More Like this

1. Mutualistic networks: moving closer to a predictive theory

   https://doi.org/10.1111/ele.13279  

   Valdovinos, Fernanda_S; Hillebrand, ed., Helmut (June 2019, Ecology Letters)

   Abstract Plant–animal mutualistic networks sustain terrestrial biodiversity and human food security. Global environmental changes threaten these networks, underscoring the urgency for developing a predictive theory on how networks respond to perturbations. Here, I synthesise theoretical advances towards predicting network structure, dynamics, interaction strengths and responses to perturbations. I find that mathematical models incorporating biological mechanisms of mutualistic interactions provide better predictions of network dynamics. Those mechanisms include trait matching, adaptive foraging, and the dynamic consumption and production of both resources and services provided by mutualisms. Models incorporating species traits better predict the potential structure of networks (fundamental niche), while theory based on the dynamics of species abundances, rewards, foraging preferences and reproductive services can predict the extremely dynamic realised structures of networks, and may successfully predict network responses to perturbations. From a theoretician's standpoint, model development must more realistically represent empirical data on interaction strengths, population dynamics and how these vary with perturbations from global change. From an empiricist's standpoint, theory needs to make specific predictions that can be tested by observation or experiments. Developing models using short‐term empirical data allows models to make longer term predictions of community dynamics. As more longer term data become available, rigorous tests of model predictions will improve. 

   more » « less
2. Macrosystems EDDIE Module 6: Understanding Uncertainty in Ecological Forecasts (Instructor Materials)

   https://doi.org/10.6073/pasta/1ce758925388a9273083c24ed0ee0c05  

   Moore, Tadhg N.; Lofton, Mary E.; Carey, Cayelan C.; Thomas, R. Quinn (December 2023, Environmental Data Initiative)

   This EDI data package contains instructional materials necessary to teach Macrosystems EDDIE Module 6: Understanding Uncertainty in Ecological Forecasts, a ~3-hour educational module for undergraduates. Ecological forecasting is an emerging approach that provides an estimate of the future state of an ecological system with uncertainty, allowing society to prepare for changes in important ecosystem services. Forecast uncertainty is derived from multiple sources, including model parameters and driver data, among others. Knowing the uncertainty associated with a forecast enables forecast users to evaluate the forecast and make more informed decisions. This module will guide students through an exploration of the sources of uncertainty within an ecological forecast, how uncertainty can be quantified, and steps that can be taken to reduce the uncertainty in a forecast that students develop for a lake ecosystem, using data from the National Ecological Observatory Network (NEON). Students will visualize data, build a model, generate a forecast with uncertainty, and then compare the contributions of various sources of forecast uncertainty to total forecast uncertainty. The flexible, three-part (A-B-C) structure of this module makes it adaptable to a range of student levels and course structures. There are two versions of the module: an R Shiny application which does not require students to code, and an RMarkdown version which requires students to read and alter R code to complete module activities. The R Shiny application is published to shinyapps.io and is available at the following link: https://macrosystemseddie.shinyapps.io/module6/. GitHub repositories are available for both the R Shiny (https://github.com/MacrosystemsEDDIE/module6) and RMarkdown versions (https://github.com/MacrosystemsEDDIE/module6_R) of the module, and both code repositories have been published with DOIs to Zenodo (R Shiny version at https://zenodo.org/doi/10.5281/zenodo.10380759 and RMarkdown version at https://zenodo.org/doi/10.5281/zenodo.10380339). Readers are referred to the module landing page for additional information (https://serc.carleton.edu/eddie/teaching_materials/modules/module6.html). 

   more » « less
3. Context-dependent representation of within- and between-model uncertainty: aggregating probabilistic predictions in infectious disease epidemiology

   https://doi.org/10.1098/rsif.2022.0659  

   Howerton, Emily; Runge, Michael C.; Bogich, Tiffany L.; Borchering, Rebecca K.; Inamine, Hidetoshi; Lessler, Justin; Mullany, Luke C.; Probert, William J.; Smith, Claire P.; Truelove, Shaun; et al (January 2023, Journal of The Royal Society Interface)

