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Deep Learning for Population Genetic Inference

Sara Sheehan, Yun S. Song • PLoS Computational Biology (2016)

Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep...

OPENALEX cc-by DOI: https://doi.org/10.1371/journal.pcbi.1004845 PMC: 4809617

Deep learning and computer vision will transform entomology

Toke T. Høye, Johanna Ärje, Kim Bjerge, Oskar Liset Pryds Hansen et al. • Proceedings of the National Academy of Sciences (2021)

ABSTRACT Most animal species on Earth are insects, and recent reports suggest that their abundance is in drastic decline. Although these reports come from a wide range of insect taxa and regions, the evidence to assess the extent of the phe...

OPENALEX cc-by DOI: https://doi.org/10.1073/pnas.2002545117 PMC: 7812775

Rapid profiling of carcinogenic types of Helicobacter pylori infection via deep learning analysis of label-free SERS spectra of human serum

Fen Li, Yu-Ting Si, Jia-Wei Tang, Zeeshan Umar et al. • Computational and Structural Biotechnology Journal (2024)

WHO classified Helicobacter pylori as a Group I carcinogen for gastric cancer as early as 1994. However, despite the high prevalence of H. pylori infection, only about 3 % of infected individuals eventually develop gastric cancer, with the ...

DOAJ Open Access (DOAJ) DOI: 10.1016/j.csbj.2024.09.008

Deep learning as a tool for ecology and evolution

Marek L. Borowiec, Rebecca B. Dikow, Paul B. Frandsen, Alexander J. McKeeken et al. • Methods in Ecology and Evolution (2022)

Abstract Deep learning is driving recent advances behind many everyday technologies, including speech and image recognition, natural language processing and autonomous driving. It is also gaining popularity in biology, where it has been use...

OPENALEX cc-by-nc DOI: https://doi.org/10.1111/2041-210x.13901

Deep Learning-Driven Predictive Modelling for Optimizing Stingless Beekeeping Yields

Noor Hafizah Khairul Anuar, Mohd Amri Md Yunus, Muhammad Ariff Baharudin, Sallehuddin Ibrahim et al. • Journal of Computing Research and Innovation (2024)

Environmental factors like temperature, solar irradiance, and rain may influence the health and productivity of stingless bees. This paper aims to investigate the best approaches applied in meliponiculture to predict beehive health and prod...

DOAJ Open Access (DOAJ)

Image-based quantification of histological features as a function of spatial location using the Tissue Positioning SystemResearch in context

Ruichen Rong, Yonglong Wei, Lin Li, Tao Wang et al. • EBioMedicine (2023)

Summary: Background: Tissues such as the liver lobule, kidney nephron, and intestinal gland exhibit intricate patterns of zonated gene expression corresponding to distinct cell types and functions. To quantitatively understand zonation, it...

DOAJ Open Access (DOAJ) DOI: 10.1016/j.ebiom.2023.104698

Applications for deep learning in ecology

Sylvain Christin, Éric Hervet, Nicolas Lecomte • Methods in Ecology and Evolution (2019)

Abstract A lot of hype has recently been generated around deep learning, a group of artificial intelligence approaches able to break accuracy records in pattern recognition. Over the course of just a few years, deep learning revolutionized ...

OPENALEX Open Access DOI: https://doi.org/10.1111/2041-210x.13256

A Cardiovascular Disease Prediction Model Based on Routine Physical Examination Indicators Using Machine Learning Methods: A Cohort Study

Xin Qian, Yu Li, Xianghui Zhang, Heng Guo et al. • Frontiers in Cardiovascular Medicine (2022)

BackgroundCardiovascular diseases (CVD) are currently the leading cause of premature death worldwide. Model-based early detection of high-risk populations for CVD is the key to CVD prevention. Thus, this research aimed to use machine learni...

DOAJ Open Access (DOAJ) DOI: 10.3389/fcvm.2022.854287

Cyclic multiplex fluorescent immunohistochemistry and machine learning reveal distinct states of astrocytes and microglia in normal aging and Alzheimer’s disease

Clara Muñoz-Castro, Ayush Noori, Colin G. Magdamo, Zhaozhi Li et al. • Journal of Neuroinflammation (2022)

Abstract Background Astrocytes and microglia react to Aβ plaques, neurofibrillary tangles, and neurodegeneration in the Alzheimer’s disease (AD) brain. Single-nuclei and single-cell RNA-seq have revealed multiple states or subpopulations of...

DOAJ Open Access (DOAJ) DOI: 10.1186/s12974-022-02383-4

On the use of aspect-based sentiment analysis of Twitter data to explore the experiences of African Americans during COVID-19

Meghna Chaudhary, Kristin Kosyluk, Sylvia Thomas, Tempestt Neal • Scientific Reports (2023)

Abstract According to data from the U.S. Center for Disease Control and Prevention, as of June 2020, a significant number of African Americans had been infected with the coronavirus disease, experiencing disproportionately higher death rate...

DOAJ Open Access (DOAJ) DOI: 10.1038/s41598-023-37592-1

A synergistic enhancement of the Ivy algorithm for GAN-based imbalanced classification

Hanjie Xu, Jian Xiong, Jinyu Wu, Xianlai Zhou et al. • Scientific Reports (2025)

Abstract The Ivy Algorithm (IVYA), a swarm intelligence algorithm inspired by plant growth, presents a novel framework for optimization. To unlock its full potential in complex, high-dimensional problems, it is crucial to address the fundam...

DOAJ Open Access (DOAJ) DOI: 10.1038/s41598-025-32510-z

Automated cell type annotation and exploration of single-cell signaling dynamics using mass cytometry

Dimitrios Kleftogiannnis, Sonia Gavasso, Benedicte Sjo Tislevoll, Nisha van der Meer et al. • iScience (2024)

Summary: Mass cytometry by time-of-flight (CyTOF) is an emerging technology allowing for in-depth characterization of cellular heterogeneity in cancer and other diseases. Unfortunately, high-dimensional analyses of CyTOF data remain quite d...

DOAJ Open Access (DOAJ) DOI: 10.1016/j.isci.2024.110261

Machine Learning in Healthcare

Hafsa Habehh, Suril Gohel • Current Genomics (2021)

Recent advancements in Artificial Intelligence (AI) and Machine Learning (ML) technology have brought on substantial strides in predicting and identifying health emergencies, disease populations, and disease state and immune response, among...

OPENALEX Open Access DOI: https://doi.org/10.2174/1389202922666210705124359 PMC: 8822225

Epistemic frontiers and the distinction between causality, information, and predictability in pattern recognition

Pablo Neirz, Héctor Allende, Carolina Saavedra • Scientific Reports (2026)

Abstract High predictive accuracy is frequently misinterpreted as evidence of causal understanding or population-level signal. Models can exploit spurious correlations, confounding, or protocol-induced artefacts, while post-hoc explanations...

DOAJ Open Access (DOAJ) DOI: 10.1038/s41598-026-52883-z

Directional Gaussian Mixture Models of the Gut Microbiome Elucidate Microbial Spatial Structure

Amey P. Pasarkar, Tyler A. Joseph, Itsik Pe’er • mSystems (2021)

ABSTRACT The gut microbiome is spatially heterogeneous, with environmental niches contributing to the distribution and composition of microbial populations. A recently developed mapping technology, MaPS-seq, aims to characterize the spatial...

DOAJ Open Access (DOAJ) DOI: 10.1128/mSystems.00817-21