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Timothée Poisot

Publications and source records attributed to Timothée Poisot.

5 recordsLinked to original sources

What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases

Food webs are complex ecological networks whose structure is both ecologically and statistically constrained, with many network properties being correlated with each other. Despite the recognition of these invariable relationships in food webs, the use of the principle of maximum entropy (MaxEnt) in network ecology is still rare. This is surprising considering that MaxEnt is a statistical tool precisely designed for understanding and predicting many different types of constrained systems. Precisely, this principle asserts that the least-biased probability distribution of a system's property, constrained by prior knowledge about that system, is the one with maximum information entropy. Here we show how MaxEnt can be used to derive many food-web properties both analytically and heuristically. First, we show how the joint degree distribution (the joint probability distribution of the numbers of prey and predators for each species in the network) can be derived analytically using the number of species and the number of interactions in food webs. Second, we present a heuristic and flexible approach of finding a network's adjacency matrix (the network's representation in matrix format) based on simulated annealing and SVD entropy. We built two heuristic models using the connectance and the joint degree sequence as statistical constraints, respectively. We compared both models' predictions against corresponding null and neutral models commonly used in network ecology using open access data of terrestrial and aquatic food webs sampled globally. We found that the heuristic model constrained by the joint degree sequence was a good predictor of many measures of food-web structure, especially the nestedness and motifs distribution. Specifically, our results suggest that the structure of terrestrial and aquatic food webs is mainly driven by their joint degree distribution.

q-bio.QM

Network embedding unveils the hidden interactions in the mammalian virome

At most 1-2% of the global virome has been sampled to date. Recent work has shown that predicting which host-virus interactions are possible but undiscovered or unrealized is, fundamentally, a network science problem. Here, we develop a novel method that combines a coarse recommender system (Linear Filtering; LF) with an imputation algorithm based on low-rank graph embedding (Singular Value Decomposition; SVD) to infer host-virus associations. This combination of techniques results in informed initial guesses based on directly measurable network properties (density, degree distribution) that are refined through SVD (which is able to leverage emerging features). Using this method, we recovered highly plausible undiscovered interactions with a strong signal of viral coevolutionary history, and revealed a global hotspot of unusually unique but unsampled (or unrealized) host-virus interactions in the Amazon rainforest. We develop several tests for quantifying the bias and realism of these predictions, and show that the LF-SVD method is robust in each aspect. We finally show that graph embedding of the imputed network can be used to improve predictions of human infection from viral genome features, showing that the global structure of the mammal-virus network provides additional insights into human disease emergence.

q-bio.QM

Sustainable computational science: the ReScience initiative

Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. James Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code, and data that produced the result. This implies new workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and software tests.

cs.DL

BiMAT: a MATLAB(R) package to facilitate the analysis and visualization of bipartite networks

The statistical analysis of the structure of bipartite ecological networks has increased in importance in recent years. Yet, both algorithms and software packages for the analysis of network structure focus on properties of unipartite networks. In response, we describe BiMAT, an object-oriented MATLAB package for the study of the structure of bipartite ecological networks. BiMAT can analyze the structure of networks, including features such as modularity and nestedness, using a selection of widely-adopted algorithms. BiMAT also includes a variety of null models for evaluating the statistical significance of network properties. BiMAT is capable of performing multi-scale analysis of structure - a potential (and under-examined) feature of many biological networks. Finally, BiMAT relies on the graphics capabilities of MATLAB to enable the visualization of the statistical structure of bipartite networks in either matrix or graph layout representations. BiMAT is available as an open-source package at http://ecotheory.biology.gatech.edu/cflores.

q-bio.QM

A simple model to study phylogeographies and speciation patterns in space

In this working paper, we present a simple theoretical framework based on network theory to study how speciation, the process by which new species appear, shapes spatial patterns of diversity. We show that this framework can be expanded to account for different types of networks and interactions, and incorporates different modes of speciation.

q-bio.PE