HetEnc: A Deep Learning Predictive Model for Multi-type Biological Dataset

10.21203/rs.2.9278/v2 ◽

2019 ◽

Author(s):

Leihong Wu ◽

Xiangwen Liu ◽

Joshua Xu

Keyword(s):

Neural Network ◽

Gene Expression ◽

Deep Learning ◽

Classification Problem ◽

Biological Data ◽

Feature Representation ◽

Biological Research ◽

Integrated Analysis ◽

Learning Approaches ◽

Feed Forward Neural Network

Abstract Background: Researchers today are generating unprecedented amounts of biological data. One trend in current biological research is integrated analysis with multi-platform data. Effective integration of multi-platform data into the solution of a single or multi-task classification problem; however, is critical and challenging. In this study, we proposed HetEnc, a novel deep learning-based approach, for information domain separation. Results: HetEnc includes both an unsupervised feature representation module and a supervised neural network module to handle multi-platform gene expression datasets. It first constructs three different encoding networks to represent the original gene expression data using high-level abstracted features. A six-layer fully-connected feed-forward neural network is then trained using these abstracted features for each targeted endpoint. We applied HetEnc to the SEQC neuroblastoma dataset to demonstrate that it outperforms other machine learning approaches. Although we used multi-platform data in feature abstraction and model training, HetEnc does not need multi-platform data for prediction, enabling a broader application of the trained model by reducing the cost of gene expression profiling for new samples to a single platform. Thus, HetEnc provides a new solution to integrated gene expression analysis, accelerating modern biological research.

Download Full-text

HetEnc: A Deep Learning Predictive Model for Multi-type Biological Dataset

10.21203/rs.2.9278/v3 ◽

2019 ◽

Author(s):

Leihong Wu ◽

Xiangwen Liu ◽

Joshua Xu

Keyword(s):

Neural Network ◽

Gene Expression ◽

Deep Learning ◽

Classification Problem ◽

Biological Data ◽

Feature Representation ◽

Biological Research ◽

Integrated Analysis ◽

Learning Approaches ◽

Feed Forward Neural Network

Abstract Background: Researchers today are generating unprecedented amounts of biological data. One trend in current biological research is integrated analysis with multi-platform data. Effective integration of multi-platform data into the solution of a single or multi-task classification problem; however, is critical and challenging. In this study, we proposed HetEnc, a novel deep learning-based approach, for information domain separation. Results: HetEnc includes both an unsupervised feature representation module and a supervised neural network module to handle multi-platform gene expression datasets. It first constructs three different encoding networks to represent the original gene expression data using high-level abstracted features. A six-layer fully-connected feed-forward neural network is then trained using these abstracted features for each targeted endpoint. We applied HetEnc to the SEQC neuroblastoma dataset to demonstrate that it outperforms other machine learning approaches. Although we used multi-platform data in feature abstraction and model training, HetEnc does not need multi-platform data for prediction, enabling a broader application of the trained model by reducing the cost of gene expression profiling for new samples to a single platform. Thus, HetEnc provides a new solution to integrated gene expression analysis, accelerating modern biological research.

Download Full-text

HetEnc: A Deep Learning Predictive Model for Multi-type Biological Dataset

10.21203/rs.2.9278/v1 ◽

2019 ◽

Author(s):

Leihong Wu ◽

Xiangwen Liu ◽

Joshua Xu

Keyword(s):

