scholarly journals Determination of biomarkers from microarray data using graph neural network and spectral clustering

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kun Yu ◽  
Weidong Xie ◽  
Linjie Wang ◽  
Shoujia Zhang ◽  
Wei Li
Keyword(s):  
Feature Selection ◽  
Microarray Data ◽  
Classification Accuracy ◽  
Spectral Clustering ◽  
Link Prediction ◽  
A Priori ◽  
Feature Selection Method ◽  
A Priori Knowledge ◽  
Graph Structure ◽  
Priori Knowledge

AbstractIn bioinformatics, the rapid development of gene sequencing technology has produced an increasing amount of microarray data. This type of data shares the typical characteristics of small sample size and high feature dimensions. Searching for biomarkers from microarray data, which expression features of various diseases, is essential for the disease classification. feature selection has therefore became fundemental for the analysis of microarray data, which designs to remove irrelevant and redundant features. There are a large number of redundant features and irrelevant features in microarray data, which severely degrade the classification effectiveness. We propose an innovative feature selection method with the goal of obtaining feature dependencies from a priori knowledge and removing redundant features using spectral clustering. In this paper, the graph structure is firstly constructed by using the gene interaction network as a priori knowledge, and then a link prediction method based on graph neural network is proposed to enhance the graph structure data. Finally, a feature selection method based on spectral clustering is proposed to determine biomarkers. The classification accuracy on DLBCL and Prostate can be improved by 10.90% and 16.22% compared to traditional methods. Link prediction provides an average classification accuracy improvement of 1.96% and 1.31%, and is up to 16.98% higher than the published method. The results show that the proposed method can have full use of a priori knowledge to effectively select disease prediction biomarkers with high classification accuracy.

A fuzzy gaussian rank aggregation ensemble feature selection method for microarray data

2021 ◽  
Vol 24 (4) ◽  
pp. 289-301
Author(s):  
B. Venkatesh ◽  
J. Anuradha
Keyword(s):  
Feature Selection ◽  
Microarray Data ◽  
Classification Accuracy ◽  
Performance Metrics ◽  
Feature Selection Method ◽  
Selection Method ◽  
Support Vector ◽  
Svm Classifier ◽  
Binary Particle Swarm Optimization ◽  
Selection Methods

In Microarray Data, it is complicated to achieve more classification accuracy due to the presence of high dimensions, irrelevant and noisy data. And also It had more gene expression data and fewer samples. To increase the classification accuracy and the processing speed of the model, an optimal number of features need to extract, this can be achieved by applying the feature selection method. In this paper, we propose a hybrid ensemble feature selection method. The proposed method has two phases, filter and wrapper phase in filter phase ensemble technique is used for aggregating the feature ranks of the Relief, minimum redundancy Maximum Relevance (mRMR), and Feature Correlation (FC) filter feature selection methods. This paper uses the Fuzzy Gaussian membership function ordering for aggregating the ranks. In wrapper phase, Improved Binary Particle Swarm Optimization (IBPSO) is used for selecting the optimal features, and the RBF Kernel-based Support Vector Machine (SVM) classifier is used as an evaluator. The performance of the proposed model are compared with state of art feature selection methods using five benchmark datasets. For evaluation various performance metrics such as Accuracy, Recall, Precision, and F1-Score are used. Furthermore, the experimental results show that the performance of the proposed method outperforms the other feature selection methods.

Seeing, Knowing, and Doing

2020 ◽  
Author(s):  
Robert Audi
Keyword(s):  
Practical Reasoning ◽  
Practical Knowledge ◽  
A Priori ◽  
Human Action ◽  
A Priori Knowledge ◽  
Rational Action ◽  
Reasons For Action ◽  
Discriminative Response ◽  
Rich Information ◽  
Priori Knowledge

This book provides an overall theory of perception and an account of knowledge and justification concerning the physical, the abstract, and the normative. It has the rigor appropriate for professionals but explains its main points using concrete examples. It accounts for two important aspects of perception on which philosophers have said too little: its relevance to a priori knowledge—traditionally conceived as independent of perception—and its role in human action. Overall, the book provides a full-scale account of perception, presents a theory of the a priori, and explains how perception guides action. It also clarifies the relation between action and practical reasoning; the notion of rational action; and the relation between propositional and practical knowledge. Part One develops a theory of perception as experiential, representational, and causally connected with its objects: as a discriminative response to those objects, embodying phenomenally distinctive elements; and as yielding rich information that underlies human knowledge. Part Two presents a theory of self-evidence and the a priori. The theory is perceptualist in explicating the apprehension of a priori truths by articulating its parallels to perception. The theory unifies empirical and a priori knowledge by clarifying their reliable connections with their objects—connections many have thought impossible for a priori knowledge as about the abstract. Part Three explores how perception guides action; the relation between knowing how and knowing that; the nature of reasons for action; the role of inference in determining action; and the overall conditions for rational action.

