LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 49

Search options

  1. Article ; Online: Reduced Deep Convolutional Activation Features (R-DeCAF) in Histopathology Images to Improve the Classification Performance for Breast Cancer Diagnosis.

    Morovati, Bahareh / Lashgari, Reza / Hajihasani, Mojtaba / Shabani, Hasti

    Journal of digital imaging

    2023  Volume 36, Issue 6, Page(s) 2602–2612

    Abstract: Breast cancer is the second most common cancer among women worldwide, and the diagnosis by pathologists is a time-consuming procedure and subjective. Computer-aided diagnosis frameworks are utilized to relieve pathologist workload by classifying the data ...

    Abstract Breast cancer is the second most common cancer among women worldwide, and the diagnosis by pathologists is a time-consuming procedure and subjective. Computer-aided diagnosis frameworks are utilized to relieve pathologist workload by classifying the data automatically, in which deep convolutional neural networks (CNNs) are effective solutions. The features extracted from the activation layer of pre-trained CNNs are called deep convolutional activation features (DeCAF). In this paper, we have analyzed that all DeCAF features are not necessarily led to higher accuracy in the classification task and dimension reduction plays an important role. We have proposed reduced DeCAF (R-DeCAF) for this purpose, and different dimension reduction methods are applied to achieve an effective combination of features by capturing the essence of DeCAF features. This framework uses pre-trained CNNs such as AlexNet, VGG-16, and VGG-19 as feature extractors in transfer learning mode. The DeCAF features are extracted from the first fully connected layer of the mentioned CNNs, and a support vector machine is used for classification. Among linear and nonlinear dimensionality reduction algorithms, linear approaches such as principal component analysis (PCA) represent a better combination among deep features and lead to higher accuracy in the classification task using a small number of features considering a specific amount of cumulative explained variance (CEV) of features. The proposed method is validated using experimental BreakHis and ICIAR datasets. Comprehensive results show improvement in the classification accuracy up to 4.3% with a feature vector size (FVS) of 23 and CEV equal to 0.15.
    MeSH term(s) Humans ; Female ; Breast Neoplasms/diagnostic imaging ; Breast Neoplasms/pathology ; Neural Networks, Computer ; Algorithms ; Diagnosis, Computer-Assisted ; Support Vector Machine
    Language English
    Publishing date 2023-08-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1033897-4
    ISSN 1618-727X ; 0897-1889
    ISSN (online) 1618-727X
    ISSN 0897-1889
    DOI 10.1007/s10278-023-00887-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article: LFP polarity changes across cortical and eccentricity in primary visual cortex.

    Khodaei, Fereshteh / Sadati, S H / Doost, Mahyar / Lashgari, Reza

    Frontiers in neuroscience

    2023  Volume 17, Page(s) 1138602

    Abstract: Local field potentials (LFPs) can evaluate neural population activity in the cortex and their interaction with other cortical areas. Analyzing current source density (CSD) rather than LFPs is very significant due to the reduction of volume conduction ... ...

    Abstract Local field potentials (LFPs) can evaluate neural population activity in the cortex and their interaction with other cortical areas. Analyzing current source density (CSD) rather than LFPs is very significant due to the reduction of volume conduction effects. Current sinks are construed as net inward transmembrane currents, while current sources are net outward ones. Despite extensive studies of LFPs and CSDs, their morphology in different cortical layers and eccentricities are still largely unknown. Because LFP polarity changes provide a measure of neural activity, they can be useful in implanting brain-computer interface (BCI) chips and effectively communicating the BCI devices to the brain. We hypothesize that sinks and sources analyses could be a way to quantitatively achieve their characteristics in response to changes in stimulus size and layer-dependent differences with increasing eccentricities. In this study, we show that stimulus properties play a crucial role in determining the flow. The present work focusses on the primary visual cortex (V1). In this study, we investigate a map of the LFP-CSD in V1 area by presenting different stimulus properties (e.g., size and type) in the visual field area of Macaque monkeys. Our aim is to use the morphology of sinks and sources to measure the input and output information in different layers as well as different eccentricities. According to the value of CSDs, the results show that the stimuli smaller than RF's size had lower strength than the others and the larger RF's stimulus size showed smaller strength than the optimized stimulus size, which indicated the suppression phenomenon. Additionally, with the increased eccentricity, CSD's strengths were increased across cortical layers.
    Language English
    Publishing date 2023-02-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2411902-7
    ISSN 1662-453X ; 1662-4548
    ISSN (online) 1662-453X
    ISSN 1662-4548
    DOI 10.3389/fnins.2023.1138602
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Book ; Online: Reduced Deep Convolutional Activation Features (R-DeCAF) in Histopathology Images to Improve the Classification Performance for Breast Cancer Diagnosis

    Morovati, Bahareh / Lashgari, Reza / Hajihasani, Mojtaba / Shabani, Hasti

    2023  

    Abstract: Breast cancer is the second most common cancer among women worldwide. Diagnosis of breast cancer by the pathologists is a time-consuming procedure and subjective. Computer aided diagnosis frameworks are utilized to relieve pathologist workload by ... ...

    Abstract Breast cancer is the second most common cancer among women worldwide. Diagnosis of breast cancer by the pathologists is a time-consuming procedure and subjective. Computer aided diagnosis frameworks are utilized to relieve pathologist workload by classifying the data automatically, in which deep convolutional neural networks (CNNs) are effective solutions. The features extracted from activation layer of pre-trained CNNs are called deep convolutional activation features (DeCAF). In this paper, we have analyzed that all DeCAF features are not necessarily led to a higher accuracy in the classification task and dimension reduction plays an important role. Therefore, different dimension reduction methods are applied to achieve an effective combination of features by capturing the essence of DeCAF features. To this purpose, we have proposed reduced deep convolutional activation features (R-DeCAF). In this framework, pre-trained CNNs such as AlexNet, VGG-16 and VGG-19 are utilized in transfer learning mode as feature extractors. DeCAF features are extracted from the first fully connected layer of the mentioned CNNs and support vector machine has been used for binary classification. Among linear and nonlinear dimensionality reduction algorithms, linear approaches such as principal component analysis (PCA) represent a better combination among deep features and lead to a higher accuracy in the classification task using small number of features considering specific amount of cumulative explained variance (CEV) of features. The proposed method is validated using experimental BreakHis dataset. Comprehensive results show improvement in the classification accuracy up to 4.3% with less computational time. Best achieved accuracy is 91.13% for 400x data with feature vector size (FVS) of 23 and CEV equals to 0.15 using pre-trained AlexNet as feature extractor and PCA as feature reduction algorithm.
    Keywords Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Artificial Intelligence
    Subject code 006 ; 004
    Publishing date 2023-01-05
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  4. Article ; Online: Brain-inspired multiple-target tracking using Dynamic Neural Fields.

    Kamkar, Shiva / Abrishami Moghaddam, Hamid / Lashgari, Reza / Erlhagen, Wolfram

    Neural networks : the official journal of the International Neural Network Society

    2022  Volume 151, Page(s) 121–131

    Abstract: Despite considerable progress in the field of automatic multi-target tracking, several problems such as data association remained challenging. On the other hand, cognitive studies have reported that humans can robustly track several objects ... ...

    Abstract Despite considerable progress in the field of automatic multi-target tracking, several problems such as data association remained challenging. On the other hand, cognitive studies have reported that humans can robustly track several objects simultaneously. Such circumstances happen regularly in daily life, and humans have evolved to handle the associated problems. Accordingly, using brain-inspired processing principles may contribute to significantly increase the performance of automatic systems able to follow the trajectories of multiple objects. In this paper, we propose a multiple-object tracking algorithm based on dynamic neural field theory which has been proven to provide neuro-plausible processing mechanisms for cognitive functions of the brain. We define several input neural fields responsible for representing previous location and orientation information as well as instantaneous linear and angular speed of the objects in successive video frames. Image processing techniques are applied to extract the critical object features including target location and orientation. Two prediction fields anticipate the objects' locations and orientations in the upcoming frame after receiving excitatory and inhibitory inputs from the input fields in a feed-forward architecture. This information is used in the data association and labeling process. We tested the proposed algorithm on a zebrafish larvae segmentation and tracking dataset and an ant-tracking dataset containing non-rigid objects with spiky movements and frequently occurring occlusions. The results showed a significant improvement in tracking metrics compared to state-of-the-art algorithms.
    MeSH term(s) Algorithms ; Animals ; Brain ; Image Processing, Computer-Assisted/methods ; Movement ; Zebrafish
    Language English
    Publishing date 2022-03-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 740542-x
    ISSN 1879-2782 ; 0893-6080
    ISSN (online) 1879-2782
    ISSN 0893-6080
    DOI 10.1016/j.neunet.2022.03.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article ; Online: CCTCOVID: COVID-19 detection from chest X-ray images using Compact Convolutional Transformers.

