scholarly journals Fighting Together against the Pandemic: Learning Multiple Models on Tomography Images for COVID-19 Diagnosis

AI ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 261-273
Author(s):  
Mario Manzo ◽  
Simone Pellino
Keyword(s):  
Network Architecture ◽  
State Of The Art ◽  
Ensemble Classification ◽  
Effective Vaccine ◽  
Rt Pcr ◽  
Neural Network Architecture ◽  
Experimental Phase ◽  
Different Types ◽  
Polymerase Chain ◽  
Better Than

COVID-19 has been a great challenge for humanity since the year 2020. The whole world has made a huge effort to find an effective vaccine in order to save those not yet infected. The alternative solution is early diagnosis, carried out through real-time polymerase chain reaction (RT-PCR) tests or thorax Computer Tomography (CT) scan images. Deep learning algorithms, specifically convolutional neural networks, represent a methodology for image analysis. They optimize the classification design task, which is essential for an automatic approach with different types of images, including medical. In this paper, we adopt a pretrained deep convolutional neural network architecture in order to diagnose COVID-19 disease from CT images. Our idea is inspired by what the whole of humanity is achieving, as the set of multiple contributions is better than any single one for the fight against the pandemic. First, we adapt, and subsequently retrain for our assumption, some neural architectures that have been adopted in other application domains. Secondly, we combine the knowledge extracted from images by the neural architectures in an ensemble classification context. Our experimental phase is performed on a CT image dataset, and the results obtained show the effectiveness of the proposed approach with respect to the state-of-the-art competitors.

scholarly journals DeepIsoFun: a deep domain adaptation approach to predict isoform functions

2018 ◽  
Vol 35 (15) ◽  
pp. 2535-2544 ◽  
Author(s):  
Dipan Shaw ◽  
Hao Chen ◽  
Tao Jiang
Keyword(s):  
Network Architecture ◽  
Domain Adaptation ◽  
Multiple Instance Learning ◽  
Training Data ◽  
Supplementary Information ◽  
Operating Characteristics ◽  
Neural Network Architecture ◽  
Receiver Operating Characteristics Curve ◽  
Gene Functions ◽  
Better Than

AbstractMotivationIsoforms are mRNAs produced from the same gene locus by alternative splicing and may have different functions. Although gene functions have been studied extensively, little is known about the specific functions of isoforms. Recently, some computational approaches based on multiple instance learning have been proposed to predict isoform functions from annotated gene functions and expression data, but their performance is far from being desirable primarily due to the lack of labeled training data. To improve the performance on this problem, we propose a novel deep learning method, DeepIsoFun, that combines multiple instance learning with domain adaptation. The latter technique helps to transfer the knowledge of gene functions to the prediction of isoform functions and provides additional labeled training data. Our model is trained on a deep neural network architecture so that it can adapt to different expression distributions associated with different gene ontology terms.ResultsWe evaluated the performance of DeepIsoFun on three expression datasets of human and mouse collected from SRA studies at different times. On each dataset, DeepIsoFun performed significantly better than the existing methods. In terms of area under the receiver operating characteristics curve, our method acquired at least 26% improvement and in terms of area under the precision-recall curve, it acquired at least 10% improvement over the state-of-the-art methods. In addition, we also study the divergence of the functions predicted by our method for isoforms from the same gene and the overall correlation between expression similarity and the similarity of predicted functions.Availability and implementationhttps://github.com/dls03/DeepIsoFun/Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals IPOMDP-Net: A Deep Neural Network for Partially Observable Multi-Agent Planning Using Interactive POMDPs

2019 ◽  
Vol 33 ◽  
pp. 6062-6069 ◽  
Author(s):  
Yanlin Han ◽  
Piotr Gmytrasiewicz
Keyword(s):  
Neural Network ◽  
Network Architecture ◽  
State Of The Art ◽  
Neural Computing ◽  
Neural Network Architecture ◽  
Markov Decision ◽  
Planning Algorithm ◽  
Multi Agent ◽  
Partially Observable ◽  
Multi Agent Planning