How Reality is Reasonable

2018 ◽  
Author(s):  
Donald C. Williams
Keyword(s):  
A Priori ◽  
A Priori Knowledge ◽  
Dimensional Manifold ◽  
The World ◽  
Being There ◽  
Ways Of Being ◽  
Fundamental Entity ◽  
Spatiotemporal Relations ◽  
Priori Knowledge

This chapter begins with a systematic presentation of the doctrine of actualism. According to actualism, all that exists is actual, determinate, and of one way of being. There are no possible objects, nor is there any indeterminacy in the world. In addition, there are no ways of being. It is proposed that actual entities stand in three fundamental relations: mereological, spatiotemporal, and resemblance relations. These relations govern the fundamental entities. Each fundamental entity stands in parthood relations, spatiotemporal relations, and resemblance relations to other entities. The resulting picture is one that represents the world as a four-dimensional manifold of actual ‘qualitied contents’—upon which all else supervenes. It is then explained how actualism accounts for classes, quantity, number, causation, laws, a priori knowledge, necessity, and induction.

How Do We Know that We’re Not Brains in Vats?

2018 ◽  
Author(s):  
Keith DeRose
Keyword(s):  
Epistemic Justification ◽  
A Priori ◽  
A Priori Knowledge ◽  
Conservative Approach ◽  
Contingent Fact ◽  
Brains In Vats ◽  
Priori Knowledge

In this chapter the contextualist Moorean account of how we know by ordinary standards that we are not brains in vats (BIVs) utilized in Chapter 1 is developed and defended, and the picture of knowledge and justification that emerges is explained. The account (a) is based on a double-safety picture of knowledge; (b) has it that our knowledge that we’re not BIVs is in an important way a priori; and (c) is knowledge that is easily obtained, without any need for fancy philosophical arguments to the effect that we’re not BIVs; and the account is one that (d) utilizes a conservative approach to epistemic justification. Special attention is devoted to defending the claim that we have a priori knowledge of the deeply contingent fact that we’re not BIVs, and to distinguishing this a prioritist account of this knowledge from the kind of “dogmatist” account prominently championed by James Pryor.

An Integrated Feature Selection Algorithm for Cancer Classification using Gene Expression Data

2019 ◽  
Vol 21 (9) ◽  
pp. 631-645 ◽  
Author(s):  
Saeed Ahmed ◽  
Muhammad Kabir ◽  
Zakir Ali ◽  
Muhammad Arif ◽  
Farman Ali ◽  
...  
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Gene Expression Data ◽  
Classification Accuracy ◽  
Early Stage ◽  
Small Sample Size ◽  
Feature Selection Method ◽  
Small Sample ◽  
Expression Data ◽  
Base Function

Aim and Objective: Cancer is a dangerous disease worldwide, caused by somatic mutations in the genome. Diagnosis of this deadly disease at an early stage is exceptionally new clinical application of microarray data. In DNA microarray technology, gene expression data have a high dimension with small sample size. Therefore, the development of efficient and robust feature selection methods is indispensable that identify a small set of genes to achieve better classification performance. Materials and Methods: In this study, we developed a hybrid feature selection method that integrates correlation-based feature selection (CFS) and Multi-Objective Evolutionary Algorithm (MOEA) approaches which select the highly informative genes. The hybrid model with Redial base function neural network (RBFNN) classifier has been evaluated on 11 benchmark gene expression datasets by employing a 10-fold cross-validation test. Results: The experimental results are compared with seven conventional-based feature selection and other methods in the literature, which shows that our approach owned the obvious merits in the aspect of classification accuracy ratio and some genes selected by extensive comparing with other methods. Conclusion: Our proposed CFS-MOEA algorithm attained up to 100% classification accuracy for six out of eleven datasets with a minimal sized predictive gene subset.

Incorporating a priori knowledge into neural networks

1995 ◽  
Vol 31 (22) ◽  
pp. 1930-1931 ◽  
Author(s):  
D. Anguita ◽  
S. Rovetta ◽  
S. Ridella ◽  
R. Zunino
Keyword(s):  
Neural Networks ◽  
A Priori ◽  
A Priori Knowledge ◽  
Priori Knowledge
Sign in / Sign up

Export Citation Format

Share Document