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  1. Article ; Online: Motor imagery classification using sparse representations: an exploratory study.

    de Menezes, José Antonio Alves / Gomes, Juliana Carneiro / de Carvalho Hazin, Vitor / Dantas, Júlio César Sousa / Rodrigues, Marcelo Cairrão Araújo / Dos Santos, Wellington Pinheiro

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 15585

    Abstract: The non-stationary nature of the EEG signal poses challenges for the classification of motor imagery. sparse representation classification (SRC) appears as an alternative for classification of untrained conditions and, therefore, useful in motor imagery. ...

    Abstract The non-stationary nature of the EEG signal poses challenges for the classification of motor imagery. sparse representation classification (SRC) appears as an alternative for classification of untrained conditions and, therefore, useful in motor imagery. Empirical mode decomposition (EMD) deals with signals of this nature and appears at the rear of the classification, supporting the generation of features. In this work we evaluate the combination of these methods in a multiclass classification problem, comparing them with a conventional method in order to determine if their performance is regular. For comparison with SRC we use multilayer perceptron (MLP). We also evaluated a hybrid approach for classification of sparse representations with MLP (RSMLP). For comparison with EMD we used filtering by frequency bands. Feature selection methods were used to select the most significant ones, specifically Random Forest and Particle Swarm Optimization. Finally, we used data augmentation to get a more voluminous base. Regarding the first dataset, we observed that the classifiers that use sparse representation have results equivalent to each other, but they outperform the conventional MLP model. SRC and SRMLP achieve an average accuracy of [Formula: see text] and [Formula: see text] respectively while the MLP is [Formula: see text], representing a gain between [Formula: see text] and [Formula: see text]. The use of EMD in relation to other feature processing techniques is not superior. However, EMD does not influence negatively, there is an opportunity for improvement. Finally, the use of data augmentation proved to be important to obtain relevant results. In the second dataset, we did not observe the same results. Models based on sparse representation (SRC, SRMLP, etc.) have on average a performance close to other conventional models, but without surpassing them. The best sparse models achieve an average accuracy of [Formula: see text] among the subjects in the base, while other model reach [Formula: see text]. The improvement of self-adaptive mechanisms that respond efficiently to the user's context is a good way to achieve improvements in motor imagery applications. However, other scenarios should be investigated, since the advantage of these methods was not proven in all datasets studied. There is still room for improvement, such as optimizing the dictionary of sparse representation in the context of motor imagery. Investing efforts in synthetically increasing the training base has also proved important to reduce the costs of this group of applications.
    Language English
    Publishing date 2023-09-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-42790-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: COVID-19's influence on cardiac function: a machine learning perspective on ECG analysis.

    Gomes, Juliana Carneiro / de Santana, Maíra Araújo / Masood, Aras Ismael / de Lima, Clarisse Lins / Dos Santos, Wellington Pinheiro

    Medical & biological engineering & computing

    2023  Volume 61, Issue 5, Page(s) 1057–1081

    Abstract: In December 2019, the spread of the SARS-CoV-2 virus to the world gave rise to probably the biggest public health problem in the world: the COVID-19 pandemic. Initially seen only as a disease of the respiratory system, COVID-19 is actually a blood ... ...

    Abstract In December 2019, the spread of the SARS-CoV-2 virus to the world gave rise to probably the biggest public health problem in the world: the COVID-19 pandemic. Initially seen only as a disease of the respiratory system, COVID-19 is actually a blood disease with effects on the respiratory tract. Considering its influence on hematological parameters, how does COVID-19 affect cardiac function? Is it possible to support the clinical diagnosis of COVID-19 from the automatic analysis of electrocardiography? In this work, we sought to investigate how COVID-19 affects cardiac function using a machine learning approach to analyze electrocardiography (ECG) signals. We used a public database of ECG signals expressed as photographs of printed signals, obtained in the context of emergency care. This database has signals associated with abnormal heartbeat, myocardial infarction, history of myocardial infarction, COVID-19, and healthy heartbeat. We propose a system to support the diagnosis of COVID-19 based on hybrid deep architectures composed of pre-trained convolutional neural networks for feature extraction and Random Forests for classification. We investigated the LeNet, ResNet, and VGG16 networks. The best results were obtained with the VGG16 and Random Forest network with 100 trees, with attribute selection using particle swarm optimization. The instance size has been reduced from 4096 to 773 attributes. In the validation step, we obtained an accuracy of 94%, kappa index of 0.91, and sensitivity, specificity, and area under the ROC curve of 100%. This work showed that the influence of COVID-19 on cardiac function is quite considerable: COVID-19 did not present confusion with any heart disease, nor with signs of healthy individuals. It is also possible to build a solution to support the clinical diagnosis of COVID-19 in the context of emergency care from a non-invasive and technologically scalable solution, based on hybrid deep learning architectures.
    MeSH term(s) Humans ; COVID-19/diagnosis ; SARS-CoV-2 ; Pandemics ; Machine Learning ; Electrocardiography ; Myocardial Infarction/diagnosis
    Language English
    Publishing date 2023-01-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 282327-5
    ISSN 1741-0444 ; 0025-696X ; 0140-0118
    ISSN (online) 1741-0444
    ISSN 0025-696X ; 0140-0118
    DOI 10.1007/s11517-023-02773-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Classification of Parkinson's disease motor phenotype: a machine learning approach.

