scholarly journals Gene prediction of aging-related diseases based on DNN and Mashup

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Junhua Ye ◽  
Shunfang Wang ◽  
Xin Yang ◽  
Xianjun Tang
Keyword(s):  
Neural Network ◽  
Biological Networks ◽  
Gene Prediction ◽  
Feature Space ◽  
Biological Information ◽  
Single Type ◽  
Protein Interaction Data ◽  
Pathogenic Genes ◽  
Tree Classifier ◽  
Association Data

Abstract Background At present, the bioinformatics research on the relationship between aging-related diseases and genes is mainly through the establishment of a machine learning multi-label model to classify each gene. Most of the existing methods for predicting pathogenic genes mainly rely on specific types of gene features, or directly encode multiple features with different dimensions, use the same encoder to concatenate and predict the final results, which will be subject to many limitations in the applicability of the algorithm. Possible shortcomings of the above include: incomplete coverage of gene features by a single type of biomics data, overfitting of small dimensional datasets by a single encoder, or underfitting of larger dimensional datasets. Methods We use the known gene disease association data and gene descriptors, such as gene ontology terms (GO), protein interaction data (PPI), PathDIP, Kyoto Encyclopedia of genes and genomes Genes (KEGG), etc, as input for deep learning to predict the association between genes and diseases. Our innovation is to use Mashup algorithm to reduce the dimensionality of PPI, GO and other large biological networks, and add new pathway data in KEGG database, and then combine a variety of biological information sources through modular Deep Neural Network (DNN) to predict the genes related to aging diseases. Result and conclusion The results show that our algorithm is more effective than the standard neural network algorithm (the Area Under the ROC curve from 0.8795 to 0.9153), gradient enhanced tree classifier and logistic regression classifier. In this paper, we firstly use DNN to learn the similar genes associated with the known diseases from the complex multi-dimensional feature space, and then provide the evidence that the assumed genes are associated with a certain disease.

scholarly journals Using deep learning to associate human genes with age-related diseases

2019 ◽  
Vol 36 (7) ◽  
pp. 2202-2208 ◽  
Author(s):  
Fabio Fabris ◽  
Daniel Palmer ◽  
Khalid M Salama ◽  
João Pedro de Magalhães ◽  
Alex A Freitas
Keyword(s):  
Feature Space ◽  
Predictive Performance ◽  
Biological Data ◽  
Classification Model ◽  
Supplementary Information ◽  
Protein Interaction Data ◽  
Modular Architecture ◽  
Age Related ◽  
Human Genes ◽  
Tree Classifier

Abstract Motivation One way to identify genes possibly associated with ageing is to build a classification model (from the machine learning field) capable of classifying genes as associated with multiple age-related diseases. To build this model, we use a pre-compiled list of human genes associated with age-related diseases and apply a novel Deep Neural Network (DNN) method to find associations between gene descriptors (e.g. Gene Ontology terms, protein–protein interaction data and biological pathway information) and age-related diseases. Results The novelty of our new DNN method is its modular architecture, which has the capability of combining several sources of biological data to predict which ageing-related diseases a gene is associated with (if any). Our DNN method achieves better predictive performance than standard DNN approaches, a Gradient Boosted Tree classifier (a strong baseline method) and a Logistic Regression classifier. Given the DNN model produced by our method, we use two approaches to identify human genes that are not known to be associated with age-related diseases according to our dataset. First, we investigate genes that are close to other disease-associated genes in a complex multi-dimensional feature space learned by the DNN algorithm. Second, using the class label probabilities output by our DNN approach, we identify genes with a high probability of being associated with age-related diseases according to the model. We provide evidence of these putative associations retrieved from the DNN model with literature support. Availability and implementation The source code and datasets can be found at: https://github.com/fabiofabris/Bioinfo2019. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals bCNN-Methylpred: Feature-Based Prediction of RNA Sequence Modification Using Branch Convolutional Neural Network

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1155
Author(s):  
Naeem Islam ◽  
Jaebyung Park
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Domain Knowledge ◽  
Feature Space ◽  
Experimental Methods ◽  
Machine Learning Techniques ◽  
Rna Modification ◽  
Biological Processes ◽  
Rna Sequence ◽  
Functional Mechanisms