   Probabilistic predictions support public health planning and decision making, especially in infectious disease emergencies. Aggregating outputs from multiple models yields more robust predictions of outcomes and associated uncertainty. While the selection of an aggregation method can be guided by retrospective performance evaluations, this is not always possible. For example, if predictions are conditional on assumptions about how the future will unfold (e.g. possible interventions), these assumptions may never materialize, precluding any direct comparison between predictions and observations. Here, we summarize literature on aggregating probabilistic predictions, illustrate various methods for infectious disease predictions via simulation, and present a strategy for choosing an aggregation method when empirical validation cannot be used. We focus on the linear opinion pool (LOP) and Vincent average, common methods that make different assumptions about between-prediction uncertainty. We contend that assumptions of the aggregation method should align with a hypothesis about how uncertainty is expressed within and between predictions from different sources. The LOP assumes that between-prediction uncertainty is meaningful and should be retained, while the Vincent average assumes that between-prediction uncertainty is akin to sampling error and should not be preserved. We provide an R package for implementation. Given the rising importance of multi-model infectious disease hubs, our work provides useful guidance on aggregation and a deeper understanding of the benefits and risks of different approaches. 

   more » « less
4. Resistance genes are distinct in protein-protein interaction networks according to drug class and gene mobility

   https://doi.org/10.1101/2024.02.05.578986  

   Moumi, Nazifa Ahmed; Brown, Connor L; Ahmed, Shafayat; Vikesland, Peter J; Pruden, Amy; Zhang, Liqing (February 2024, bioRxiv)

   Abstract With growing calls for increased surveillance of antibiotic resistance as an escalating global health threat, improved bioinformatic tools are needed for tracking antibiotic resistance genes (ARGs) across One Health domains. Most studies to date profile ARGs using sequence homology, but such approaches provide limited information about the broader context or function of the ARG in bacterial genomes. Here we introduce a new pipeline for identifying ARGs in genomic data that employs machine learning analysis of Protein-Protein Interaction Networks (PPINs) as a means to improve predictions of ARGs while also providing vital information about the context, such as gene mobility. A random forest model was trained to effectively differentiate between ARGs and nonARGs and was validated using the PPINs of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, andEnterobacter cloacae), which represent urgent threats to human health because they tend to be multi-antibiotic resistant. The pipeline exhibited robustness in discriminating ARGs from nonARGs, achieving an average area under the precision-recall curve of 88%. We further identified that the neighbors of ARGs, i.e., genes connected to ARGs by only one edge, were disproportionately associated with mobile genetic elements, which is consistent with the understanding that ARGs tend to be mobile compared to randomly sampled genes in the PPINs. This pipeline showcases the utility of PPINs in discerning distinctive characteristics of ARGs within a broader genomic context and in differentiating ARGs from nonARGs through network-based attributes and interaction patterns. The code for running the pipeline is publicly available athttps://github.com/NazifaMoumi/PPI-ARG-ESKAPE 

   more » « less
5. Stability and Multigroup Fairness in Ranking with Uncertain Predictions

   Devic, Siddartha; Korolova, Aleksandra; Kempe, David; Sharan, Vatsal (February 2024, Proceedings of the 41st International Conference on Machine Learning)

   Salakhutdinov, Ruslan; Kolter, Zico; Heller, Katherine; Weller, Adrian; Oliver, Nuria; Scarlett, Jonathan; Berkenkamp, Felix (Ed.)

   Rankings are ubiquitous across many applications, from search engines to hiring committees. In practice, many rankings are derived from the output of predictors. However, when predictors trained for classification tasks have intrinsic uncertainty, it is not obvious how this uncertainty should be represented in the derived rankings. Our work considers ranking functions: maps from individual predictions for a classification task to distributions over rankings. We focus on two aspects of ranking functions: stability to perturbations in predictions and fairness towards both individuals and subgroups. Not only is stability an important requirement for its own sake, but — as we show — it composes harmoniously with individual fairness in the sense of Dwork et al. (2012). While deterministic ranking functions cannot be stable aside from trivial scenarios, we show that the recently proposed uncertainty aware (UA) ranking functions of Singh et al. (2021) are stable. Our main result is that UA rankings also achieve group fairness through successful composition with multiaccurate or multicalibrated predictors. Our work demonstrates that UA rankings naturally interpolate between group and individual level fairness guarantees, while simultaneously satisfying stability guarantees important whenever machine-learned predictions are used. 

   more » « less