This paper introduces the IPOMDP-net, a neural network architecture for multi-agent planning under partial observability. It embeds an interactive partially observable Markov decision process (I-POMDP) model and a QMDP planning algorithm that solves the model in a neural network architecture. The IPOMDP-net is fully differentiable and allows for end-to-end training. In the learning phase, we train an IPOMDP-net on various fixed and randomly generated environments in a reinforcement learning setting, assuming observable reinforcements and unknown (randomly initialized) model functions. In the planning phase, we test the trained network on new, unseen variants of the environments under the planning setting, using the trained model to plan without reinforcements. Empirical results show that our model-based IPOMDP-net outperforms the other state-of-the-art modelfree network and generalizes better to larger, unseen environments. Our approach provides a general neural computing architecture for multi-agent planning using I-POMDPs. It suggests that, in a multi-agent setting, having a model of other agents benefits our decision-making, resulting in a policy of higher quality and better generalizability.

scholarly journals Efficient Semantic Segmentation Using Multi-Path Decoder

2020 ◽  
Vol 10 (18) ◽  
pp. 6386
Author(s):  
Xing Bai ◽  
Jun Zhou
Keyword(s):  
Neural Network ◽  
Real Time ◽  
Network Architecture ◽  
Resource Constraints ◽  
Cost Effective ◽  
Semantic Segmentation ◽  
Classification Model ◽  
Neural Network Architecture ◽  
Great Progress ◽  
Different Types

Benefiting from the booming of deep learning, the state-of-the-art models achieved great progress. But they are huge in terms of parameters and floating point operations, which makes it hard to apply them to real-time applications. In this paper, we propose a novel deep neural network architecture, named MPDNet, for fast and efficient semantic segmentation under resource constraints. First, we use a light-weight classification model pretrained on ImageNet as the encoder. Second, we use a cost-effective upsampling datapath to restore prediction resolution and convert features for classification into features for segmentation. Finally, we propose to use a multi-path decoder to extract different types of features, which are not ideal to process inside only one convolutional neural network. The experimental results of our model outperform other models aiming at real-time semantic segmentation on Cityscapes. Based on our proposed MPDNet, we achieve 76.7% mean IoU on Cityscapes test set with only 118.84GFLOPs and achieves 37.6 Hz on 768 × 1536 images on a standard GPU.

scholarly journals Prevalence of Adhesion and Regulation of Biofilm-Related Genes in Different Clones ofStaphylococcus aureus

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Salman Sahab Atshan ◽  
Mariana Nor Shamsudin ◽  
Zamberi Sekawi ◽  
Leslie Than Thian Lung ◽  
Rukman Awang Hamat ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Biofilm Formation ◽  
Clinical Information ◽  
Microtiter Plate ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Microtiter Plate Assay ◽  
High Prevalence ◽  
Different Types ◽  
Polymerase Chain

Clinical information about genotypically different clones of biofilm-producingStaphylococcus aureusis largely unknown. We examined whether different clones of methicillin-sensitive and methicillin-resistantS. aureus(MSSA and MRSA) differ with respect to staphylococcal microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) in biofilm formation. The study used 60 different types ofspaand determined the phenotypes, the prevalence of the 13 MSCRAMM, and biofilm genes for each clone. The current investigation was carried out using a modified Congo red agar (MCRA), a microtiter plate assay (MPA), polymerase chain reaction (PCR), and reverse transcriptase polymerase chain reaction (RT-PCR). Clones belonging to the samespatype were found to have similar properties in adheringto thepolystyrene microtiter plate surface. However, their ability to produce slime on MCRA medium was different. PCR experiments showed that 60 clones of MSSA and MRSA were positive for 5 genes (out of 9 MSCRAMM genes).icaADBCgenes were found to be present in all the 60 clones tested indicating a high prevalence, and these genes were equally distributed among the clones associated with MSSA and those with MRSA. The prevalence of other MSCRAMM genes among MSSA and MRSA clones was found to be variable. MRSA and MSSA gene expression (MSCRAMM andicaADBC) was confirmed by RT-PCR.

