Advancements in artificial intelligence (AI) have transformed many scientific fields, with microbiology and microbiome research now experiencing significant breakthroughs through machine learning and deep learning applications. This review provides a comprehensive overview of AI-driven approaches tailored for microbiology and microbiome studies, emphasizing both technical advancements and biological insights. We begin with an introduction to foundational AI techniques, including primary machine learning paradigms and various deep learning architectures, and offer guidance on choosing between machine learning and deep learning methods based on specific research goals. The primary section on application scenarios spans diverse research areas, from taxonomic profiling, functional annotation & prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, clinical microbiology, to prevention & therapeutics. Finally, we discuss challenges unique to this field, including the balance between interpretability and complexity, the "small n, large p" problem, and the critical need for standardized benchmarking datasets to validate and compare models. Together, this review underscores AI's transformative role in microbiology and microbiome research, paving the way for innovative methodologies and applications that enhance our understanding of microbial life and its impact on our planet and our health.

Accurate weather forecasting is of paramount importance for a wide range of practical applications, drawing substantial scientific and societal interest. However, the intricacies of weather systems pose substantial challenges to accurate predictions. This research introduces a multilayer perceptron model tailored for weather forecasting in Itoshima, Kyushu, Japan. Our meticulously designed architecture demonstrates superior performance compared to existing models, surpassing benchmarks such as Long Short-Term Memory and Recurrent Neural Networks.

The generation of synthetic tabular data that preserves differential privacy is a problem of growing importance. While traditional marginal-based methods have achieved impressive results, recent work has shown that deep learning-based approaches tend to lag behind. In this work, we present Differentially-Private TaBular AutoRegressive Transformer (DP-TBART), a transformer-based autoregressive model that maintains differential privacy and achieves performance competitive with marginal-based methods on a wide variety of datasets, capable of even outperforming state-of-the-art methods in certain settings. We also provide a theoretical framework for understanding the limitations of marginal-based approaches and where deep learning-based approaches stand to contribute most. These results suggest that deep learning-based techniques should be considered as a viable alternative to marginal-based methods in the generation of differentially private synthetic tabular data.

The development of phase-based techniques has accelerated the pace of X-ray imaging. Dark-field images are sensitive to inhomogeneities on a length scale below the system's spatial resolution, and phase contrast images are improved for detailed visibility. A new technique for X-raying luggage to find trace levels of explosives was developed by a team of researchers from University College London, Nylers Ltd., and XPCI Technology Ltd. They demonstrated how dark-field produces a texture specific to the substance being photographed and how combining it with traditional attenuation improves the ability to distinguish amongst threat materials. They have also published their work in Nature Communications journal, which involves adapting a conventional X-ray detector and using a deep-learning application to better detect hazardous chemicals in luggage.

Abstract: Although existing monocular depth estimation methods have made great progress, predicting an accurate absolute depth map from a single image is still challenging due to the limited modeling capacity of networks and the scale ambiguity issue. In this paper, we introduce a fully Visual Attention-based Depth (VADepth) network, where spatial attention and channel attention are applied to all stages. By continuously extracting the dependencies of features along the spatial and channel dimensions over a long distance, VADepth network can effectively preserve important details and suppress interfering features to better perceive the scene structure for more accurate depth estimates. In addition, we utilize geometric priors to form scale constraints for scale-aware model training. Specifically, we construct a novel scale-aware loss using the distance between the camera and a plane fitted by the ground points corresponding to the pixels of the rectangular area in the bottom middle of the image.

In recent years, deep learning-based methods have emerged as promising tools for de novo drug design. Most of these methods are ligand-based, where an initial target-specific ligand data set is necessary to design potent molecules with optimized properties. Although there have been attempts to develop alternative ways to design target-specific ligand data sets, availability of such data sets remains a challenge while designing molecules against novel target proteins. In this work, we propose a deep learning-based method, where the knowledge of the active site structure of the target protein is sufficient to design new molecules. First, a graph attention model was used to learn the structure and features of the amino acids in the active site of proteins that are experimentally known to form protein–ligand complexes.

Summary: A new AI algorithm can predict the onset of Alzheimer's disease with an accuracy of over 99% by analyzing fMRI brain scans. Researchers from Kaunas University, Lithuania developed a deep learning-based method that can predict the possible onset of Alzheimer's disease from brain images with an accuracy of over 99 percent. The method was developed while analyzing functional MRI images obtained from 138 subjects and performed better in terms of accuracy, sensitivity, and specificity than previously developed methods. According to World Health Organisation, Alzheimer's disease is the most frequent cause of dementia, contributing to up to 70 percent of dementia cases. Worldwide, approximately 24 million people are affected, and this number is expected to double every 20 years.

MIT researchers have developed a way to produce holograms almost instantly. They say the deep learning-based method is so efficient that it could run on a smartphone. A new method called tensor holography could enable the creation of holograms for virtual reality, 3D printing, medical imaging, and more -- and it can run on a smartphone. Despite years of hype, virtual reality headsets have yet to topple TV or computer screens as the go-to devices for video viewing. One reason: VR can make users feel sick.

Facial pose estimation has gained a lot of attentions in many practical applications, such as human-robot interaction, gaze estimation and driver monitoring. Meanwhile, end-to-end deep learning-based facial pose estimation is becoming more and more popular. However, facial pose estimation suffers from a key challenge: the lack of sufficient training data for many poses, especially for large poses. Inspired by the observation that the faces under close poses look similar, we reformulate the facial pose estimation as a label distribution learning problem, considering each face image as an example associated with a Gaussian label distribution rather than a single label, and construct a convolutional neural network which is trained with a multi-loss function on AFLW dataset and 300WLP dataset to predict the facial poses directly from color image. Extensive experiments are conducted on several popular benchmarks, including AFLW2000, BIWI, AFLW and AFW, where our approach shows a significant advantage over other state-of-the-art methods.

Researchers at King Saud University, in Saudi Arabia, have developed a new approach to detect cyberbullying on Twitter using deep learning called OCDD. In contrast with other deep-learning approaches, which extract features from tweets and feed them to a classifier, their method represents a tweet as a set of word vectors. In recent years, cyberbullying on social media has become a huge and widely discussed issue. Cyberbullying entails the use of online communication channels to bully other users by sending intimidating, threatening or abusive messages. This can have psychological and sometimes life-threatening consequences for the victims.