to see a wide spectrum of applications using HiChIP data in deciphering the mechanism of gene regulation.AvailabilityDeepExpression is freely available at https://github.com/wanwenzeng/[email protected], [email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems

2017 ◽  
Author(s):  
Anthony Szedlak ◽  
Spencer Sims ◽  
Nicholas Smith ◽  
Giovanni Paternostro ◽  
Carlo Piermarocchi
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Cell Cycle ◽  
Time Series ◽  
Time Series Data ◽  
Series Data ◽  
Data Sets ◽  
Expression Data ◽  
Time Series Gene Expression ◽  
Human Cervical Cancer

AbstractModern time series gene expression and other omics data sets have enabled unprecedented resolution of the dynamics of cellular processes such as cell cycle and response to pharmaceutical compounds. In anticipation of the proliferation of time series data sets in the near future, we use the Hopfield model, a recurrent neural network based on spin glasses, to model the dynamics of cell cycle in HeLa (human cervical cancer) and S. cerevisiae cells. We study some of the rich dynamical properties of these cyclic Hopfield systems, including the ability of populations of simulated cells to recreate experimental expression data and the effects of noise on the dynamics. Next, we use a genetic algorithm to identify sets of genes which, when selectively inhibited by local external fields representing gene silencing compounds such as kinase inhibitors, disrupt the encoded cell cycle. We find, for example, that inhibiting the set of four kinases BRD4, MAPK1, NEK7, and YES1 in HeLa cells causes simulated cells to accumulate in the M phase. Finally, we suggest possible improvements and extensions to our model.Author SummaryCell cycle – the process in which a parent cell replicates its DNA and divides into two daughter cells – is an upregulated process in many forms of cancer. Identifying gene inhibition targets to regulate cell cycle is important to the development of effective therapies. Although modern high throughput techniques offer unprecedented resolution of the molecular details of biological processes like cell cycle, analyzing the vast quantities of the resulting experimental data and extracting actionable information remains a formidable task. Here, we create a dynamical model of the process of cell cycle using the Hopfield model (a type of recurrent neural network) and gene expression data from human cervical cancer cells and yeast cells. We find that the model recreates the oscillations observed in experimental data. Tuning the level of noise (representing the inherent randomness in gene expression and regulation) to the “edge of chaos” is crucial for the proper behavior of the system. We then use this model to identify potential gene targets for disrupting the process of cell cycle. This method could be applied to other time series data sets and used to predict the effects of untested targeted perturbations.

scholarly journals scGNN: a novel graph neural network framework for single-cell RNA-Seq analyses

2020 ◽  
Author(s):  
Juexin Wang ◽  
Anjun Ma ◽  
Yuzhou Chang ◽  
Jianting Gong ◽  
Yuexu Jiang ◽  
...  
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Single Cell ◽  
Neural Development ◽  
Expression Patterns ◽  
Gaussian Model ◽  
Postmortem Brain ◽  
Differential Mechanism ◽  
Disease Study ◽  
Cell Cell

ABSTRACTSingle-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and dynamics of tissues, organisms, and complex diseases, but its analyses still suffer from multiple grand challenges, including the sequencing sparsity and complex differential patterns in gene expression. We introduce the scGNN (single-cell graph neural network) to provide a hypothesis-free deep learning framework for scRNA-Seq analyses. This framework formulates and aggregates cell-cell relationships with graph neural networks and models heterogeneous gene expression patterns using a left-truncated mixture Gaussian model. scGNN integrates three iterative multi-modal autoencoders and outperforms existing tools for gene imputation and cell clustering on four benchmark scRNA-Seq datasets. In an Alzheimer’s disease study with 13,214 single nuclei from postmortem brain tissues, scGNN successfully illustrated disease-related neural development and the differential mechanism. scGNN provides an effective representation of gene expression and cell-cell relationships. It is also a novel and powerful framework that can be applied to scRNA-Seq analyses.

scholarly journals Application of Gene Expression Programming, Artificial Neural Network and Multilinear Regression in Predicting Hydrochar Physicochemical Properties

2020 ◽  
Author(s):  
Jibril Abdulsalam ◽  
Abiodun Ismail Lawal ◽  
Ramadimetja Lizah Setsepu ◽  
Moshood Onifade ◽  
Samson Bada
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Artificial Neural Network ◽  
Performance Metrics ◽  
Gene Expression Programming ◽  
Mean Bias Error ◽  
Energy Yield ◽  
Multilinear Regression ◽  
Soft Computing Techniques ◽  
Artificial Neural

