CAUSAL INFERENCE WITH A CONTINUOUS TREATMENT AND OUTCOME: ALTERNATIVE ESTIMATORS FOR PARAMETRIC DOSE-RESPONSE FUNCTIONS WITH APPLICATIONS.

Causal inference with a continuous treatment is a relatively under-explored problem. In this dissertation, we adopt the potential outcomes framework. Potential outcomes are responses that would be seen for a unit under all possible treatments. In an observational study where the treatment is continuous, the potential outcomes are an uncountably infinite set indexed by treatment dose. We parameterize this unobservable set as a linear combination of a finite number of basis functions whose coefficients vary across units. This leads to new techniques for estimating the population average dose-response function (ADRF). Some techniques require a model for the treatment assignment given covariates, some require a model for predicting the potential outcomes from covariates, and some require both. We develop these techniques using a framework of estimating functions, compare them to existing methods for continuous treatments, and simulate their performance in a population where the ADRF is linear and the models for the treatment and/or outcomes may be misspecified. We also extend the comparisons to a data set of lottery winners in Massachusetts. Next, we describe the methods and functions in the R package causaldrf using data from the National Medical Expenditure Survey (NMES) and Infant Health and Development Program (IHDP) as examples. Additionally, we analyze the National Growth and Health Study (NGHS) data set and deal with the issue of missing data. Lastly, we discuss future research goals and possible extensions.

Inductive Theorem Proving and Computer Algebra in the Mathweb Software Bus

Reasoning systems have reached a high degree of maturity in the last decade. However, even the most successful systems are usually not general purpose problem solvers but are typically specialised on problems in a certain domain. The MathWeb SOftware Bus (Mathweb-SB) is a system for combining reasoning specialists via a common osftware bus. We described the integration of the lambda-clam systems, a reasoning specialist for proofs by induction, into the MathWeb-SB. Due to this integration, lambda-clam now offers its theorem proving expertise to other systems in the MathWeb-SB. On the other hand, lambda-clam can use the services of any reasoning specialist already integrated. We focus on the latter and describe first experimnents on proving theorems by induction using the computational power of the MAPLE system within lambda-clam.

The renormalization group via statistical inference

In physics, one attempts to infer the rules governing a system given only the results of imperfect measurements. Hence, microscopic theories may be effectively indistinguishable experimentally. We develop an operationally motivated procedure to identify the corresponding equivalence classes of states, and argue that the renormalization group (RG) arises from the inherent ambiguities associated with the classes: one encounters flow parameters as, e.g., a regulator, a scale, or a measure of precision, which specify representatives in a given equivalence class. This provides a unifying framework and reveals the role played by information in renormalization. We validate this idea by showing that it justifies the use of low-momenta n-point functions as statistically relevant observables around a Gaussian hypothesis. These results enable the calculation of distinguishability in quantum field theory. Our methods also provide a way to extend renormalization techniques to effective models which are not based on the usual quantum-field formalism, and elucidates the relationships between various type of RG.

Metoda projektów w uczeniu się i nauczaniu fizyki w gimnazjum

Wydział Studiów Edukacyjnych: Zakład Pedeutologii

Phylogenetic inference's algorithms

Phylogenetic inference consist in the search of an evolutionary tree to explain the best way possible genealogical relationships of a set of species. Phylogenetic analysis has a large number of applications in areas such as biology, ecology, paleontology, etc. There are several criterias which has been defined in order to infer phylogenies, among which are the maximum parsimony and maximum likelihood. The first one tries to find the phylogenetic tree that minimizes the number of evolutionary steps needed to describe the evolutionary history among species, while the second tries to find the tree that has the highest probability of produce the observed data according to an evolutionary model. The search of a phylogenetic tree can be formulated as a multi-objective optimization problem, which aims to find trees which satisfy simultaneously (and as much as possible) both criteria of parsimony and likelihood. Due to the fact that these criteria are different there won't be a single optimal solution (a single tree), but a set of compromise solutions. The solutions of this set are called "Pareto Optimal". To find this solutions, evolutionary algorithms are being used with success nowadays.This algorithms are a family of techniques, which aren’t exact, inspired by the process of natural selection. They usually find great quality solutions in order to resolve convoluted optimization problems. The way this algorithms works is based on the handling of a set of trial solutions (trees in the phylogeny case) using operators, some of them exchanges information between solutions, simulating DNA crossing, and others apply aleatory modifications, simulating a mutation. The result of this algorithms is an approximation to the set of the “Pareto Optimal” which can be shown in a graph with in order that the expert in the problem (the biologist when we talk about inference) can choose the solution of the commitment which produces the higher interest. In the case of optimization multi-objective applied to phylogenetic inference, there is open source software tool, called MO-Phylogenetics, which is designed for the purpose of resolving inference problems with classic evolutionary algorithms and last generation algorithms. REFERENCES [1] C.A. Coello Coello, G.B. Lamont, D.A. van Veldhuizen. Evolutionary algorithms for solving multi-objective problems. Spring. Agosto 2007 [2] C. Zambrano-Vega, A.J. Nebro, J.F Aldana-Montes. MO-Phylogenetics: a phylogenetic inference software tool with multi-objective evolutionary metaheuristics. Methods in Ecology and Evolution. En prensa. Febrero 2016.

