Evolutionary tree reconstruction

It is described how Minimum Description Length (MDL) can be applied to the problem of DNA and protein evolutionary tree reconstruction. If there is a set of mutations that transform a common ancestor into a set of the known sequences, and this description is shorter than the information to encode the known sequences directly, then strong evidence for an evolutionary relationship has been found. A heuristic algorithm is described that searches for the simplest tree (smallest MDL) that finds close to optimal trees on the test data. Various ways of extending the MDL theory to more complex evolutionary relationships are discussed

HBST: A Hamming Distance embedding Binary Search Tree for Visual Place Recognition

Reliable and efficient Visual Place Recognition is a major building block of modern SLAM systems. Leveraging on our prior work, in this paper we present a Hamming Distance embedding Binary Search Tree (HBST) approach for binary Descriptor Matching and Image Retrieval. HBST allows for descriptor Search and Insertion in logarithmic time by exploiting particular properties of binary Feature descriptors. We support the idea behind our search structure with a thorough analysis on the exploited descriptor properties and their effects on completeness and complexity of search and insertion. To validate our claims we conducted comparative experiments for HBST and several state-of-the-art methods on a broad range of publicly available datasets. HBST is available as a compact open-source C++ header-only library.Comment: Submitted to IEEE Robotics and Automation Letters (RA-L) 2018 with International Conference on Intelligent Robots and Systems (IROS) 2018 option, 8 pages, 10 figure

A Framework for Index Bulk Loading and Dynamization

In this paper we investigate automated methods for externalizing internal memory data structures. We consider a class of balanced trees that we call weight-balanced partitioning trees (or wp-trees) for indexing a set of points in Rd. Well-known examples of wp-trees include fed-trees, BBD-trees, pseudo quad trees, and BAR trees. These trees are defined with fixed degree and are thus suited for internal memory implementations. Given an efficient wp-tree construction algorithm, we present a general framework for automatically obtaining a new dynamic external data structure. Using this framework together with a new general construction (bulk loading) technique of independent interest, we obtain data structures with guaranteed good update performance in terms of I /O transfers. Our approach gives considerably improved construction and update I/O bounds of e.g. fed-trees and BBD-trees

Energy-Efficient Algorithms

We initiate the systematic study of the energy complexity of algorithms (in addition to time and space complexity) based on Landauer's Principle in physics, which gives a lower bound on the amount of energy a system must dissipate if it destroys information. We propose energy-aware variations of three standard models of computation: circuit RAM, word RAM, and transdichotomous RAM. On top of these models, we build familiar high-level primitives such as control logic, memory allocation, and garbage collection with zero energy complexity and only constant-factor overheads in space and time complexity, enabling simple expression of energy-efficient algorithms. We analyze several classic algorithms in our models and develop low-energy variations: comparison sort, insertion sort, counting sort, breadth-first search, Bellman-Ford, Floyd-Warshall, matrix all-pairs shortest paths, AVL trees, binary heaps, and dynamic arrays. We explore the time/space/energy trade-off and develop several general techniques for analyzing algorithms and reducing their energy complexity. These results lay a theoretical foundation for a new field of semi-reversible computing and provide a new framework for the investigation of algorithms.Comment: 40 pages, 8 pdf figures, full version of work published in ITCS 201