RNA modification is vital to various cellular and biological processes. Among the existing RNA modifications, N6-methyladenosine (m6A) is considered the most important modification owing to its involvement in many biological processes. The prediction of m6A sites is crucial because it can provide a better understanding of their functional mechanisms. In this regard, although experimental methods are useful, they are time consuming. Previously, researchers have attempted to predict m6A sites using computational methods to overcome the limitations of experimental methods. Some of these approaches are based on classical machine-learning techniques that rely on handcrafted features and require domain knowledge, whereas other methods are based on deep learning. However, both methods lack robustness and yield low accuracy. Hence, we develop a branch-based convolutional neural network and a novel RNA sequence representation. The proposed network automatically extracts features from each branch of the designated inputs. Subsequently, these features are concatenated in the feature space to predict the m6A sites. Finally, we conduct experiments using four different species. The proposed approach outperforms existing state-of-the-art methods, achieving accuracies of 94.91%, 94.28%, 88.46%, and 94.8% for the H. sapiens, M. musculus, S. cerevisiae, and A. thaliana datasets, respectively.

scholarly journals Combine and conquer: event reconstruction with Bayesian Ensemble Neural Networks

2021 ◽  
Vol 2021 (4) ◽  
Author(s):  
Jack Y. Araz ◽  
Michael Spannowsky
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Top Quark ◽  
Feature Space ◽  
Training Sample ◽  
Bayesian Techniques ◽  
Training Sample Size ◽  
Event Reconstruction ◽  
Neural Network Classifiers ◽  
Quark Jets

Abstract Ensemble learning is a technique where multiple component learners are combined through a protocol. We propose an Ensemble Neural Network (ENN) that uses the combined latent-feature space of multiple neural network classifiers to improve the representation of the network hypothesis. We apply this approach to construct an ENN from Convolutional and Recurrent Neural Networks to discriminate top-quark jets from QCD jets. Such ENN provides the flexibility to improve the classification beyond simple prediction combining methods by linking different sources of error correlations, hence improving the representation between data and hypothesis. In combination with Bayesian techniques, we show that it can reduce epistemic uncertainties and the entropy of the hypothesis by simultaneously exploiting various kinematic correlations of the system, which also makes the network less susceptible to a limitation in training sample size.

scholarly journals Neural network model for multimodal recognition of human aggression

2020 ◽  
pp. 132-149
Author(s):  
М.Ю. Уздяев
Keyword(s):  
Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Feature Space ◽  
Smart Environments ◽  
High Fidelity ◽  
Cyberphysical Systems ◽  
Human Aggression ◽  
Proposed Model ◽  
User Actions

Увеличение количества пользователей социокиберфизических систем, умных пространств, систем интернета вещей актуализирует проблему выявления деструктивных действий пользователей, таких как агрессия. При этом, деструктивные действия пользователей могут быть представлены в различных модальностях: двигательная активность тела, сопутствующее выражение лица, невербальное речевое поведение, вербальное речевое поведение. В статье рассматривается нейросетевая модель многомодального распознавания человеческой агрессии, основанная на построении промежуточного признакового пространства, инвариантного виду обрабатываемой модальности. Предлагаемая модель позволяет распознавать с высокой точностью агрессию в условиях отсутствия или недостатка информации какой-либо модальности. Экспериментальное исследование показало 81:8% верных распознаваний на наборе данных IEMOCAP. Также приводятся результаты экспериментов распознавания агрессии на наборе данных IEMOCAP для 15 различных сочетаний обозначенных выше модальностей. Growing user base of socio-cyberphysical systems, smart environments, IoT (Internet of Things) systems actualizes the problem of revealing of destructive user actions, such as various acts of aggression. Thereby destructive user actions can be represented in different modalities: locomotion, facial expression, associated with it, non-verbal speech behavior, verbal speech behavior. This paper considers a neural network model of multi-modal recognition of human aggression, based on the establishment of an intermediate feature space, invariant to the actual modality, being processed. The proposed model ensures high-fidelity aggression recognition in the cases when data on certain modality are scarce or lacking. Experimental research showed 81.8% correct recognition instances on the IEMOCAP dataset. Also, experimental results are given concerning aggression recognition on the IEMOCAP dataset for 15 different combinations of the modalities, outlined above.

