Alignment-Free Z-Curve Genomic Cepstral Coefficients and Machine Learning for Classification of Viruses

2018 ◽  
pp. 290-301 ◽  
Author(s):  
Emmanuel Adetiba ◽  
Oludayo O. Olugbara ◽  
Tunmike B. Taiwo ◽  
Marion O. Adebiyi ◽  
Joke A. Badejo ◽  
...  
Keyword(s):  
Machine Learning ◽  
Alignment Free ◽  
Cepstral Coefficients ◽  
Z Curve

scholarly journals Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study

2020 ◽  
Author(s):  
Gurjit S. Randhawa ◽  
Maximillian P.M. Soltysiak ◽  
Hadi El Roz ◽  
Camila P.E. de Souza ◽  
Kathleen A. Hill ◽  
...  
Keyword(s):  
Machine Learning ◽  
Death Rate ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Rank Correlation ◽  
Taxonomic Classification ◽  
Supervised Machine Learning ◽  
Biological Knowledge ◽  
Alignment Free

AbstractAs of February 20, 2020, the 2019 novel coronavirus (renamed to COVID-19) spread to 30 countries with 2130 deaths and more than 75500 confirmed cases. COVID-19 is being compared to the infamous SARS coronavirus, which resulted, between November 2002 and July 2003, in 8098 confirmed cases worldwide with a 9.6% death rate and 774 deaths. Though COVID-19 has a death rate of 2.8% as of 20 February, the 75752 confirmed cases in a few weeks (December 8, 2019 to February 20, 2020) are alarming, with cases likely being under-reported given the comparatively longer incubation period. Such outbreaks demand elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic planning, containment, and treatment. This paper identifies an intrinsic COVID-19 genomic signature and uses it together with a machine learning-based alignment-free approach for an ultra-fast, scalable, and highly accurate classification of whole COVID-19 genomes. The proposed method combines supervised machine learning with digital signal processing for genome analyses, augmented by a decision tree approach to the machine learning component, and a Spearman’s rank correlation coefficient analysis for result validation. These tools are used to analyze a large dataset of over 5000 unique viral genomic sequences, totalling 61.8 million bp. Our results support a hypothesis of a bat origin and classify COVID-19 as Sarbecovirus, within Betacoronavirus. Our method achieves high levels of classification accuracy and discovers the most relevant relationships among over 5,000 viral genomes within a few minutes, ab initio, using raw DNA sequence data alone, and without any specialized biological knowledge, training, gene or genome annotations. This suggests that, for novel viral and pathogen genome sequences, this alignment-free whole-genome machine-learning approach can provide a reliable real-time option for taxonomic classification.

Machine Learning Classification of Low-grade and High-grade Chondrosarcomas Based on MRI-based Texture Analysis

2019 ◽  
Author(s):  
S. Gitto ◽  
D. Albano ◽  
V. Chianca ◽  
R. Cuocolo ◽  
L. Ugga ◽  
...  
Keyword(s):  
Machine Learning ◽  
Texture Analysis ◽  
Low Grade ◽  
High Grade ◽  
Machine Learning Classification

A Brief Survey on Text Classification Using Various Machine Learning Techniques

2018 ◽  
Vol 8 (1) ◽  
pp. 14
Author(s):  
Padmavathi .S ◽  
M. Chidambaram
Keyword(s):  
Machine Learning ◽  
Text Classification ◽  
Fixed Number ◽  
Machine Learning Techniques ◽  
Online Information ◽  
Rule Based ◽  
Learning Techniques ◽  
Machine Learning Approach ◽  
Rule Based Approach

Text classification has grown into more significant in managing and organizing the text data due to tremendous growth of online information. It does classification of documents in to fixed number of predefined categories. Rule based approach and Machine learning approach are the two ways of text classification. In rule based approach, classification of documents is done based on manually defined rules. In Machine learning based approach, classification rules or classifier are defined automatically using example documents. It has higher recall and quick process. This paper shows an investigation on text classification utilizing different machine learning techniques.

Classification of Observations through Combination of the Dimension Reduction and the Cluster Analysis

2017 ◽  
Vol 7 (8) ◽  
pp. 30
Author(s):  
Hyeuk Kim
Keyword(s):  
Machine Learning ◽  
Principal Component Analysis ◽  
Cluster Analysis ◽  
Unsupervised Learning ◽  
Principal Component ◽  
Component Analysis ◽  
Baseball Players ◽  
Partitioning Around Medoids ◽  
Different Characteristics

Unsupervised learning in machine learning divides data into several groups. The observations in the same group have similar characteristics and the observations in the different groups have the different characteristics. In the paper, we classify data by partitioning around medoids which have some advantages over the k-means clustering. We apply it to baseball players in Korea Baseball League. We also apply the principal component analysis to data and draw the graph using two components for axis. We interpret the meaning of the clustering graphically through the procedure. The combination of the partitioning around medoids and the principal component analysis can be used to any other data and the approach makes us to figure out the characteristics easily.

