iEnhancer-ECNN: identifying enhancers and their strength using ensembles of convolutional neural networks

Abstract Background Enhancers are non-coding DNA fragments which are crucial in gene regulation (e.g. transcription and translation). Having high locational variation and free scattering in 98% of non-encoding genomes, enhancer identification is, therefore, more complicated than other genetic factors. To address this biological issue, several in silico studies have been done to identify and classify enhancer sequences among a myriad of DNA sequences using computational advances. Although recent studies have come up with improved performance, shortfalls in these learning models still remain. To overcome limitations of existing learning models, we introduce iEnhancer-ECNN, an efficient prediction framework using one-hot encoding and k-mers for data transformation and ensembles of convolutional neural networks for model construction, to identify enhancers and classify their strength. The benchmark dataset from Liu et al.’s study was used to develop and evaluate the ensemble models. A comparative analysis between iEnhancer-ECNN and existing state-of-the-art methods was done to fairly assess the model performance. Results Our experimental results demonstrates that iEnhancer-ECNN has better performance compared to other state-of-the-art methods using the same dataset. The accuracy of the ensemble model for enhancer identification (layer 1) and enhancer classification (layer 2) are 0.769 and 0.678, respectively. Compared to other related studies, improvements in the Area Under the Receiver Operating Characteristic Curve (AUC), sensitivity, and Matthews’s correlation coefficient (MCC) of our models are remarkable, especially for the model of layer 2 with about 11.0%, 46.5%, and 65.0%, respectively. Conclusions iEnhancer-ECNN outperforms other previously proposed methods with significant improvement in most of the evaluation metrics. Strong growths in the MCC of both layers are highly meaningful in assuring the stability of our models.

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IEnhancer-ECNN: Identifying enhancers and their strength using ensembles of convolutional neural networks

10.26686/wgtn.14315879.v1 ◽

2021 ◽

Author(s):

QH Nguyen ◽

TH Nguyen-Vo ◽

NQK Le ◽

TTT Do ◽

S Rahardja ◽

...

Keyword(s):

Neural Networks ◽

Convolutional Neural Networks ◽

Dna Sequences ◽

State Of The Art ◽

Characteristic Curve ◽

Learning Models ◽

In Silico Studies ◽

Layer 2 ◽

Art Methods ◽

Enhancer Identification

© 2019 The Author(s). Background: Enhancers are non-coding DNA fragments which are crucial in gene regulation (e.g. transcription and translation). Having high locational variation and free scattering in 98% of non-encoding genomes, enhancer identification is, therefore, more complicated than other genetic factors. To address this biological issue, several in silico studies have been done to identify and classify enhancer sequences among a myriad of DNA sequences using computational advances. Although recent studies have come up with improved performance, shortfalls in these learning models still remain. To overcome limitations of existing learning models, we introduce iEnhancer-ECNN, an efficient prediction framework using one-hot encoding and k-mers for data transformation and ensembles of convolutional neural networks for model construction, to identify enhancers and classify their strength. The benchmark dataset from Liu et al.'s study was used to develop and evaluate the ensemble models. A comparative analysis between iEnhancer-ECNN and existing state-of-the-art methods was done to fairly assess the model performance. Results: Our experimental results demonstrates that iEnhancer-ECNN has better performance compared to other state-of-the-art methods using the same dataset. The accuracy of the ensemble model for enhancer identification (layer 1) and enhancer classification (layer 2) are 0.769 and 0.678, respectively. Compared to other related studies, improvements in the Area Under the Receiver Operating Characteristic Curve (AUC), sensitivity, and Matthews's correlation coefficient (MCC) of our models are remarkable, especially for the model of layer 2 with about 11.0%, 46.5%, and 65.0%, respectively. Conclusions: iEnhancer-ECNN outperforms other previously proposed methods with significant improvement in most of the evaluation metrics. Strong growths in the MCC of both layers are highly meaningful in assuring the stability of our models.

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IEnhancer-ECNN: Identifying enhancers and their strength using ensembles of convolutional neural networks

10.26686/wgtn.14315879 ◽

2021 ◽

Author(s):

QH Nguyen ◽

TH Nguyen-Vo ◽

NQK Le ◽

TTT Do ◽

S Rahardja ◽

...