    Shirahige, Lívia / Leimig, Brenda / Baltar, Adriana / Bezerra, Amanda / de Brito, Caio Vinícius Ferreira / do Nascimento, Yasmin Samara Oliveira / Gomes, Juliana Carneiro / Teo, Wei-Peng / Dos Santos, Wellignton Pinheiro / Cairrão, Marcelo / Fonseca, André / Monte-Silva, Kátia

    Journal of neural transmission (Vienna, Austria : 1996)

    2022  Volume 129, Issue 12, Page(s) 1447–1461

    Abstract: To assess the cortical activity in people with Parkinson's disease (PwP) with different motor phenotype (tremor-dominant-TD and postural instability and gait difficulty-PIGD) and to compare with controls. Twenty-four PwP (during OFF and ON medication) ... ...

    Abstract To assess the cortical activity in people with Parkinson's disease (PwP) with different motor phenotype (tremor-dominant-TD and postural instability and gait difficulty-PIGD) and to compare with controls. Twenty-four PwP (during OFF and ON medication) and twelve age-/sex-/handedness-matched healthy controls underwent electrophysiological assessment of spectral ratio analysis through electroencephalography (EEG) at resting state and during the hand movement. We performed a machine learning method with 35 attributes extracted from EEG. To verify the efficiency of the proposed phenotype-based EEG classification the random forest and random tree were tested (performed 30 times, using a tenfolds cross validation in Weka environment). The analyses based on phenotypes indicated a slowing down of cortical activity during OFF medication state in PwP. PD with TD phenotype presented this characteristic at resting and the individuals with PIGD presented during the hand movement. During the ON state, there is no difference between phenotypes at resting nor during the hand movement. PD phenotypes may influence spectral activity measured by EEG. Random forest machine learning provides a slightly more accurate, sensible and specific approach to distinguish different PD phenotypes. The phenotype of PD might be a clinical characteristic that could influence cortical activity.
    MeSH term(s) Humans ; Parkinson Disease/drug therapy ; Gait Disorders, Neurologic/drug therapy ; Tremor ; Phenotype ; Machine Learning ; Postural Balance/physiology
    Language English
    Publishing date 2022-11-06
    Publishing country Austria
    Document type Journal Article
    ZDB-ID 184163-4
    ISSN 1435-1463 ; 0300-9564
    ISSN (online) 1435-1463
    ISSN 0300-9564
    DOI 10.1007/s00702-022-02552-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Covid-19 rapid test by combining a Random Forest-based web system and blood tests.

    Barbosa, Valter Augusto de Freitas / Gomes, Juliana Carneiro / de Santana, Maíra Araújo / de Lima, Clarisse Lins / Calado, Raquel Bezerra / Bertoldo Júnior, Cláudio Roberto / Albuquerque, Jeniffer Emidio de Almeida / de Souza, Rodrigo Gomes / de Araújo, Ricardo Juarez Escorel / Mattos Júnior, Luiz Alberto Reis / de Souza, Ricardo Emmanuel / Dos Santos, Wellington Pinheiro

    Journal of biomolecular structure & dynamics

    2021  Volume 40, Issue 22, Page(s) 11948–11967

    Abstract: The disease caused by the new type of coronavirus, Covid-19, has posed major public health challenges for many countries. With its rapid spread, since the beginning of the outbreak in December 2019, the disease transmitted by SARS-CoV-2 has already ... ...