Best Architecture of an Artificial Neural Network to Model Prefilming Airblast Atomization: Not So Deep Learning

2021 ◽  
Author(s):  
Geoffroy Chaussonnet ◽  
Sebastian Gepperth ◽  
Simon Holz ◽  
Rainer Koch ◽  
Hans-Jörg Bauer
Keyword(s):  
Neural Network ◽  
Artificial Neural Network ◽  
Feature Space ◽  
Middle Layer ◽  
Ann Model ◽  
Deformation Velocity ◽  
The Mean ◽  
Artificial Neural ◽  
Artificial Neural Network Ann ◽  
Domain Of Parameters

Abstract A fully connected Artificial Neural Network (ANN) is used to predict the mean spray characteristics of prefilming airblast atomization. The model is trained from the planar prefilmer experiment from the PhD thesis of Gepperth (2020). The output of the ANN model are the Sauter Mean Diameter, the mean droplet axial velocity, the mean ligament length and the mean ligament deformation velocity. The training database contains 322 different operating points. Two types of model input quantities are investigated and compared. First, nine dimensional parameters are used as inputs for the model. Second, nine non-dimensional groups commonly used for liquid atomization are derived from the first set of inputs. The best architecture is determined after testing over 10000 randomly drawn ANN architectures, with up to 10 layers and up to 128 neurons per layer. The striking results is that for both types of model, the best architectures consist of only 3 hidden layer in the shape of a diabolo. This shape recalls the shape of an autoencoder, where the middle layer would be the feature space of reduced dimensionality. It was found that the model with dimensional input quantities always shows a lower test and validation errors than the one with non-dimensional input quantities. In general, the two types of models provide comparable accuracy, better than typical correlations of SMD and droplet velocity. Finally the extrapolation capability of the models was assessed by a training them on a confined domain of parameters and testing them outside this domain.

scholarly journals Optimal Network Alignment with Graphlet Degree Vectors

2010 ◽  
Vol 9 ◽  
pp. CIN.S4744 ◽  
Author(s):  
Tijana Milenković ◽  
Weng Leong Ng ◽  
Wayne Hayes ◽  
NatašA PržUlj
Keyword(s):  
Cost Function ◽  
Network Topology ◽  
Biological Networks ◽  
Phylogenetic Trees ◽  
Biological Function ◽  
Network Alignment ◽  
New Method ◽  
Biological Information ◽  
Global Alignment ◽  
Sequence Alignments

Important biological information is encoded in the topology of biological networks. Comparative analyses of biological networks are proving to be valuable, as they can lead to transfer of knowledge between species and give deeper insights into biological function, disease, and evolution. We introduce a new method that uses the Hungarian algorithm to produce optimal global alignment between two networks using any cost function. We design a cost function based solely on network topology and use it in our network alignment. Our method can be applied to any two networks, not just biological ones, since it is based only on network topology. We use our new method to align protein-protein interaction networks of two eukaryotic species and demonstrate that our alignment exposes large and topologically complex regions of network similarity. At the same time, our alignment is biologically valid, since many of the aligned protein pairs perform the same biological function. From the alignment, we predict function of yet unannotated proteins, many of which we validate in the literature. Also, we apply our method to find topological similarities between metabolic networks of different species and build phylogenetic trees based on our network alignment score. The phylogenetic trees obtained in this way bear a striking resemblance to the ones obtained by sequence alignments. Our method detects topologically similar regions in large networks that are statistically significant. It does this independent of protein sequence or any other information external to network topology.

scholarly journals Kernel-blending connection approximated by a neural network for image classification

2020 ◽  
Vol 6 (4) ◽  
pp. 467-476
Author(s):  
Xinxin Liu ◽  
Yunfeng Zhang ◽  
Fangxun Bao ◽  
Kai Shao ◽  
Ziyi Sun ◽  
...  
Keyword(s):  
Neural Network ◽  
Image Classification ◽  
Function Approximation ◽  
Feature Space ◽  
Neural Network Learning ◽  
Network Learning ◽  
Hinge Loss ◽  
The Neural Network ◽  
Good Classification ◽  
Kernel Mapping

AbstractThis paper proposes a kernel-blending connection approximated by a neural network (KBNN) for image classification. A kernel mapping connection structure, guaranteed by the function approximation theorem, is devised to blend feature extraction and feature classification through neural network learning. First, a feature extractor learns features from the raw images. Next, an automatically constructed kernel mapping connection maps the feature vectors into a feature space. Finally, a linear classifier is used as an output layer of the neural network to provide classification results. Furthermore, a novel loss function involving a cross-entropy loss and a hinge loss is proposed to improve the generalizability of the neural network. Experimental results on three well-known image datasets illustrate that the proposed method has good classification accuracy and generalizability.

Sign in / Sign up

Export Citation Format

Share Document