Abstract Globally, the provision of energy is becoming an absolute necessity. Biomass resources are abundant and have been described as a potential alternative source of energy. However, it is important to assess the fuel characteristics of the various available biomass sources. Soft computing techniques are presented in this study to predict the mass yield (MY), energy yield (EY), and higher heating value (HHV) of hydrothermally carbonized biomass by using Gene Expression Programming (GEP), multiple-input single output-artificial neural network (MISO-ANN), and Multilinear regression (MLR). The three techniques were compared using statistical performance metrics. The coefficient of determination (R2), mean absolute error (MAE), and mean bias error (MBE) were used to evaluate the performance of the models. The MISO-ANN with 5-10-10-1 and 5-15-15-1 network architectures provided the most satisfactory performance of the three proposed models (R2 = 0.976, 0.955, 0.996; MAE = 2.24, 2.11, 0.93; MBE = 0.16, 0.37, 0.12) for MY, EY and HHV respectively. The GEP technique’s ability to predict hydrochar properties based on the input parameters was found to be satisfactory, while MLR provided an unsatisfactory predictive model. Sensitivity analysis was conducted, and the analysis revealed that volatile matter (VM) and temperature (Temp) have more influence on the MY, EY, and HHV.

scholarly journals Evaluation of Genotype-Based Gene Expression Model Performance: A Cross-Framework and Cross-Dataset Study

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1531
Author(s):  
Vânia Tavares ◽  
Joana Monteiro ◽  
Evangelos Vassos ◽  
Jonathan Coleman ◽  
Diana Prata
Keyword(s):  
Gene Expression ◽  
Frontal Cortex ◽  
Model Performance ◽  
Variation Method ◽  
Expression Model ◽  
The Brain ◽  
Gene Expression Model ◽  
And Training ◽  
Predict Gene Expression ◽  
Fold Cross Validation

Predicting gene expression from genotyped data is valuable for studying inaccessible tissues such as the brain. Herein we present eGenScore, a polygenic/poly-variation method, and compare it with PrediXcan, a method based on regularized linear regression using elastic nets. While both methods have the same purpose of predicting gene expression based on genotype, they carry important methodological differences. We compared the performance of expression quantitative trait loci (eQTL) models to predict gene expression in the frontal cortex, comparing across these frameworks (eGenScore vs. PrediXcan) and training datasets (BrainEAC, which is brain-specific, vs. GTEx, which has data across multiple tissues). In addition to internal five-fold cross-validation, we externally validated the gene expression models using the CommonMind Consortium database. Our results showed that (1) PrediXcan outperforms eGenScore regardless of the training database used; and (2) when using PrediXcan, the performance of the eQTL models in frontal cortex is higher when trained with GTEx than with BrainEAC.

scholarly journals Deciphering gene regulation from gene expression dynamics using deep neural network

2018 ◽  
Author(s):  
Jingxiang Shen ◽  
Mariela D. Petkova ◽  
Yuhai Tu ◽  
Feng Liu ◽  
Chao Tang
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Machine Learning ◽  
Gene Regulation ◽  
Gene Network ◽  
Deep Neural Network ◽  
Biological Functions ◽  
Gene Regulation Network ◽  
Regulation Network ◽  
Gene Expression Dynamics

AbstractComplex biological functions are carried out by the interaction of genes and proteins. Uncovering the gene regulation network behind a function is one of the central themes in biology. Typically, it involves extensive experiments of genetics, biochemistry and molecular biology. In this paper, we show that much of the inference task can be accomplished by a deep neural network (DNN), a form of machine learning or artificial intelligence. Specifically, the DNN learns from the dynamics of the gene expression. The learnt DNN behaves like an accurate simulator of the system, on which one can perform in-silico experiments to reveal the underlying gene network. We demonstrate the method with two examples: biochemical adaptation and the gap-gene patterning in fruit fly embryogenesis. In the first example, the DNN can successfully find the two basic network motifs for adaptation – the negative feedback and the incoherent feed-forward. In the second and much more complex example, the DNN can accurately predict behaviors of essentially all the mutants. Furthermore, the regulation network it uncovers is strikingly similar to the one inferred from experiments. In doing so, we develop methods for deciphering the gene regulation network hidden in the DNN “black box”. Our interpretable DNN approach should have broad applications in genotype-phenotype mapping.SignificanceComplex biological functions are carried out by gene regulation networks. The mapping between gene network and function is a central theme in biology. The task usually involves extensive experiments with perturbations to the system (e.g. gene deletion). Here, we demonstrate that machine learning, or deep neural network (DNN), can help reveal the underlying gene regulation for a given function or phenotype with minimal perturbation data. Specifically, after training with wild-type gene expression dynamics data and a few mutant snapshots, the DNN learns to behave like an accurate simulator for the genetic system, which can be used to predict other mutants’ behaviors. Furthermore, our DNN approach is biochemically interpretable, which helps uncover possible gene regulatory mechanisms underlying the observed phenotypic behaviors.

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