Species Tree Estimation from Gene Trees by Minimizing Deep Coalescence and Maximizing Quartet Consistency: A Comparative Study and the Presence of Pseudo Species Tree Terraces.

Species tree estimation from multilocus data sets is extremely challenging, especially in the presence of gene tree heterogeneity across the genome due to incomplete lineage sorting (ILS). Summary methods have been developed which estimate gene trees and then combine the gene trees to estimate a species tree by optimizing various optimization scores. In this study, we have extended and adapted the concept of phylogenetic terraces to species tree estimation by "summarizing" a set of gene trees, where multiple species trees with distinct topologies may have exactly the same optimality score (i.e., quartet score, extra lineage score, etc.). We particularly investigated the presence and impacts of equally optimal trees in species tree estimation from multilocus data using summary methods by taking ILS into account. We analyzed two of the most popular ILS-aware optimization criteria: maximize quartet consistency (MQC) and minimize deep coalescence (MDC). Methods based on MQC are provably statistically consistent, whereas MDC is not a consistent criterion for species tree estimation. We present a comprehensive comparative study of these two optimality criteria. Our experiments, on a collection of data sets simulated under ILS, indicate that MDC may result in competitive or identical quartet consistency score as MQC, but could be significantly worse than MQC in terms of tree accuracy-demonstrating the presence and impacts of equally optimal species trees. This is the first known study that provides the conditions for the data sets to have equally optimal trees in the context of phylogenomic inference using summary methods. [Gene tree; incomplete lineage sorting; phylogenomic analysis, species tree; summary method.].

A Multi-Level Task Framework for Event Sequence Analysis.

Despite the development of numerous visual analytics tools for event sequence data across various domains, including but not limited to healthcare, digital marketing, and user behavior analysis, comparing these domain-specific investigations and transferring the results to new datasets and problem areas remain challenging. Task abstractions can help us go beyond domain-specific details, but existing visualization task abstractions are insufficient for event sequence visual analytics because they primarily focus on multivariate datasets and often overlook automated analytical techniques. To address this gap, we propose a domain-agnostic multi-level task framework for event sequence analytics, derived from an analysis of 58 papers that present event sequence visualization systems. Our framework consists of four levels: objective, intent, strategy, and technique. Overall objectives identify the main goals of analysis. Intents comprises five high-level approaches adopted at each analysis step: augment data, simplify data, configure data, configure visualization, and manage provenance. Each intent is accomplished through a number of strategies, for instance, data simplification can be achieved through aggregation, summarization, or segmentation. Finally, each strategy can be implemented by a set of techniques depending on the input and output components. We further show that each technique can be expressed through a quartet of action-input-output-criteria. We demonstrate the framework's descriptive power through case studies and discuss its similarities and differences with previous event sequence task taxonomies.