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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. 

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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). 

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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. 

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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 

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5. One Pixel Can Change the Diagnosis: Adversarial andNon-Adversarial Robustness and Uncertainty in BreastUltrasound Classification Model

   https://doi.org/10.1609/aaaiss.v7i1.36927  

   Huang, Kuan; Sahel, Noorul; Karki, Dikshya; Xu, Meng; Wang, Yingfeng (November 2025, Proceedings of the AAAI Symposium Series)

   Deep learning models have strong potential for automating breast ultrasound (BUS) image classification to support early cancer detection. However, their vulnerability to small input perturbations poses a challenge for clinical reliability. This study examines how minimal pixel-level changes affect classification performance and predictive uncertainty, using the BUSI dataset and a ResNet-50 classifier. Two perturbation types are evaluated: (1) adversarial perturbations via the One Pixel Attack and (2) non-adversarial, device-related noise simulated by setting a single pixel to black. Robustness is assessed alongside uncertainty estimation using Monte Carlo Dropout, with metrics including Expected Kullback–Leibler divergence (EKL), Predictive Variance (PV), and Mutual Information (MI) for epistemic uncertainty, and Maximum Class Probability (MP) for aleatoric uncertainty. Both perturbations reduced accuracy, producing 17 and 29 “fooled” test samples, defined as cases classified correctly before but incorrectly after perturbation, for the adversarial and non-adversarial settings, respectively. Samples that remained correct are referred to as “unfooled.” Across all metrics, uncertainty increased after perturbation for both groups, and fooled samples had higher uncertainty than unfooled samples even before perturbation. We also identify spatially localized “uncertainty-decreasing” regions, where individual single-pixel blackouts both flipped predictions and reduced uncertainty, creating overconfident errors. These regions represent high-risk vulnerabilities that could be exploited in adversarial attacks or addressed through targeted robustness training and uncertainty-aware safeguards. Overall, combining perturbation analysis with uncertainty quantification provides valuable insights into model weaknesses and can inform the design of safer, more reliable AI systems for BUS diagnosis. 

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