The Past, Present, and Future of Multidimensional Scaling

Multidimensional scaling (MDS) has established itself as a standard tool for statisticians and applied researchers. Its success is due to its simple and easily interpretable representation of potentially complex structural data. These data are typically embedded into a 2-dimensional map, where the objects of interest (items, attributes, stimuli, respondents, etc.) correspond to points such that those that are near to each other are empirically similar, and those that are far apart are different. In this paper, we pay tribute to several important developers of MDS and give a subjective overview of milestones in MDS developments. We also discuss the present situation of MDS and give a brief outlook on its future

A nonspatial methodology for the analysis of two-way proximity data incorporating the distance-density hypothesis

This paper presents a nonspatial operationalization of the Krumhansl (1978, 1982) distancedensity model of similarity. This model assumes that the similarity between two objects i and j is a function of both the interpoint distance between i and j and the density of other stimulus points in the regions surrounding i and j . We review this conceptual model and associated empirical evidence for such a specification. A nonspatial, tree-fitting methodology is described which is sufficiently flexible to fit a number of competing hypotheses of similarity formation. A sequential, unconstrained minimization algorithm is technically presented together with various program options. Three applications are provided which demonstrate the flexibility of the methodology. Finally, extensions to spatial models, three-way analyses, and hybrid models are discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45746/1/11336_2005_Article_BF02295285.pd

A new stochastic path-length tree methodology for constructing communication networks

Network analysis has become a popular method for identifying the communication structure in a system where positional and relational aspects are important. In this paper, a maximum likelihood based methodology is presented that allows for the analysis of binary sociometric data. This methodology provides a network representation via estimated path-length or additive trees that indicate the distance between all pairs of members. The methodology is distinguished from traditional hierarchical clustering based procedures by its direct consideration of the asymmetry in a typical communication process, the simultaneous representation of structural characteristics (e.g., clique membership, clique cohesiveness), and the identification of the specialized communication roles of each member (e.g., opinion leader, liaison). A penalty function algorithm is developed and its performance is investigated via a Monte Carlo analysis with synthetic data. An application examining information flows among managers is presented. Finally, directions for future research are suggested.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29291/1/0000352.pd

Cell assembly dynamics of sparsely-connected inhibitory networks: a simple model for the collective activity of striatal projection neurons

Striatal projection neurons form a sparsely-connected inhibitory network, and this arrangement may be essential for the appropriate temporal organization of behavior. Here we show that a simplified, sparse inhibitory network of Leaky-Integrate-and-Fire neurons can reproduce some key features of striatal population activity, as observed in brain slices [Carrillo-Reid et al., J. Neurophysiology 99 (2008) 1435{1450]. In particular we develop a new metric to determine the conditions under which sparse inhibitory networks form anti-correlated cell assemblies with time-varying activity of individual cells. We found that under these conditions the network displays an input-specific sequence of cell assembly switching, that effectively discriminates similar inputs. Our results support the proposal [Ponzi and Wickens, PLoS Comp Biol 9 (2013) e1002954] that GABAergic connections between striatal projection neurons allow stimulus-selective, temporally-extended sequential activation of cell assemblies. Furthermore, we help to show how altered intrastriatal GABAergic signaling may produce aberrant network-level information processing in disorders such as Parkinson's and Huntington's diseases.Comment: 22 pages, 9 figure

Changing Choices

Changing choices psychological relativity theory unifying theory transformation parameters psychology psygologie koornstra choice dynamics The book contains a unifying theory on how the common object space is metrically transformed by individuals with different transformation parameters, due to their other previous experiences, to individually different psychological spaces for judgment on the one hand and preference on the other hand. Individual experiences also change generally, whereby the psychological spaces also change generally for each individual. The theory, therefore, is a psychological relativity theory of perception, judgment, preference, and choice dynamics. This book is a must read for all behavioural, economic, and social scientists with theoretical interest and some understanding of multidimensional data analyses. It integrates more than twenty theories on perception, judgment, preference, and risk decisions into one mathematical theory. Knowledge of advanced mathematics and modern geometry is not needed, because the mathematical subsections can be skipped without loss of understanding, due to their explanation and illustration by figures in the text

