Predicting tipping points in mutualistic networks through dimension reduction

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1714958115/-/DCSupplemental.Peer reviewedPublisher PD

Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that – in many cases – adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future

Cortical Learning of Recognition Categories: A Resolution of the Exemplar Vs. Prototype Debate

Do humans and animals learn exemplars or prototypes when they categorize objects and events in the world? How are different degrees of abstraction realized through learning by neurons in inferotemporal and prefrontal cortex? How do top-down expectations influence the course of learning? Thirty related human cognitive experiments (the 5-4 category structure) have been used to test competing views in the prototype-exemplar debate. In these experiments, during the test phase, subjects unlearn in a characteristic way items that they had learned to categorize perfectly in the training phase. Many cognitive models do not describe how an individual learns or forgets such categories through time. Adaptive Resonance Theory (ART) neural models provide such a description, and also clarify both psychological and neurobiological data. Matching of bottom-up signals with learned top-down expectations plays a key role in ART model learning. Here, an ART model is used to learn incrementally in response to 5-4 category structure stimuli. Simulation results agree with experimental data, achieving perfect categorization in training and a good match to the pattern of errors exhibited by human subjects in the testing phase. These results show how the model learns both prototypes and certain exemplars in the training phase. ART prototypes are, however, unlike the ones posited in the traditional prototype-exemplar debate. Rather, they are critical patterns of features to which a subject learns to pay attention based on past predictive success and the order in which exemplars are experienced. Perturbations of old memories by newly arriving test items generate a performance curve that closely matches the performance pattern of human subjects. The model also clarifies exemplar-based accounts of data concerning amnesia.Defense Advanced Projects Research Agency SyNaPSE program (Hewlett-Packard Company, DARPA HR0011-09-3-0001; HRL Laboratories LLC #801881-BS under HR0011-09-C-0011); Science of Learning Centers program of the National Science Foundation (NSF SBE-0354378

Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities

Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems that undergo both recoverable and unrecoverable transitions, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community\u27s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities

Measuring, Predicting and Visualizing Short-Term Change in Word Representation and Usage in VKontakte Social Network

Language in social media is extremely dynamic: new words emerge, trend and disappear, while the meaning of existing words can fluctuate over time. Such dynamics are especially notable during a period of crisis. This work addresses several important tasks of measuring, visualizing and predicting short term text representation shift, i.e. the change in a word's contextual semantics, and contrasting such shift with surface level word dynamics, or concept drift, observed in social media streams. Unlike previous approaches on learning word representations from text, we study the relationship between short-term concept drift and representation shift on a large social media corpus - VKontakte posts in Russian collected during the Russia-Ukraine crisis in 2014-2015. Our novel contributions include quantitative and qualitative approaches to (1) measure short-term representation shift and contrast it with surface level concept drift; (2) build predictive models to forecast short-term shifts in meaning from previous meaning as well as from concept drift; and (3) visualize short-term representation shift for example keywords to demonstrate the practical use of our approach to discover and track meaning of newly emerging terms in social media. We show that short-term representation shift can be accurately predicted up to several weeks in advance. Our unique approach to modeling and visualizing word representation shifts in social media can be used to explore and characterize specific aspects of the streaming corpus during crisis events and potentially improve other downstream classification tasks including real-time event detection

Early Warning Analysis for Social Diffusion Events

There is considerable interest in developing predictive capabilities for social diffusion processes, for instance to permit early identification of emerging contentious situations, rapid detection of disease outbreaks, or accurate forecasting of the ultimate reach of potentially viral ideas or behaviors. This paper proposes a new approach to this predictive analytics problem, in which analysis of meso-scale network dynamics is leveraged to generate useful predictions for complex social phenomena. We begin by deriving a stochastic hybrid dynamical systems (S-HDS) model for diffusion processes taking place over social networks with realistic topologies; this modeling approach is inspired by recent work in biology demonstrating that S-HDS offer a useful mathematical formalism with which to represent complex, multi-scale biological network dynamics. We then perform formal stochastic reachability analysis with this S-HDS model and conclude that the outcomes of social diffusion processes may depend crucially upon the way the early dynamics of the process interacts with the underlying network's community structure and core-periphery structure. This theoretical finding provides the foundations for developing a machine learning algorithm that enables accurate early warning analysis for social diffusion events. The utility of the warning algorithm, and the power of network-based predictive metrics, are demonstrated through an empirical investigation of the propagation of political memes over social media networks. Additionally, we illustrate the potential of the approach for security informatics applications through case studies involving early warning analysis of large-scale protests events and politically-motivated cyber attacks

Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process

In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators

Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process

In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators