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General General

Network science characteristics of brain-derived neuronal cultures deciphered from quantitative phase imaging data.

In Scientific reports ; h5-index 158.0

Understanding the mechanisms by which neurons create or suppress connections to enable communication in brain-derived neuronal cultures can inform how learning, cognition and creative behavior emerge. While prior studies have shown that neuronal cultures possess self-organizing criticality properties, we further demonstrate that in vitro brain-derived neuronal cultures exhibit a self-optimization phenomenon. More precisely, we analyze the multiscale neural growth data obtained from label-free quantitative microscopic imaging experiments and reconstruct the in vitro neuronal culture networks (microscale) and neuronal culture cluster networks (mesoscale). We investigate the structure and evolution of neuronal culture networks and neuronal culture cluster networks by estimating the importance of each network node and their information flow. By analyzing the degree-, closeness-, and betweenness-centrality, the node-to-node degree distribution (informing on neuronal interconnection phenomena), the clustering coefficient/transitivity (assessing the "small-world" properties), and the multifractal spectrum, we demonstrate that murine neurons exhibit self-optimizing behavior over time with topological characteristics distinct from existing complex network models. The time-evolving interconnection among murine neurons optimizes the network information flow, network robustness, and self-organization degree. These findings have complex implications for modeling neuronal cultures and potentially on how to design biological inspired artificial intelligence.

Yin Chenzhong, Xiao Xiongye, Balaban Valeriu, Kandel Mikhail E, Lee Young Jae, Popescu Gabriel, Bogdan Paul


General General

Convolutional Neural Network Based Approach to in Silico Non-Anticipating Prediction of Antigenic Distance for Influenza Virus.

In Viruses ; h5-index 58.0

Evaluation of the antigenic similarity degree between the strains of the influenza virus is highly important for vaccine production. The conventional method used to measure such a degree is related to performing the immunological assays of hemagglutinin inhibition. Namely, the antigenic distance between two strains is calculated on the basis of HI assays. Usually, such distances are visualized by using some kind of antigenic cartography method. The known drawback of the HI assay is that it is rather time-consuming and expensive. In this paper, we propose a novel approach for antigenic distance approximation based on deep learning in the feature spaces induced by hemagglutinin protein sequences and Convolutional Neural Networks (CNNs). To apply a CNN to compare the protein sequences, we utilize the encoding based on the physical and chemical characteristics of amino acids. By varying (hyper)parameters of the CNN architecture design, we find the most robust network. Further, we provide insight into the relationship between approximated antigenic distance and antigenicity by evaluating the network on the HI assay database for the H1N1 subtype. The results indicate that the best-trained network gives a high-precision approximation for the ground-truth antigenic distances, and can be used as a good exploratory tool in practical tasks.

Forghani Majid, Khachay Michael


antigenic distance, convolutional neural network, evolution, influenza, vaccine

General General

Identification of risk factors and symptoms of SARS-CoV-2 (COVID-19) using biomedical literature and social media data: Integrative and Consensus study.

In Journal of medical Internet research ; h5-index 88.0

BACKGROUND : In December 2019, Coronavirus disease 2019 (COVID-19) outbreak started in China and rapidly spread around the world. Lack of any vaccine or optimized intervention raised the importance of characterizing risk factors and symptoms for the early identification and successful treatment of COVID-19 patients.

OBJECTIVE : This study aims to investigate and analyze biomedical literature and public social media data to understand the association of risk factors and symptoms with various outcomes of COVID-19 patients.

METHODS : Through semantic analysis, we collected 45 retrospective cohort studies, which evaluated 303 clinical and demographic variables across 13 different outcomes of COVID-19 patients, and 84,140 Twitter posts from 1,036 COVID-19 positive users. Machine-learning tools to extract biomedical information were introduced to identify uncommon or novel symptoms mentioning in social media. We then examined and compared two datasets to expand our landscape of risk factors and symptoms related to COVID-19.

RESULTS : From the biomedical literature, approximately 90% of clinical and demographic variables showed inconsistent associations with COVID-19 outcomes. Consensus analysis identified 72 risk factors that were specifically associated with individual outcomes. From the social media data, 51 symptoms were characterized and analyzed. By comparing social media data with biomedical literature, we identified 25 novel symptoms that were specifically mentioned in social media but have been not previously well characterized. Furthermore, there were certain combinations of symptoms that were frequently mentioned together in social media.

