The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

How to Construct Polar Codes

A method for efficiently constructing polar codes is presented and analyzed. Although polar codes are explicitly defined, straightforward construction is intractable since the resulting polar bit-channels have an output alphabet that grows exponentially with he code length. Thus the core problem that needs to be solved is that of faithfully approximating a bit-channel with an intractably large alphabet by another channel having a manageable alphabet size. We devise two approximation methods which "sandwich" the original bit-channel between a degraded and an upgraded version thereof. Both approximations can be efficiently computed, and turn out to be extremely close in practice. We also provide theoretical analysis of our construction algorithms, proving that for any fixed $\epsilon > 0$ and all sufficiently large code lengths $n$, polar codes whose rate is within $\epsilon$ of channel capacity can be constructed in time and space that are both linear in $n$