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General General

DAR-Net: Dense Attentional Residual Network for Vehicle Detection in Aerial Images.

In Computational intelligence and neuroscience

With the rapid development of deep learning and the wide usage of Unmanned Aerial Vehicles (UAVs), CNN-based algorithms of vehicle detection in aerial images have been widely studied in the past several years. As a downstream task of the general object detection, there are some differences between the vehicle detection in aerial images and the general object detection in ground view images, e.g., larger image areas, smaller target sizes, and more complex background. In this paper, to improve the performance of this task, a Dense Attentional Residual Network (DAR-Net) is proposed. The proposed network employs a novel dense waterfall residual block (DW res-block) to effectively preserve the spatial information and extract high-level semantic information at the same time. A multiscale receptive field attention (MRFA) module is also designed to select the informative feature from the feature maps and enhance the ability of multiscale perception. Based on the DW res-block and MRFA module, to protect the spatial information, the proposed framework adopts a new backbone that only downsamples the feature map 3 times; i.e., the total downsampling ratio of the proposed backbone is 8. These designs could alleviate the degradation problem, improve the information flow, and strengthen the feature reuse. In addition, deep-projection units are used to reduce the impact of information loss caused by downsampling operations, and the identity mapping is applied to each stage of the proposed backbone to further improve the information flow. The proposed DAR-Net is evaluated on VEDAI, UCAS-AOD, and DOTA datasets. The experimental results demonstrate that the proposed framework outperforms other state-of-the-art algorithms.

Li Kaifeng, Wang Bin

2021

Internal Medicine Internal Medicine

Automatic Classification Between COVID-19 and Non-COVID-19 Pneumonia Using Symptoms, Comorbidities, and Laboratory Findings: The Khorshid COVID Cohort Study.

In Frontiers in medicine

Coronavirus disease-2019, also known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was a disaster in 2020. Accurate and early diagnosis of coronavirus disease-2019 (COVID-19) is still essential for health policymaking. Reverse transcriptase-polymerase chain reaction (RT-PCR) has been performed as the operational gold standard for COVID-19 diagnosis. We aimed to design and implement a reliable COVID-19 diagnosis method to provide the risk of infection using demographics, symptoms and signs, blood markers, and family history of diseases to have excellent agreement with the results obtained by the RT-PCR and CT-scan. Our study primarily used sample data from a 1-year hospital-based prospective COVID-19 open-cohort, the Khorshid COVID Cohort (KCC) study. A sample of 634 patients with COVID-19 and 118 patients with pneumonia with similar characteristics whose RT-PCR and chest CT scan were negative (as the control group) (dataset 1) was used to design the system and for internal validation. Two other online datasets, namely, some symptoms (dataset 2) and blood tests (dataset 3), were also analyzed. A combination of one-hot encoding, stability feature selection, over-sampling, and an ensemble classifier was used. Ten-fold stratified cross-validation was performed. In addition to gender and symptom duration, signs and symptoms, blood biomarkers, and comorbidities were selected. Performance indices of the cross-validated confusion matrix for dataset 1 were as follows: sensitivity of 96% [confidence interval, CI, 95%: 94-98], specificity of 95% [90-99], positive predictive value (PPV) of 99% [98-100], negative predictive value (NPV) of 82% [76-89], diagnostic odds ratio (DOR) of 496 [198-1,245], area under the ROC (AUC) of 0.96 [0.94-0.97], Matthews Correlation Coefficient (MCC) of 0.87 [0.85-0.88], accuracy of 96% [94-98], and Cohen's Kappa of 0.86 [0.81-0.91]. The proposed algorithm showed excellent diagnosis accuracy and class-labeling agreement, and fair discriminant power. The AUC on the datasets 2 and 3 was 0.97 [0.96-0.98] and 0.92 [0.91-0.94], respectively. The most important feature was white blood cell count, shortness of breath, and C-reactive protein for datasets 1, 2, and 3, respectively. The proposed algorithm is, thus, a promising COVID-19 diagnosis method, which could be an amendment to simple blood tests and screening of symptoms. However, the RT-PCR and chest CT-scan, performed as the gold standard, are not 100% accurate.

Marateb Hamid Reza, Ziaie Nezhad Farzad, Mohebian Mohammad Reza, Sami Ramin, Haghjooy Javanmard Shaghayegh, Dehghan Niri Fatemeh, Akafzadeh-Savari Mahsa, Mansourian Marjan, Mañanas Miquel Angel, Wolkewitz Martin, Binder Harald

2021

COVID-19, computer-aided diagnosis, machine learning, screening, validation studies

General General

Effective and scalable single-cell data alignment with non-linear canonical correlation analysis.