Unsupervised Deraining: Where Asymmetric Contrastive Learning Meets Self-similarity

Most of the existing learning-based deraining methods are supervisedly trained on synthetic rainy-clean pairs. The domain gap between the synthetic and real rain makes them less generalized to complex real rainy scenes. Moreover, the existing methods mainly utilize the property of the image or rain layers independently, while few of them have considered their mutually exclusive relationship. To solve above dilemma, we explore the intrinsic intra-similarity within each layer and inter-exclusiveness between two layers and propose an unsupervised non-local contrastive learning (NLCL) deraining method. The non-local self-similarity image patches as the positives are tightly pulled together, rain patches as the negatives are remarkably pushed away, and vice versa. On one hand, the intrinsic self-similarity knowledge within positive/negative samples of each layer benefits us to discover more compact representation; on the other hand, the mutually exclusive property between the two layers enriches the discriminative decomposition. Thus, the internal self-similarity within each layer (similarity) and the external exclusive relationship of the two layers (dissimilarity) serving as a generic image prior jointly facilitate us to unsupervisedly differentiate the rain from clean image. We further discover that the intrinsic dimension of the non-local image patches is generally higher than that of the rain patches. This motivates us to design an asymmetric contrastive loss to precisely model the compactness discrepancy of the two layers for better discriminative decomposition. In addition, considering that the existing real rain datasets are of low quality, either small scale or downloaded from the internet, we collect a real large-scale dataset under various rainy kinds of weather that contains high-resolution rainy images.Comment: 16 pages, 15 figures. arXiv admin note: substantial text overlap with arXiv:2203.1150

