scholarly journals PARROT is a flexible recurrent neural network framework for analysis of large protein datasets

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Daniel Griffith ◽  
Alex S Holehouse
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
High Throughput ◽  
Recurrent Neural Network ◽  
Transcriptional Activation ◽  
Network Architecture ◽  
Learning Approaches ◽  
Large Protein ◽  
Protein Datasets

The rise of high-throughput experiments has transformed how scientists approach biological questions. The ubiquity of large-scale assays that can test thousands of samples in a day has necessitated the development of new computational approaches to interpret this data. Among these tools, machine learning approaches are increasingly being utilized due to their ability to infer complex nonlinear patterns from high-dimensional data. Despite their effectiveness, machine learning (and in particular deep learning) approaches are not always accessible or easy to implement for those with limited computational expertise. Here we present PARROT, a general framework for training and applying deep learning-based predictors on large protein datasets. Using an internal recurrent neural network architecture, PARROT is capable of tackling both classification and regression tasks while only requiring raw protein sequences as input. We showcase the potential uses of PARROT on three diverse machine learning tasks: predicting phosphorylation sites, predicting transcriptional activation function of peptides generated by high-throughput reporter assays, and predicting the fibrillization propensity of amyloid beta with data generated by deep mutational scanning. Through these examples, we demonstrate that PARROT is easy to use, performs comparably to state-of-the-art computational tools, and is applicable for a wide array of biological problems.

scholarly journals PARROT: a flexible recurrent neural network framework for analysis of large protein datasets

2021 ◽  
Author(s):  
Daniel Griffith ◽  
Alex S Holehouse
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
High Throughput ◽  
Recurrent Neural Network ◽  
Transcriptional Activation ◽  
Network Architecture ◽  
Learning Approaches ◽  
Large Protein ◽  
Protein Datasets

The rise of high-throughput experiments has transformed how scientists approach biological questions. The ubiquity of large-scale assays that can test thousands of samples in a day has necessitated the development of new computational approaches to interpret this data. Among these tools, machine learning approaches are increasingly being utilized due to their ability to infer complex non-linear patterns from high-dimensional data. Despite their effectiveness, machine learning (and in particular deep learning) approaches are not always accessible or easy to implement for those with limited computational expertise. Here we present PARROT, a general framework for training and applying deep learning-based predictors on large protein datasets. Using an internal recurrent neural network architecture, PARROT is capable of tackling both classification and regression tasks while only requiring raw protein sequences as input. We showcase the potential uses of PARROT on three diverse machine learning tasks: predicting phosphorylation sites, predicting transcriptional activation function of peptides generated by high-throughput reporter assays, and predicting the fibrillization propensity of amyloid-beta with data generated by deep mutational scanning. Through these examples, we demonstrate that PARROT is easy to use, performs comparably to state-of-the-art computational tools, and is applicable for a wide array of biological problems.

scholarly journals A Framework for Sentiment Analysis of Telugu Tweets

2020 ◽  
Vol 9 (6) ◽  
pp. 523-525
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Social Media ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Recurrent Neural Network ◽  
English Language ◽  
Research Work ◽  
Learning Approaches ◽  
Text Data

Now a day Social Media like Facebook, twitter and Instagram is major Sources for people to share their emotions based on the current situations in society. By knowing the interesting patterns in it, a government/appropriate person for that situation can take good and useful decisions. Sentiment analysis is a method where people can extract the useful information from the text like the emotions (happy, sad, and neutral) of people. Much research work was been underdoing in the area of sentiment analysis. Among that work the Machine learning and Deep learning approaches plays a maximum role. Existing works on sentiment analysis is going in the English language. In this paper, proposed a novel framework that specifically designed to do sentiment analysis of the text data, that available in the telugu language. The proposed framework was integrated with the word embedding model Word2Vec, language translator and deep learning approaches like Recurrent Neural Network and Navie base algorithms to collect and analyse the sentiment in tweeter data that present in telugu language. The results shows effective in terms of accuracy, precision and specificity.

