scholarly journals Representation Learning of Genomic Sequence Motifs with Convolutional Neural Networks

2018 ◽  
Author(s):  
Peter K. Koo ◽  
Sean R. Eddy
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Genomic Sequence ◽  
Representation Learning ◽  
Computational Genomics ◽  
The Other ◽  
Sequence Motif ◽  
Sequence Motifs ◽  
Filter Size

AbstractAlthough convolutional neural networks (CNNs) have been applied to a variety of computational genomics problems, there remains a large gap in our understanding of how they build representations of regulatory genomic sequences. Here we perform systematic experiments on synthetic sequences to reveal how CNN architecture, specifically convolutional filter size and max-pooling, influences the extent that sequence motif representations are learned by first layer filters. We find that CNNs designed to foster hierarchical representation learning of sequence motifs - assembling partial features into whole features in deeper layers - tend to learn distributed representations, i.e. partial motifs. On the other hand, CNNs that are designed to limit the ability to hierarchically build sequence motif representations in deeper layers tend to learn more interpretable localist representations, i.e. whole motifs. We then validate that this representation learning principle established from synthetic sequences generalizes to in vivo sequences.

scholarly journals Improving representations of genomic sequence motifs in convolutional networks with exponential activations

2020 ◽  
Author(s):  
Peter K. Koo ◽  
Matt Ploenzke
Keyword(s):  
Neural Networks ◽  
Dna Sequences ◽  
Test Performance ◽  
Genomic Sequence ◽  
Comprehensive Analysis ◽  
Sequence Motifs ◽  
Deep Convolutional Neural Networks ◽  
Convolutional Networks ◽  
Learned Features

ABSTRACTDeep convolutional neural networks (CNNs) trained on regulatory genomic sequences tend to build representations in a distributed manner, making it a challenge to extract learned features that are biologically meaningful, such as sequence motifs. Here we perform a comprehensive analysis on synthetic sequences to investigate the role that CNN activations have on model interpretability. We show that employing an exponential activation to first layer filters consistently leads to interpretable and robust representations of motifs compared to other commonly used activations. Strikingly, we demonstrate that CNNs with better test performance do not necessarily imply more interpretable representations with attribution methods. We find that CNNs with exponential activations significantly improve the efficacy of recovering biologically meaningful representations with attribution methods. We demonstrate these results generalise to real DNA sequences across several in vivo datasets. Together, this work demonstrates how a small modification to existing CNNs, i.e. setting exponential activations in the first layer, can significantly improve the robustness and interpretabilty of learned representations directly in convolutional filters and indirectly with attribution methods.

scholarly journals Separable convolutional neural networks for facial expressions recognition

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Andry Chowanda
Keyword(s):  
Neural Networks ◽  
Social Interactions ◽  
Facial Expressions ◽  
Convolutional Neural Networks ◽  
The Other ◽  
Computational Power ◽  
Facial Cues ◽  
Emotional Recognition ◽  
Testing Accuracy ◽  
Facial Expressions Recognition

AbstractSocial interactions are important for us, humans, as social creatures. Emotions play an important part in social interactions. They usually express meanings along with the spoken utterances to the interlocutors. Automatic facial expressions recognition is one technique to automatically capture, recognise, and understand emotions from the interlocutor. Many techniques proposed to increase the accuracy of emotions recognition from facial cues. Architecture such as convolutional neural networks demonstrates promising results for emotions recognition. However, most of the current models of convolutional neural networks require an enormous computational power to train and process emotional recognition. This research aims to build compact networks with depthwise separable layers while also maintaining performance. Three datasets and three other similar architectures were used to be compared with the proposed architecture. The results show that the proposed architecture performed the best among the other architectures. It achieved up to 13% better accuracy and 6–71% smaller and more compact than the other architectures. The best testing accuracy achieved by the architecture was 99.4%.

scholarly journals INFERRING THE SCALE AND CONTENT OF A MAP USING DEEP LEARNING

2020 ◽  
Vol XLIII-B4-2020 ◽  
pp. 17-24
Author(s):  
G. Touya ◽  
F. Brisebard ◽  
F. Quinton ◽  
A. Courtial
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Visually Impaired ◽  
The Other ◽  
Visually Impaired People ◽  
Impaired People ◽  
Tactile Maps

Abstract. Visually impaired people cannot use classical maps but can learn to use tactile relief maps. These tactile maps are crucial at school to learn geography and history as well as the other students. They are produced manually by professional transcriptors in a very long and costly process. A platform able to generate tactile maps from maps scanned from geography textbooks could be extremely useful to these transcriptors, to fasten their production. As a first step towards such a platform, this paper proposes a method to infer the scale and the content of the map from its image. We used convolutional neural networks trained with a few hundred maps from French geography textbooks, and the results show promising results to infer labels about the content of the map (e.g. ”there are roads, cities and administrative boundaries”), and to infer the extent of the map (e.g. a map of France or of Europe).

