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Paul Tupper

Publications and source records attributed to Paul Tupper.

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Linear and Sublinear Diversities

Diversities are an extension of the concept of a metric space which assign a non-negative value to every finite set of points, rather than just pairs. A general theory of diversities has been developed which exhibits many deep analogies to metric space theory but also veers off in new directions. Just as many of the most important aspects of metric space theory involve metrics defined on $\mathbb{R}^k$, many applications of diversity theory require a specialized theory for diversities defined on $\mathbb{R}^k$, as we develop here. We focus on two fundamental classes of diversities defined on $\mathbb{R}^k$: those that are Minkowski linear and those that are Minkowski sublinear. Many well-known functions in convex analysis belong to these classes, including diameter, circumradius and mean width. We derive surprising characterizations of these classes, and establish elegant connections between them. Motivated by classical results in metric geometry, and connections with combinatorial optimization, we then examine embeddability of finite diversities into $\mathbb{R}^k$. We prove that a finite diversity can be embedded into a linear diversity exactly when it is of negative type and that it can be embedded into a sublinear diversity exactly when it corresponds to a generalized circumradius.

math.MG

Optimal Dosing Schedules for Substances Inducing Tolerance

Many drugs used therapeutically or recreationally induce tolerance: the effect of the substance decreases with repeated use. This phenomenon may reduce the efficacy of the substance unless dosage is increased beyond what is healthy for the individual. Restoring the effect of the substance can often be obtained by taking a break from consumption. We propose designing dosing schedules that maximize the desired effect of the substance with a given total consumption, while factoring in the effect of tolerance. We provide a simple mathematical model of response to consumption and tolerance that can be fit from data on substance administration and response. Using this model with given parameters, we determine optimal consumption schedules to maximize a given objective. We illustrate with the example of caffeine, where we provide a schedule of consumption for a user who values the effects of caffeine on all days but needs extra alertness on some days of the week.

math.DS

Lattice Diversities

Diversities are a generalization of metric spaces, where instead of the non-negative function being defined on pairs of points, it is defined on arbitrary finite sets of points. Diversities have a well-developed theory. This includes the concept of a diversity tight span that extends the metric tight span in a natural way. Here we explore the generalization of diversities to lattices. Instead of defining diversities on finite subsets of a set we consider diversities defined on members of an arbitrary lattice (with a 0). We show that many of the basic properties of diversities continue to hold. However, the natural map from a lattice diversity to its tight span is not a lattice homomorphism, preventing the development of a complete tight span theory as in the metric and diversity cases.

math.MG

Generalizing Outside the Training Set: When Can Neural Networks Learn Identity Effects?

Often in language and other areas of cognition, whether two components of an object are identical or not determine whether it is well formed. We call such constraints identity effects. When developing a system to learn well-formedness from examples, it is easy enough to build in an identify effect. But can identity effects be learned from the data without explicit guidance? We provide a simple framework in which we can rigorously prove that algorithms satisfying simple criteria cannot make the correct inference. We then show that a broad class of algorithms including deep neural networks with standard architecture and training with backpropagation satisfy our criteria, dependent on the encoding of inputs. Finally, we demonstrate our theory with computational experiments in which we explore the effect of different input encodings on the ability of algorithms to generalize to novel inputs.

cs.CL

Fra\"iss\'e Limits for Relational Metric Structures

The general theory developed by Ben Yaacov for metric structures provides Fra\"iss\'e limits which are approximately ultrahomogeneous. We show here that this result can be strengthened in the case of relational metric structures. We give an extra condition that guarantees exact ultrahomogenous limits. The condition is quite general. We apply it to stochastic processes, the class of diversities, and its subclass of $L_1$ diversities.

math.LO

Discrete symbolic optimization and Boltzmann sampling by continuous neural dynamics: Gradient Symbolic Computation

Gradient Symbolic Computation is proposed as a means of solving discrete global optimization problems using a neurally plausible continuous stochastic dynamical system. Gradient symbolic dynamics involves two free parameters that must be adjusted as a function of time to obtain the global maximizer at the end of the computation. We provide a summary of what is known about the GSC dynamics for special cases of settings of the parameters, and also establish that there is a schedule for the two parameters for which convergence to the correct answer occurs with high probability. These results put the empirical results already obtained for GSC on a sound theoretical footing.

cs.CL

Open Problem Statement: Minimal Distortion Embeddings of Diversities in $\ell_1$

We state an open problem in the theory of diversities: what is the worst case minimal distortion embedding of a diversity on $n$ points in $\ell_1$. This problem is the diversity analogue of a famous problem in metric geometry: what is the worst case minimal distortion embedding of an $n$-point metric space in $\ell_1$. We explain the problem, state some special classes of diversities for which the answer is known, and show why the standard techniques from the metric space case do not work. We then outline some possible lines of attack for the problem that are not yet fully explored.

math.MG

Stability and Fluctuations in a Simple Model of Phonetic Category Change

In spoken languages, speakers divide up the space of phonetic possibilities into different regions, corresponding to different phonemes. We consider a simple exemplar model of how this division of phonetic space varies over time among a population of language users. In the particular model we consider, we show that, once the system is initialized with a given set of phonemes, that phonemes do not become extinct: all phonemes will be maintained in the system for all time. This is in contrast to what is observed in more complex models. Furthermore, we show that the boundaries between phonemes fluctuate and we quantitatively study the fluctuations in a simple instance of our model. These results prepare the ground for more sophisticated models in which some phonemes go extinct or new phonemes emerge through other processes.

cs.CL

Which Learning Algorithms Can Generalize Identity-Based Rules to Novel Inputs?

