A view of Estimation of Distribution Algorithms through the lens of Expectation-Maximization

We show that a large class of Estimation of Distribution Algorithms, including, but not limited to, Covariance Matrix Adaption, can be written as a Monte Carlo Expectation-Maximization algorithm, and as exact EM in the limit of infinite samples. Because EM sits on a rigorous statistical foundation and has been thoroughly analyzed, this connection provides a new coherent framework with which to reason about EDAs

Unifying Projected Entangled Pair States contractions

The approximate contraction of a Projected Entangled Pair States (PEPS) tensor network is a fundamental ingredient of any PEPS algorithm, required for the optimization of the tensors in ground state search or time evolution, as well as for the evaluation of expectation values. An exact contraction is in general impossible, and the choice of the approximating procedure determines the efficiency and accuracy of the algorithm. We analyze different previous proposals for this approximation, and show that they can be understood via the form of their environment, i.e. the operator that results from contracting part of the network. This provides physical insight into the limitation of various approaches, and allows us to introduce a new strategy, based on the idea of clusters, that unifies previous methods. The resulting contraction algorithm interpolates naturally between the cheapest and most imprecise and the most costly and most precise method. We benchmark the different algorithms with finite PEPS, and show how the cluster strategy can be used for both the tensor optimization and the calculation of expectation values. Additionally, we discuss its applicability to the parallelization of PEPS and to infinite systems (iPEPS).Comment: 28 pages, 15 figures, accepted versio

Open Science principles for accelerating trait-based science across the Tree of Life.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges