Prevalence of processed foods in major US grocery stores.

The offering of grocery stores is a strong driver of consumer decisions. While highly processed foods such as packaged products, processed meat and sweetened soft drinks have been increasingly associated with unhealthy diets, information on the degree of processing characterizing an item in a store is not straightforward to obtain, limiting the ability of individuals to make informed choices. GroceryDB, a database with over 50,000 food items sold by Walmart, Target and Whole Foods, shows the degree of processing of food items and potential alternatives in the surrounding food environment.

NetMedPy: A Python package for Large-Scale Network Medicine Screening.

Network medicine leverages the quantification of information flow within sub-cellular networks to elucidate disease etiology and comorbidity, as well as to predict drug efficacy and identify potential therapeutic targets. However, current Network Medicine toolsets often lack computationally efficient data processing pipelines that support diverse scoring functions, network distance metrics, and null models. These limitations hamper their application in large-scale molecular screening, hypothesis testing, and ensemble modeling.

GroceryDB: Prevalence of Processed Food in Grocery Stores.

The offering of grocery stores is a strong driver of consumer decisions, shaping their diet and long-term health. While highly processed food like packaged products, processed meat, and sweetened soft drinks have been increasingly associated with unhealthy diet, information on the degree of processing characterizing an item in a store is not straightforward to obtain, limiting the ability of individuals to make informed choices. Here we introduce GroceryDB, a database with over 50,000 food items sold by Walmart, Target, and Wholefoods, unveiling how big data can be harnessed to empower consumers and policymakers with systematic access to the degree of processing of the foods they select, and the potential alternatives in the surrounding food environment.

The clinical trials puzzle: How network effects limit drug discovery.

The depth of knowledge offered by post-genomic medicine has carried the promise of new drugs, and cures for multiple diseases. To explore the degree to which this capability has materialized, we extract meta-data from 356,403 clinical trials spanning four decades, aiming to offer mechanistic insights into the innovation practices in drug discovery. We find that convention dominates over innovation, as over 96% of the recorded trials focus on previously tested drug targets, and the tested drugs target only 12% of the human interactome.

A network-based normalized impact measure reveals successful periods of scientific discovery across discipline.

The impact of a scientific publication is often measured by the number of citations it receives from the scientific community. However, citation count is susceptible to well-documented variations in citation practices across time and discipline, limiting our ability to compare different scientific achievements. Previous efforts to account for citation variations often rely on a priori discipline labels of papers, assuming that all papers in a discipline are identical in their subject matter.

Noncoding RNAs improve the predictive power of network medicine.

Network medicine has improved the mechanistic understanding of disease, offering quantitative insights into disease mechanisms, comorbidities, and novel diagnostic tools and therapeutic treatments. Yet, most network-based approaches rely on a comprehensive map of protein-protein interactions (PPI), ignoring interactions mediated by noncoding RNAs (ncRNAs). Here, we systematically combine experimentally confirmed binding interactions mediated by ncRNA with PPI, constructing a comprehensive network of all physical interactions in the human cell.

Quantifying hierarchy and prestige in US ballet academies as social predictors of career success.

In the recent decade, we have seen major progress in quantifying the behaviors and the impact of scientists, resulting in a quantitative toolset capable of monitoring and predicting the career patterns of the profession. It is unclear, however, if this toolset applies to other creative domains beyond the sciences. In particular, while performance in the arts has long been difficult to quantify objectively, research suggests that professional networks and prestige of affiliations play a similar role to those observed in science, hence they can reveal patterns underlying successful careers.

Machine learning prediction of the degree of food processing.

Despite the accumulating evidence that increased consumption of ultra-processed food has adverse health implications, it remains difficult to decide what constitutes processed food. Indeed, the current processing-based classification of food has limited coverage and does not differentiate between degrees of processing, hindering consumer choices and slowing research on the health implications of processed food. Here we introduce a machine learning algorithm that accurately predicts the degree of processing for any food, indicating that over 73% of the US food supply is ultra-processed.

Improving the generalizability of protein-ligand binding predictions with AI-Bind.

Identifying novel drug-target interactions is a critical and rate-limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, here we show that state-of-the-art models fail to generalize to novel (i.e.

Accelerating network layouts using graph neural networks.

Graph layout algorithms used in network visualization represent the first and the most widely used tool to unveil the inner structure and the behavior of complex networks. Current network visualization software relies on the force-directed layout (FDL) algorithm, whose high computational complexity makes the visualization of large real networks computationally prohibitive and traps large graphs into high energy configurations, resulting in hard-to-interpret "hairball" layouts. Here we use Graph Neural Networks (GNN) to accelerate FDL, showing that deep learning can address both limitations of FDL: it offers a 10 to 100 fold improvement in speed while also yielding layouts which are more informative.

Genomics and phenomics of body mass index reveals a complex disease network.

Elevated body mass index (BMI) is heritable and associated with many health conditions that impact morbidity and mortality. The study of the genetic association of BMI across a broad range of common disease conditions offers the opportunity to extend current knowledge regarding the breadth and depth of adiposity-related diseases. We identify 906 (364 novel) and 41 (6 novel) genome-wide significant loci for BMI among participants of European (N~1.

Fragmentation of outage clusters during the recovery of power distribution grids.

The understanding of recovery processes in power distribution grids is limited by the lack of realistic outage data, especially large-scale blackout datasets. By analyzing data from three electrical companies across the United States, we find that the recovery duration of an outage is connected with the downtime of its nearby outages and blackout intensity (defined as the peak number of outages during a blackout), but is independent of the number of customers affected. We present a cluster-based recovery framework to analytically characterize the dependence between outages, and interpret the dominant role blackout intensity plays in recovery.

