Shuffled linear regression concerns itself with linear models with an unknown correspondence between the input and the output. This correspondence is usually represented by a permutation matrix II*. The model we are interested in has one more complication which is that the design matrix is itself latent and is observed with noise. This is considered as a type of errors-in-variables (EIV) model. Our interest lies in the recovery of the permutation matrix. We propose an estimator for II* based on the total least squares (TLS) technique, a common method of estimation used in EIV model. The estimation problem can be viewed as approximating one matrix by another of lower rank and the quantity it seeks to minimize is the sum of the smallest singular values squared. Due to identifiability issue, we evaluate the proposed estimator by the normalized Procrustes quadratic loss which allows for an orthogonal rotation of the estimated design matrix. Our main result provides an upper bound on this quantity which states that it is required that the signal-to-noise ratio to go to infinity in order for the loss to go to zero. On the computational front, since the problem of permutation recovery is NP-hard to solve, we propose a simple and efficient algorithm named alternating LAP/TLS algorithm (ALTA) to approximate the estimator, and we use it to empirically examine the main result. The main idea of the algorithm is to alternate between estimating the unknown coefficient matrix using the TLS method and estimating the latent permutation matrix by solving a linear assignment problem (LAP) which runs in polynomial time. Lastly, we propose a hypothesis testing procedure based on graph matching which we apply in the field of digital humanities, on character social networks constructed from novel series.

No description available.

It is becoming increasingly important to understand biological networks in order to understand complex diseases, identify novel, safer protein targets for therapies and design efficient drugs. 'Systems biology' has emerged as a discipline to uncover biological networks through genomic data. Computational methods for identifying these networks become immensely important and have been growing in number in parallel to increasing amount of genomic data under the discipline of 'Systems Biology'. In this thesis we introduced novel computational methods for identifying topological and dynamic properties of biological networks. Biological data is available in various forms. Experimental data on the interactions between biological components provides a connectivity map of the system as a network of interactions and time series or steady state experiments on concentrations or activity levels of biological constituents will give a dynamic picture of the web of these interactions. Biological data is scarce usually relative to the number of components in the networks and subject to high levels of noise. The data is available from various resources however it can have missing information and inconsistencies. Hence it is critical to design intelligent computational methods that can incorporate data from different resources while considering noise component. This thesis is organized as follows; Chapter 1 and 2 will introduce the basic concepts for biological network types. Chapter 2 will give a background on biochemical network identification data types and computational approaches for reverse engineering of these networks. Chapter 3 will introduce our novel constrained total least squares approach for recovering network topology and dynamics through noisy measurements. We proved our method to be superior over existing reverse engineering methods. Chapter 4 is an extension of chapter 3 where a Bayesian parameter estimation algorithm is presented that is capable of incorporating noisy time series and prior information for the connectivity of network. The quality of prior information is critical to be able to infer dynamics of the networks. The major drawback of prior connectivity data is the presence of false negatives, missing links. Hence, powerful link prediction methods are necessary to be able to identify missing links. At this junction a novel link prediction method is introduced in Chapter 5. This method is capable of predicting missing links in a connectivity data. An application of this method on protein-protein association data from a literature mining database will be demonstrated. In chapter 6 a further extension into link prediction applications will be given. An interesting application of these methods is the drug adverse effect prediction. Adverse effects are the major reason for the failure of drugs in pharmaceutical industry, therefore it is very important to identify potential toxicity risks in the early drug development process. Motivated by this chapter 6 introduces our computational framework that integrates drug-target, drug-side effect, pathway-target and mouse phenotype-mouse genes data to predict side effects. Chapter 7 will give the significant findings and overall achievements of the thesis. Subsequent steps will be suggested that can follow the work presented here to improve network prediction methods.