Neural Network ◽

Gene Expression ◽

Deep Learning ◽

Classification Problem ◽

Biological Data ◽

Feature Representation ◽

Biological Research ◽

Integrated Analysis ◽

Learning Approaches ◽

Feed Forward Neural Network

Abstract Motivation Researchers today are generating unprecedented amounts of biological data. One trend in current biological research is integrated analysis with multi-platform data. Effective integration of multi-platform data into the solution of a single or multi-task classification problem; however, is critical and challenging. In this study, we proposed HetEnc, a novel deep learning-based approach, for information domain separation. Results HetEnc includes both an unsupervised feature representation module and a supervised neural network module to handle multi-platform gene expression datasets. It first constructs three different encoding networks to represent the original gene expression data using high-level abstracted features. A six-layer fully-connected feed-forward neural network is then trained using these abstracted features for each targeted endpoint. We applied HetEnc to the SEQC neuroblastoma dataset to demonstrate that it outperforms other machine learning approaches. Although we used multi-platform data in feature abstraction and model training, HetEnc does not need multi-platform data for prediction, enabling a broader application of the trained model by reducing the cost of gene expression profiling for new samples to a single platform. Thus, HetEnc provides a new solution to integrated gene expression analysis, accelerating modern biological research. Availability and Implementation The source code for HetEnc is available at: https://github.com/seldas/HetEnc_Code.

Download Full-text

A convolutional neural network for predicting transcriptional regulators of genes in Arabidopsis transcriptome data reveals classification based on positive regulatory interactions

10.1101/618926 ◽

2019 ◽

Cited By ~ 3

Author(s):

Dan MacLean

Keyword(s):

Neural Network ◽

Gene Expression ◽

Neural Networks ◽

Deep Learning ◽

Convolutional Neural Network ◽

Convolutional Neural Networks ◽

Expression Profiles ◽

Biological Data ◽

Expression Data ◽

Data Set

AbstractGene Regulatory networks that control gene expression are widely studied yet the interactions that make them up are difficult to predict from high throughput data. Deep Learning methods such as convolutional neural networks can perform surprisingly good classifications on a variety of data types and the matrix-like gene expression profiles would seem to be ideal input data for deep learning approaches. In this short study I compiled training sets of expression data using the Arabidopsis AtGenExpress global stress expression data set and known transcription factor-target interactions from the Arabidopsis PLACE database. I built and optimised convolutional neural networks with a best model providing 95 % accuracy of classification on a held-out validation set. Investigation of the activations within this model revealed that classification was based on positive correlation of expression profiles in short sections. This result shows that a convolutional neural network can be used to make classifications and reveal the basis of those calssifications for gene expression data sets, indicating that a convolutional neural network is a useful and interpretable tool for exploratory classification of biological data. The final model is available for download and as a web application.

Download Full-text

Deep Learning-Based Approach to Fast Power Allocation in SISO SWIPT Systems with a Power-Splitting Scheme

Applied Sciences ◽

10.3390/app10103634 ◽

2020 ◽

Vol 10 (10) ◽

pp. 3634

Author(s):

Huynh Thanh Thien ◽

Pham-Viet Tuan ◽

Insoo Koo

Keyword(s):

Neural Network ◽

Deep Learning ◽

High Performance ◽

Short Term Memory ◽

Computation Time ◽

Power Splitting ◽

Learning Approaches ◽

Feed Forward Neural Network ◽

Transmit Power ◽

Single Input Single Output

Recently, simultaneous wireless information and power transfer (SWIPT) systems, which can supply efficiently throughput and energy, have emerged as a potential research area in fifth-generation (5G) system. In this paper, we study SWIPT with multi-user, single-input single-output (SISO) system. First, we solve the transmit power optimization problem, which provides the optimal strategy for getting minimum power while satisfying sufficient signal-to-noise ratio (SINR) and harvested energy requirements to ensure receiver circuits work in SWIPT systems where receivers are equipped with a power-splitting structure. Although optimization algorithms are able to achieve relatively high performance, they often entail a significant number of iterations, which raises many issues in computation costs and time for real-time applications. Therefore, we aim at providing a deep learning-based approach, which is a promising solution to address this challenging issue. Deep learning architectures used in this paper include a type of Deep Neural Network (DNN): the Feed-Forward Neural Network (FFNN) and three types of Recurrent Neural Network (RNN): the Layer Recurrent Network (LRN), the Nonlinear AutoRegressive network with eXogenous inputs (NARX), and Long Short-Term Memory (LSTM). Through simulations, we show that the deep learning approaches can approximate a complex optimization algorithm that optimizes transmit power in SWIPT systems with much less computation time.