CONCLUSIONS : Identified outcome-specific risk factors, symptoms, and combinations of symptoms may serve as surrogate indicators to identify COVID-19 patients and predict their clinical outcomes providing appropriate treatments.


Jeon Jouhyun, Baruah Gaurav, Sarabadani Sarah, Palanica Adam


General General

Face Mask Detection using Transfer Learning of InceptionV3

ArXiv Preprint

The world is facing a huge health crisis due to the rapid transmission of coronavirus (COVID-19). Several guidelines were issued by the World Health Organization (WHO) for protection against the spread of coronavirus. According to WHO, the most effective preventive measure against COVID-19 is wearing a mask in public places and crowded areas. It is very difficult to monitor people manually in these areas. In this paper, a transfer learning model is proposed to automate the process of identifying the people who are not wearing mask. The proposed model is built by fine-tuning the pre-trained state-of-the-art deep learning model, InceptionV3. The proposed model is trained and tested on the Simulated Masked Face Dataset (SMFD). Image augmentation technique is adopted to address the limited availability of data for better training and testing of the model. The model outperformed the other recently proposed approaches by achieving an accuracy of 99.9% during training and 100% during testing.

G. Jignesh Chowdary, Narinder Singh Punn, Sanjay Kumar Sonbhadra, Sonali Agarwal


Ophthalmology Ophthalmology

Automatic detection of non-perfusion areas in diabetic macular edema from fundus fluorescein angiography for decision making using deep learning.

In Scientific reports ; h5-index 158.0

Vision loss caused by diabetic macular edema (DME) can be prevented by early detection and laser photocoagulation. As there is no comprehensive detection technique to recognize NPA, we proposed an automatic detection method of NPA on fundus fluorescein angiography (FFA) in DME. The study included 3,014 FFA images of 221 patients with DME. We use 3 convolutional neural networks (CNNs), including DenseNet, ResNet50, and VGG16, to identify non-perfusion regions (NP), microaneurysms, and leakages in FFA images. The NPA was segmented using attention U-net. To validate its performance, we applied our detection algorithm on 249 FFA images in which the NPA areas were manually delineated by 3 ophthalmologists. For DR lesion classification, area under the curve is 0.8855 for NP regions, 0.9782 for microaneurysms, and 0.9765 for leakage classifier. The average precision of NP region overlap ratio is 0.643. NP regions of DME in FFA images are identified based a new automated deep learning algorithm. This study is an in-depth study from computer-aided diagnosis to treatment, and will be the theoretical basis for the application of intelligent guided laser.

Jin Kai, Pan Xiangji, You Kun, Wu Jian, Liu Zhifang, Cao Jing, Lou Lixia, Xu Yufeng, Su Zhaoan, Yao Ke, Ye Juan


Radiology Radiology

A multi-task, multi-stage deep transfer learning model for early prediction of neurodevelopment in very preterm infants.

In Scientific reports ; h5-index 158.0

Survivors following very premature birth (i.e., ≤ 32 weeks gestational age) remain at high risk for neurodevelopmental impairments. Recent advances in deep learning techniques have made it possible to aid the early diagnosis and prognosis of neurodevelopmental deficits. Deep learning models typically require training on large datasets, and unfortunately, large neuroimaging datasets with clinical outcome annotations are typically limited, especially in neonates. Transfer learning represents an important step to solve the fundamental problem of insufficient training data in deep learning. In this work, we developed a multi-task, multi-stage deep transfer learning framework using the fusion of brain connectome and clinical data for early joint prediction of multiple abnormal neurodevelopmental (cognitive, language and motor) outcomes at 2 years corrected age in very preterm infants. The proposed framework maximizes the value of both available annotated and non-annotated data in model training by performing both supervised and unsupervised learning. We first pre-trained a deep neural network prototype in a supervised fashion using 884 older children and adult subjects, and then re-trained this prototype using 291 neonatal subjects without supervision. Finally, we fine-tuned and validated the pre-trained model using 33 preterm infants. Our proposed model identified very preterm infants at high-risk for cognitive, language, and motor deficits at 2 years corrected age with an area under the receiver operating characteristic curve of 0.86, 0.66 and 0.84, respectively. Employing such a deep learning model, once externally validated, may facilitate risk stratification at term-equivalent age for early identification of long-term neurodevelopmental deficits and targeted early interventions to improve clinical outcomes in very preterm infants.

He Lili, Li Hailong, Wang Jinghua, Chen Ming, Gozdas Elveda, Dillman Jonathan R, Parikh Nehal A