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

Electronics ◽  
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.

scholarly journals Analysis of the Nosema Cells Identification for Microscopic Images

Sensors ◽  
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%.

scholarly journals SENTIMENT ANALYSIS OF ELECTRIC CARS USING RECURRENT NEURAL NETWORK METHOD IN INDONESIAN TWEETS

Kursor ◽  
2020 ◽  
Vol 10 (4) ◽  
Author(s):  
Felisia Handayani ◽  
Metty Mustikasari
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Recurrent Neural Network ◽  
Confusion Matrix ◽  
Data Representation ◽  
Sequential Data ◽  
Communication Tool ◽  
Electric Cars

Sentiment analysis is computational research of the opinions of many people who are textually expressed against a particular topic. Twitter is the most popular communication tool among Internet users today to express their opinions. Deep Learning is a solution to allow computers to learn from experience and understand the world in terms of the hierarchy concept. Deep Learning objectives replace manual assignments with learning. The development of deep learning has a set of algorithms that focus on learning data representation. The recurrent Neural Network is one of the machine learning methods included in Deep learning because the data is processed through multi-players. RNN is also an algorithm that can recall the input with internal memory, therefore it is suitable for machine learning problems involving sequential data. The study aims to test models that have been created from tweets that are positive, negative, and neutral sentiment to determine the accuracy of the models. The models have been created using the Recurrent Neural Network when applied to tweet classifications to mark the individual classes of Indonesian-language tweet data sentiment. From the experiments conducted, results on the built system showed that the best test results in the tweet data with the RNN method using Confusion Matrix are with Precision 0.618, Recall 0.507 and Accuracy 0.722 on the data amounted to 3000 data and comparative data training and data testing of ratio data 80:20

scholarly journals Comparison between Deep Learning and Tree-Based Machine Learning Approaches for Landslide Susceptibility Mapping

Water ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 2664
Author(s):  
Sunil Saha ◽  
Jagabandhu Roy ◽  
Tusar Kanti Hembram ◽  
Biswajeet Pradhan ◽  
Abhirup Dikshit ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Landslide Susceptibility ◽  
Learning Model ◽  
Susceptibility Mapping ◽  
Landslide Susceptibility Mapping ◽  
Learning Approaches ◽  
Statistical Measures ◽  
Deep Learning Model

The efficiency of deep learning and tree-based machine learning approaches has gained immense popularity in various fields. One deep learning model viz. convolution neural network (CNN), artificial neural network (ANN) and four tree-based machine learning models, namely, alternative decision tree (ADTree), classification and regression tree (CART), functional tree and logistic model tree (LMT), were used for landslide susceptibility mapping in the East Sikkim Himalaya region of India, and the results were compared. Landslide areas were delimited and mapped as landslide inventory (LIM) after gathering information from historical records and periodic field investigations. In LIM, 91 landslides were plotted and classified into training (64 landslides) and testing (27 landslides) subsets randomly to train and validate the models. A total of 21 landslide conditioning factors (LCFs) were considered as model inputs, and the results of each model were categorised under five susceptibility classes. The receiver operating characteristics curve and 21 statistical measures were used to evaluate and prioritise the models. The CNN deep learning model achieved the priority rank 1 with area under the curve of 0.918 and 0.933 by using the training and testing data, quantifying 23.02% and 14.40% area as very high and highly susceptible followed by ANN, ADtree, CART, FTree and LMT models. This research might be useful in landslide studies, especially in locations with comparable geophysical and climatological characteristics, to aid in decision making for land use planning.

scholarly journals Designing deep neural networks for continual learning in an open world

2021 ◽  
Author(s):  
◽  
Martin Mundt
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Network Architecture ◽  
Neural Network Training ◽  
Neural Network Architecture ◽  
Neural Architecture ◽  
Network Training ◽  
Classification Tasks ◽  
Continual Learning

