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Machine learning and deep learning applications in microbiome research

Ricardo Hernández Medina, Svetlana Kutuzova, Knud Nor Nielsen, Joachim Johansen et al. • ISME Communications (2022)

The many microbial communities around us form interactive and dynamic ecosystems called microbiomes. Though concealed from the naked eye, microbiomes govern and influence macroscopic systems including human health, plant resilience, and bio...

OPENALEX cc-by DOI: https://doi.org/10.1038/s43705-022-00182-9 PMC: 9723725

A State-of-the-Art Survey on Deep Learning Theory and Architectures

Md Zahangir Alom, Tarek M. Taha, Chris Yakopcic, Stefan K.E. Westberg et al. • Electronics (2019)

In recent years, deep learning has garnered tremendous success in a variety of application domains. This new field of machine learning has been growing rapidly and has been applied to most traditional application domains, as well as some ne...

OPENALEX cc-by DOI: https://doi.org/10.3390/electronics8030292

Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology

Thomas Hu, Mayar Allam, Shuangyi Cai, Walter Henderson et al. • Nature Communications (2023)

Abstract Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell Spatially resolved Metabolic (scSpaMet) framework for joint protein-metabolite pr...

DOAJ Open Access (DOAJ) DOI: 10.1038/s41467-023-43917-5

Intelligent diagnosis with Chinese electronic medical records based on convolutional neural networks

Xiaozheng Li, Huazhen Wang, Huixin He, Jixiang Du et al. • BMC Bioinformatics (2019)

Abstract Background Benefiting from big data, powerful computation and new algorithmic techniques, we have been witnessing the renaissance of deep learning, particularly the combination of natural language processing (NLP) and deep neural n...

DOAJ Open Access (DOAJ) DOI: 10.1186/s12859-019-2617-8

Deep Learning for PET Image Reconstruction

Andrew J. Reader, Guillaume Corda-D’Incan, Abolfazl Mehranian, Casper O. da Costa-Luis et al. • IEEE Transactions on Radiation and Plasma Medical Sciences (2020)

This article reviews the use of a subdiscipline of artificial intelligence (AI), deep learning, for the reconstruction of images in positron emission tomography (PET). Deep learning can be used either directly or as a component of conventio...

OPENALEX Open Access DOI: https://doi.org/10.1109/trpms.2020.3014786

DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs

Fenglei Li, Qiaoyu Hu, Xianglei Zhang, Renhong Sun et al. • Nature Communications (2022)

The rational design of PROTACs is difficult due to their obscure structure-activity relationship. Here the authors present a deep neural network model - DeepPROTACs - for predicting the degradation capacity of a proposed PROTAC molecule....

DOAJ Open Access (DOAJ) DOI: 10.1038/s41467-022-34807-3

MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites

Chengqi Wang, Yibo Dong, Chang Li, Jenna Oberstaller et al. • Genome Biology (2023)

Abstract Malaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab initio deep learning f...

DOAJ Open Access (DOAJ) DOI: 10.1186/s13059-023-03063-z

Spatiotemporal prediction of sneeze pollutants in enclosed spaces: a CNN-LSTM approach validated by field measurements and CFD-Robotics arm twin system

Mingyu Zhao, Shujia Zhang, Ke Li, Yanru Zhang et al. • Frontiers in Robotics and AI (2026)

Densely populated enclosed environments, characterized by complex thermal stratification and overlapping breathing zones, represent high-risk clusters for the airborne transmission of respiratory pathogens. To address the dual challenges of...

DOAJ Open Access (DOAJ) DOI: 10.3389/frobt.2026.1846010

An overview of deep learning in medical imaging focusing on MRI

Alexander Selvikvåg Lundervold, Arvid Lundervold • Zeitschrift für Medizinische Physik (2018)

What has happened in machine learning lately, and what does it mean for the future of medical image analysis? Machine learning has witnessed a tremendous amount of attention over the last few years. The current boom started around 2009 when...

OPENALEX cc-by DOI: https://doi.org/10.1016/j.zemedi.2018.11.002

Deep learning in food category recognition

Yudong Zhang, Lijia Deng, Hengde Zhu, Wei Wang et al. • Information Fusion (2023)

Integrating artificial intelligence with food category recognition has been a field of interest for research for the past few decades. It is potentially one of the next steps in revolutionizing human interaction with food. The modern advent...

OPENALEX cc-by DOI: https://doi.org/10.1016/j.inffus.2023.101859

Deep learning applications and challenges in big data analytics

Maryam Mousaarab Najafabadi, Flavio Villanustre, Taghi M. Khoshgoftaar, Naeem Seliya et al. • Journal Of Big Data (2015)

Abstract Big Data Analytics and Deep Learning are two high-focus of data science. Big Data has become important as many organizations both public and private have been collecting massive amounts of domain-specific information, which can con...

OPENALEX cc-by DOI: https://doi.org/10.1186/s40537-014-0007-7

Presenting the students’ academic achievement causal model based on goal orientation

EBRAHIM NASIRI, ALI POUR-SAFAR, MAHDOKHT TAHERI, ABDULLAH SEDIGHI PASHAKY et al. • Journal of Advances in Medical Education and Professionalism (2017)

Introduction: Several factors play a role in academic achievement, individual’s excellence and capability to do actions and tasks that the learner is in charge of in learning areas. The main goal of this study was to present academic ach...

DOAJ Open Access (DOAJ)

A learning‐based energy management strategy for hybrid energy storage systems with compressed air and solid oxide fuel cells

Yundie Guan, Xiangyu Zhang, Zheming Liang, Tao Chen • IET Renewable Power Generation (2025)

Abstract The intermittency and volatility of renewable energy have been major challenges in modern power systems. This paper proposes a self‐adaptive energy management strategy based on deep reinforcement learning (DRL) to integrate renewab...

DOAJ Open Access (DOAJ) DOI: 10.1049/rpg2.13192

ACtriplet: An improved deep learning model for activity cliffs prediction by integrating triplet loss and pre-training

Xinxin Yu, Yimeng Wang, Long Chen, Weihua Li et al. • Journal of Pharmaceutical Analysis (2025)

Activity cliffs (ACs) are generally defined as pairs of similar compounds that only differ by a minor structural modification but exhibit a large difference in their binding affinity for a given target. ACs offer crucial insights that aid m...

DOAJ Open Access (DOAJ) DOI: 10.1016/j.jpha.2025.101317