A primer for microbiome time-series analysis

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coenen, A. R., Hu, S. K., Luo, E., Muratore, D., & Weitz, J. S. A primer for microbiome time-series analysis. Frontiers in Genetics, 11, (2020): 310, doi:10.3389/fgene.2020.00310.Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.This work was supported by the Simons Foundation (SCOPE award ID 329108) and the National Science Foundation (NSF Bio Oc 1829636)

A multidimensional perspective on microbial interactions

Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts.R01 GM121950 - NIGMS NIH HHSPublished versio

Learning shape correspondence with anisotropic convolutional neural networks

Establishing correspondence between shapes is a fundamental problem in geometry processing, arising in a wide variety of applications. The problem is especially difficult in the setting of non-isometric deformations, as well as in the presence of topological noise and missing parts, mainly due to the limited capability to model such deformations axiomatically. Several recent works showed that invariance to complex shape transformations can be learned from examples. In this paper, we introduce an intrinsic convolutional neural network architecture based on anisotropic diffusion kernels, which we term Anisotropic Convolutional Neural Network (ACNN). In our construction, we generalize convolutions to non-Euclidean domains by constructing a set of oriented anisotropic diffusion kernels, creating in this way a local intrinsic polar representation of the data (`patch'), which is then correlated with a filter. Several cascades of such filters, linear, and non-linear operators are stacked to form a deep neural network whose parameters are learned by minimizing a task-specific cost. We use ACNNs to effectively learn intrinsic dense correspondences between deformable shapes in very challenging settings, achieving state-of-the-art results on some of the most difficult recent correspondence benchmarks

Dynamical Networks of Social Influence: Modern Trends and Perspectives

Dynamics and control of processes over social networks, such as the evolution of opinions, social influence and interpersonal appraisals, diffusion of information and misinformation, emergence and dissociation of communities, are now attracting significant attention from the broad research community that works on systems, control, identification and learning. To provide an introduction to this rapidly developing area, a Tutorial Session was included into the program of IFAC World Congress 2020. This paper provides a brief summary of the three tutorial lectures, covering the most “mature” directions in analysis of social networks and dynamics over them: 1) formation of opinions under social influence; 2) identification and learning for analysis of a network’s structure; 3) dynamics of interpersonal appraisals

Closed loop interactions between spiking neural network and robotic simulators based on MUSIC and ROS

In order to properly assess the function and computational properties of simulated neural systems, it is necessary to account for the nature of the stimuli that drive the system. However, providing stimuli that are rich and yet both reproducible and amenable to experimental manipulations is technically challenging, and even more so if a closed-loop scenario is required. In this work, we present a novel approach to solve this problem, connecting robotics and neural network simulators. We implement a middleware solution that bridges the Robotic Operating System (ROS) to the Multi-Simulator Coordinator (MUSIC). This enables any robotic and neural simulators that implement the corresponding interfaces to be efficiently coupled, allowing real-time performance for a wide range of configurations. This work extends the toolset available for researchers in both neurorobotics and computational neuroscience, and creates the opportunity to perform closed-loop experiments of arbitrary complexity to address questions in multiple areas, including embodiment, agency, and reinforcement learning

Central Bank Transparency: Where, Why, and with What Effects?

Greater transparency in central bank operations is the most dramatic change in the conduct of monetary policy in recent years. In this paper we present new information on its extent and effects. We show that the trend is general: a large number of central banks have moved in the direction of greater transparency since the late 1990s. We then analyze the determinants and effects of central bank transparency in an integrated empirical framework. Transparency is greater in countries with more stable and developed political systems and deeper and more developed financial markets. Our preliminary analysis suggests broadly favorable if relatively weak impacts on inflation and output variability.

Towards precise completion of deformable shapes

According to Aristotle, “the whole is greater than the sum of its parts”. This statement was adopted to explain human perception by the Gestalt psychology school of thought in the twentieth century. Here, we claim that when observing a part of an object which was previously acquired as a whole, one could deal with both partial correspondence and shape completion in a holistic manner. More specifically, given the geometry of a full, articulated object in a given pose, as well as a partial scan of the same object in a different pose, we address the new problem of matching the part to the whole while simultaneously reconstructing the new pose from its partial observation. Our approach is data-driven and takes the form of a Siamese autoencoder without the requirement of a consistent vertex labeling at inference time; as such, it can be used on unorganized point clouds as well as on triangle meshes. We demonstrate the practical effectiveness of our model in the applications of single-view deformable shape completion and dense shape correspondence, both on synthetic and real-world geometric data, where we outperform prior work by a large margin

How much structure in empirical models?

This chapter highlights the problems that structural methods and SVAR approaches have when estimating DSGE models and examining their ability to capture important features of the data. We show that structural methods are subject to severe identification problems due, in large part, to the nature of DSGE models. The problems can be patched up in a number of ways but solved only if DSGEs are completely reparametrized or respecified. The potential misspecification of the structural relationships give Bayesian methods an hedge over classical ones in structural estimation. SVAR approaches may face invertibility problems but simple diagnostics can help to detect and remedy these problems. A pragmatic empirical approach ought to use the flexibility of SVARs against potential misspecification of the structural relationships but must firmly tie SVARs to the class of DSGE models which could have have generated the data.DSGE models, SVAR models, Identification, Invertibility, Misspecification, Small Samples.