The preservation of soil health has been identified as one of the main challenges of the XXI century given its vast (and potentially threatening) ramifications in agriculture, human health and biodiversity. Here, we provide the first deep investigation of the predictive potential of machine-learning models to understand the connections between soil and biological phenotypes. Indeed, we investigate an integrative framework performing accurate machine-learning-based prediction of plant phenotypes from biological, chemical and physical properties of the soil via two models: random forest and Bayesian neural network. We show that prediction is improved, as evidenced by higher weighted F1 scores, when incorporating into the models environmental features like soil physicochemical properties and microbial population density in addition to the microbiome information. Furthermore, by exploring multiple data preprocessing strategies such as normalization, zero replacement, and data augmentation, we confirm that human decisions have a huge impact on the predictive performance. In particular, we show that the naive total sum scaling normalization that is commonly used in microbiome research is not the optimal strategy to maximize predictive power. In addition, we find that accurately defined labels are more important than normalization, taxonomic level or model characteristics. That is, if humans are unable to classify the samples and provide accurate labels, the performance of machine-learning models will be limited. Lastly, we present strategies for domain scientists via a full model selection decision tree to identify the human choices that maximize the prediction power of the models. Our work is accompanied by open source reproducible scripts (https://github.com/solislemuslab/soil-microbiome-nn) for maximum outreach among the microbiome research community.

Recent advancements in the acquisition of various brain data sources have created new opportunities for integrating multimodal brain data to assist in early detection of complex brain disorders. However, current data integration approaches typically need a complete set of biomedical data modalities, which may not always be feasible, as some modalities are only available in large-scale research cohorts and are prohibitive to collect in routine clinical practice. Especially in studies of brain diseases, research cohorts may include both neuroimaging data and genetic data, but for practical clinical diagnosis, we often need to make disease predictions only based on neuroimages. As a result, it is desired to design machine learning models which can use all available data (different data could provide complementary information) during training but conduct inference using only the most common data modality. We propose a new incomplete multimodal data integration approach that employs transformers and generative adversarial networks to effectively exploit auxiliary modalities available during training in order to improve the performance of a unimodal model at inference. We apply our new method to predict cognitive degeneration and disease outcomes using the multimodal imaging genetic data from Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Experimental results demonstrate that our approach outperforms the related machine learning and deep learning methods by a significant margin.

Machine learning can pinpoint "genes of importance" that help crops to grow with less fertilizer, according to a new study published in Nature Communications. It can also predict additional traits in plants and disease outcomes in animals, illustrating its applications beyond agriculture. Using genomic data to predict outcomes in agriculture and medicine is both a promise and challenge for systems biology. Researchers have been working to determine how to best use the vast amount of genomic data available to predict how organisms respond to changes in nutrition, toxins and pathogen exposure--which in turn would inform crop improvement, disease prognosis, epidemiology and public health. However, accurately predicting such complex outcomes in agriculture and medicine from genome-scale information remains a significant challenge.

A new study identifies genes that enable plants to grow with less fertilizer. Machine learning, a type of artificial intelligence used to detect patterns in data, can pinpoint "genes of importance" that help crops grow with less fertilizer, according to a U.S. National Science Foundation-funded study published in Nature Communications. It can also predict additional traits in plants and disease outcomes in animals, illustrating its applications beyond agriculture. "This is an excellent example of how NSF-supported scientists lead the way in using AI and cutting-edge computational approaches to accelerate translation of basic plant genomic research and discoveries to the field," said Diane Okamuro, a program director in NSF's Division of Integrative Organismal Systems. Using genomic data to predict outcomes in agriculture and medicine is both a promise and challenge for systems biology.

Machine learning can pinpoint "genes of importance" that help crops to grow with less fertilizer, according to a new study published in Nature Communications. It can also predict additional traits in plants and disease outcomes in animals, illustrating its applications beyond agriculture. Using genomic data to predict outcomes in agriculture and medicine is both a promise and challenge for systems biology. Researchers have been working to determine how to best use the vast amount of genomic data available to predict how organisms respond to changes in nutrition, toxins, and pathogen exposure-;which in turn would inform crop improvement, disease prognosis, epidemiology, and public health. However, accurately predicting such complex outcomes in agriculture and medicine from genome-scale information remains a significant challenge. In the Nature Communications study, NYU researchers and collaborators in the U.S. and Taiwan tackled this challenge using machine learning, a type of artificial intelligence used to detect patterns in data.

Machine learning can pinpoint "genes of importance" that help crops to grow with less fertilizer, according to a new study published in Nature Communications. It can also predict additional traits in plants and disease outcomes in animals, illustrating its applications beyond agriculture. Using genomic data to predict outcomes in agriculture and medicine is both a promise and challenge for systems biology. Researchers have been working to determine how to best use the vast amount of genomic data available to predict how organisms respond to changes in nutrition, toxins, and pathogen exposure--which in turn would inform crop improvement, disease prognosis, epidemiology, and public health. However, accurately predicting such complex outcomes in agriculture and medicine from genome-scale information remains a significant challenge.

The intent of this work is to speed up drug repurposing, which is not a new concept -- think Botox injections, first approved to treat crossed eyes and now a migraine treatment and top cosmetic strategy to reduce the appearance of wrinkles. But getting to those new uses typically involves a mix of serendipity and time-consuming and expensive randomized clinical trials to ensure that a drug deemed effective for one disorder will be useful as a treatment for something else. The Ohio State University researchers created a framework that combines enormous patient care-related datasets with high-powered computation to arrive at repurposed drug candidates and the estimated effects of those existing medications on a defined set of outcomes. Though this study focused on proposed repurposing of drugs to prevent heart failure and stroke in patients with coronary artery disease, the framework is flexible -- and could be applied to most diseases. "This work shows how artificial intelligence can be used to'test' a drug on a patient, and speed up hypothesis generation and potentially speed up a clinical trial," said senior author Ping Zhang, assistant professor of computer science and engineering and biomedical informatics at Ohio State.

Health care leaders are embracing AI. But by conducting an extensive review of case studies and research literature, we've found that their AI initiatives are predominantly focused on developing algorithms that can predict a problem such as cancer in order to make diagnoses better, faster, and less expensively. Rarely, are their organizations devoting resources to AI efforts aimed at understanding why diseases occur. To intervene as effectively as possible, both kinds of algorithms are crucial. To be clear, we are not downplaying the importance of predictive analytics to help diagnose patients.

Health care leaders are embracing AI. But by conducting an extensive review of case studies and research literature, we've found that their AI initiatives are predominantly focused on developing algorithms that can predict a problem such as cancer in order to make diagnoses better, faster, and less expensively. Rarely, are their organizations devoting resources to AI efforts aimed at understanding why diseases occur. To intervene as effectively as possible, both kinds of algorithms are crucial. To be clear, we are not downplaying the importance of predictive analytics to help diagnose patients.