    Marefat, Abdolreza / Marefat, Mahdieh / Hassannataj Joloudari, Javad / Nematollahi, Mohammad Ali / Lashgari, Reza

    Frontiers in public health

    2023  Volume 11, Page(s) 1025746

    Abstract: COVID-19 is a novel virus that attacks the upper respiratory tract and the lungs. Its person-to-person transmissibility is considerably rapid and this has caused serious problems in approximately every facet of individuals' lives. While some infected ... ...

    Abstract COVID-19 is a novel virus that attacks the upper respiratory tract and the lungs. Its person-to-person transmissibility is considerably rapid and this has caused serious problems in approximately every facet of individuals' lives. While some infected individuals may remain completely asymptomatic, others have been frequently witnessed to have mild to severe symptoms. In addition to this, thousands of death cases around the globe indicated that detecting COVID-19 is an urgent demand in the communities. Practically, this is prominently done with the help of screening medical images such as Computed Tomography (CT) and X-ray images. However, the cumbersome clinical procedures and a large number of daily cases have imposed great challenges on medical practitioners. Deep Learning-based approaches have demonstrated a profound potential in a wide range of medical tasks. As a result, we introduce a transformer-based method for automatically detecting COVID-19 from X-ray images using Compact Convolutional Transformers (CCT). Our extensive experiments prove the efficacy of the proposed method with an accuracy of 99.22% which outperforms the previous works.
    MeSH term(s) Humans ; COVID-19/diagnostic imaging ; X-Rays ; Health Personnel ; Tomography, X-Ray Computed
    Language English
    Publishing date 2023-02-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711781-9
    ISSN 2296-2565 ; 2296-2565
    ISSN (online) 2296-2565
    ISSN 2296-2565
    DOI 10.3389/fpubh.2023.1025746
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: Exploring Methodological Approaches of Experimental Studies in the Field of Neuroarchitecture: A Systematic Review.

    Rad, Parastou Naghibi / Behzadi, Farzaneh / Yazdanfar, Seyed Abbas / Ghamari, Hessam / Zabeh, Erfan / Lashgari, Reza

    HERD

    2023  Volume 16, Issue 2, Page(s) 284–309

    Abstract: Objectives: This systematic review aims to strengthen the relationship between architecture and neuroscience by classifying data measurement techniques in the field of neuroarchitecture with a focus on the most practical and common methodological ... ...

    Abstract Objectives: This systematic review aims to strengthen the relationship between architecture and neuroscience by classifying data measurement techniques in the field of neuroarchitecture with a focus on the most practical and common methodological approaches. It classifies data recording techniques in different architectural categories (e.g., interior, urban, built environment).
    Backgrounds: With regard to urban life developments and technological breakthroughs, studies of human interactions with environments have been expanding in recent years. Additionally, recent advances in neuroscience have allowed architects to find out more about human experiences in built environments, but there are few valid frameworks about what methodologies and instruments are more common to conduct experimental tasks in this interdisciplinary field.
    Methods: Twenty-eight experimental studies were selected based on the preferred reporting items for systematic reviews and meta-analyses literature search extension (PRISMA) systematic review protocol and a comprehensive analysis. The task-space of selected articles was categorized into three subfields, namely, "interior design," "urban design," and "building design" based on environments and their stimuli. As for this context-based categorization, recording techniques and methodology were distinguished for each subfield division.
    Results: More than 50% of the studies were incorporated in the first two categories, and the EEG recording was the most frequently employed neuroimaging technique thanks to the technical efficacy of its setup and the high temporal resolution of its electrophysiological signals.
    Conclusion: In this study, a summary of techniques and methodological approaches applied in the field is provided in a nut shell, and a general framework of instruments is presented to help scholars to carry out more practical research in the future leading to designing built environments more efficiently.
    MeSH term(s) Humans ; Built Environment
    Language English
    Publishing date 2023-01-20
    Publishing country United States
    Document type Systematic Review ; Journal Article ; Review
    ZDB-ID 2525547-2
    ISSN 2167-5112 ; 1937-5867
    ISSN (online) 2167-5112
    ISSN 1937-5867
    DOI 10.1177/19375867221133135
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Ripples in macaque V1 and V4 are modulated by top-down visual attention.