Download Full-text

Review of the Applications of Deep Learning in Bioinformatics

Current Bioinformatics ◽

10.2174/1574893615999200711165743 ◽

2021 ◽

Vol 15 (8) ◽

pp. 898-911

Author(s):

Yongqing Zhang ◽

Jianrong Yan ◽

Siyu Chen ◽

Meiqin Gong ◽

Dongrui Gao ◽

...

Keyword(s):

Deep Learning ◽

Drug Discovery ◽

Biomedical Imaging ◽

State Of The Art ◽

Black Box ◽

Medical Data ◽

Biological Data ◽

High Dimensional ◽

Biological Research ◽

Process Data

Rapid advances in biological research over recent years have significantly enriched biological and medical data resources. Deep learning-based techniques have been successfully utilized to process data in this field, and they have exhibited state-of-the-art performances even on high-dimensional, nonstructural, and black-box biological data. The aim of the current study is to provide an overview of the deep learning-based techniques used in biology and medicine and their state-of-the-art applications. In particular, we introduce the fundamentals of deep learning and then review the success of applying such methods to bioinformatics, biomedical imaging, biomedicine, and drug discovery. We also discuss the challenges and limitations of this field, and outline possible directions for further research.

Download Full-text

Detection of Malicious Software by Analyzing Distinct Artifacts Using Machine Learning and Deep Learning Algorithms

Electronics ◽

10.3390/electronics10141694 ◽

2021 ◽

Vol 10 (14) ◽

pp. 1694

Author(s):

Mathew Ashik ◽

A. Jyothish ◽

S. Anandaram ◽

P. Vinod ◽

Francesco Mercaldo ◽

...

Keyword(s):

Neural Network ◽

Machine Learning ◽

Deep Learning ◽

Support Vector ◽

Malware Analysis ◽

Learning Approaches ◽

Dynamic Features ◽

System Calls ◽

Prevention Methods ◽

Structural Aspects

Malware is one of the most significant threats in today’s computing world since the number of websites distributing malware is increasing at a rapid rate. Malware analysis and prevention methods are increasingly becoming necessary for computer systems connected to the Internet. This software exploits the system’s vulnerabilities to steal valuable information without the user’s knowledge, and stealthily send it to remote servers controlled by attackers. Traditionally, anti-malware products use signatures for detecting known malware. However, the signature-based method does not scale in detecting obfuscated and packed malware. Considering that the cause of a problem is often best understood by studying the structural aspects of a program like the mnemonics, instruction opcode, API Call, etc. In this paper, we investigate the relevance of the features of unpacked malicious and benign executables like mnemonics, instruction opcodes, and API to identify a feature that classifies the executable. Prominent features are extracted using Minimum Redundancy and Maximum Relevance (mRMR) and Analysis of Variance (ANOVA). Experiments were conducted on four datasets using machine learning and deep learning approaches such as Support Vector Machine (SVM), Naïve Bayes, J48, Random Forest (RF), and XGBoost. In addition, we also evaluate the performance of the collection of deep neural networks like Deep Dense network, One-Dimensional Convolutional Neural Network (1D-CNN), and CNN-LSTM in classifying unknown samples, and we observed promising results using APIs and system calls. On combining APIs/system calls with static features, a marginal performance improvement was attained comparing models trained only on dynamic features. Moreover, to improve accuracy, we implemented our solution using distinct deep learning methods and demonstrated a fine-tuned deep neural network that resulted in an F1-score of 99.1% and 98.48% on Dataset-2 and Dataset-3, respectively.

