Simple Parsimonious Types and Logarithmic Space

We present a functional characterization of deterministic logspace-computable predicates based on a variant (although not a subsystem) of propositional linear logic, which we call parsimonious logic. The resulting calculus is simply-typed and contains no primitive besides those provided by the underlying logical system, which makes it one of the simplest higher-order languages capturing logspace currently known. Completeness of the calculus uses the descriptive complexity characterization of logspace (we encode first-order logic with deterministic closure), whereas soundness is established by executing terms on a token machine (using the geometry of interaction)

Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression

The nonlinearity of dynamics in systems biology makes it hard to infer them from experimental data. Simple linear models are computationally efficient, but cannot incorporate these important nonlinearities. An adaptive method based on the S-system formalism, which is a sensible representation of nonlinear mass-action kinetics typically found in cellular dynamics, maintains the efficiency of linear regression. We combine this approach with adaptive model selection to obtain efficient and parsimonious representations of cellular dynamics. The approach is tested by inferring the dynamics of yeast glycolysis from simulated data. With little computing time, it produces dynamical models with high predictive power and with structural complexity adapted to the difficulty of the inference problem.Comment: 14 pages, 2 figure

Latent tree models

Latent tree models are graphical models defined on trees, in which only a subset of variables is observed. They were first discussed by Judea Pearl as tree-decomposable distributions to generalise star-decomposable distributions such as the latent class model. Latent tree models, or their submodels, are widely used in: phylogenetic analysis, network tomography, computer vision, causal modeling, and data clustering. They also contain other well-known classes of models like hidden Markov models, Brownian motion tree model, the Ising model on a tree, and many popular models used in phylogenetics. This article offers a concise introduction to the theory of latent tree models. We emphasise the role of tree metrics in the structural description of this model class, in designing learning algorithms, and in understanding fundamental limits of what and when can be learned

Inference of Ancestral Recombination Graphs through Topological Data Analysis

The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Gal\'apagos Islands.Comment: 33 pages, 12 figures. The accompanying software, instructions and example files used in the manuscript can be obtained from https://github.com/RabadanLab/TARGe

Using The Censored Gamma Distribution for Modeling Fractional Response Variables with an Application to Loss Given Default

Regression models for limited continuous dependent variables having a non-negligible probability of attaining exactly their limits are presented. The models differ in the number of parameters and in their flexibility. Fractional data being a special case of limited dependent data, the models also apply to variables that are a fraction or a proportion. It is shown how to fit these models and they are applied to a Loss Given Default dataset from insurance to which they provide a good fit

Time and Space Bounds for Reversible Simulation

We prove a general upper bound on the tradeoff between time and space that suffices for the reversible simulation of irreversible computation. Previously, only simulations using exponential time or quadratic space were known. The tradeoff shows for the first time that we can simultaneously achieve subexponential time and subquadratic space. The boundary values are the exponential time with hardly any extra space required by the Lange-McKenzie-Tapp method and the ($\log 3$)th power time with square space required by the Bennett method. We also give the first general lower bound on the extra storage space required by general reversible simulation. This lower bound is optimal in that it is achieved by some reversible simulations.Comment: 11 pages LaTeX, Proc ICALP 2001, Lecture Notes in Computer Science, Vol xxx Springer-Verlag, Berlin, 200