scholarly journals TMAinspiration: Decode Interdependencies in Multifactorial Tissue Microarray Data

2016 ◽  
Vol 15 ◽  
pp. CIN.S39112 ◽  
Author(s):  
Florian Boecker ◽  
Horst Buerger ◽  
Nikhil V. Mallela ◽  
Eberhard Korsching
Keyword(s):  
Breast Cancer ◽  
Tissue Microarray ◽  
Microarray Data ◽  
Cellular Network ◽  
Cooperative Behavior ◽  
A Priori ◽  
A Priori Knowledge ◽  
Protein Markers ◽  
Ranking Scheme ◽  
Self Consistent

There are no satisfying tools in tissue microarray (TMA) data analysis up to now to analyze the cooperative behavior of all measured markers in a multifactorial TMA approach. The developed tool TMAinspiration is not only offering an analysis option to close this gap but also offering an ecosystem consisting of quality control concepts and supporting scripts to make this approach a platform for informed practice and further research. The TMAinspiration method is specifically focusing on the demands of the TMA analysis by controlling errors and noise by a generalized regression scheme while at the same time avoiding to introduce a priori too many constraints into the analysis of the data. So, we are testing partitions of a proximity table to find an optimal support for a ranking scheme of molecular dependencies. The idea of combining several partitions to one ensemble, which is balancing the optimization process, is based on the main assumption that all these perspectives on the cellular network need to be self-consistent. Several application examples in breast cancer and one in squamous cell carcinoma demonstrate that this procedure is nicely confirming a priori knowledge on the expression characteristics of protein markers, while also integrating many new results discovered in the treasury of a bigger TMA experiment. The code and software are now freely available at: http://complex-systems.unimuenster.de/tma_inspiration.html .

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.

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.

scholarly journals Integrating ensemble systems biology feature selection and bimodal deep neural network for breast cancer prognosis prediction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Li-Hsin Cheng ◽  
Te-Cheng Hsu ◽  
Che Lin
Keyword(s):  
Breast Cancer ◽  
Neural Network ◽  
Feature Selection ◽  
Systems Biology ◽  
Ensemble Learning ◽  
Microarray Data ◽  
Deep Neural Network ◽  
Prediction Models ◽  
Biological Knowledge ◽  
Prognosis Prediction

AbstractBreast cancer is a heterogeneous disease. To guide proper treatment decisions for each patient, robust prognostic biomarkers, which allow reliable prognosis prediction, are necessary. Gene feature selection based on microarray data is an approach to discover potential biomarkers systematically. However, standard pure-statistical feature selection approaches often fail to incorporate prior biological knowledge and select genes that lack biological insights. Besides, due to the high dimensionality and low sample size properties of microarray data, selecting robust gene features is an intrinsically challenging problem. We hence combined systems biology feature selection with ensemble learning in this study, aiming to select genes with biological insights and robust prognostic predictive power. Moreover, to capture breast cancer's complex molecular processes, we adopted a multi-gene approach to predict the prognosis status using deep learning classifiers. We found that all ensemble approaches could improve feature selection robustness, wherein the hybrid ensemble approach led to the most robust result. Among all prognosis prediction models, the bimodal deep neural network (DNN) achieved the highest test performance, further verified by survival analysis. In summary, this study demonstrated the potential of combining ensemble learning and bimodal DNN in guiding precision medicine.

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