In Nucleic acids research ; h5-index 217.0

Data alignment is one of the first key steps in single cell analysis for integrating multiple datasets and performing joint analysis across studies. Data alignment is challenging in extremely large datasets, however, as the major of the current single cell data alignment methods are not computationally efficient. Here, we present VIPCCA, a computational framework based on non-linear canonical correlation analysis for effective and scalable single cell data alignment. VIPCCA leverages both deep learning for effective single cell data modeling and variational inference for scalable computation, thus enabling powerful data alignment across multiple samples, multiple data platforms, and multiple data types. VIPCCA is accurate for a range of alignment tasks including alignment between single cell RNAseq and ATACseq datasets and can easily accommodate millions of cells, thereby providing researchers unique opportunities to tackle challenges emerging from large-scale single-cell atlas.

Hu Jialu, Chen Mengjie, Zhou Xiang

2021-Dec-06

General General

CoCoNet-boosting RNA contact prediction by convolutional neural networks.

In Nucleic acids research ; h5-index 217.0

Co-evolutionary models such as direct coupling analysis (DCA) in combination with machine learning (ML) techniques based on deep neural networks are able to predict accurate protein contact or distance maps. Such information can be used as constraints in structure prediction and massively increase prediction accuracy. Unfortunately, the same ML methods cannot readily be applied to RNA as they rely on large structural datasets only available for proteins. Here, we demonstrate how the available smaller data for RNA can be used to improve prediction of RNA contact maps. We introduce an algorithm called CoCoNet that is based on a combination of a Coevolutionary model and a shallow Convolutional Neural Network. Despite its simplicity and the small number of trained parameters, the method boosts the positive predictive value (PPV) of predicted contacts by about 70% with respect to DCA as tested by cross-validation of about eighty RNA structures. However, the direct inclusion of the CoCoNet contacts in 3D modeling tools does not result in a proportional increase of the 3D RNA structure prediction accuracy. Therefore, we suggest that the field develops, in addition to contact PPV, metrics which estimate the expected impact for 3D structure modeling tools better. CoCoNet is freely available and can be found at https://github.com/KIT-MBS/coconet.

Zerihun Mehari B, Pucci Fabrizio, Schug Alexander

2021-Dec-06

Pathology Pathology

Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.

In Nucleic acids research ; h5-index 217.0

Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC-ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids.

Andreopoulos William B, Geller Alexander M, Lucke Miriam, Balewski Jan, Clum Alicia, Ivanova Natalia N, Levy Asaf

2021-Dec-06

General General

Towards Responsible Artificial Intelligence in Long-term Care: A Scoping Review on Practical Approaches.

In The Gerontologist

BACKGROUND AND OBJECTIVES : Artificial intelligence (AI) is widely positioned to become a key element of intelligent technologies used in the long-term care (LTC) for older adults. The increasing relevance and adoption of AI has encouraged debate over the societal and ethical implications of introducing and scaling AI. This scoping review investigates how the design and implementation of AI technologies in LTC is addressed responsibly: so called responsible innovation (RI).

RESEARCH DESIGN AND METHODS : We conducted a systematic literature search in five electronic databases using concepts related to LTC, AI and RI. We then performed a descriptive and thematic analysis to map the key concepts, types of evidence and gaps in the literature.

RESULTS : After reviewing 3,339 papers, 25 papers were identified that met our inclusion criteria. From this literature, we extracted three overarching themes: user-oriented AI innovation; framing AI as a solution to RI issues; and context-sensitivity. Our results provide an overview of measures taken and recommendations provided to address responsible AI innovation in LTC.

DISCUSSION AND IMPLICATIONS : The review underlines the importance of the context of use when addressing responsible AI innovation in LTC. However, limited empirical evidence actually details how responsible AI innovation is addressed in context. Therefore, we recommend expanding empirical studies on RI at the level of specific AI technologies and their local contexts of use. Also, we call for more specific frameworks for responsible AI innovation in LTC to flexibly guide researchers and innovators. Future frameworks should clearly distinguish between RI processes and outcomes.

Lukkien Dirk R M, Nap Henk Herman, Buimer Hendrik P, Peine Alexander, Boon Wouter P C, Ket Johannes C F, Minkman Mirella M N, Moors Ellen H M

2021-Dec-06

Ethics, Intelligent technology, Responsible innovation