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Ecosystems are among the most interesting and well-studied examples of self-organized complex systems. Community ecology, the study of how species interact with each other and the environment, has a rich tradition. Over the last few years, there has been a growing theoretical and experimental interest in these problems from the physics and quantitative biology communities. Here, we give an overview of community ecology, highlighting the deep connections between ecology and statistical physics. We start by introducing the two classes of mathematical models that have served as the workhorses of community ecology: Consumer Resource Models (CRM) and the generalized Lotka-Volterra models (GLV). We place a special emphasis on graphical methods and general principles. We then review recent works showing a deep and surprising connection between ecological dynamics and constrained optimization. We then shift our focus by analyzing these same models in "high-dimensions" (i.e. in the limit where the number of species and resources in the ecosystem becomes large) and discuss how such complex ecosystems can be analyzed using methods from the statistical physics of disordered systems such as the cavity method and Random Matrix Theory., Comment: 48 pages, 9 figures, Les Houches Theoretical Biophysics Summer School 2023

Ecosystems are commonly organized into trophic levels -- organisms that occupy the same level in a food chain (e.g., plants, herbivores, carnivores). A fundamental question in theoretical ecology is how the interplay between trophic structure, diversity, and competition shapes the properties of ecosystems. To address this problem, we analyze a generalized Consumer Resource Model with three trophic levels using the zero-temperature cavity method and numerical simulations. We find that intra-trophic diversity gives rise to ``emergent competition'' between species within a trophic level due to feedbacks mediated by other trophic levels. This emergent competition gives rise to a crossover from a regime of top-down control (populations are limited by predators) to a regime of bottom-up control (populations are limited by primary producers) and is captured by a simple order parameter related to the ratio of surviving species in different trophic levels. We show that our theoretical results agree with empirical observations, suggesting that the theoretical approach outlined here can be used to understand complex ecosystems with multiple trophic levels., Comment: Main text: 10.5 pages, 7 figures (Total: 18 pages)

Faster-than-Nyquist (FTN) signaling is an attractive transmission technique which accelerates data symbols beyond the Nyquist rate to improve the spectral efficiency; however, at the expense of higher computational complexity to remove the introduced intersymbol interference (ISI). In this work, we introduce a novel FTN signaling transmission technique, named coordinate interleaved FTN (CI-FTN) signaling that exploits the ISI at the transmitter to generate constructive interference for every pair of the counter-clockwise rotated binary phase shift keying (BPSK) data symbols. In particular, the proposed CI- FTN signaling interleaves the in-phase (I) and the quadrature (Q) components of the counter-clockwise rotated BPSK symbols to guarantee that every pair of consecutive symbols has the same sign, and hence, has constructive ISI. At the receiver, we propose a low-complexity detector that makes use of the constructive ISI introduced at the transmitter. Simulation results show the merits of the CI-FTN signaling and the proposed low-complexity detector compared to conventional Nyquist and FTN signaling.

Sound recordings are used in various ecological studies, including acoustic wildlife monitoring. Such surveys require automatic detection of target sound events. However, current detectors, especially those relying on band-limited energy, are severely impacted by wind. The rapid dynamics of this noise invalidate standard noise estimators, and no satisfactory method for dealing with it exists in bioacoustics, where simple training and generalization between conditions are important. We propose to estimate the transient noise level by fitting short-term spectrum models to a wavelet packet representation. This estimator is then combined with log-spectral subtraction to stabilize the background level. The resulting adjusted wavelet series can be analysed by standard energy detectors. We use real monitoring data to tune this workflow, and test it on two acoustic surveys of birds. Additionally, we show how the estimator can be incorporated in a denoising method to restore sound. The proposed noise-robust workflow greatly reduced the number of false alarms in the surveys, compared to unadjusted energy detection. As a result, the survey efficiency (precision of the estimated call density) improved for both species. Denoising was also more effective when using the short-term estimate, whereas standard wavelet shrinkage with a constant noise estimate struggled to remove the effects of wind. In contrast to existing methods, the proposed estimator can adjust for transient broadband noises without requiring additional hardware or extensive tuning to each species. It improved the detection workflow based on very little training data, making it particularly attractive for detection of rare species., Comment: 34 pages, 5 figures, 2 supplementary figures

Recent work suggests that cross-feeding -- the secretion and consumption of metabolic biproducts by microbes -- is essential for understanding microbial ecology. Yet how cross-feeding and competition combine to give rise to ecosystem-level properties remains poorly understood. To address this question, we analytically analyze the Microbial Consumer Resource Model (MiCRM), a prominent ecological model commonly used to study microbial communities. Our mean-field solution exploits the fact that unlike replicas, the cavity method does not require the existence of a Lyapunov function. We use our solution to derive new species-packing bounds for diverse ecosystems in the presence of cross-feeding, as well as simple expressions for species richness and the abundance of secreted resources as a function of cross-feeding (metabolic leakage) and competition. Our results show how a complex interplay between competition for resources and cooperation resulting from metabolic exchange combine to shape the properties of microbial ecosystems., Comment: 23 pages, 6 figures, 4 pages main text