    Abstract The disease caused by the new type of coronavirus, Covid-19, has posed major public health challenges for many countries. With its rapid spread, since the beginning of the outbreak in December 2019, the disease transmitted by SARS-CoV-2 has already caused over 2 million deaths to date. In this work, we propose a web solution, called Heg.IA, to optimize the diagnosis of Covid-19 through the use of artificial intelligence. Our system aims to support decision-making regarding to diagnosis of Covid-19 and to the indication of hospitalization on regular ward, semi-ICU or ICU based on decision a Random Forest architecture with 90 trees. The main idea is that healthcare professionals can insert 41 hematological parameters from common blood tests and arterial gasometry into the system. Then, Heg.IA will provide a diagnostic report. The system reached good results for both Covid-19 diagnosis and to recommend hospitalization. For the first scenario we found average results of accuracy of 92.891%±0.851, kappa index of 0.858 ± 0.017, sensitivity of 0.936 ± 0.011, precision of 0.923 ± 0.011, specificity of 0.921 ± 0.012 and area under ROC of 0.984 ± 0.003. As for the indication of hospitalization, we achieved excellent performance of accuracies above 99% and more than 0.99 for the other metrics in all situations. By using a computationally simple method, based on the classical decision trees, we were able to achieve high diagnosis performance. Heg.IA system may be a way to overcome the testing unavailability in the context of Covid-19.Communicated by Ramaswamy H. Sarma.
    MeSH term(s) Humans ; COVID-19/diagnosis ; SARS-CoV-2 ; COVID-19 Testing ; Random Forest ; Artificial Intelligence ; Hematologic Tests
    Language English
    Publishing date 2021-08-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2021.1966509
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Covid-19 diagnosis by combining RT-PCR and pseudo-convolutional machines to characterize virus sequences.

    Gomes, Juliana Carneiro / Masood, Aras Ismael / Silva, Leandro Honorato de S / da Cruz Ferreira, Janderson Romário B / Freire Júnior, Agostinho Antônio / Rocha, Allana Laís Dos Santos / de Oliveira, Letícia Castro Portela / da Silva, Nathália Regina Cauás / Fernandes, Bruno José Torres / Dos Santos, Wellington Pinheiro

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 11545

    Abstract: The Covid-19 pandemic, a disease transmitted by the SARS-CoV-2 virus, has already caused the infection of more than 120 million people, of which 70 million have been recovered, while 3 million people have died. The high speed of infection has led to the ... ...

    Abstract The Covid-19 pandemic, a disease transmitted by the SARS-CoV-2 virus, has already caused the infection of more than 120 million people, of which 70 million have been recovered, while 3 million people have died. The high speed of infection has led to the rapid depletion of public health resources in most countries. RT-PCR is Covid-19's reference diagnostic method. In this work we propose a new technique for representing DNA sequences: they are divided into smaller sequences with overlap in a pseudo-convolutional approach and represented by co-occurrence matrices. This technique eliminates multiple sequence alignment. Through the proposed method, it is possible to identify virus sequences from a large database: 347,363 virus DNA sequences from 24 virus families and SARS-CoV-2. When comparing SARS-CoV-2 with virus families with similar symptoms, we obtained [Formula: see text] for sensitivity and [Formula: see text] for specificity with MLP classifier and 30% overlap. When SARS-CoV-2 is compared to other coronaviruses and healthy human DNA sequences, we obtained [Formula: see text] for sensitivity and [Formula: see text] for specificity with MLP and 50% overlap. Therefore, the molecular diagnosis of Covid-19 can be optimized by combining RT-PCR and our pseudo-convolutional method to identify DNA sequences for SARS-CoV-2 with greater specificity and sensitivity.
    MeSH term(s) COVID-19 Nucleic Acid Testing/methods ; Computational Biology/methods ; DNA, Viral ; Humans ; Machine Learning ; Reverse Transcriptase Polymerase Chain Reaction/methods ; SARS-CoV-2/genetics ; Sensitivity and Specificity ; Support Vector Machine ; Viruses/genetics
    Chemical Substances DNA, Viral
    Language English
    Publishing date 2021-06-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-90766-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Covid-19 Dynamic Monitoring and Real-Time Spatio-Temporal Forecasting.

    da Silva, Cecilia Cordeiro / de Lima, Clarisse Lins / da Silva, Ana Clara Gomes / Silva, Eduardo Luiz / Marques, Gabriel Souza / de Araújo, Lucas Job Brito / Albuquerque Júnior, Luiz Antônio / de Souza, Samuel Barbosa Jatobá / de Santana, Maíra Araújo / Gomes, Juliana Carneiro / Barbosa, Valter Augusto de Freitas / Musah, Anwar / Kostkova, Patty / Dos Santos, Wellington Pinheiro / da Silva Filho, Abel Guilhermino

    Frontiers in public health

    2021  Volume 9, Page(s) 641253

    Abstract: Background: ...