Keyword(s):

Neural Networks ◽

Convolutional Neural Networks ◽

Dna Sequences ◽

State Of The Art ◽

Characteristic Curve ◽

Learning Models ◽

In Silico Studies ◽

Layer 2 ◽

Art Methods ◽

Enhancer Identification

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Sentiment Classification Using Convolutional Neural Networks

Applied Sciences ◽

10.3390/app9112347 ◽

2019 ◽

Vol 9 (11) ◽

pp. 2347 ◽

Cited By ~ 18

Author(s):

Hannah Kim ◽

Young-Seob Jeong

Keyword(s):

Neural Network ◽

Neural Networks ◽

Convolutional Neural Networks ◽

Text Classification ◽

State Of The Art ◽

Sentiment Classification ◽

Learning Models ◽

Text Data ◽

Textual Data ◽

Better Than

As the number of textual data is exponentially increasing, it becomes more important to develop models to analyze the text data automatically. The texts may contain various labels such as gender, age, country, sentiment, and so forth. Using such labels may bring benefits to some industrial fields, so many studies of text classification have appeared. Recently, the Convolutional Neural Network (CNN) has been adopted for the task of text classification and has shown quite successful results. In this paper, we propose convolutional neural networks for the task of sentiment classification. Through experiments with three well-known datasets, we show that employing consecutive convolutional layers is effective for relatively longer texts, and our networks are better than other state-of-the-art deep learning models.

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DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout

Bioinformatics ◽

10.1093/bioinformatics/btz593 ◽

2019 ◽

Vol 36 (2) ◽

pp. 470-477 ◽

Cited By ~ 2

Author(s):

Badri Adhikari

Keyword(s):

Neural Networks ◽

Long Range ◽

Convolutional Neural Networks ◽

High Throughput Sequencing ◽

State Of The Art ◽

Deep Convolutional Neural Networks ◽

Contact Prediction ◽

Learning Techniques ◽

Medium Range ◽

Art Methods

Abstract Motivation Exciting new opportunities have arisen to solve the protein contact prediction problem from the progress in neural networks and the availability of a large number of homologous sequences through high-throughput sequencing. In this work, we study how deep convolutional neural networks (ConvNets) may be best designed and developed to solve this long-standing problem. Results With publicly available datasets, we designed and trained various ConvNet architectures. We tested several recent deep learning techniques including wide residual networks, dropouts and dilated convolutions. We studied the improvements in the precision of medium-range and long-range contacts, and compared the performance of our best architectures with the ones used in existing state-of-the-art methods. The proposed ConvNet architectures predict contacts with significantly more precision than the architectures used in several state-of-the-art methods. When trained using the DeepCov dataset consisting of 3456 proteins and tested on PSICOV dataset of 150 proteins, our architectures achieve up to 15% higher precision when L/2 long-range contacts are evaluated. Similarly, when trained using the DNCON2 dataset consisting of 1426 proteins and tested on 84 protein domains in the CASP12 dataset, our single network achieves 4.8% higher precision than the ensembled DNCON2 method when top L long-range contacts are evaluated. Availability and implementation DEEPCON is available at https://github.com/badriadhikari/DEEPCON/.

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Adaptive Region Embedding for Text Classification

Proceedings of the AAAI Conference on Artificial Intelligence ◽

10.1609/aaai.v33i01.33017314 ◽

2019 ◽

Vol 33 ◽

pp. 7314-7321

Author(s):

Liuyu Xiang ◽

Xiaoming Jin ◽

Lan Yi ◽

Guiguang Ding

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Convolutional Neural Networks ◽

Text Classification ◽

State Of The Art ◽

Context Information ◽

Great Success ◽

Recurrent Networks ◽

Learning Models ◽

Benchmark Datasets

Deep learning models such as convolutional neural networks and recurrent networks are widely applied in text classification. In spite of their great success, most deep learning models neglect the importance of modeling context information, which is crucial to understanding texts. In this work, we propose the Adaptive Region Embedding to learn context representation to improve text classification. Specifically, a metanetwork is learned to generate a context matrix for each region, and each word interacts with its corresponding context matrix to produce the regional representation for further classification. Compared to previous models that are designed to capture context information, our model contains less parameters and is more flexible. We extensively evaluate our method on 8 benchmark datasets for text classification. The experimental results prove that our method achieves state-of-the-art performances and effectively avoids word ambiguity.