The New Zealand National Policy Statement for Freshwater Management 2020 sets several targets for freshwater quality, six of which are measurements of rivers; others relate to lakes. Each regional council is required to monitor freshwater quality and to respond as prescribed in order to meet the targets. One target of particular public interest is based on four criteria determined from recent E. coli readings, and concerns the health risk of swimming in a river. However, the inherent variability of the data makes it difficult to determine the water quality state and trend reliably, particularly using traditional methods based on percentiles. Therefore, in this study we return to the parametric lognormal model of E. coli distribution, from which the official criteria were developed. We interpret the classification system in terms of the parametric model and show that the parametric model can reduce uncertainty and can incorporate more useful information, especially from very high E. coli readings, and is suitable for censored data. We apply the parametric model for state and trend to 135 sites in the Manawat\=u-Whanganui region.

We often wish to classify objects by their shapes. Indeed, the study of shapes is an important part of many scientific fields such as evolutionary biology, structural biology, image processing, and archaeology. The most widely-used method of shape analysis, Geometric Morphometrics, assumes that that the mathematical space in which shapes are represented is linear. However, it has long been known that shape space is, in fact, rather more complicated, and certainly non-linear. Diffeomorphic methods that take this non-linearity into account, and so give more accurate estimates of the distances among shapes, exist but have rarely been applied to real-world problems. Using a machine classifier, we tested the ability of several of these methods to describe and classify the shapes of a variety of organic and man-made objects. We find that one method, the Square-Root Velocity Function (SRVF), is superior to all others, including a standard Geometric Morphometric method (eigenshapes). We also show that computational shape classifiers outperform human experts, and that the SRVF shortest-path between shapes can be used to estimate the shapes of intermediate steps in evolutionary series. Diffeomorphic shape analysis methods, we conclude, now provide practical and effective solutions to many shape description and classification problems in the natural and human sciences., Comment: 7 pages, 6 figures

BACKGROUND: In object oriented (OO) software systems, class size has been acknowledged as having an indirect effect on the relationship between certain artifact characteristics, captured via metrics, and faultproneness, and therefore it is recommended to control for size when designing fault prediction models. AIM: To use robust statistical methods to assess whether there is evidence of any true effect of class size on fault prediction models. METHOD: We examine the potential mediation and moderation effects of class size on the relationships between OO metrics and number of faults. We employ regression analysis and bootstrapping-based methods to investigate the mediation and moderation effects in two widely-used datasets comprising seventeen systems. RESULTS: We find no strong evidence of a significant mediation or moderation effect of class size on the relationships between OO metrics and faults. In particular, size appears to have a more significant mediation effect on CBO and Fan-out than other metrics, although the evidence is not consistent in all examined systems. On the other hand, size does appear to have a significant moderation effect on WMC and CBO in most of the systems examined. Again, the evidence provided is not consistent across all examined systems CONCLUSION: We are unable to confirm if class size has a significant mediation or moderation effect on the relationships between OO metrics and the number of faults. We contend that class size does not fully explain the relationships between OO metrics and the number of faults, and it does not always affect the strength/magnitude of these relationships. We recommend that researchers consider the potential mediation and moderation effect of class size when building their prediction models, but this should be examined independently for each system., Comment: Conference paper, 11 pages, 8 figures, 7 tables

Regulatory T cells (Tregs) play a crucial role in mediating immune response. Yet an algorithmic understanding of the role of Tregs in adaptive immunity remains lacking. Here, we present a biophysically realistic model of Treg mediated self-tolerance in which Tregs bind to self-antigens and locally inhibit the proliferation of nearby activated T cells. By exploiting a duality between ecological dynamics and constrained optimization, we show that Tregs tile the potential antigen space while simultaneously minimizing the overlap between Treg activation profiles. We find that for sufficiently high Treg diversity, Treg mediated self-tolerance is robust to fluctuations in self-antigen concentrations but lowering the Treg diversity results in a sharp transition -- related to the Gardner transition in perceptrons -- to a regime where changes in self-antigen concentrations can result in an auto-immune response. We propose a novel experimental test of this transition in immune-deficient mice and discuss potential implications for autoimmune diseases., Comment: 8 pages, 4 figures + Appendix; Accepted at PNAS