    Abstract Background:
    MeSH term(s) Brazil/epidemiology ; COVID-19/epidemiology ; Epidemiological Monitoring ; Forecasting ; Humans ; Linear Models ; Neural Networks, Computer ; Spatio-Temporal Analysis ; Support Vector Machine
    Language English
    Publishing date 2021-04-08
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2711781-9
    ISSN 2296-2565 ; 2296-2565
    ISSN (online) 2296-2565
    ISSN 2296-2565
    DOI 10.3389/fpubh.2021.641253
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Optimizing the molecular diagnosis of Covid-19 by combining RT-PCR and a pseudo-convolutional machine learning approach to characterize virus DNA sequences

    Gomes, Juliana Carneiro / de S. Silva, Leandro Honorato / Ferreira, Janderson / Júnior, Agostinho A. F. / dos Santos Rocha, Allana Lais / Castro, Letícia / da Silva, Nathália R. C. / Fernandes, Bruno J. T. / dos Santos, Wellington Pinheiro

    bioRxiv

    Abstract: The proliferation of the SARS-Cov-2 virus to the whole world caused more than 250,000 deaths worldwide and over 4 million confirmed cases. The severity of Covid-19, the exponential rate at which the virus proliferates, and the rapid exhaustion of the ... ...

    Abstract The proliferation of the SARS-Cov-2 virus to the whole world caused more than 250,000 deaths worldwide and over 4 million confirmed cases. The severity of Covid-19, the exponential rate at which the virus proliferates, and the rapid exhaustion of the public health resources are critical factors. The RT-PCR with virus DNA identification is still the benchmark Covid-19 diagnosis method. In this work we propose a new technique for representing DNA sequences: they are divided into smaller sequences with overlap in a pseudo-convolutional approach, and represented by co-occurrence matrices. This technique analyzes the DNA sequences obtained by the RT-PCR method, eliminating sequence alignment. Through the proposed method, it is possible to identify virus sequences from a large database: 347,363 virus DNA sequences from 24 virus families and SARS-Cov-2. Experiments with all 24 virus families and SARS-Cov-2 (multi-class scenario) resulted 0.822222 ± 0.05613 for sensitivity and 0.99974 ± 0.00001 for specificity using Random Forests with 100 trees and 30% overlap. When we compared SARS-Cov-2 with similar-symptoms virus families, we got 0.97059 ± 0.03387 for sensitivity, and 0.99187 ± 0.00046 for specificity with MLP classifier and 30% overlap. In the real test scenario, in which SARS-Cov-2 is compared to Coronaviridae and healthy human DNA sequences, we got 0.98824 ± 001198 for sensitivity and 0.99860 ± 0.00020 for specificity with MLP and 50% overlap. Therefore, the molecular diagnosis of Covid-19 can be optimized by combining RT-PCR and our pseudo-convolutional method to identify SARS-Cov-2 DNA sequences faster with higher specificity and sensitivity.
    Keywords covid19
    Publisher BioRxiv
    Document type Article ; Online
    DOI 10.1101/2020.06.02.129775
    Database COVID19

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  8. Article ; Online: Optimizing the molecular diagnosis of Covid-19 by combining RT-PCR and a pseudo-convolutional machine learning approach to characterize virus DNA sequences

    Gomes, Juliana Carneiro / Masood, Aras Ismael / de S. Silva, Leandro Honorato / Ferreira, Janderson / Júnior, Agostinho A. F. / dos Santos Rocha, Allana Lais / Castro, Letícia / da Silva, Nathália R. C. / Fernandes, Bruno J. T. / dos Santos, Wellington Pinheiro

    bioRxiv

    Abstract: The proliferation of the SARS-Cov-2 virus to the whole world caused more than 250,000 deaths worldwide and over 4 million confirmed cases. The severity of Covid-19, the exponential rate at which the virus proliferates, and the rapid exhaustion of the ... ...

