scholarly journals Mutual Information for Explainable Deep Learning of Multiscale Systems

2021 ◽  
pp. 110551
Author(s):  
Søren Taverniers ◽  
Eric J. Hall ◽  
Markos A. Katsoulakis ◽  
Daniel M. Tartakovsky
Author(s):  
Yang Xu ◽  
Priyojit Das ◽  
Rachel Patton McCord

Abstract Motivation Deep learning approaches have empowered single-cell omics data analysis in many ways and generated new insights from complex cellular systems. As there is an increasing need for single cell omics data to be integrated across sources, types, and features of data, the challenges of integrating single-cell omics data are rising. Here, we present an unsupervised deep learning algorithm that learns discriminative representations for single-cell data via maximizing mutual information, SMILE (Single-cell Mutual Information Learning). Results Using a unique cell-pairing design, SMILE successfully integrates multi-source single-cell transcriptome data, removing batch effects and projecting similar cell types, even from different tissues, into the shared space. SMILE can also integrate data from two or more modalities, such as joint profiling technologies using single-cell ATAC-seq, RNA-seq, DNA methylation, Hi-C, and ChIP data. When paired cells are known, SMILE can integrate data with unmatched feature, such as genes for RNA-seq and genome wide peaks for ATAC-seq. Integrated representations learned from joint profiling technologies can then be used as a framework for comparing independent single source data. Supplementary information Supplementary data are available at Bioinformatics online. The source code of SMILE including analyses of key results in the study can be found at: https://github.com/rpmccordlab/SMILE.


Author(s):  
Bob D. de Vos ◽  
Bas van der Velden ◽  
Jörg Sander ◽  
Kenneth Gilhuijs ◽  
Marius Staring ◽  
...  

Entropy ◽  
2018 ◽  
Vol 20 (11) ◽  
pp. 823 ◽  
Author(s):  
Hui Fang ◽  
Victoria Wang ◽  
Motonori Yamaguchi

Deep Learning (DL) networks are recent revolutionary developments in artificial intelligence research. Typical networks are stacked by groups of layers that are further composed of many convolutional kernels or neurons. In network design, many hyper-parameters need to be defined heuristically before training in order to achieve high cross-validation accuracies. However, accuracy evaluation from the output layer alone is not sufficient to specify the roles of the hidden units in associated networks. This results in a significant knowledge gap between DL’s wider applications and its limited theoretical understanding. To narrow the knowledge gap, our study explores visualization techniques to illustrate the mutual information (MI) in DL networks. The MI is a theoretical measurement, reflecting the relationship between two sets of random variables even if their relationship is highly non-linear and hidden in high-dimensional data. Our study aims to understand the roles of DL units in classification performance of the networks. Via a series of experiments using several popular DL networks, it shows that the visualization of MI and its change patterns between the input/output with the hidden layers and basic units can facilitate a better understanding of these DL units’ roles. Our investigation on network convergence suggests a more objective manner to potentially evaluate DL networks. Furthermore, the visualization provides a useful tool to gain insights into the network performance, and thus to potentially facilitate the design of better network architectures by identifying redundancy and less-effective network units.


Entropy ◽  
2021 ◽  
Vol 23 (7) ◽  
pp. 862
Author(s):  
Sungyeop Lee ◽  
Junghyo Jo

Deep learning methods have had outstanding performances in various fields. A fundamental query is why they are so effective. Information theory provides a potential answer by interpreting the learning process as the information transmission and compression of data. The information flows can be visualized on the information plane of the mutual information among the input, hidden, and output layers. In this study, we examine how the information flows are shaped by the network parameters, such as depth, sparsity, weight constraints, and hidden representations. Here, we adopt autoencoders as models of deep learning, because (i) they have clear guidelines for their information flows, and (ii) they have various species, such as vanilla, sparse, tied, variational, and label autoencoders. We measured their information flows using Rényi’s matrix-based α-order entropy functional. As learning progresses, they show a typical fitting phase where the amounts of input-to-hidden and hidden-to-output mutual information both increase. In the last stage of learning, however, some autoencoders show a simplifying phase, previously called the “compression phase”, where input-to-hidden mutual information diminishes. In particular, the sparsity regularization of hidden activities amplifies the simplifying phase. However, tied, variational, and label autoencoders do not have a simplifying phase. Nevertheless, all autoencoders have similar reconstruction errors for training and test data. Thus, the simplifying phase does not seem to be necessary for the generalization of learning.


2021 ◽  
Author(s):  
Xinjie Lan ◽  
Bin Zhu ◽  
Charles Boncelet ◽  
Kenneth Barner

Entropy ◽  
2020 ◽  
Vol 22 (4) ◽  
pp. 484 ◽  
Author(s):  
Jose-Agustin Almaraz-Damian ◽  
Volodymyr Ponomaryov ◽  
Sergiy Sadovnychiy ◽  
Heydy Castillejos-Fernandez

In this paper, a new Computer-Aided Detection (CAD) system for the detection and classification of dangerous skin lesions (melanoma type) is presented, through a fusion of handcraft features related to the medical algorithm ABCD rule (Asymmetry Borders-Colors-Dermatoscopic Structures) and deep learning features employing Mutual Information (MI) measurements. The steps of a CAD system can be summarized as preprocessing, feature extraction, feature fusion, and classification. During the preprocessing step, a lesion image is enhanced, filtered, and segmented, with the aim to obtain the Region of Interest (ROI); in the next step, the feature extraction is performed. Handcraft features such as shape, color, and texture are used as the representation of the ABCD rule, and deep learning features are extracted using a Convolutional Neural Network (CNN) architecture, which is pre-trained on Imagenet (an ILSVRC Imagenet task). MI measurement is used as a fusion rule, gathering the most important information from both types of features. Finally, at the Classification step, several methods are employed such as Linear Regression (LR), Support Vector Machines (SVMs), and Relevant Vector Machines (RVMs). The designed framework was tested using the ISIC 2018 public dataset. The proposed framework appears to demonstrate an improved performance in comparison with other state-of-the-art methods in terms of the accuracy, specificity, and sensibility obtained in the training and test stages. Additionally, we propose and justify a novel procedure that should be used in adjusting the evaluation metrics for imbalanced datasets that are common for different kinds of skin lesions.


Sign in / Sign up

Export Citation Format

Share Document