Machine learning approaches for ELNES/XANES

Microscopy ◽  
2020 ◽  
Vol 69 (2) ◽  
pp. 92-109 ◽  
Author(s):  
Teruyasu Mizoguchi ◽  
Shin Kiyohara
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Decision Tree ◽  
Hierarchical Clustering ◽  
Data Augmentation ◽  
Xanes Spectrum ◽  
Feedforward Neural Network ◽  
Material Structure ◽  
Learning Approaches ◽  
Edge Structure

Abstract Materials characterization is indispensable for materials development. In particular, spectroscopy provides atomic configuration, chemical bonding and vibrational information, which are crucial for understanding the mechanism underlying the functions of a material. Despite its importance, the interpretation of spectra using human-driven methods, such as manual comparison of experimental spectra with reference/simulated spectra, is becoming difficult owing to the rapid increase in experimental spectral data. To overcome the limitations of such methods, we develop new data-driven approaches based on machine learning. Specifically, we use hierarchical clustering, a decision tree and a feedforward neural network to investigate the electron energy loss near edge structures (ELNES) spectrum, which is identical to the X-ray absorption near edge structure (XANES) spectrum. Hierarchical clustering and the decision tree are used to interpret and predict ELNES/XANES, while the feedforward neural network is used to obtain hidden information about the material structure and properties from the spectra. Further, we construct a prediction model that is robust against noise by data augmentation. Finally, we apply our method to noisy spectra and predict six properties accurately. In summary, the proposed approaches can pave the way for fast and accurate spectrum interpretation/prediction as well as local measurement of material functions.

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%.

SCONES: Self-Consistent Neural Network for Protein Stability Prediction Upon Mutation

2021 ◽  
Author(s):  
Yashas Samaga B L ◽  
Shampa Raghunathan ◽  
U. Deva Priyakumar
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Protein Stability ◽  
Data Augmentation ◽  
Stability Prediction ◽  
Structural Environment ◽  
Self Consistent ◽  
The Difference ◽  
Protein Sequence Space ◽  
New Machine

<div>Engineering proteins to have desired properties by mutating amino acids at specific sites is commonplace. Such engineered proteins must be stable to function. Experimental methods used to determine stability at throughputs required to scan the protein sequence space thoroughly are laborious. To this end, many machine learning based methods have been developed to predict thermodynamic stability changes upon mutation. These methods have been evaluated for symmetric consistency by testing with hypothetical reverse mutations. In this work, we propose transitive data augmentation, evaluating transitive consistency, and a new machine learning based method, first of its kind, that incorporates both symmetric and transitive properties into the architecture. Our method, called SCONES, is an interpretable neural network that estimates a residue's contributions towards protein stability dG in its local structural environment. The difference between independently predicted contributions of the reference and mutant residues in a missense mutation is reported as dG. We show that this self-consistent machine learning architecture is immune to many common biases in datasets, relies less on data than existing methods, and is robust to overfitting.</div><div><br></div>

scholarly journals Applying of machine learning in the construction of a voice-controlled interface on the example of a music player

2019 ◽  
Vol 13 ◽  
pp. 302-309
Author(s):  
Jakub Basiakowski
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Convolutional Neural Network ◽  
Feedforward Neural Network ◽  
Hidden Layer ◽  
Music Player ◽  
The Impact

The following paper presents the results of research on the impact of machine learning in the construction of a voice-controlled interface. Two different models were used for the analysys: a feedforward neural network containing one hidden layer and a more complicated convolutional neural network. What is more, a comparison of the applied models was presented. This comparison was performed in terms of quality and the course of training.

scholarly journals Near-Optimal Sparse Neural Trees for Supervised Learning

2021 ◽  
Author(s):  
Tanujit Chakraborty
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Decision Tree ◽  
Classification Tree ◽  
Mathematical Formulation ◽  
Machine Learning Algorithms ◽  
Optimal Decision ◽  
Feed Forward ◽  
Feed Forward Network ◽  
Tree Algorithms

Decision tree algorithms have been among the most popular algorithms for interpretable (transparent) machine learning since the early 1980s. On the other hand, deep learning methods have boosted the capacity of machine learning algorithms and are now being used for non-trivial applications in various applied domains. But training a fully-connected deep feed-forward network by gradient-descent backpropagation is slow and requires arbitrary choices regarding the number of hidden units and layers. In this paper, we propose near-optimal neural regression trees, intending to make it much faster than deep feed-forward networks and for which it is not essential to specify the number of hidden units in the hidden layers of the neural network in advance. The key idea is to construct a decision tree and then simulate the decision tree with a neural network. This work aims to build a mathematical formulation of neural trees and gain the complementary benefits of both sparse optimal decision trees and neural trees. We propose near-optimal sparse neural trees (NSNT) that is shown to be asymptotically consistent and robust in nature. Additionally, the proposed NSNT model obtain a fast rate of convergence which is near-optimal up to some logarithmic factor. We comprehensively benchmark the proposed method on a sample of 80 datasets (40 classification datasets and 40 regression datasets) from the UCI machine learning repository. We establish that the proposed method is likely to outperform the current state-of-the-art methods (random forest, XGBoost, optimal classification tree, and near-optimal nonlinear trees) for the majority of the datasets.

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.