Metastability and dynamics of stem cells: from direct observations to inference at the single cell level

Organismal development, homeostasis, and pathology are rooted in inherently probabilistic events. From gene expression to cellular differentiation, rates and likelihoods shape the form and function of biology. Processes ranging from growth to cancer homeostasis to reprogramming of stem cells all require transitions between distinct phenotypic states, and these occur at defined rates. Therefore, measuring the fidelity and dynamics with which such transitions occur is central to understanding natural biological phenomena and is critical for therapeutic interventions.

While these processes may produce robust population-level behaviors, decisions are made by individual cells. In certain circumstances, these minuscule computing units effectively roll dice to determine their fate. And while the 'omics' era has provided vast amounts of data on what these populations are doing en masse, the behaviors of the underlying units of these processes get washed out in averages.

Therefore, in order to understand the behavior of a sample of cells, it is critical to reveal how its underlying components, or mixture of cells in distinct states, each contribute to the overall phenotype. As such, we must first define what states exist in the population, determine what controls the stability of these states, and measure in high dimensionality the dynamics with which these cells transition between states.

To address a specific example of this general problem, we investigate the heterogeneity and dynamics of mouse embryonic stem cells (mESCs). While a number of reports have identified particular genes in ES cells that switch between 'high' and 'low' metastable expression states in culture, it remains unclear how levels of many of these regulators combine to form states in transcriptional space. Using a method called single molecule mRNA fluorescent in situ hybridization (smFISH), we quantitatively measure and fit distributions of core pluripotency regulators in single cells, identifying a wide range of variabilities between genes, but each explained by a simple model of bursty transcription. From this data, we also observed that strongly bimodal genes appear to be co-expressed, effectively limiting the occupancy of transcriptional space to two primary states across genes studied here. However, these states also appear punctuated by the conditional expression of the most highly variable genes, potentially defining smaller substates of pluripotency.

Having defined the transcriptional states, we next asked what might control their stability or persistence. Surprisingly, we found that DNA methylation, a mark normally associated with irreversible developmental progression, was itself differentially regulated between these two primary states. Furthermore, both acute or chronic inhibition of DNA methyltransferase activity led to reduced heterogeneity among the population, suggesting that metastability can be modulated by this strong epigenetic mark.

Finally, because understanding the dynamics of state transitions is fundamental to a variety of biological problems, we sought to develop a high-throughput method for the identification of cellular trajectories without the need for cell-line engineering. We achieved this by combining cell-lineage information gathered from time-lapse microscopy with endpoint smFISH for measurements of final expression states. Applying a simple mathematical framework to these lineage-tree associated expression states enables the inference of dynamic transitions. We apply our novel approach in order to infer temporal sequences of events, quantitative switching rates, and network topology among a set of ESC states.

Taken together, we identify distinct expression states in ES cells, gain fundamental insight into how a strong epigenetic modifier enforces the stability of these states, and develop and apply a new method for the identification of cellular trajectories using scalable in situ readouts of cellular state.

Simple approximate MAP inference for Dirichlet processes mixtures

The Dirichlet process mixture model (DPMM) is a ubiquitous, flexible Bayesian nonparametric statistical model. However, full probabilistic inference in this model is analytically intractable, so that computationally intensive techniques such as Gibbs sampling are required. As a result, DPMM-based methods, which have considerable potential, are restricted to applications in which computational resources and time for inference is plentiful. For example, they would not be practical for digital signal processing on embedded hardware, where computational resources are at a serious premium. Here, we develop a simplified yet statistically rigorous approximate maximum a-posteriori (MAP) inference algorithm for DPMMs. This algorithm is as simple as DP-means clustering, solves the MAP problem as well as Gibbs sampling, while requiring only a fraction of the computational effort. (For freely available code that implements the MAP-DP algorithm for Gaussian mixtures see http://www.maxlittle.net/.) Unlike related small variance asymptotics (SVA), our method is non-degenerate and so inherits the “rich get richer” property of the Dirichlet process. It also retains a non-degenerate closed-form likelihood which enables out-of-sample calculations and the use of standard tools such as cross-validation. We illustrate the benefits of our algorithm on a range of examples and contrast it to variational, SVA and sampling approaches from both a computational complexity perspective as well as in terms of clustering performance. We demonstrate the wide applicabiity of our approach by presenting an approximate MAP inference method for the infinite hidden Markov model whose performance contrasts favorably with a recently proposed hybrid SVA approach. Similarly, we show how our algorithm can applied to a semiparametric mixed-effects regression model where the random effects distribution is modelled using an infinite mixture model, as used in longitudinal progression modelling in population health science. Finally, we propose directions for future research on approximate MAP inference in Bayesian nonparametrics.

