Geometric and Topological Combinatorics

The 2007 Oberwolfach meeting “Geometric and Topological Combinatorics” presented a great variety of investigations where topological and algebraic methods are brought into play to solve combinatorial and geometric problems, but also where geometric and combinatorial ideas are applied to topological questions

Implementation strategies for hyperspectral unmixing using Bayesian source separation

Bayesian Positive Source Separation (BPSS) is a useful unsupervised approach for hyperspectral data unmixing, where numerical non-negativity of spectra and abundances has to be ensured, such in remote sensing. Moreover, it is sensible to impose a sum-to-one (full additivity) constraint to the estimated source abundances in each pixel. Even though non-negativity and full additivity are two necessary properties to get physically interpretable results, the use of BPSS algorithms has been so far limited by high computation time and large memory requirements due to the Markov chain Monte Carlo calculations. An implementation strategy which allows one to apply these algorithms on a full hyperspectral image, as typical in Earth and Planetary Science, is introduced. Effects of pixel selection, the impact of such sampling on the relevance of the estimated component spectra and abundance maps, as well as on the computation times, are discussed. For that purpose, two different dataset have been used: a synthetic one and a real hyperspectral image from Mars.Comment: 10 pages, 6 figures, submitted to IEEE Transactions on Geoscience and Remote Sensing in the special issue on Hyperspectral Image and Signal Processing (WHISPERS

Stable isotope sourcing using sampling

Stable isotope sourcing is used to estimate proportional contributions of sources to a mixture, such as in the analysis of animal diets, plant nutrient use, geochemistry, pollution, and forensics. We focus on animal ecology because of the particular complexities due to the process of digestion and assimilation. Parameter estimation has been a challenge because there are often many sources and few isotopes leading to an underconstrained linear system for the diet probability vector. This dissertation offers three primary contributions to the mixing model community. (1) We detail and provide an R implementation of a better algorithm (SISUS) for representing possible solutions in the underconstrained case (many sources, few isotopes) when no variance is considered (Phillips and Gregg, 2003). (2) We provide general methods for performing frequentist estimation in the perfectly-constrained case using the delta method and the bootstrap, which extends previous work applying the delta method to two- and three-source problems (Phillips and Gregg, 2001). (3) We propose two Bayesian models, the implicit representation model estimating the population mean diet through the mean mixture isotope ratio, and the explicit representation model estimating the population mean diet through mixture-specific diets given individual isotope ratios. Secondary contributions include (4) estimation using summaries from the literature in lieu of observation-level data, (5) multiple methods for incorporating isotope ratio discrimination (fractionation) in the analysis, (6) the use of measurement error to account for and partition more uncertainty, (7) estimation improvements by pooling multiple estimates, and (8) detailing scenarios when one model is preferred over another. We show that the Bayesian explicit representation model provides more precise diet estimates than other models when measurement error is small and informed by the necessary calibration measurements