Complementary Object Tracking Using Average Peak-to-Correlation Energy

2021 ◽  
Author(s):  
Kosuke Honda ◽  
Hamido Fujita
Keyword(s):  
Neural Networks ◽  
Object Tracking ◽  
Convolutional Neural Networks ◽  
Correlation Energy ◽  
Target Object ◽  
The Other ◽  
Tracking Performance ◽  
Correlation Filter ◽  
Evaluation Index ◽  
Siamese Network

In recent years, template-based methods such as Siamese network trackers and Correlation Filter (CF) based trackers have achieved state-of-the-art performance in several benchmarks. Recent Siamese network trackers use deep features extracted from convolutional neural networks to locate the target. However, the tracking performance of these trackers decreases when there are similar distractors to the object and the target object is deformed. On the other hand, correlation filter (CF)-based trackers that use handcrafted features (e.g., HOG features) to spatially locate the target. These two approaches have complementary characteristics due to differences in learning methods, features used, and the size of search regions. Also, we found that these trackers are complementary in terms of performance in benchmarking. Therefore, we propose the “Complementary Tracking framework using Average peak-to-correlation energy” (CTA). CTA is the generic object tracking framework that connects CF-trackers and Siamese-trackers in parallel and exploits the complementary features of these. In CTA, when a tracking failure of the Siamese tracker is detected using Average peak-to-correlation energy (APCE), which is an evaluation index of the response map matrix, the CF-trackers correct the output. In experimental on OTB100, CTA significantly improves the performance over the original tracker for several combinations of Siamese-trackers and CF-rackers.

scholarly journals Efficient implementation of convolutional neural networks in the data processing of two-photon in vivo imaging

2019 ◽  
Vol 35 (17) ◽  
pp. 3208-3210 ◽  
Author(s):  
Yangzhen Wang ◽  
Feng Su ◽  
Shanshan Wang ◽  
Chaojuan Yang ◽  
Yonglu Tian ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Detection Methods ◽  
Supplementary Information ◽  
Imaging Data ◽  
Two Photon ◽  
Processing Power ◽  
Fluctuation Method ◽  
The Brain

Abstract Motivation Functional imaging at single-neuron resolution offers a highly efficient tool for studying the functional connectomics in the brain. However, mainstream neuron-detection methods focus on either the morphologies or activities of neurons, which may lead to the extraction of incomplete information and which may heavily rely on the experience of the experimenters. Results We developed a convolutional neural networks and fluctuation method-based toolbox (ImageCN) to increase the processing power of calcium imaging data. To evaluate the performance of ImageCN, nine different imaging datasets were recorded from awake mouse brains. ImageCN demonstrated superior neuron-detection performance when compared with other algorithms. Furthermore, ImageCN does not require sophisticated training for users. Availability and implementation ImageCN is implemented in MATLAB. The source code and documentation are available at https://github.com/ZhangChenLab/ImageCN. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Model Architecture of CNN for Recognition the Pandava Mask

Jurnal INFORM ◽  
2020 ◽  
Vol 5 (2) ◽  
pp. 99
Author(s):  
Andi Sanjaya ◽  
Endang Setyati ◽  
Herman Budianto
Keyword(s):  
Neural Networks ◽  
Data Processing ◽  
Convolutional Neural Networks ◽  
Research Result ◽  
Trial Result ◽  
Trial Data ◽  
The Other ◽  
Architectural Model ◽  
Input Layer

This research was conducted to observe the use of architectural model Convolutional Neural Networks (CNN) LeNEt, which was suitable to use for Pandava mask objects. The Data processing in the research was 200 data for each class or similar with 1000 trial data. Architectural model CNN LeNET used input layer 32x32, 64x64, 128x128, 224x224 and 256x256. The trial result with the input layer 32x32 succeeded, showing a faster time compared to the other layer. The result of accuracy value and validation was not under fitted or overfit. However, when the activation of the second dense process as changed from the relu to sigmoid, the result was better in sigmoid, in the tem of time, and the possibility of overfitting was less. The research result had a mean accuracy value of 0.96.

scholarly journals Computational Prediction of Intrinsically Disordered Proteins Based on Protein Sequences and Convolutional Neural Networks

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Hao He ◽  
Yong Yang
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Intrinsically Disordered Proteins ◽  
Prediction Method ◽  
Computational Prediction ◽  
Disordered Proteins ◽  
Biological Functions ◽  
Intrinsically Disordered ◽  
Central Residue

Intrinsically disordered proteins (IDPs) possess at least one region that lacks a single stable structure in vivo, which makes them play an important role in a variety of biological functions. We propose a prediction method for IDPs based on convolutional neural networks (CNNs) and feature selection. The combination of sequence and evolutionary properties is used to describe the differences between disordered and ordered regions. Especially, to highlight the correlation between the target residue and adjacent residues, multiple windows are selected to preprocess the protein sequence through the selected properties. The shorter windows reflect the characteristics of the central residue, and the longer windows reflect the characteristics of the surroundings around the central residue. Moreover, to highlight the specificity of sequence and evolutionary properties, they are preprocessed, respectively. After that, the preprocessed properties are combined into feature matrices as the input of the constructed CNN. Our method is training as well as testing based on the DisProt database. The simulation results show that the proposed method can predict IDPs effectively, and the performance is competitive in comparison with IsUnstruct and ESpritz.

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