Spectrum scarcity necessitates innovative, spectral-efficient strategies to meet the ever-growing demand for high data rates. Faster-than-Nyquist (FTN) signaling emerges as a compelling spectral-efficient transmission method that pushes transmit data symbols beyond the Nyquist limit, offering enhanced spectral efficiency (SE). While FTN signaling maintains SE with the same energy and bandwidth as the Nyquist signaling, it introduces increased complexity, particularly at higher modulation levels. This complexity predominantly arises from the detection process, which seeks to mitigate the intentional intersymbol interference generated by FTN signaling. Another challenge involves the generation of reliable log-likelihood ratios (LLRs) vital for soft channel decoders. In this study, we introduce a lookup table (LUT) aided soft output semidefinite relaxation (soSDR) based sub-optimal FTN detector, which can be extended to higher modulation levels. This detector possesses polynomial computational complexity, given the negligible complexity associated with soft value generation. Our study assesses the performance of this soft output detector against that of the optimal FTN detector, Bahl, Cocke, Jelinek and Raviv (BCJR) algorithm as the benchmark. The likelihood values produced by our LUT aided semidefinite relaxation (SDR) based FTN signaling detector show promising viability in coded scenario., Comment: Updated version (v4) accepted at IEEE ICC 2024

The Earth system is accumulating energy due to human-induced activities. More than 90 percent of this energy has been stored in the ocean as heat since 1970, with about 64 percent of that in the upper 700 m. Differences in upper ocean heat content anomaly (OHCA) estimates, however, exist. Here, we evaluate spread in upper OHCA estimates arising from choices in instrumental bias corrections and mapping methods, in addition to the effect of using a common ocean mask. The same dataset was mapped by six research groups for 1970 to 2008, with six instrumental bias corrections applied to expendable bathythermograph (XBT) data. We find that use of a common ocean mask may impact estimation of global OHCA by +- 13 percent. Uncertainty due to mapping method dominates over XBT bias correction at a global scale and is largest in the Indian Ocean and in the eddy-rich and frontal regions of all basins. Uncertainty due to XBT bias correction is largest in the Pacific Ocean within 30N to 30S. In both mapping and XBT cases, spread is higher since the 1990s. Important differences in spatial trends among mapping methods are found in the well-observed Northwest Atlantic and the poorly-observed Southern Ocean. Although our results cannot identify the best mapping or bias correction schemes, they identify where and when greater uncertainties exist, and so where further refinements may yield the largest improvements. Our results highlight the need for a future international coordination to evaluate performance of existing mapping methods., Comment: Submitted to AMS Journal of Climate (30 July 2020). Feedback welcome. Please email: abhishek.abhisheksavita@utas.edu.au

Many time series problems feature epidemic changes - segments where a parameter deviates from a background baseline. The number and location of such changes can be estimated in a principled way by existing detection methods, providing that the background level is stable and known. However, practical data often contains nuisance changes in background level, which interfere with standard estimation techniques. Furthermore, such changes often differ from the target segments only in duration, and appear as false alarms in the detection results. To solve these issues, we propose a two-level detector that models and separates nuisance and signal changes. As part of this method, we developed a new, efficient approach to simultaneously estimate unknown, but fixed, background level and detect epidemic changes. The analytic and computational properties of the proposed methods are established, including consistency and convergence. We demonstrate via simulations that our two-level detector provides accurate estimation of changepoints under a nuisance process, while other state-of-the-art detectors fail. Using real-world genomic and demographic datasets, we demonstrate that our method can identify and localise target events while separating out seasonal variations and experimental artefacts., Comment: 33 pages, 5 figures

We show that the COVID-19 pandemic under social distancing exhibits universal dynamics. The cumulative numbers of both infections and deaths quickly cross over from exponential growth at early times to a longer period of power law growth, before eventually slowing. In agreement with a recent statistical forecasting model by the IHME, we show that this dynamics is well described by the erf function. Using this functional form, we perform a data collapse across countries and US states with very different population characteristics and social distancing policies, confirming the universal behavior of the COVID-19 outbreak. We show that the predictive power of statistical models is limited until a few days before curves flatten, forecast deaths and infections assuming current policies continue and compare our predictions to the IHME models. We present simulations showing this universal dynamics is consistent with disease transmission on scale-free networks and random networks with non-Markovian transmission dynamics., Comment: 19 pages, 14 figures

Contemporary Niche Theory is a useful framework for understanding how organisms interact with each other and with their shared environment. Its graphical representation, popularized by Tilman's Resource Ratio Hypothesis, facilitates the analysis of the equilibrium structure of complex dynamical models including species coexistence. This theory has been applied primarily to resource competition since its early beginnings. Here, we integrate mutualism into niche theory by expanding Tilman's graphical representation to the analysis of consumer-resource dynamics of plant-pollinator networks. We graphically explain the qualitative phenomena previously found by numerical simulations, including the effects on community dynamics of nestedness, adaptive foraging, and pollinator invasions. Our graphical approach promotes the unification of niche and network theories, and deepens the synthesis of different types of interactions within a consumer-resource framework., Comment: 41 pages, 8 figures