Deep learning with neural networks seems to have largely replaced traditional design of computer vision systems. Automated methods to learn a plethora of parameters are now used in favor of previously practiced selection of explicit mathematical operators for a specific task. The entailed promise is that practitioners no longer need to take care of every individual step, but rather focus on gathering big amounts of data for neural network training. As a consequence, both a shift in mindset towards a focus on big datasets, as well as a wave of conceivable applications based exclusively on deep learning can be observed. This PhD dissertation aims to uncover some of the only implicitly mentioned or overlooked deep learning aspects, highlight unmentioned assumptions, and finally introduce methods to address respective immediate weaknesses. In the author’s humble opinion, these prevalent shortcomings can be tied to the fact that the involved steps in the machine learning workflow are frequently decoupled. Success is predominantly measured based on accuracy measures designed for evaluation with static benchmark test sets. Individual machine learning workflow components are assessed in isolation with respect to available data, choice of neural network architecture, and a particular learning algorithm, rather than viewing the machine learning system as a whole in context of a particular application. Correspondingly, in this dissertation, three key challenges have been identified: 1. Choice and flexibility of a neural network architecture. 2. Identification and rejection of unseen unknown data to avoid false predictions. 3. Continual learning without forgetting of already learned information. These latter challenges have already been crucial topics in older literature, alas, seem to require a renaissance in modern deep learning literature. Initially, it may appear that they pose independent research questions, however, the thesis posits that the aspects are intertwined and require a joint perspective in machine learning based systems. In summary, the essential question is thus how to pick a suitable neural network architecture for a specific task, how to recognize which data inputs belong to this context, which ones originate from potential other tasks, and ultimately how to continuously include such identified novel data in neural network training over time without overwriting existing knowledge. Thus, the central emphasis of this dissertation is to build on top of existing deep learning strengths, yet also acknowledge mentioned weaknesses, in an effort to establish a deeper understanding of interdependencies and synergies towards the development of unified solution mechanisms. For this purpose, the main portion of the thesis is in cumulative form. The respective publications can be grouped according to the three challenges outlined above. Correspondingly, chapter 1 is focused on choice and extendability of neural network architectures, analyzed in context of popular image classification tasks. An algorithm to automatically determine neural network layer width is introduced and is first contrasted with static architectures found in the literature. The importance of neural architecture design is then further showcased on a real-world application of defect detection in concrete bridges. Chapter 2 is comprised of the complementary ensuing questions of how to identify unknown concepts and subsequently incorporate them into continual learning. A joint central mechanism to distinguish unseen concepts from what is known in classification tasks, while enabling consecutive training without forgetting or revisiting older classes, is proposed. Once more, the role of the chosen neural network architecture is quantitatively reassessed. Finally, chapter 3 culminates in an overarching view, where developed parts are connected. Here, an extensive survey further serves the purpose to embed the gained insights in the broader literature landscape and emphasizes the importance of a common frame of thought. The ultimately presented approach thus reflects the overall thesis’ contribution to advance neural network based machine learning towards a unified solution that ties together choice of neural architecture with the ability to learn continually and the capability to automatically separate known from unknown data.

scholarly journals Landslide Susceptibility Prediction Modeling Based on Remote Sensing and a Novel Deep Learning Algorithm of a Cascade-Parallel Recurrent Neural Network

Sensors ◽  
2020 ◽  
Vol 20 (6) ◽  
pp. 1576 ◽  
Author(s):  
Li Zhu ◽  
Lianghao Huang ◽  
Linyu Fan ◽  
Jinsong Huang ◽  
Faming Huang ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Remote Sensing ◽  
Deep Learning ◽  
Environmental Factors ◽  
Recurrent Neural Network ◽  
Landslide Susceptibility ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Predictive Rate

Landslide susceptibility prediction (LSP) modeling is an important and challenging problem. Landslide features are generally uncorrelated or nonlinearly correlated, resulting in limited LSP performance when leveraging conventional machine learning models. In this study, a deep-learning-based model using the long short-term memory (LSTM) recurrent neural network and conditional random field (CRF) in cascade-parallel form was proposed for making LSPs based on remote sensing (RS) images and a geographic information system (GIS). The RS images are the main data sources of landslide-related environmental factors, and a GIS is used to analyze, store, and display spatial big data. The cascade-parallel LSTM-CRF consists of frequency ratio values of environmental factors in the input layers, cascade-parallel LSTM for feature extraction in the hidden layers, and cascade-parallel full connection for classification and CRF for landslide/non-landslide state modeling in the output layers. The cascade-parallel form of LSTM can extract features from different layers and merge them into concrete features. The CRF is used to calculate the energy relationship between two grid points, and the extracted features are further smoothed and optimized. As a case study, the cascade-parallel LSTM-CRF was applied to Shicheng County of Jiangxi Province in China. A total of 2709 landslide grid cells were recorded and 2709 non-landslide grid cells were randomly selected from the study area. The results show that, compared with existing main traditional machine learning algorithms, such as multilayer perception, logistic regression, and decision tree, the proposed cascade-parallel LSTM-CRF had a higher landslide prediction rate (positive predictive rate: 72.44%, negative predictive rate: 80%, total predictive rate: 75.67%). In conclusion, the proposed cascade-parallel LSTM-CRF is a novel data-driven deep learning model that overcomes the limitations of traditional machine learning algorithms and achieves promising results for making LSPs.

scholarly journals Analysis of deep learning models for network anomaly detection in Internet of Things

2021 ◽  
pp. 28-37
Author(s):  
Diana Gaifilina ◽  
Igor Kotenko
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Internet Of Things ◽  
Anomaly Detection ◽  
Recurrent Neural Network ◽  
Network Traffic ◽  
Learning Models ◽  
Network Anomaly Detection ◽  
Machine Learning Models

Introduction: The article discusses the problem of choosing deep learning models for detecting anomalies in Internet of Things (IoT) network traffic. This problem is associated with the necessity to analyze a large number of security events in order to identify the abnormal behavior of smart devices. A powerful technology for analyzing such data is machine learning and, in particular, deep learning. Purpose: Development of recommendations for the selection of deep learning models for anomaly detection in IoT network traffic. Results: The main results of the research are comparative analysis of deep learning models, and recommendations on the use of deep learning models for anomaly detection in IoT network traffic. Multilayer perceptron, convolutional neural network, recurrent neural network, long short-term memory, gated recurrent units, and combined convolutional-recurrent neural network were considered the basic deep learning models. Additionally, the authors analyzed the following traditional machine learning models: naive Bayesian classifier, support vector machines, logistic regression, k-nearest neighbors, boosting, and random forest. The following metrics were used as indicators of anomaly detection efficiency: accuracy, precision, recall, and F-measure, as well as the time spent on training the model. The constructed models demonstrated a higher accuracy rate for anomaly detection in large heterogeneous traffic typical for IoT, as compared to conventional machine learning methods. The authors found that with an increase in the number of neural network layers, the completeness of detecting anomalous connections rises. This has a positive effect on the recognition of unknown anomalies, but increases the number of false positives. In some cases, preparing traditional machine learning models takes less time. This is due to the fact that the application of deep learning methods requires more resources and computing power. Practical relevance: The results obtained can be used to build systems for network anomaly detection in Internet of Things traffic.

scholarly journals Cross-situational word learning with multimodal neural networks

2021 ◽  
Author(s):  
Wai Keen Vong ◽  
Brenden M. Lake
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Word Learning ◽  
Network Architecture ◽  
Question Answering ◽  
Cognitive Models ◽  
Learning Approaches ◽  
Neural Network Learning ◽  
Single Epoch

In order to learn the mappings from words to referents, children must integrate co-occurrence information across individually ambiguous pairs of scenes and utterances, a challenge known as cross-situational word learning. In machine learning, recent multimodal neural networks have been shown to learn meaningful visual-linguistic mappings from cross-situational data, as needed to solve problems such as image captioning and visual question answering. These networks are potentially appealing as cognitive models because they can learn from raw visual and linguistic stimuli, something previous cognitive models have not addressed. In this paper, we examine whether recent machine learning approaches can help explain various behavioral phenomena from the psychological literature on cross-situational word learning. We consider two variants of a multimodal neural network architecture, and look at seven different phenomena associated with cross-situational word learning, and word learning more generally. Our results show that these networks can learn word-referent mappings from a single epoch of training, matching the amount of training found in cross-situational word learning experiments. Additionally, these networks capture some, but not all of the phenomena we studied, with all of the failures related to reasoning via mutual exclusivity. These results provide insight into the kinds of phenomena that arise naturally from relatively generic neural network learning algorithms, and which word learning phenomena require additional inductive biases.

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