Learning from samples using coherent lower previsions

Het hoofdonderwerp van dit werk is het afleiden, voorstellen en bestuderen van voorspellende en parametrische gevolgtrekkingsmodellen die gebaseerd zijn op de theorie van coherente onderprevisies. Een belangrijk nevenonderwerp is het vinden en bespreken van extreme onderwaarschijnlijkheden. In het hoofdstuk ‘Modeling uncertainty’ geef ik een inleidend overzicht van de theorie van coherente onderprevisies ─ ook wel theorie van imprecieze waarschijnlijkheden genoemd ─ en de ideeën waarop ze gestoeld is. Deze theorie stelt ons in staat onzekerheid expressiever ─ en voorzichtiger ─ te beschrijven. Dit overzicht is origineel in de zin dat ze meer dan andere inleidingen vertrekt van de intuitieve theorie van coherente verzamelingen van begeerlijke gokken. Ik toon in het hoofdstuk ‘Extreme lower probabilities’ hoe we de meest extreme vormen van onzekerheid kunnen vinden die gemodelleerd kunnen worden met onderwaarschijnlijkheden. Elke andere onzekerheidstoestand beschrijfbaar met onderwaarschijnlijkheden kan geformuleerd worden in termen van deze extreme modellen. Het belang van de door mij bekomen en uitgebreid besproken resultaten in dit domein is voorlopig voornamelijk theoretisch. Het hoofdstuk ‘Inference models’ behandelt leren uit monsters komende uit een eindige, categorische verzameling. De belangrijkste basisveronderstelling die ik maak is dat het bemonsteringsproces omwisselbaar is, waarvoor ik een nieuwe definitie geef in termen van begeerlijke gokken. Mijn onderzoek naar de gevolgen van deze veronderstelling leidt ons naar enkele belangrijke representatiestellingen: onzekerheid over (on)eindige rijen monsters kan gemodelleerd worden in termen van categorie-aantallen (-frequenties). Ik bouw hier op voort om voor twee populaire gevolgtrekkingsmodellen voor categorische data ─ het voorspellende imprecies Dirichlet-multinomiaalmodel en het parametrische imprecies Dirichletmodel ─ een verhelderende afleiding te geven, louter vertrekkende van enkele grondbeginselen; deze modellen pas ik toe op speltheorie en het leren van Markov-ketens. In het laatste hoofdstuk, ‘Inference models for exponential families’, verbreed ik de blik tot niet-categorische exponentiële-familie-bemonsteringsmodellen; voorbeelden zijn normale bemonstering en Poisson-bemonstering. Eerst onderwerp ik de exponentiële families en de aanverwante toegevoegde parametrische en voorspellende previsies aan een grondig onderzoek. Deze aanverwante previsies worden gebruikt in de klassieke Bayesiaanse gevolgtrekkingsmodellen gebaseerd op toegevoegd updaten. Ze dienen als grondslag voor de nieuwe, door mij voorgestelde imprecieze-waarschijnlijkheidsgevolgtrekkingsmodellen. In vergelijking met de klassieke Bayesiaanse aanpak, laat de mijne toe om voorzichtiger te zijn bij de beschrijving van onze kennis over het bemonsteringsmodel; deze voorzichtigheid wordt weerspiegeld door het op deze modellen gebaseerd gedrag (getrokken besluiten, gemaakte voorspellingen, genomen beslissingen). Ik toon ten slotte hoe de voorgestelde gevolgtrekkingsmodellen gebruikt kunnen worden voor classificatie door de naïeve credale classificator.This thesis's main subject is deriving, proposing, and studying predictive and parametric inference models that are based on the theory of coherent lower previsions. One important side subject also appears: obtaining and discussing extreme lower probabilities. In the chapter ‘Modeling uncertainty’, I give an introductory overview of the theory of coherent lower previsions ─ also called the theory of imprecise probabilities ─ and its underlying ideas. This theory allows us to give a more expressive ─ and a more cautious ─ description of uncertainty. This overview is original in the sense that ─ more than other introductions ─ it is based on the intuitive theory of coherent sets of desirable gambles. I show in the chapter ‘Extreme lower probabilities’ how to obtain the most extreme forms of uncertainty that can be modeled using lower probabilities. Every other state of uncertainty describable by lower probabilities can be formulated in terms of these extreme ones. The importance of the results in this area obtained and extensively discussed by me is currently mostly theoretical. The chapter ‘Inference models’ treats learning from samples from a finite, categorical space. My most basic assumption about the sampling process is that it is exchangeable, for which I give a novel definition in terms of desirable gambles. My investigation of the consequences of this assumption leads us to some important representation theorems: uncertainty about (in)finite sample sequences can be modeled entirely in terms of category counts (frequencies). I build on this to give an elucidating derivation from first principles for two popular inference models for categorical data ─ the predictive imprecise Dirichlet-multinomial model and the parametric imprecise Dirichlet model; I apply these models to game theory and learning Markov chains. In the last chapter, ‘Inference models for exponential families’, I enlarge the scope to exponential family sampling models; examples are normal sampling and Poisson sampling. I first thoroughly investigate exponential families and the related conjugate parametric and predictive previsions used in classical Bayesian inference models based on conjugate updating. These previsions serve as a basis for the new imprecise-probabilistic inference models I propose. Compared to the classical Bayesian approach, mine allows to be much more cautious when trying to express what we know about the sampling model; this caution is reflected in behavior (conclusions drawn, predictions made, decisions made) based on these models. Lastly, I show how the proposed inference models can be used for classification with the naive credal classifier