Tagging terms in text

Terminology ◽  
2022 ◽  
Author(s):  
Ayla Rigouts Terryn ◽  
Véronique Hoste ◽  
Els Lefever
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Language Processing ◽  
Conditional Random Fields ◽  
Traditional Approach ◽  
Learning Approaches ◽  
Term Extraction ◽  
The Neural Network ◽  
Predicted Probability ◽  
Automatic Term Extraction

Abstract As with many tasks in natural language processing, automatic term extraction (ATE) is increasingly approached as a machine learning problem. So far, most machine learning approaches to ATE broadly follow the traditional hybrid methodology, by first extracting a list of unique candidate terms, and classifying these candidates based on the predicted probability that they are valid terms. However, with the rise of neural networks and word embeddings, the next development in ATE might be towards sequential approaches, i.e., classifying each occurrence of each token within its original context. To test the validity of such approaches for ATE, two sequential methodologies were developed, evaluated, and compared: one feature-based conditional random fields classifier and one embedding-based recurrent neural network. An additional comparison was added with a machine learning interpretation of the traditional approach. All systems were trained and evaluated on identical data in multiple languages and domains to identify their respective strengths and weaknesses. The sequential methodologies were proven to be valid approaches to ATE, and the neural network even outperformed the more traditional approach. Interestingly, a combination of multiple approaches can outperform all of them separately, showing new ways to push the state-of-the-art in ATE.

Analysis of Kinase Inhibitors and Druggability of Kinase-Targets Using Machine Learning Techniques

2012 ◽  
pp. 155-165
Author(s):  
S. Prasanthi ◽  
S.Durga Bhavani ◽  
T. Sobha Rani ◽  
Raju S. Bapi
Keyword(s):  
Machine Learning ◽  
Decision Tree ◽  
Kinase Inhibitors ◽  
Kinase Inhibitor ◽  
Classification Problem ◽  
Machine Learning Techniques ◽  
Learning Approaches ◽  
Decision Tree Classifier ◽  
Data Set ◽  
Learning Techniques

Vast majority of successful drugs or inhibitors achieve their activity by binding to, and modifying the activity of a protein leading to the concept of druggability. A target protein is druggable if it has the potential to bind the drug-like molecules. Hence kinase inhibitors need to be studied to understand the specificity of a kinase inhibitor in choosing a particular kinase target. In this paper we focus on human kinase drug target sequences since kinases are known to be potential drug targets. Also we do a preliminary analysis of kinase inhibitors in order to study the problem in the protein-ligand space in future. The identification of druggable kinases is treated as a classification problem in which druggable kinases are taken as positive data set and non-druggable kinases are chosen as negative data set. The classification problem is addressed using machine learning techniques like support vector machine (SVM) and decision tree (DT) and using sequence-specific features. One of the challenges of this classification problem is due to the unbalanced data with only 48 druggable kinases available against 509 non-drugggable kinases present at Uniprot. The accuracy of the decision tree classifier obtained is 57.65 which is not satisfactory. A two-tier architecture of decision trees is carefully designed such that recognition on the non-druggable dataset also gets improved. Thus the overall model is shown to achieve a final performance accuracy of 88.37. To the best of our knowledge, kinase druggability prediction using machine learning approaches has not been reported in literature.

scholarly journals A Machine Learning View on Momentum and Reversal Trading

Algorithms ◽  
2018 ◽  
Vol 11 (11) ◽  
pp. 170 ◽  
Author(s):  
Zhixi Li ◽  
Vincent Tam
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Stock Market ◽  
Short Term Memory ◽  
Predictive Ability ◽  
Trading Strategies ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Learning Approaches ◽  
Learning Techniques

Momentum and reversal effects are important phenomena in stock markets. In academia, relevant studies have been conducted for years. Researchers have attempted to analyze these phenomena using statistical methods and to give some plausible explanations. However, those explanations are sometimes unconvincing. Furthermore, it is very difficult to transfer the findings of these studies to real-world investment trading strategies due to the lack of predictive ability. This paper represents the first attempt to adopt machine learning techniques for investigating the momentum and reversal effects occurring in any stock market. In the study, various machine learning techniques, including the Decision Tree (DT), Support Vector Machine (SVM), Multilayer Perceptron Neural Network (MLP), and Long Short-Term Memory Neural Network (LSTM) were explored and compared carefully. Several models built on these machine learning approaches were used to predict the momentum or reversal effect on the stock market of mainland China, thus allowing investors to build corresponding trading strategies. The experimental results demonstrated that these machine learning approaches, especially the SVM, are beneficial for capturing the relevant momentum and reversal effects, and possibly building profitable trading strategies. Moreover, we propose the corresponding trading strategies in terms of market states to acquire the best investment returns.

scholarly journals From Characters to Time Intervals: New Paradigms for Evaluation and Neural Parsing of Time Normalizations

2018 ◽  
Vol 6 ◽  
pp. 343-356 ◽  
Author(s):  
Egoitz Laparra ◽  
Dongfang Xu ◽  
Steven Bethard
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Comparative Analysis ◽  
State Of The Art ◽  
Learning Approaches ◽  
Semantic Parsing ◽  
Time Intervals ◽  
Semantic Composition ◽  
Previous State ◽  
New Scoring

This paper presents the first model for time normalization trained on the SCATE corpus. In the SCATE schema, time expressions are annotated as a semantic composition of time entities. This novel schema favors machine learning approaches, as it can be viewed as a semantic parsing task. In this work, we propose a character level multi-output neural network that outperforms previous state-of-the-art built on the TimeML schema. To compare predictions of systems that follow both SCATE and TimeML, we present a new scoring metric for time intervals. We also apply this new metric to carry out a comparative analysis of the annotations of both schemes in the same corpus.

Sign in / Sign up

Export Citation Format

Share Document