Computational reverse mathematics and foundational analysis

Reverse mathematics studies which subsystems of second order arithmetic are equivalent to key theorems of ordinary, non-set-theoretic mathematics. The main philosophical application of reverse mathematics proposed thus far is foundational analysis, which explores the limits of different foundations for mathematics in a formally precise manner. This paper gives a detailed account of the motivations and methodology of foundational analysis, which have heretofore been largely left implicit in the practice. It then shows how this account can be fruitfully applied in the evaluation of major foundational approaches by a careful examination of two case studies: a partial realization of Hilbert's program due to Simpson [1988], and predicativism in the extended form due to Feferman and Sch\"{u}tte. Shore [2010, 2013] proposes that equivalences in reverse mathematics be proved in the same way as inequivalences, namely by considering only $\omega$-models of the systems in question. Shore refers to this approach as computational reverse mathematics. This paper shows that despite some attractive features, computational reverse mathematics is inappropriate for foundational analysis, for two major reasons. Firstly, the computable entailment relation employed in computational reverse mathematics does not preserve justification for the foundational programs above. Secondly, computable entailment is a $\Pi^1_1$ complete relation, and hence employing it commits one to theoretical resources which outstrip those available within any foundational approach that is proof-theoretically weaker than $\Pi^1_1\text{-}\mathsf{CA}_0$.Comment: Submitted. 41 page

Spatial Aggregation: Theory and Applications

Visual thinking plays an important role in scientific reasoning. Based on the research in automating diverse reasoning tasks about dynamical systems, nonlinear controllers, kinematic mechanisms, and fluid motion, we have identified a style of visual thinking, imagistic reasoning. Imagistic reasoning organizes computations around image-like, analogue representations so that perceptual and symbolic operations can be brought to bear to infer structure and behavior. Programs incorporating imagistic reasoning have been shown to perform at an expert level in domains that defy current analytic or numerical methods. We have developed a computational paradigm, spatial aggregation, to unify the description of a class of imagistic problem solvers. A program written in this paradigm has the following properties. It takes a continuous field and optional objective functions as input, and produces high-level descriptions of structure, behavior, or control actions. It computes a multi-layer of intermediate representations, called spatial aggregates, by forming equivalence classes and adjacency relations. It employs a small set of generic operators such as aggregation, classification, and localization to perform bidirectional mapping between the information-rich field and successively more abstract spatial aggregates. It uses a data structure, the neighborhood graph, as a common interface to modularize computations. To illustrate our theory, we describe the computational structure of three implemented problem solvers -- KAM, MAPS, and HIPAIR --- in terms of the spatial aggregation generic operators by mixing and matching a library of commonly used routines.Comment: See http://www.jair.org/ for any accompanying file

Projective schemes: What is Computable in low degree?

This article first presents two examples of algorithms that extracts information on scheme out of its defining equations. We also give a review on the notion of Castelnuovo-Mumford regularity, its main properties (in particular its relation to computational issues) and different ways that were used to estimate it

Counting, generating and sampling tree alignments

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical sets of matches between identical pairs of trees. This ambiguity is uninformative, and detrimental to any probabilistic analysis.In this work, we consider tree alignments up to equivalence. Our first result is a precise asymptotic enumeration of tree alignments, obtained from a context-free grammar by mean of basic analytic combinatorics. Our second result focuses on alignments between two given ordered trees $S$ and $T$. By refining our grammar to align specific trees, we obtain a decomposition scheme for the space of alignments, and use it to design an efficient dynamic programming algorithm for sampling alignments under the Gibbs-Boltzmann probability distribution. This generalizes existing tree alignment algorithms, and opens the door for a probabilistic analysis of the space of suboptimal RNA secondary structures alignments.Comment: ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, Jun 2016, Trujillo, Spain. 201