    Doostmohammadi, Jafar / Gieselmann, Marc Alwin / van Kempen, Jochem / Lashgari, Reza / Yoonessi, Ali / Thiele, Alexander

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 5, Page(s) e2210698120

    Abstract: Sharp-wave ripples (SWRs) are highly synchronous neuronal activity events. They have been predominantly observed in the hippocampus during offline states such as pause in exploration, slow-wave sleep, and quiescent wakefulness. SWRs have been linked to ... ...

    Abstract Sharp-wave ripples (SWRs) are highly synchronous neuronal activity events. They have been predominantly observed in the hippocampus during offline states such as pause in exploration, slow-wave sleep, and quiescent wakefulness. SWRs have been linked to memory consolidation, spatial navigation, and spatial decision-making. Recently, SWRs have been reported during visual search, a form of remote spatial exploration, in macaque hippocampus. However, the association between SWRs and multiple forms of awake conscious and goal-directed behavior is unknown. We report that ripple activity occurs in macaque visual areas V1 and V4 during focused spatial attention. The occurrence of ripples is modulated by stimulus characteristics, increased by attention toward the receptive field, and by the size of the attentional focus. During attention cued to the receptive field, the monkey's reaction time in detecting behaviorally relevant events was reduced by ripples. These results show that ripple activity is not limited to hippocampal activity during offline states, rather they occur in the neocortex during active attentive states and vigilance behaviors.
    MeSH term(s) Animals ; Macaca ; Hippocampus/physiology ; Wakefulness/physiology ; Neocortex ; Sleep/physiology
    Language English
    Publishing date 2023-01-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2210698120
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article: Pre-stimulus Alpha Activity Modulates Face and Object Processing in the Intra-Parietal Sulcus, a MEG Study.

    Dehaghani, Narjes Soltani / Maess, Burkhard / Khosrowabadi, Reza / Lashgari, Reza / Braeutigam, Sven / Zarei, Mojtaba

    Frontiers in human neuroscience

    2022  Volume 16, Page(s) 831781

    Abstract: Face perception is crucial in all social animals. Recent studies have shown that pre-stimulus oscillations of brain activity modulate the perceptual performance of face vs. non-face stimuli, specifically under challenging conditions. However, it is ... ...

    Abstract Face perception is crucial in all social animals. Recent studies have shown that pre-stimulus oscillations of brain activity modulate the perceptual performance of face vs. non-face stimuli, specifically under challenging conditions. However, it is unclear if this effect also occurs during simple tasks, and if so in which brain regions. Here we used magnetoencephalography (MEG) and a 1-back task in which participants decided if the two sequentially presented stimuli were the same or not in each trial. The aim of the study was to explore the effect of pre-stimulus alpha oscillation on the perception of face (human and monkey) and non-face stimuli. Our results showed that pre-stimulus activity in the left occipital face area (OFA) modulated responses in the intra-parietal sulcus (IPS) at around 170 ms after the presentation of human face stimuli. This effect was also found after participants were shown images of motorcycles. In this case, the IPS was modulated by pre-stimulus activity in the right OFA and the right fusiform face area (FFA). We conclude that pre-stimulus modulation of post-stimulus response also occurs during simple tasks and is therefore independent of behavioral responses.
    Language English
    Publishing date 2022-05-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2425477-0
    ISSN 1662-5161
    ISSN 1662-5161
    DOI 10.3389/fnhum.2022.831781
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: Automated prediction of COVID-19 mortality outcome using clinical and laboratory data based on hierarchical feature selection and random forest classifier.