scholarly journals Development of Enhanced Primer Sets for Detection of Norovirus

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Byoung-Hwa Kong ◽  
Sung-Geun Lee ◽  
Sang-Ha Han ◽  
Ji-Young Jin ◽  
Weon-Hwa Jheong ◽  
...  
Keyword(s):  
Rt Pcr ◽  
Chain Reaction ◽  
Viral Pathogen ◽  
Food Borne ◽  
Polymerase Chain ◽  
Primer Sets ◽  
Global Increase ◽  
Seminested Pcr ◽  
Diagnosis Of Infection ◽  
Better Than

Norovirus (NV) is a major viral pathogen that causes nonbacterial acute gastroenteritis and outbreaks of food-borne disease. The genotype of NV most frequently responsible for NV outbreaks is GII.4, which accounts for 60–80% of cases. Moreover, original and new NV variant types have been continuously emerging, and their emergence is related to the recent global increase in NV infection. In this study, we developed advanced primer sets (NKI-F/R/F2, NKII-F/R/R2) for the detection of NV, including the variant types. The new primer sets were compared with conventional primer sets (GI-F1/R1/F2, SRI-1/2/3, GII-F1/R1/F2, and SRII-1/2/3) to evaluate their efficiency when using clinical and environmental samples. Using reverse transcription polymerase chain reaction (RT-PCR) and seminested PCR, NV GI and GII were detected in 91.7% (NKI-F/R/F2), 89.3% (NKII-F/R/R2), 54.2% (GI-F1/R1/F2), 52.5% (GII-F1/R1/F2), 25.0% (SRI-1/2/3), and 32.2% (SRII-1/2/3) of clinical and environmental specimens. Therefore, our primer sets perform better than conventional primer sets in the detection of emerged types of NV and could be used in the future for epidemiological diagnosis of infection with the virus.

scholarly journals Backbone Cannot Be Trained at Once: Rolling Back to Pre-Trained Network for Person Re-Identification

2019 ◽  
Vol 33 ◽  
pp. 8859-8867 ◽  
Author(s):  
Youngmin Ro ◽  
Jongwon Choi ◽  
Dae Ung Jo ◽  
Byeongho Heo ◽  
Jongin Lim ◽  
...  
Keyword(s):  
Network Architecture ◽  
State Of The Art ◽  
Fine Tuning ◽  
Neural Network Architecture ◽  
Large Dataset ◽  
Low Level ◽  
Tuning Method ◽  
Improved Performance ◽  
High Level ◽  
Tuning Strategy

In person re-identification (ReID) task, because of its shortage of trainable dataset, it is common to utilize fine-tuning method using a classification network pre-trained on a large dataset. However, it is relatively difficult to sufficiently finetune the low-level layers of the network due to the gradient vanishing problem. In this work, we propose a novel fine-tuning strategy that allows low-level layers to be sufficiently trained by rolling back the weights of high-level layers to their initial pre-trained weights. Our strategy alleviates the problem of gradient vanishing in low-level layers and robustly trains the low-level layers to fit the ReID dataset, thereby increasing the performance of ReID tasks. The improved performance of the proposed strategy is validated via several experiments. Furthermore, without any addons such as pose estimation or segmentation, our strategy exhibits state-of-the-art performance using only vanilla deep convolutional neural network architecture.

scholarly journals Robustness of Neural Network Emulations of Radiative Transfer Parameterizations in a State-of-the-Art General Circulation Model