Download Full-text

Analysis of the Nosema Cells Identification for Microscopic Images

Sensors ◽

10.3390/s21093068 ◽

2021 ◽

Vol 21 (9) ◽

pp. 3068

Author(s):

Soumaya Dghim ◽

Carlos M. Travieso-González ◽

Radim Burget

Keyword(s):

Neural Network ◽

Machine Learning ◽

Image Processing ◽

Deep Learning ◽

The Other ◽

Support Vector ◽

Learning Approaches ◽

Microscopic Images ◽

Trained Neural Network ◽

Nosema Disease

The use of image processing tools, machine learning, and deep learning approaches has become very useful and robust in recent years. This paper introduces the detection of the Nosema disease, which is considered to be one of the most economically significant diseases today. This work shows a solution for recognizing and identifying Nosema cells between the other existing objects in the microscopic image. Two main strategies are examined. The first strategy uses image processing tools to extract the most valuable information and features from the dataset of microscopic images. Then, machine learning methods are applied, such as a neural network (ANN) and support vector machine (SVM) for detecting and classifying the Nosema disease cells. The second strategy explores deep learning and transfers learning. Several approaches were examined, including a convolutional neural network (CNN) classifier and several methods of transfer learning (AlexNet, VGG-16 and VGG-19), which were fine-tuned and applied to the object sub-images in order to identify the Nosema images from the other object images. The best accuracy was reached by the VGG-16 pre-trained neural network with 96.25%.

Download Full-text

Deep Learning Methods for Heart Sounds Classification: A Systematic Review

Entropy ◽

10.3390/e23060667 ◽

2021 ◽

Vol 23 (6) ◽

pp. 667

Author(s):

Wei Chen ◽

Qiang Sun ◽

Xiaomin Chen ◽

Gangcai Xie ◽

Huiqun Wu ◽

...

Keyword(s):

Neural Network ◽

Systematic Review ◽

Deep Learning ◽

Heart Sounds ◽

Learning Approaches ◽

Automated Classification ◽

Learning Methods ◽

Artificial Intelligence Technology ◽

Medical Big Data ◽

Effective Models

The automated classification of heart sounds plays a significant role in the diagnosis of cardiovascular diseases (CVDs). With the recent introduction of medical big data and artificial intelligence technology, there has been an increased focus on the development of deep learning approaches for heart sound classification. However, despite significant achievements in this field, there are still limitations due to insufficient data, inefficient training, and the unavailability of effective models. With the aim of improving the accuracy of heart sounds classification, an in-depth systematic review and an analysis of existing deep learning methods were performed in the present study, with an emphasis on the convolutional neural network (CNN) and recurrent neural network (RNN) methods developed over the last five years. This paper also discusses the challenges and expected future trends in the application of deep learning to heart sounds classification with the objective of providing an essential reference for further study.

Download Full-text

Deep Learning for Laryngopharyngeal Reflux Diagnosis

Applied Sciences ◽

10.3390/app11114753 ◽

2021 ◽

Vol 11 (11) ◽

pp. 4753

Author(s):

Gen Ye ◽

Chen Du ◽

Tong Lin ◽

Yan Yan ◽

Jack Jiang

Keyword(s):

Deep Learning ◽

Speech Processing ◽

Data Augmentation ◽

Laryngopharyngeal Reflux ◽

Ph Monitoring ◽

Binary Classification ◽

Classification Problem ◽

Learning Approaches ◽

Learning Techniques ◽

Auc Value

(1) Background: Deep learning has become ubiquitous due to its impressive performance in various domains, such as varied as computer vision, natural language and speech processing, and game-playing. In this work, we investigated the performance of recent deep learning approaches on the laryngopharyngeal reflux (LPR) diagnosis task. (2) Methods: Our dataset is composed of 114 subjects with 37 pH-positive cases and 77 control cases. In contrast to prior work based on either reflux finding score (RFS) or pH monitoring, we directly take laryngoscope images as inputs to neural networks, as laryngoscopy is the most common and simple diagnostic method. The diagnosis task is formulated as a binary classification problem. We first tested a powerful backbone network that incorporates residual modules, attention mechanism and data augmentation. Furthermore, recent methods in transfer learning and few-shot learning were investigated. (3) Results: On our dataset, the performance is the best test classification accuracy is 73.4%, while the best AUC value is 76.2%. (4) Conclusions: This study demonstrates that deep learning techniques can be applied to classify LPR images automatically. Although the number of pH-positive images used for training is limited, deep network can still be capable of learning discriminant features with the advantage of technique.

Download Full-text