Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons

Mining Object Parts from CNNs via Active Question-Answering

Given a convolutional neural network (CNN) that is pre-trained for object classification, this paper proposes to use active question-answering to semanticize neural patterns in conv-layers of the CNN and mine part concepts. For each part concept, we mine neural patterns in the pre-trained CNN, which are related to the target part, and use these patterns to construct an And-Or graph (AOG) to represent a four-layer semantic hierarchy of the part. As an interpretable model, the AOG associates different CNN units with different explicit object parts. We use an active human-computer communication to incrementally grow such an AOG on the pre-trained CNN as follows. We allow the computer to actively identify objects, whose neural patterns cannot be explained by the current AOG. Then, the computer asks human about the unexplained objects, and uses the answers to automatically discover certain CNN patterns corresponding to the missing knowledge. We incrementally grow the AOG to encode new knowledge discovered during the active-learning process. In experiments, our method exhibits high learning efficiency. Our method uses about 1/6-1/3 of the part annotations for training, but achieves similar or better part-localization performance than fast-RCNN methods.Comment: Published in CVPR 201

User-friendly Support for Common Concepts in a Lightweight Verifier

Machine verification of formal arguments can only increase our confidence in the correctness of those arguments, but the costs of employing machine verification still outweigh the benefits for some common kinds of formal reasoning activities. As a result, usability is becoming increasingly important in the design of formal verification tools. We describe the "aartifact" lightweight verification system, designed for processing formal arguments involving basic, ubiquitous mathematical concepts. The system is a prototype for investigating potential techniques for improving the usability of formal verification systems. It leverages techniques drawn both from existing work and from our own efforts. In addition to a parser for a familiar concrete syntax and a mechanism for automated syntax lookup, the system integrates (1) a basic logical inference algorithm, (2) a database of propositions governing common mathematical concepts, and (3) a data structure that computes congruence closures of expressions involving relations found in this database. Together, these components allow the system to better accommodate the expectations of users interested in verifying formal arguments involving algebraic and logical manipulations of numbers, sets, vectors, and related operators and predicates. We demonstrate the reasonable performance of this system on typical formal arguments and briefly discuss how the system's design contributed to its usability in two case studies