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S2A: Scale-Attention-Aware Networks for Video Super-Resolution

Entropy ◽

10.3390/e23111398 ◽

2021 ◽

Vol 23 (11) ◽

pp. 1398

Author(s):

Taian Guo ◽

Tao Dai ◽

Ling Liu ◽

Zexuan Zhu ◽

Shu-Tao Xia

Keyword(s):

Neural Networks ◽

Convolutional Neural Networks ◽

State Of The Art ◽

Super Resolution ◽

Art Methods ◽

Multiple Frames ◽

Feature Expression

Convolutional Neural Networks (CNNs) have been widely used in video super-resolution (VSR). Most existing VSR methods focus on how to utilize the information of multiple frames, while neglecting the feature correlations of the intermediate features, thus limiting the feature expression of the models. To address this problem, we propose a novel SAA network, that is, Scale-and-Attention-Aware Networks, to apply different attention to different temporal-length streams, while further exploring both spatial and channel attention on separate streams with a newly proposed Criss-Cross Channel Attention Module (C3AM). Experiments on public VSR datasets demonstrate the superiority of our method over other state-of-the-art methods in terms of both quantitative and qualitative metrics.

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Levenshtein Augmentation Improves Performance of SMILES Based Deep-Learning Synthesis Prediction

10.26434/chemrxiv.12562121 ◽

2020 ◽

Author(s):

Dean Sumner ◽

Jiazhen He ◽

Amol Thakkar ◽

Ola Engkvist ◽

Esben Jannik Bjerrum

Keyword(s):

Neural Networks ◽

Pattern Recognition ◽

Deep Learning ◽

Recurrent Neural Networks ◽

Data Augmentation ◽

State Of The Art ◽

Sequence Similarity ◽

Learning Models ◽

Underlying Network

<p>SMILES randomization, a form of data augmentation, has previously been shown to increase the performance of deep learning models compared to non-augmented baselines. Here, we propose a novel data augmentation method we call “Levenshtein augmentation” which considers local SMILES sub-sequence similarity between reactants and their respective products when creating training pairs. The performance of Levenshtein augmentation was tested using two state of the art models - transformer and sequence-to-sequence based recurrent neural networks with attention. Levenshtein augmentation demonstrated an increase performance over non-augmented, and conventionally SMILES randomization augmented data when used for training of baseline models. Furthermore, Levenshtein augmentation seemingly results in what we define as <i>attentional gain </i>– an enhancement in the pattern recognition capabilities of the underlying network to molecular motifs.</p>

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Deep Malaria Parasite Detection in Thin Blood Smear Microscopic Images

Applied Sciences ◽

10.3390/app11052284 ◽

2021 ◽

Vol 11 (5) ◽

pp. 2284

Author(s):

Asma Maqsood ◽

Muhammad Shahid Farid ◽

Muhammad Hassan Khan ◽

Marcin Grzegorzek

Keyword(s):

Neural Networks ◽

Deep Learning ◽

Red Blood Cells ◽

Convolutional Neural Networks ◽

Blood Cells ◽

Superior Performance ◽

Learning Models ◽

Infected Female ◽

The World ◽

Augmentation Techniques

Malaria is a disease activated by a type of microscopic parasite transmitted from infected female mosquito bites to humans. Malaria is a fatal disease that is endemic in many regions of the world. Quick diagnosis of this disease will be very valuable for patients, as traditional methods require tedious work for its detection. Recently, some automated methods have been proposed that exploit hand-crafted feature extraction techniques however, their accuracies are not reliable. Deep learning approaches modernize the world with their superior performance. Convolutional Neural Networks (CNN) are vastly scalable for image classification tasks that extract features through hidden layers of the model without any handcrafting. The detection of malaria-infected red blood cells from segmented microscopic blood images using convolutional neural networks can assist in quick diagnosis, and this will be useful for regions with fewer healthcare experts. The contributions of this paper are two-fold. First, we evaluate the performance of different existing deep learning models for efficient malaria detection. Second, we propose a customized CNN model that outperforms all observed deep learning models. It exploits the bilateral filtering and image augmentation techniques for highlighting features of red blood cells before training the model. Due to image augmentation techniques, the customized CNN model is generalized and avoids over-fitting. All experimental evaluations are performed on the benchmark NIH Malaria Dataset, and the results reveal that the proposed algorithm is 96.82% accurate in detecting malaria from the microscopic blood smears.