Algorithms for Strong Nash Equilibrium with More than Two Agents

Strong Nash equilibrium (SNE) is an appealing solu-tion concept when rational agents can form coalitions. A strategy profile is an SNE if no coalition of agents can benefit by deviating. We present the first general– purpose algorithms for SNE finding in games with more than two agents. An SNE must simultaneously be a Nash equilibrium (NE) and the optimal solution of mul-tiple non–convex optimization problems. This makes even the derivation of necessary and sufficient mathe-matical equilibrium constraints difficult. We show that forcing an SNE to be resilient only to pure–strategy de-viations by coalitions, unlike for NEs, is only a nec-essary condition here. Second, we show that the ap-plication of Karush–Kuhn–Tucker conditions leads to another set of necessary conditions that are not suffi-cient. Third, we show that forcing the Pareto efficiency of an SNE for each coalition with respect to coalition correlated strategies is sufficient but not necessary. We then develop a tree search algorithm for SNE finding. At each node, it calls an oracle to suggest a candidate SNE and then verifies the candidate. We show that our new necessary conditions can be leveraged to make the oracle more powerful. Experiments validate the overall approach and show that the new conditions significantly reduce search tree size compared to using NE condi-tions alone

An Algorithmic Theory of Dependent Regularizers, Part 1: Submodular Structure

We present an exploration of the rich theoretical connections between several classes of regularized models, network flows, and recent results in submodular function theory. This work unifies key aspects of these problems under a common theory, leading to novel methods for working with several important models of interest in statistics, machine learning and computer vision. In Part 1, we review the concepts of network flows and submodular function optimization theory foundational to our results. We then examine the connections between network flows and the minimum-norm algorithm from submodular optimization, extending and improving several current results. This leads to a concise representation of the structure of a large class of pairwise regularized models important in machine learning, statistics and computer vision. In Part 2, we describe the full regularization path of a class of penalized regression problems with dependent variables that includes the graph-guided LASSO and total variation constrained models. This description also motivates a practical algorithm. This allows us to efficiently find the regularization path of the discretized version of TV penalized models. Ultimately, our new algorithms scale up to high-dimensional problems with millions of variables

Interpretable Machine Learning for Electro-encephalography

While behavioral, genetic and psychological markers can provide important information about brain health, research in that area over the last decades has much focused on imaging devices such as magnetic resonance tomography (MRI) to provide non-invasive information about cognitive processes. Unfortunately, MRI based approaches, able to capture the slow changes in blood oxygenation levels, cannot capture electrical brain activity which plays out on a time scale up to three orders of magnitude faster. Electroencephalography (EEG), which has been available in clinical settings for over 60 years, is able to measure brain activity based on rapidly changing electrical potentials measured non-invasively on the scalp. Compared to MRI based research into neurodegeneration, EEG based research has, over the last decade, received much less interest from the machine learning community. But generally, EEG in combination with sophisticated machine learning offers great potential such that neglecting this source of information, compared to MRI or genetics, is not warranted. In collaborating with clinical experts, the ability to link any results provided by machine learning to the existing body of research is especially important as it ultimately provides an intuitive or interpretable understanding. Here, interpretable means the possibility for medical experts to translate the insights provided by a statistical model into a working hypothesis relating to brain function. To this end, we propose in our first contribution a method allowing for ultra-sparse regression which is applied on EEG data in order to identify a small subset of important diagnostic markers highlighting the main differences between healthy brains and brains affected by Parkinson's disease. Our second contribution builds on the idea that in Parkinson's disease impaired functioning of the thalamus causes changes in the complexity of the EEG waveforms. The thalamus is a small region in the center of the brain affected early in the course of the disease. Furthermore, it is believed that the thalamus functions as a pacemaker - akin to a conductor of an orchestra - such that changes in complexity are expressed and quantifiable based on EEG. We use these changes in complexity to show their association with future cognitive decline. In our third contribution we propose an extension of archetypal analysis embedded into a deep neural network. This generative version of archetypal analysis allows to learn an appropriate representation where every sample of a data set can be decomposed into a weighted sum of extreme representatives, the so-called archetypes. This opens up an interesting possibility of interpreting a data set relative to its most extreme representatives. In contrast, clustering algorithms describe a data set relative to its most average representatives. For Parkinson's disease, we show based on deep archetypal analysis, that healthy brains produce archetypes which are different from those produced by brains affected by neurodegeneration