Nova Reader - Subject

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

2021-04-05T00:00

Learning biological properties from sequence data is a logical step toward generative and predictive artificial intelligence for biology. Here, we propose scaling a deep contextual language model with unsupervised learning to sequences spanning evolutionary diversity. We find that without prior knowledge, information emerges in the learned representations on fundamental properties of proteins such as secondary structure, contacts, and biological activity. We show the learned representations are useful across benchmarks for remote homology detection, prediction of secondary structure, long-range residue–residue contacts, and mutational effect. Unsupervised representation learning enables state-of-the-art supervised prediction of mutational effect and secondary structure and improves state-of-the-art features for long-range contact prediction.

In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. In the life sciences, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity. Protein language modeling at the scale of evolution is a logical step toward predictive and generative artificial intelligence for biology. To this end, we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. The resulting model contains information about biological properties in its representations. The representations are learned from sequence data alone. The learned representation space has a multiscale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. Information about secondary and tertiary structure is encoded in the representations and can be identified by linear projections. Representation learning produces features that generalize across a range of applications, enabling state-of-the-art supervised prediction of mutational effect and secondary structure and improving state-of-the-art features for long-range contact prediction.

Exposure density and neighborhood disparities in COVID-19 infection risk

2021-03-16T00:00

We present a computational approach to measure exposure density at high spatial and temporal resolution to understand neighborhood disparities in transmission risk of COVID-19. By integrating geolocation data and granular land-use information, we are able to establish both the extent of activity in a particular neighborhood and the nature of that activity across residential, nonresidential, and outdoor activities. We then analyze the differential behavioral response to social-distancing policies based on local risk factors, built-environment characteristics, and socioeconomic inequality. Our results highlight the significant disparities in health outcomes for racial and ethnic minorities and lower-income households. Exposure density provides an additional metric to further explain and understand the disparate impact of COVID-19 on vulnerable communities.

Although there is increasing awareness of disparities in COVID-19 infection risk among vulnerable communities, the effect of behavioral interventions at the scale of individual neighborhoods has not been fully studied. We develop a method to quantify neighborhood activity behaviors at high spatial and temporal resolutions and test whether, and to what extent, behavioral responses to social-distancing policies vary with socioeconomic and demographic characteristics. We define exposure density (Exρ

) as a measure of both the localized volume of activity in a defined area and the proportion of activity occurring in distinct land-use types. Using detailed neighborhood data for New York City, we quantify neighborhood exposure density using anonymized smartphone geolocation data over a 3-mo period covering more than 12 million unique devices and rasterize granular land-use information to contextualize observed activity. Next, we analyze disparities in community social distancing by estimating variations in neighborhood activity by land-use type before and after a mandated stay-at-home order. Finally, we evaluate the effects of localized demographic, socioeconomic, and built-environment density characteristics on infection rates and deaths in order to identify disparities in health outcomes related to exposure risk. Our findings demonstrate distinct behavioral patterns across neighborhoods after the stay-at-home order and that these variations in exposure density had a direct and measurable impact on the risk of infection. Notably, we find that an additional 10% reduction in exposure density city-wide could have saved between 1,849 and 4,068 lives during the study period, predominantly in lower-income and minority communities.

The echo chamber effect on social media

2021-02-23T00:00

We explore the key differences between the main social media platforms and how they are likely to influence information spreading and the formation of echo chambers. To assess the different dynamics, we perform a comparative analysis on more than 100 million pieces of content concerning controversial topics (e.g., gun control, vaccination, abortion) from Gab, Facebook, Reddit, and Twitter. The analysis focuses on two main dimensions: 1) homophily in the interaction networks and 2) bias in the information diffusion toward like-minded peers. Our results show that the aggregation in homophilic clusters of users dominates online dynamics. However, a direct comparison of news consumption on Facebook and Reddit shows higher segregation on Facebook.

Social media may limit the exposure to diverse perspectives and favor the formation of groups of like-minded users framing and reinforcing a shared narrative, that is, echo chambers. However, the interaction paradigms among users and feed algorithms greatly vary across social media platforms. This paper explores the key differences between the main social media platforms and how they are likely to influence information spreading and echo chambers’ formation. We perform a comparative analysis of more than 100 million pieces of content concerning several controversial topics (e.g., gun control, vaccination, abortion) from Gab, Facebook, Reddit, and Twitter. We quantify echo chambers over social media by two main ingredients: 1) homophily in the interaction networks and 2) bias in the information diffusion toward like-minded peers. Our results show that the aggregation of users in homophilic clusters dominate online interactions on Facebook and Twitter. We conclude the paper by directly comparing news consumption on Facebook and Reddit, finding higher segregation on Facebook.