MilkyBase, a database of human milk composition as a function of maternal-, infant- and measurement conditions.

This study describes the development of a database, called MilkyBase, of the biochemical composition of human milk. The data were selected, digitized and curated partly by machine-learning, partly manually from publications. The database can be used to find patterns in the milk composition as a function of maternal-, infant- and measurement conditions and as a platform for users to put their own data in the format shown here.

Visualizing novel connections and genetic similarities across diseases using a network-medicine based approach.

Understanding the genetic relationships between human disorders could lead to better treatment and prevention strategies, especially for individuals with multiple comorbidities. A common resource for studying genetic-disease relationships is the GWAS Catalog, a large and well curated repository of SNP-trait associations from various studies and populations. Some of these populations are contained within mega-biobanks such as the Million Veteran Program (MVP), which has enabled the genetic classification of several diseases in a large well-characterized and heterogeneous population.

Network-medicine framework for studying disease trajectories in U.S. veterans.

A better understanding of the sequential and temporal aspects in which diseases occur in patient's lives is essential for developing improved intervention strategies that reduce burden and increase the quality of health services. Here we present a network-based framework to study disease relationships using Electronic Health Records from > 9 million patients in the United States Veterans Health Administration (VHA) system. We create the Temporal Disease Network, which maps the sequential aspects of disease co-occurrence among patients and demonstrate that network properties reflect clinical aspects of the respective diseases.

Dynamics of ranking.

Virtually anything can be and is ranked; people, institutions, countries, words, genes. Rankings reduce complex systems to ordered lists, reflecting the ability of their elements to perform relevant functions, and are being used from socioeconomic policy to knowledge extraction. A century of research has found regularities when temporal rank data is aggregated.

Quantifying NFT-driven networks in crypto art.

The evolution of the art ecosystem is driven by largely invisible networks, defined by undocumented interactions between artists, institutions, collectors and curators. The emergence of cryptoart, and the NFT-based digital marketplace around it, offers unprecedented opportunities to examine the mechanisms that shape the evolution of networks that define artistic practice. Here we mapped the Foundation platform, identifying over 48,000 artworks through the associated NFTs listed by over 15,000 artists, allowing us to characterize the patterns that govern the networks that shape artistic success.

Recovery coupling in multilayer networks.

The increased complexity of infrastructure systems has resulted in critical interdependencies between multiple networks-communication systems require electricity, while the normal functioning of the power grid relies on communication systems. These interdependencies have inspired an extensive literature on coupled multilayer networks, assuming a hard interdependence, where a component failure in one network causes failures in the other network, resulting in a cascade of failures across multiple systems. While empirical evidence of such hard failures is limited, the repair and recovery of a network requires resources typically supplied by other networks, resulting in documented interdependencies induced by the recovery process.

Network medicine framework for identifying drug-repurposing opportunities for COVID-19.

The COVID-19 pandemic has highlighted the need to quickly and reliably prioritize clinically approved compounds for their potential effectiveness for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Here, we deployed algorithms relying on artificial intelligence, network diffusion, and network proximity, tasking each of them to rank 6,340 drugs for their expected efficacy against SARS-CoV-2. To test the predictions, we used as ground truth 918 drugs experimentally screened in VeroE6 cells, as well as the list of drugs in clinical trials that capture the medical community's assessment of drugs with potential COVID-19 efficacy.

Uncovering the genetic blueprint of the nervous system.

Despite rapid advances in connectome mapping and neuronal genetics, we lack theoretical and computational tools to unveil, in an experimentally testable fashion, the genetic mechanisms that govern neuronal wiring. Here we introduce a computational framework to link the adjacency matrix of a connectome to the expression patterns of its neurons, helping us uncover a set of genetic rules that govern the interactions between neurons in contact. The method incorporates the biological realities of the system, accounting for noise from data collection limitations, as well as spatial restrictions.

A systematic comprehensive longitudinal evaluation of dietary factors associated with acute myocardial infarction and fatal coronary heart disease.

Environmental factors, and in particular diet, are known to play a key role in the development of Coronary Heart Disease. Many of these factors were unveiled by detailed nutritional epidemiology studies, focusing on the role of a single nutrient or food at a time. Here, we apply an Environment-Wide Association Study approach to Nurses' Health Study data to explore comprehensively and agnostically the association of 257 nutrients and 117 foods with coronary heart disease risk (acute myocardial infarction and fatal coronary heart disease).

Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19.

The current pandemic has highlighted the need for methodologies that can quickly and reliably prioritize clinically approved compounds for their potential effectiveness for SARS-CoV-2 infections. In the past decade, network medicine has developed and validated multiple predictive algorithms for drug repurposing, exploiting the sub-cellular network-based relationship between a drug's targets and disease genes. Here, we deployed algorithms relying on artificial intelligence, network diffusion, and network proximity, tasking each of them to rank 6,340 drugs for their expected efficacy against SARS-CoV-2.

Synthetic ablations in the nervous system.

Synthetic lethality, the finding that the simultaneous knockout of two or more individually nonessential genes leads to cell or organism death, has offered a systematic framework to explore cellular function, and also offered therapeutic applications. Yet the concept lacks its parallel in neuroscience-a systematic knowledge base on the role of double or higher order ablations in the functioning of a neural system. Here, we use the framework of network control to systematically predict the effects of ablating neuron pairs and triplets on the gentle touch response.