    Abstract The proliferation of the SARS-Cov-2 virus to the whole world caused more than 250,000 deaths worldwide and over 4 million confirmed cases. The severity of Covid-19, the exponential rate at which the virus proliferates, and the rapid exhaustion of the public health resources are critical factors. The RT-PCR with virus DNA identification is still the benchmark Covid-19 diagnosis method. In this work we propose a new technique for representing DNA sequences: they are divided into smaller sequences with overlap in a pseudo-convolutional approach, and represented by co-occurrence matrices. This technique analyzes the DNA sequences obtained by the RT-PCR method, eliminating sequence alignment. Through the proposed method, it is possible to identify virus sequences from a large database: 347,363 virus DNA sequences from 24 virus families and SARS-Cov-2. Experiments with all 24 virus families and SARS-Cov-2 (multi-class scenario) resulted 0.822222 ± 0.05613 for sensitivity and 0.99974 ± 0.00001 for specificity using Random Forests with 100 trees and 30% overlap. When we compared SARS-Cov-2 with similar-symptoms virus families, we got 0.97059 ± 0.03387 for sensitivity, and 0.99187 ± 0.00046 for specificity with MLP classifier and 30% overlap. In the real test scenario, in which SARS-Cov-2 is compared to Coronaviridae and healthy human DNA sequences, we got 0.98824 ± 001198 for sensitivity and 0.99860 ± 0.00020 for specificity with MLP and 50% overlap. Therefore, the molecular diagnosis of Covid-19 can be optimized by combining RT-PCR and our pseudo-convolutional method to identify SARS-Cov-2 DNA sequences faster with higher specificity and sensitivity.
    Keywords covid19
    Publisher BioRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.06.02.129775
    Database COVID19

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  9. Article ; Online: Heg.IA: An intelligent system to support diagnosis of Covid-19 based on blood tests

    Barbosa, Valter Augusto de Freitas / Gomes, Juliana Carneiro / de Santana, Maira Araujo / Albuquerque, Jeniffer Emidio de Almeida / de Souza, Rodrigo Gomes / de Souza, Ricardo Emmanuel / dos Santos, Wellington Pinheiro

    medRxiv

    Abstract: A new kind of coronavirus, the SARS-Cov2, started the biggest pandemic of the century. It has already killed more than 250,000 people. Because of this, it is necessary quick and precise diagnosis test. The current gold standard is the RT-PCR with DNA ... ...

    Abstract A new kind of coronavirus, the SARS-Cov2, started the biggest pandemic of the century. It has already killed more than 250,000 people. Because of this, it is necessary quick and precise diagnosis test. The current gold standard is the RT-PCR with DNA sequencing and identification, but its results takes too long to be available. Tests base on IgM/IgG antibodies have been used, but their sensitivity and specificity may be very low. Many studies have been demonstrating the Covid-19 impact in hematological parameters. This work proposes an intelligent system to support Covid-19 diagnosis based on blood testing. We tested several machine learning methods, and we achieved high classification performance: 95.159% +- 0.693 of overall accuracy, kappa index of 0.903 +- 0.014, sensitivity of 0.968 +- 0.007, precision of 0.938 +- 0.010 and specificity of 0.936 +- 0.011. These results were achieved using classical and low computational cost classifiers, with Bayes Network being the best of them. In addition, only 24 blood tests were needed. This points to the possibility of a new rapid test with low cost. The desktop version of the system is fully functional and available for free use.
    Keywords covid19
    Language English
    Publishing date 2020-05-18
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.05.14.20102533
    Database COVID19

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  10. Article ; Online: IKONOS: An intelligent tool to support diagnosis of Covid-19 by texture analysis of x-ray images

    Gomes, Juliana Carneiro / Barbosa, Valter Augusto de Freitas / de Santana, Maira Araujo / Bandeira, Jonathan / Valenca, Meuser Jorge Silva / de Souza, Ricardo Emmanuel / Ismael, Aras Masood / dos Santos, Wellington Pinheiro

    medRxiv

    Abstract: In late 2019, the SARS-Cov-2 spread worldwide. The virus has high rates of proliferation and causes severe respiratory symptoms, such as pneumonia. There is still no specific treatment and diagnosis for the disease. The standard diagnostic method for ... ...

    Abstract In late 2019, the SARS-Cov-2 spread worldwide. The virus has high rates of proliferation and causes severe respiratory symptoms, such as pneumonia. There is still no specific treatment and diagnosis for the disease. The standard diagnostic method for pneumonia is chest X-ray image. There are many advantages to using Covid-19 diagnostic X-rays: low cost, fast and widely available. We propose an intelligent system to support diagnosis by X-ray images.We tested Haralick and Zernike moments for feature extraction. Experiments with classic classifiers were done. Support vector machines stood out, reaching an average accuracy of 89:78%, average recall and sensitivity of 0:8979, and average precision and specificity of 0:8985 and 0:9963 respectively. The system is able to differentiate Covid-19 from viral and bacterial pneumonia, with low computational cost.
    Keywords covid19
    Language English
    Publishing date 2020-05-09
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.05.05.20092346
    Database COVID19

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