2021 ◽  
Author(s):  
Alexei Belochitski ◽  
Vladimir Krasnopolsky
Keyword(s):  
Neural Network ◽  
Radiative Transfer ◽  
Network Architecture ◽  
General Circulation ◽  
State Of The Art ◽  
Circulation Model ◽  
Set Design ◽  
Neural Network Architecture ◽  
Parametric Change ◽  
Model Components

Abstract. The ability of Machine-Learning (ML) based model components to generalize to the previously unseen inputs, and the resulting stability of the models that use these components, has been receiving a lot of recent attention, especially when it comes to ML-based parameterizations. At the same time, ML-based emulators of existing parameterizations can be stable, accurate, and fast when used in the model they were specifically designed for. In this work we show that shallow-neural-network-based emulators of radiative transfer parameterizations developed almost a decade ago for a state-of-the-art GCM are robust with respect to the substantial structural and parametric change in the host model: when used in two seven month-long experiments with the new model, they not only remain stable, but generate realistic output. Aspects of neural network architecture and training set design potentially contributing to stability of ML-based model components are discussed.

scholarly journals Deep learning regression model for antimicrobial peptide design

2019 ◽  
Author(s):  
Jacob Witten ◽  
Zack Witten
Keyword(s):  
Neural Network ◽  
Antimicrobial Peptides ◽  
Network Architecture ◽  
State Of The Art ◽  
Machine Learning Techniques ◽  
Neural Network Architecture ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Naturally Occurring ◽  
Learning Techniques

AbstractAntimicrobial peptides (AMPs) are naturally occurring or synthetic peptides that show promise for treating antibiotic-resistant pathogens. Machine learning techniques are increasingly used to identify naturally occurring AMPs, but there is a dearth of purely computational methods to design novel effective AMPs, which would speed AMP development. We collected a large database, Giant Repository of AMP Activities (GRAMPA), containing AMP sequences and associated MICs. We designed a convolutional neural network to perform combined classification and regression on peptide sequences to quantitatively predict AMP activity against Escherichia coli. Our predictions outperformed the state of the art at AMP classification and were also effective at regression, for which there were no publicly available comparisons. We then used our model to design novel AMPs and experimentally demonstrated activity of these AMPs against the pathogens E. coli, Pseudomonas aeruginosa, and Staphylococcus aureus. Data, code, and neural network architecture and parameters are available at https://github.com/zswitten/Antimicrobial-Peptides.

scholarly journals PlanetScope Radiometric Normalization and Sentinel-2 Super-Resolution (2.5 m): A Straightforward Spectral-Spatial Fusion of Multi-Satellite Multi-Sensor Images Using Residual Convolutional Neural Networks

2020 ◽  
Vol 12 (15) ◽  
pp. 2366
Author(s):  
Nicolas Latte ◽  
Philippe Lejeune
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Network Architecture ◽  
State Of The Art ◽  
Super Resolution ◽  
Neural Network Architecture ◽  
Research Areas ◽  
Novel Method ◽  
Spatial Fusion ◽  
Sentinel 2

Sentinel-2 (S2) imagery is used in many research areas and for diverse applications. Its spectral resolution and quality are high but its spatial resolutions, of at most 10 m, is not sufficient for fine scale analysis. A novel method was thus proposed to super-resolve S2 imagery to 2.5 m. For a given S2 tile, the 10 S2 bands (four at 10 m and six at 20 m) were fused with additional images acquired at higher spatial resolution by the PlanetScope (PS) constellation. The radiometric inconsistencies between PS microsatellites were normalized. Radiometric normalization and super-resolution were achieved simultaneously using state-of–the-art super-resolution residual convolutional neural networks adapted to the particularities of S2 and PS imageries (including masks of clouds and shadows). The method is described in detail, from image selection and downloading to neural network architecture, training, and prediction. The quality was thoroughly assessed visually (photointerpretation) and quantitatively, confirming that the proposed method is highly spatially and spectrally accurate. The method is also robust and can be applied to S2 images acquired worldwide at any date.

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