System stability plays an important role in electric power systems. With the development of electric power system, the scale of the electric grid is now becoming larger and larger, and many renewable energy resources are integrated in the grid. However, at the same time, the stability and safety issues of electric power system are becoming more complicated. Frequency and phasors are two critical parameters of the system stability. Obtaining these two parameters have been great challenges for decades. Researchers have provided various kinds of algorithms for frequency tracking and phasor estimation. Among them, Least Squares (LS) algorithm is one of the most commonly used algorithm. This thesis studies the LS algorithm and the Total Least Squares (TLS) algorithm working on frequency tracking and phasor estimation. In order to test the performance of the two algorithms, some simulations have been made in the Matlab. The Total Vector Error (TVE) is a commonly used performance criteria, and the TVE results of the two algorithms are compared. The TLS algorithm performs better than LS algorithm when the frequencies of all harmonic components are given.

Tato práce se zabývá metodou úplně nejmenších čtverc·, která slouží pro odhad parametr· v lineárních modelech. V práci je uveden základní popis metody a její asymptotické vlastnosti. Je vysvětleno, jakým zp·sobem lze v konceptu metody využít neparametrický bootstrap pro hledání odhadu. Vlastnosti bootstrap od- had· jsou pak simulovány na pseudo náhodně vygenerovaných datech. Simulace jsou prováděny pro dvourozměrný parametr v r·zných nastaveních základního modelu. Jednotlivé bootstrap odhady jsou v rovině řazeny pomocí Mahalanobis a Tukey statistical depth function. Simulace potvrzují, že bootstrap odhad dává dostatečně dobré výsledky, aby se dal využít pro reálné situace.

No description available.

A linear regression model, where covariates and a response are subject to errors, is considered in this thesis. For so-called errors-in-variables (EIV) model, suitable error structures are proposed, various unknown parameter estimation techniques are performed, and recent algebraic and statistical results are summarized. An extension of the total least squares (TLS) estimate in the EIV model-the EIV estimate-is invented. Its invariant (with respect to scale) and equivariant (with respect to the covariates' rotation, to the change of covariates direction, and to the interchange of covariates) properties are derived. Moreover, it is shown that the EIV estimate coincides with any unitarily invariant penalizing solution to the EIV problem. It is demonstrated that the asymptotic normality of the EIV estimate is computationally useless for a construction of confidence intervals or hypothesis testing. A proper bootstrap procedure is constructed to overcome such an issue. The validity of the bootstrap technique is proved. A simulation study and a real data example assure of its appropriateness. Strong and uniformly strong mixing errors are taken into account instead of the independent ones. For such a case, the strong consistency and the asymptotic normality of the EIV estimate are shown. Despite of that, their...

We investigate possible usage of Errors-in-Variables estimator (EIV), when esti- mating structural equations models (SEM). Structural equations modelling pro- vides framework for analysing complex relations among set of random variables where for example the response variable in one equation plays role of the predic- tor in another equation. First an overview of SEM and some common covariance based estimators is provided. Special case of linear regression model is investi- gated, showing that the covariance based estimators yield the same results as ordinary least squares. A compact review of EIV models follows, Errors-in-Variables models are re- gression models where not only response but also predictors are assumed to be measured with an error. Main contribution of this paper then lies in defining modifications of the EIV estimator to fit in the SEM framework. General opti- mization problem to estimate the parameters of structural equations model with errors-in-variables si postulated. Several modifications of two stage least squares are also proposed for future research. Equation-wise Errors-in-Variables estimator is proposed to estimate the coeffi- cients of structural equations model. The coefficients of every structural equation are estimated separately using EIV estimator. Some theoretical conditions...

In manufacturing, metrological inspection is a time-consuming process. The higher the required precision in inspection, the longer the inspection time. This is due to both slow devices that collect measurement data and slow computational methods that process the data. The goal of this work is to propose methods to speed up some of these processes. Conventional measurement devices like Coordinate Measuring Machines (CMMs) have high precision but low measurement speed while new digitizer technologies have high speed but low precision. Using these devices in synergy gives a significant improvement in the measurement speed without loss of precision. The method of synergistic integration of an advanced digitizer with a CMM is discussed. Computational aspects of the inspection process are addressed next. Once a part is measured, measurement data is compared against its model to check for tolerances. This comparison is a time-consuming process on conventional CPUs. We developed and benchmarked some GPU accelerations. Finally, naive data fitting methods can produce misleading results in cases with non-uniform data. Weighted total least-squares methods can compensate for non-uniformity. We show how they can be accelerated with GPUs, using plane fitting as an example. / Thesis / Doctor of Philosophy (PhD)