Learning and control

2018 ◽  
Author(s):  
Ivan Herreros
Keyword(s):  
Machine Learning ◽  
Reinforcement Learning ◽  
Brain Function ◽  
Control Strategies ◽  
Learning Problems ◽  
Animal Learning ◽  
Feed Forward Control ◽  
Machine Learning Applications ◽  
And Control

This chapter discusses basic concepts from control theory and machine learning to facilitate a formal understanding of animal learning and motor control. It first distinguishes between feedback and feed-forward control strategies, and later introduces the classification of machine learning applications into supervised, unsupervised, and reinforcement learning problems. Next, it links these concepts with their counterparts in the domain of the psychology of animal learning, highlighting the analogies between supervised learning and classical conditioning, reinforcement learning and operant conditioning, and between unsupervised and perceptual learning. Additionally, it interprets innate and acquired actions from the standpoint of feedback vs anticipatory and adaptive control. Finally, it argues how this framework of translating knowledge between formal and biological disciplines can serve us to not only structure and advance our understanding of brain function but also enrich engineering solutions at the level of robot learning and control with insights coming from biology.

Multiclass machine learning classification of functional brain images for Parkinson's disease stage prediction

2020 ◽  
Vol 13 (5) ◽  
pp. 508-523 ◽  
Author(s):  
Guan‐Hua Huang ◽  
Chih‐Hsuan Lin ◽  
Yu‐Ren Cai ◽  
Tai‐Been Chen ◽  
Shih‐Yen Hsu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Disease Stage ◽  
Brain Images ◽  
Functional Brain ◽  
Machine Learning Classification

scholarly journals Classification of Brainwaves for Sleep Stages by High-Dimensional FFT Features from EEG Signals

2020 ◽  
Vol 10 (5) ◽  
pp. 1797 ◽  
Author(s):  
Mera Kartika Delimayanti ◽  
Bedy Purnama ◽  
Ngoc Giang Nguyen ◽  
Mohammad Reza Faisal ◽  
Kunti Robiatul Mahmudah ◽  
...  
Keyword(s):  
Machine Learning ◽  
Sleep Stage ◽  
Machine Learning Algorithms ◽  
High Dimensional ◽  
Sleep Stages ◽  
Eeg Signals ◽  
Stage Classification ◽  
Sleep Stage Classification ◽  
Low Dimensional

Manual classification of sleep stage is a time-consuming but necessary step in the diagnosis and treatment of sleep disorders, and its automation has been an area of active study. The previous works have shown that low dimensional fast Fourier transform (FFT) features and many machine learning algorithms have been applied. In this paper, we demonstrate utilization of features extracted from EEG signals via FFT to improve the performance of automated sleep stage classification through machine learning methods. Unlike previous works using FFT, we incorporated thousands of FFT features in order to classify the sleep stages into 2–6 classes. Using the expanded version of Sleep-EDF dataset with 61 recordings, our method outperformed other state-of-the art methods. This result indicates that high dimensional FFT features in combination with a simple feature selection is effective for the improvement of automated sleep stage classification.

scholarly journals Machine learning algorithm improved automated droplet classification of ddPCR for detection of BRAF V600E in paraffin-embedded samples

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gabriel A. Colozza-Gama ◽  
Fabiano Callegari ◽  
Nikola Bešič ◽  
Ana C. de J. Paviza ◽  
Janete M. Cerutti
Keyword(s):  
Machine Learning ◽  
Sanger Sequencing ◽  
Learning Algorithm ◽  
Absolute Quantification ◽  
Braf V600e Mutation ◽  
Braf V600e ◽  
Driver Genes ◽  
Quantitative Classification ◽  
Cancer Driver

AbstractSomatic mutations in cancer driver genes can help diagnosis, prognosis and treatment decisions. Formalin-fixed paraffin-embedded (FFPE) specimen is the main source of DNA for somatic mutation detection. To overcome constraints of DNA isolated from FFPE, we compared pyrosequencing and ddPCR analysis for absolute quantification of BRAF V600E mutation in the DNA extracted from FFPE specimens and compared the results to the qualitative detection information obtained by Sanger Sequencing. Sanger sequencing was able to detect BRAF V600E mutation only when it was present in more than 15% total alleles. Although the sensitivity of ddPCR is higher than that observed for Sanger, it was less consistent than pyrosequencing, likely due to droplet classification bias of FFPE-derived DNA. To address the droplet allocation bias in ddPCR analysis, we have compared different algorithms for automated droplet classification and next correlated these findings with those obtained from pyrosequencing. By examining the addition of non-classifiable droplets (rain) in ddPCR, it was possible to obtain better qualitative classification of droplets and better quantitative classification compared to no rain droplets, when considering pyrosequencing results. Notable, only the Machine learning k-NN algorithm was able to automatically classify the samples, surpassing manual classification based on no-template controls, which shows promise in clinical practice.

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