    Amini, Nasrin / Mahdavi, Mahdi / Choubdar, Hadi / Abedini, Atefeh / Shalbaf, Ahmad / Lashgari, Reza

    Computer methods in biomechanics and biomedical engineering

    2022  Volume 26, Issue 2, Page(s) 160–173

    Abstract: Early prediction of COVID-19 mortality outcome can decrease expiration risk by alerting healthcare personnel to assure efficient resource allocation and treatment planning. This study introduces a machine learning framework for the prediction of COVID-19 ...

    Abstract Early prediction of COVID-19 mortality outcome can decrease expiration risk by alerting healthcare personnel to assure efficient resource allocation and treatment planning. This study introduces a machine learning framework for the prediction of COVID-19 mortality using demographics, vital signs, and laboratory blood tests (complete blood count (CBC), coagulation, kidney, liver, blood gas, and general). 41 features from 244 COVID-19 patients were recorded on the first day of admission. In this study, first, the features in each of the eight categories were investigated. Afterward, features that have an area under the receiver operating characteristic curve (AUC) above 0.6 and the
    MeSH term(s) Humans ; COVID-19/diagnosis ; Random Forest ; Algorithms ; Neural Networks, Computer ; ROC Curve
    Language English
    Publishing date 2022-03-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2071764-7
    ISSN 1476-8259 ; 1025-5842
    ISSN (online) 1476-8259
    ISSN 1025-5842
    DOI 10.1080/10255842.2022.2050906
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article ; Online: Neural oscillatory characteristics of feedback-associated activity in globus pallidus interna.

    Choubdar, Hadi / Mahdavi, Mahdi / Rostami, Zahra / Zabeh, Erfan / Gillies, Martin J / Green, Alexander L / Aziz, Tipu Z / Lashgari, Reza

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 4141

    Abstract: Neural oscillatory activities in basal ganglia have prominent roles in cognitive processes. However, the characteristics of oscillatory activities during cognitive tasks have not been extensively explored in human Globus Pallidus internus (GPi). This ... ...

    Abstract Neural oscillatory activities in basal ganglia have prominent roles in cognitive processes. However, the characteristics of oscillatory activities during cognitive tasks have not been extensively explored in human Globus Pallidus internus (GPi). This study aimed to compare oscillatory characteristics of GPi between dystonia and Parkinson's Disease (PD). A dystonia and a PD patient performed the Intra-Extra-Dimension shift (IED) task during both on and off-medication states. During the IED task, patients had to correctly choose between two visual stimuli containing shapes or lines based on a hidden rule via trial and error. Immediate auditory and visual feedback was provided upon the choice to inform participants if they chose correctly. Bilateral GPi Local Field Potentials (LFP) activity was recorded via externalized DBS leads. Transient high gamma activity (~ 100-150 Hz) was observed immediately after feedback in the dystonia patient. Moreover, these bursts were phase synchronous between left and right GPi with an antiphase clustering of phase differences. In contrast, no synchronous high gamma activity was detected in the PD patient with or without dopamine administration. The off-med PD patient also displayed enhanced low frequency clusters, which were ameliorated by medication. The current study provides a rare report of antiphase homotopic synchrony in human GPi, potentially related to incorporating and processing feedback information. The absence of these activities in off and on-med PD patient indicates the potential presence of impaired medication independent feedback processing circuits. Together, these findings suggest a potential role for GPi's synchronized activity in shaping feedback processing mechanisms required in cognitive tasks.
    MeSH term(s) Humans ; Globus Pallidus ; Dystonia/therapy ; Feedback ; Deep Brain Stimulation/methods ; Parkinson Disease/drug therapy ; Dystonic Disorders/therapy
    Language English
    Publishing date 2023-03-13
    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/s41598-023-30832-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top