Hochdurchsatzverfahren quantifizieren eine Vielzahl zellulärer Komponenten, können aber selten deren Interaktionen beschreiben. Daher wurden in den letzten 20 Jahren verschiedenste Netzwerk-Rekonstruktionsmethoden entwickelt. Insbesondere Perturbationsdaten erlauben dabei Rückschlüsse über funktionelle Mechanismen in der Genregulierung, Signal Transduktion, intra-zellulärer Kommunikation und anderen Prozessen zu ziehen. Dennoch bleibt Netzwerkinferenz ein ungelöstes Problem, weil die meisten Methoden auf ungeeigneten Annahmen basieren und die Identifizierbarkeit von Netzwerkkanten nicht aufklären. Diesbezüglich beschreibt diese Dissertation eine neue Rekonstruktionsmethode, die auf einfachen Annahmen von Perturbationsausbreitung basiert. Damit ist sie in verschiedensten Zusammenhängen anwendbar und übertrifft andere Methoden in Standard-Benchmarks. Für MAPK und PI3K Signalwege in einer Adenokarzinom-Zellline generiert sie plausible Netzwerkhypothesen, die unterschiedliche Sensitivitäten von PI3K-Mutanten gegenüber verschiedener Inhibitoren überzeugend erklären. Weiterhin wird gezeigt, dass sich Netzwerk-Identifizierbarkeit durch ein intuitives Max-Flow Problem beschreiben lässt. Dieses analytische Resultat erlaubt effektive, identifizierbare Netzwerke zu ermitteln und das experimentelle Design aufwändiger Perturbationsexperimente zu optimieren. Umfangreiche Tests zeigen, dass der Ansatz im Vergleich zu zufällig generierten Perturbationssequenzen die Anzahl der für volle Identifizierbarkeit notwendigen Perturbationen auf unter ein Drittel senkt. Schließlich beschreibt die Dissertation eine mathematische Weiterentwicklung der Modular Response Analysis. Es wird gezeigt, dass sich das Problem als analytisch lösbare orthogonale Regression approximieren lässt. Dies erlaubt eine drastische Reduzierung des nummerischen Aufwands, womit sich deutlich größere Netzwerke rekonstruieren und neueste Hochdurchsatz-Perturbationsdaten auswerten lassen. / 'Omics' technologies provide extensive quantifications of components of biological systems but rarely characterize the interactions between them. To fill this gap, various network reconstruction methods have been developed over the past twenty years. Using perturbation data, these methods can deduce functional mechanisms in gene regulation, signal transduction, intra-cellular communication and many other cellular processes. Nevertheless, this reverse engineering problem remains essentially unsolved because inferred networks are often based on inapt assumptions, lack interpretability as well as a rigorous description of identifiability. To overcome these shortcoming, this thesis first presents a novel inference method which is based on a simple response logic. The underlying assumptions are so mild that the approach is suitable for a wide range of applications while also outperforming existing methods in standard benchmark data sets. For MAPK and PI3K signalling pathways in an adenocarcinoma cell line, it derived plausible network hypotheses, which explain distinct sensitivities of PI3K mutants to targeted inhibitors. Second, an intuitive maximum-flow problem is shown to describe identifiability of network interactions. This analytical result allows to devise identifiable effective network models in underdetermined settings and to optimize the design of costly perturbation experiments. Benchmarked on a database of human pathways, full network identifiability is obtained with less than a third of the perturbations that are needed in random experimental designs. Finally, the thesis presents mathematical advances within Modular Response Analysis (MRA), which is a popular framework to quantify network interaction strengths. It is shown that MRA can be approximated as an analytically solvable total least squares problem. This insight drastically reduces computational complexity, which allows to model much bigger networks and to handle novel large-scale perturbation data.