We propose a novel framework for the analysis of learning algorithms that allows us to say when such algorithms can and cannot generalize certain patterns from training data to test data. In particular we focus on situations where the rule that must be learned concerns two components of a stimulus being identical. We call such a basis for discrimination an identity-based rule. Identity-based rules have proven to be difficult or impossible for certain types of learning algorithms to acquire from limited datasets. This is in contrast to human behaviour on similar tasks. Here we provide a framework for rigorously establishing which learning algorithms will fail at generalizing identity-based rules to novel stimuli. We use this framework to show that such algorithms are unable to generalize identity-based rules to novel inputs unless trained on virtually all possible inputs. We demonstrate these results computationally with a multilayer feedforward neural network.

cs.CL

A Universal Separable Diversity

The Urysohn space is a separable complete metric space with two fundamental properties: (a) universality: every separable metric space can be isometrically embedded in it; (b) ultrahomogeneity: every finite isometry between two finite subspaces can be extended to an auto-isometry of the whole space. The Urysohn space is uniquely determined up to isometry within separable metric spaces by these two properties. We introduce an analogue of the Urysohn space for diversities, a recently developed variant of the concept of a metric space. In a diversity any finite set of points is assigned a non-negative value, extending the notion of a metric which only applies to unordered pairs of points. We construct the unique separable complete diversity that it is ultrahomogeneous and universal with respect to separable diversities.

math.MG

Convergence of a Metropolized Integrator for Stochastic Differential Equations with Variable Diffusion Coefficient

We present an explicit method for simulating stochastic differential equations (SDEs) that have variable diffusion coefficients and satisfy the detailed balance condition with respect to a known equilibrium density. In Tupper and Yang (2012), we proposed a framework for such systems in which, instead of a diffusion coefficient and a drift coefficient, a modeller specifies a diffusion coefficient and a equilibrium density, and then assumes detailed balance with respect to this equilibrium density. We proposed a numerical method for such systems that works directly with the diffusion coefficient and equilibrium density, rather than the drift coefficient, and uses a Metropolis-Hastings rejection process to preserve the equilibrium density exactly. Here we show that the method is weakly convergent with order 1/2 for such systems with smooth coefficients. We perform numerical experiments demonstrating the convergence of the method for systems not covered by our theorem, including systems with discontinuous diffusion coefficients and equilibrium densities.

math.NA

Continuous and Tractable models for the Variation of Evolutionary Rates

We propose a continuous model for evolutionary rate variation across sites and over the tree and derive exact transition probabilities under this model. Changes in rate are modelled using the CIR process, a diffusion widely used in financial applications. The model directly extends the standard gamma distributed rates across site model, with one additional parameter governing changes in rate down the tree. The parameters of the model can be estimated directly from two well-known statistics: the index of dispersion and the gamma shape parameter of the rates across sites model. The CIR model can be readily incorporated into probabilistic models for sequence evolution. We provide here an exact formula for the likelihood of a three taxa tree. Larger trees can be evaluated using Monte-Carlo methods.

math.PR

The Effects of Thermonuclear Reaction Rate Variations on Nova Nucleosynthesis: A Sensitivity Study

We investigate the effects of thermonuclear reaction rate uncertainties on nova nucleosynthesis. One-zone nucleosynthesis calculations have been performed by adopting temperature-density-time profiles of the hottest hydrogen-burning zone (i.e., the region in which most of the nucleosynthesis takes place). We obtain our profiles from 7 different, recently published, hydrodynamic nova simulations covering peak temperatures in the range from Tpeak=0.145-0.418 GK. For each of these profiles, we individually varied the rates of 175 reactions within their associated errors and analyzed the resulting abundance changes of 142 isotopes in the mass range below A=40. In total, we performed 7350 nuclear reaction network calculations. We use the most recent thermonuclear reaction rate evaluations for the mass ranges A=1-20 and A=20-40. For the theoretical astrophysicist, our results indicate the extent to which nova nucleosynthesis calculations depend on presently uncertain nuclear physics input, while for the experimental nuclear physicist our results represent at least a qualitative guide for future measurements at stable and radioactive ion beam facilities. We find that present reaction rate estimates are reliable for predictions of Li, Be, C and N abundances in nova nucleosynthesis. However, rate uncertainties of several reactions have to be reduced significantly in order to predict more reliable O, F, Ne, Na, Mg, Al, Si, S, Cl and Ar abundances. Results are presented in tabular form for each adopted nova simulation.

astro-ph