Improved inference in the evaluation of mutual fund performance using bootstrap methods

Two new methodologies are introduced to improve inference in the evaluation of mutual fund performance against benchmarks. First, the benchmark models are estimated using panel methods with both fund and time effects. Second, the non-normality of individual mutual fund returns is accounted for by using panel bootstrap methods. We also augment the standard benchmark factors with fund-specific characteristics, such as fund size. Using a dataset of UK equity mutual fund returns, we find that fund size has a negative effect on the average fund manager’s benchmark-adjusted performance. Further, when we allow for time effects and the non-normality of fund returns, we find that there is no evidence that even the best performing fund managers can significantly out-perform the augmented benchmarks after fund management charges are taken into account.

Preference inference based on Pareto models

In this paper, we consider Preference Inference based on a generalised form of Pareto order. Preference Inference aims at reasoning over an incomplete specification of user preferences. We focus on two problems. The Preference Deduction Problem (PDP) asks if another preference statement can be deduced (with certainty) from a set of given preference statements. The Preference Consistency Problem (PCP) asks if a set of given preference statements is consistent, i.e., the statements are not contradicting each other. Here, preference statements are direct comparisons between alternatives (strict and non-strict). It is assumed that a set of evaluation functions is known by which all alternatives can be rated. We consider Pareto models which induce order relations on the set of alternatives in a Pareto manner, i.e., one alternative is preferred to another only if it is preferred on every component of the model. We describe characterisations for deduction and consistency based on an analysis of the set of evaluation functions, and present algorithmic solutions and complexity results for PDP and PCP, based on Pareto models in general and for a special case. Furthermore, a comparison shows that the inference based on Pareto models is less cautious than some other types of well-known preference model.

Evaluation of two methods for computational HLA haplotypes inference using a real dataset

info:eu-repo/semantics/publishedVersion

Evaluation of two methods for computational HLA haplotypes inference using a real dataset

info:eu-repo/semantics/publishedVersion

ANALYSE THE VULNERABILITY IN THE MARANHÃO ILHA, BRAZIL, USING GIS TECHNIQUES AND GEOSPATIAL INFERENCE

Vulnerability and sustainability studies of an area help to assess both its level of exposure and capacity to support possible environmental impacts, and it is of primordial importance for proposals of the Legislation on Zoning, Allotment, Land Use/land cover, aiming to stimulate those areas indicated for urban growth, to discourage growth of overcrowded areas, to detect sections with restrictive use, as well as districts for permanent protection. This paper aims to analyze the vulnerability in the Maranhão Ilha, using GIS techniques, geospatial inference intersected with relevant social-environmental indicators.Estudos de vulnerabilidade e de sustentabilidade de uma área ajudam a avaliar o seu grau de exposição e sua capacidade de suporte a possíveis impactos ambientais, sendo fundamental para propostas de Lei de Zoneamento, Parcelamento, Uso e Ocupação do Solo, tendo por finalidade orientar as áreas onde deverá haver estímulo para o crescimento urbano; contenção da malha urbana; detecção de locais com possibilidade de uso restritivo, bem como locais de proteção permanente. Este trabalho propõe analisar o índice de vulnerabilidade a perda de solo da Ilha do Maranhão com base na metodologia proposta por (CREPANI, et al. 2001) e em técnicas de inferência espacial com apoio na AHP (Análise Hierárquica de Processo).

Six Curses

This creative writing work was selected for publication in a bi-lingual anthology, published in China, as suitable to be culturally applicable to both Chinese and Australian social contexts. The poem raises six social/ethical issues and comments on them. It is based on research into Chinese traditional poetry that focuses on an image, and after each image this poem provides an ethical comment. It is based in the ethical hypothesis that moral evaluation of individual and social behaviour can not be achieved without ethical judgement which questions social norms. In particular, the poem questions the validity of fundamentalism – the belief in religious, scientific and moral absolutes. This is a key issue in contemporary research into the effect of religion on politics. It also draws on contemporary psychological theory, especially the concept of narcissism. The sociological basis of the work is in drawing parallels between eastern and western ethical issues, stressing similarity by inference. The imagery on which the poem is based selects objects such a single ‘stone’ that take on symbolic connotations common to both Australian and Chinese readers. This is innovative, since very little creative writing has been dome to address commonalities between Australian and Chinese ethical thinking, especially by adopting Chinese motifs.

Towards integrated assessments for urban development

The role of sustainability in urban design is becoming increasingly important as Australia’s cities continue to grow, putting pressure on existing infrastructure such as water, energy and transport. To optimise an urban design many different aspects such as water, energy, transport, costs need to be taken into account integrally. Integrated software applications assessing urban designs on a large variety of aspects are hardly available. With the upcoming next generation of the Internet often referred to as the Semantic Web, data can become more machine-interpretable by developing ontologies that can support the development of integrated software systems. Software systems can use these ontologies to perform an intelligent task such as assessing an urban design on a particular aspect. When ontologies of different applications are aligned, they can share information resulting in interoperability. Inference such as compliancy checks and classifications can support aligning the ontologies. A proof of concept implementation has been made to demonstrate and validate the usefulness of machine interpretable ontologies for urban designs.