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Using spatial-temporal ensembles of convolutional neural networks for lumen segmentation in ureteroscopy

International Journal of Computer Assisted Radiology and Surgery ◽

10.1007/s11548-021-02376-3 ◽

2021 ◽

Author(s):

Jorge F. Lazo ◽

Aldo Marzullo ◽

Sara Moccia ◽

Michele Catellani ◽

Benoit Rosa ◽

...

Keyword(s):

Neural Networks ◽

Convolutional Neural Networks ◽

State Of The Art ◽

Automatic Segmentation ◽

Temporal Information ◽

Invasive Technique ◽

Dice Similarity Coefficient ◽

Specular Reflections ◽

Lumen Segmentation ◽

Previous State

Abstract Purpose Ureteroscopy is an efficient endoscopic minimally invasive technique for the diagnosis and treatment of upper tract urothelial carcinoma. During ureteroscopy, the automatic segmentation of the hollow lumen is of primary importance, since it indicates the path that the endoscope should follow. In order to obtain an accurate segmentation of the hollow lumen, this paper presents an automatic method based on convolutional neural networks (CNNs). Methods The proposed method is based on an ensemble of 4 parallel CNNs to simultaneously process single and multi-frame information. Of these, two architectures are taken as core-models, namely U-Net based in residual blocks ($$m_1$$ m 1 ) and Mask-RCNN ($$m_2$$ m 2 ), which are fed with single still-frames I(t). The other two models ($$M_1$$ M 1 , $$M_2$$ M 2 ) are modifications of the former ones consisting on the addition of a stage which makes use of 3D convolutions to process temporal information. $$M_1$$ M 1 , $$M_2$$ M 2 are fed with triplets of frames ($$I(t-1)$$ I ( t - 1 ) , I(t), $$I(t+1)$$ I ( t + 1 ) ) to produce the segmentation for I(t). Results The proposed method was evaluated using a custom dataset of 11 videos (2673 frames) which were collected and manually annotated from 6 patients. We obtain a Dice similarity coefficient of 0.80, outperforming previous state-of-the-art methods. Conclusion The obtained results show that spatial-temporal information can be effectively exploited by the ensemble model to improve hollow lumen segmentation in ureteroscopic images. The method is effective also in the presence of poor visibility, occasional bleeding, or specular reflections.

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Image Classification for the Automatic Feature Extraction in Human Worn Fashion Data

Mathematics ◽

10.3390/math9060624 ◽

2021 ◽

Vol 9 (6) ◽

pp. 624

Author(s):

Stefan Rohrmanstorfer ◽

Mikhail Komarov ◽

Felix Mödritscher

Keyword(s):

Neural Networks ◽

Feature Extraction ◽

Image Classification ◽

Convolutional Neural Networks ◽

Data Augmentation ◽

State Of The Art ◽

Image Data ◽

Classification Model ◽

Upper Body ◽

Automatic Feature Extraction

With the always increasing amount of image data, it has become a necessity to automatically look for and process information in these images. As fashion is captured in images, the fashion sector provides the perfect foundation to be supported by the integration of a service or application that is built on an image classification model. In this article, the state of the art for image classification is analyzed and discussed. Based on the elaborated knowledge, four different approaches will be implemented to successfully extract features out of fashion data. For this purpose, a human-worn fashion dataset with 2567 images was created, but it was significantly enlarged by the performed image operations. The results show that convolutional neural networks are the undisputed standard for classifying images, and that TensorFlow is the best library to build them. Moreover, through the introduction of dropout layers, data augmentation and transfer learning, model overfitting was successfully prevented, and it was possible to incrementally improve the validation accuracy of the created dataset from an initial 69% to a final validation accuracy of 84%. More distinct apparel like trousers, shoes and hats were better classified than other upper body clothes.

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