SUMMARY: Next-Generation Sequencing is widely used as a tool for identifying and quantifying microorganisms pooled together in either natural or designed samples. However, a prominent obstacle is achieving correct quantification when the pooled microbes are genetically related. In such cases, the outcome mostly depends on the method used for assigning reads to the individual targets. To address this challenge, we have developed Exodus-a reference-based Python algorithm for quantification of genomes, including those that are highly similar, when they are sequenced together in a single mix. To test Exodus' performance, we generated both empirical and in silico next-generation sequencing data of mixed genomes. When applying Exodus to these data, we observed median error rates varying between 0% and 0.21% as a function of the complexity of the mix. Importantly, no false negatives were recorded, demonstrating that Exodus' likelihood of missing an existing genome is very low, even if the genome's relative abundance is low and similar genomes are present in the same mix. Taken together, these data position Exodus as a reliable tool for identifying and quantifying genomes in mixed samples. Exodus is open source and free to use at: https://github.com/ilyavs/exodus. AVAILABILITY AND IMPLEMENTATION: Exodus is implemented in Python within a Snakemake framework. It is available on GitHub alongside a docker containing the required dependencies: https://github.com/ilyavs/exodus. The data underlying this article will be shared on reasonable request to the corresponding author. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Verizon media (VZM) native advertising serves billions of impressions daily, reaching a yearly run-rate of many hundred of million USD. Driving VZM native models for predicting advertise (ad) event probabilities, such as clicks and conversions, is OFFSET - a feature enhanced collaborative-filtering ( CF) based e vent prediction algorithm. The predicted probabilities are then used in VZM native auctions to determine which ads to present for each serving event. Dynamic creative optimization (DCO) is a new VZM native product that was launched recently and is gaining increasingly more attention from advertisers. The DCO product allows advertisers to provide several assets per each native ad attribute, creating a plurality of combinations for each DCO ad. Since different combinations may appeal to different crowds, it may be beneficial to present certain combinations more frequently than others to maximize revenue. Inspired by the success of our Carousel asset optimization product, we present a post-auction successive elimination based approach for ranking DCO combinations according to their measured click through rates (CTR). This reinforcement learning multi-arm bandit like solution was evaluated during an online beta test phase done with selected advertisers, showing 21.8% CTR and 21.5% revenue lifts over a control bucket serving all combinations uniformly at random. The good performance of our DCO product attracts advertisers and it already shows a yearly run-rate of several million USD in revenue.

We present an overview of JTL (the Java Tools Language, pronounced "Gee-tel"), a novel language for querying JAVA [8] programs. JTL was designed to serve the development of source code software tools for JAVA, and as a small language which to aid programming language extensions to JAVA. Applications include definition of pointcuts for aspect-oriented programming, fixing type constraints for generic programming, specification of encapsulation policies, definition of micro-patterns, etc. We argue that the JTL expression of each of these is systematic, concise, intuitive and general.JTL relies on a simply-typed relational database for program representation, rather than an abstract syntax tree. The underlying semantics of the language is restricted to queries formulated in First Order Predicate Logic augmented with transitive closure (FOPL).Special effort was taken to ensure terse, yet readable expression of logical conditions. The JTL pattern public abstract class, for example, matches all abstract classes which are publicly accessible, while class (public clone();) matches all classes in which method clone is public. To this end, JTL relies on a DATALOG-like syntax and semantics, enriched with quantifiers and pattern matching which all but entirely eliminate the need for recursive calls.JTL's query analyzer gives special attention to the fragility of the "closed world assumption" in examining JAVA software, and determines whether a query relies on such an assumption.The performance of the JTL interpreter is comparable to that of JQuery after it generated its database cache, and at least an order of magnitude faster when the cache has to be rebuilt.