ADVANCES ON BILINEAR MODELING OF BIOCHEMICAL BATCH PROCESSES

[EN] This thesis is aimed to study the implications of the statistical modeling approaches proposed for the bilinear modeling of batch processes, develop new techniques to overcome some of the problems that have not been yet solved and apply them to data of biochemical processes. The study, discussion and development of the new methods revolve around the four steps of the modeling cycle, from the alignment, preprocessing and calibration of batch data to the monitoring of batches trajectories. Special attention is given to the problem of the batch synchronization, and its effect on the modeling from different angles. The manuscript has been divided into four blocks. First, a state-of- the-art of the latent structures based-models in continuous and batch processes and traditional univariate and multivariate statistical process control systems is carried out. The second block of the thesis is devoted to the preprocessing of batch data, in particular, to the equalization and synchronization of batch trajectories. The first section addresses the problem of the lack of equalization in the variable trajectories. The different types of unequalization scenarios that practitioners might finnd in batch processes are discussed and the solutions to equalize batch data are introduced. In the second section, a theoretical study of the nature of batch processes and of the synchronization of batch trajectories as a prior step to bilinear modeling is carried out. The topics under discussion are i) whether the same synchronization approach must be applied to batch data in presence of different types of asynchronisms, and ii) whether synchronization is always required even though the length of the variable trajectories are constant across batches. To answer these questions, a thorough study of the most common types of asynchronisms that may be found in batch data is done. Furthermore, two new synchronization techniques are proposed to solve the current problems in post-batch and real-time synchronization. To improve fault detection and classification, new unsupervised control charts and supervised fault classifiers based on the information generated by the batch synchronization are also proposed. In the third block of the manuscript, a research work is performed on the parameter stability associated with the most used synchronization methods and principal component analysis (PCA)-based Batch Multivariate Statistical Process Control methods. The results of this study have revealed that accuracy in batch synchronization has a profound impact on the PCA model parameters stability. Also, the parameter stability is closely related to the type of preprocessing performed in batch data, and the type of model and unfolding used to transform the three-way data structure to two-way. The setting of the parameter stability, the source of variability remaining after preprocessing and the process dynamics should be balanced in such a way that multivariate statistical models are accurate in fault detection and diagnosis and/or in online prediction. Finally, the fourth block introduces a graphical user-friendly interface developed in Matlab code for batch process understanding and monitoring. To perform multivariate analysis, the last developments in process chemometrics, including the methods proposed in this thesis, are implemented.[ES] La presente tesis doctoral tiene como objetivo estudiar las implicaciones de los métodos estadísticos propuestos para la modelización bilineal de procesos por lotes, el desarrollo de nuevas técnicas para solucionar algunos de los problemas más complejos aún por resolver en esta línea de investigación y aplicar los nuevos métodos a datos provenientes de procesos bioquímicos para su evaluación estadística. El estudio, la discusión y el desarrollo de los nuevos métodos giran en torno a las cuatro fases del ciclo de modelización: desde la sincronización, ecualización, preprocesamiento y calibración de los datos, a la monitorización de las trayectorias de las variables del proceso. Se presta especial atención al problema de la sincronización y su efecto en la modelización estadística desde distintas perspectivas. El manuscrito se ha dividido en cuatro grandes bloques. En primer lugar, se realiza una revisión bibliográfica de las técnicas de proyección sobre estructuras latentes para su aplicación en procesos continuos y por lotes, y del diseño de sistemas de control basados en modelos estadísticos multivariantes. El segundo bloque del documento versa sobre el preprocesamiento de los datos, en concreto, sobre la ecualización y la sincronización. La primera parte aborda el problema de la falta de ecualización en las trayectorias de las variables. Se discuten las diferentes políticas de muestreo que se pueden encontrar en procesos por lotes y las soluciones para ecualizar las variables. En la segunda parte de esta sección, se realiza un estudio teórico sobre la naturaleza de los procesos por lotes y de la sincronización de las trayectorias como paso previo a la modelización bilineal. Los temas bajo discusión son: i) si se debe utilizar el mismo enfoque de sincronización en lotes afectados por diferentes tipos de asincronismos, y ii) si la sincronización es siempre necesaria aún y cuando las trayectorias de las variables tienen la misma duración en todos los lotes. Para responder a estas preguntas, se lleva a cabo un estudio exhaustivo de los tipos más comunes de asincronismos que se pueden encontrar en este tipo de datos. Además, se proponen dos nuevas técnicas de sincronización para resolver los problemas existentes en aplicaciones post-morten y en tiempo real. Para mejorar la detección de fallos y la clasificación, también se proponen nuevos gráficos de control no supervisados y clasificadores de fallos supervisados en base a la información generada por la sincronización de los lotes. En el tercer bloque del manuscrito se realiza un estudio de la estabilidad de los parámetros asociados a los métodos de sincronización y a los métodos estadístico multivariante basados en el Análisis de Componentes Principales (PCA) más utilizados para el control de procesos. Los resultados de este estudio revelan que la precisión de la sincronización de las trayectorias tiene un impacto significativo en la estabilidad de los parámetros de los modelos PCA. Además, la estabilidad paramétrica está estrechamente relacionada con el tipo de preprocesamiento realizado en los datos de los lotes, el tipo de modelo a justado y el despliegue utilizado para transformar la estructura de datos de tres a dos dimensiones. El ajuste de la estabilidad de los parámetros, la fuente de variabilidad que queda después del preprocesamiento de los datos y la captura de las dinámicas del proceso deben ser a justados de forma equilibrada de tal manera que los modelos estadísticos multivariantes sean precisos en la detección y diagnóstico de fallos y/o en la predicción en tiempo real. Por último, el cuarto bloque del documento describe una interfaz gráfica de usuario que se ha desarrollado en código Matlab para la comprensión y la supervisión de procesos por lotes. Para llevar a cabo los análisis multivariantes, se han implementado los últimos desarrollos en la quimiometría de proc[CA] Aquesta tesi doctoral te com a objectiu estudiar les implicacions dels mètodes de modelització estadística proposats per a la modelització bilineal de processos per lots, el desenvolupament de noves tècniques per resoldre els problemes encara no resolts en aquesta línia de recerca i aplicar els nous mètodes a les dades dels processos bioquímics. L'estudi, la discussió i el desenvolupament dels nous mètodes giren entorn a les quatre fases del cicle de modelització, des de l'alineació, preprocessament i el calibratge de les dades provinents de lots, a la monitorització de les trajectòries. Es presta especial atenció al problema de la sincronització per lots, i el seu efecte sobre el modelatge des de diferents angles. El manuscrit s'ha dividit en quatre grans blocs. En primer lloc, es realitza una revisió bibliogràfica dels principals mètodes basats en tècniques de projecció sobre estructures latents en processos continus i per lots, així com dels sistemes de control estadístics multivariats. El segon bloc del document es dedica a la preprocessament de les dades provinents de lots, en particular, l' equalització i la sincronització. La primera part aborda el problema de la manca d'equalització en les trajectòries de les variables. Es discuteixen els diferents tipus d'escenaris en que les variables estan mesurades a distints intervals i les solucions per equalitzar-les en processos per lots. A la segona part d'aquesta secció es porta a terme un estudi teòric de la naturalesa dels processos per lots i de la sincronització de les trajectòries de lots com a pas previ al modelatge bilineal. Els temes en discussió són: i) si el mateix enfocament de sincronització ha de ser aplicat a les dades del lot en presència de diferents tipus de asincronismes, i ii) si la sincronització sempre es requereix tot i que la longitud de les trajectòries de les variables són constants en tots el lots. Per respondre a aquestes preguntes, es du a terme un estudi exhaustiu dels tipus més comuns de asincronismes que es poden trobar en les dades provinents de lots. A més, es proposen dues noves tècniques de sincronització per resoldre els problemes existents la sincronització post-morten i en temps real. Per millorar la detecció i la classificació de anomalies, també es proposen nous gràfics de control no supervisats i classificadors de falla supervisats dissenyats en base a la informació generada per la sincronització de lots. En el tercer bloc del manuscrit es realitza un treball de recerca sobre l'estabilitat dels paràmetres associats als mètodes de sincronització i als mètodes estadístics multivariats basats en l'Anàlisi de Components Principals (PCA) més utilitzats per al control de processos. Els resultats d'aquest estudi revelen que la precisió en la sincronització per lots te un profund impacte en l'estabilitat dels paràmetres dels models PCA. A més, l'estabilitat paramètrica està estretament relacionat amb el tipus de preprocessament realitzat en les dades provinents de lots, el tipus de model i el desplegament utilitzat per transformar l'estructura de dades de tres a dos dimensions. L'ajust de l'estabilitat dels paràmetres, la font de variabilitat que queda després del preprocessament i la captura de la dinàmica de procés ha de ser equilibrada de tal manera que els models estadístics multivariats són precisos en la detecció i diagnòstic de fallades i/o en la predicció en línia. Finalment, el quart bloc del document introdueix una interfície gràfica d'usuari que s'ha dissenyat e implementat en Matlab per a la comprensió i la supervisió de processos per lots. Per dur a terme aquestes anàlisis multivariats, s'han implementat els últims desenvolupaments en la quimiometria de processos, incloent-hi els mètodes proposats en aquesta tesi.González Martínez, JM. (2015). ADVANCES ON BILINEAR MODELING OF BIOCHEMICAL BATCH PROCESSES [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/55684TESISPremios Extraordinarios de tesis doctorale

Cosmic Voids: structure, dynamics and galaxies

In this review we discuss several aspects of Cosmic Voids. Voids are a major component of the large scale distribution of matter and galaxies in the Universe. They are of instrumental importance for understanding the emergence of the Cosmic Web. Their relatively simple shape and structure makes them into useful tools for extracting the value of a variety cosmic parameters, possibly including even that of the influence of dark energy. Perhaps most promising and challenging is the issue of the galaxies found within their realm. Not only does the pristine environment of voids provide a promising testing ground for assessing the role of environment on the formation and evolution of galaxies, the dearth of dwarf galaxies may even represent a serious challenge to the standard view of cosmic structure formation.Comment: 29 pages, 12 figures, invited review COSPA2008, Pohang, Korea. Modern Physics Letters A, accepted. For high-res version see http://www.astro.rug.nl/~weygaert/voids.cospa2008.weygaert.pd

A machine learning approach to the unsupervised segmentation of mitochondria in subcellular electron microscopy data

Recent advances in cellular and subcellular microscopy demonstrated its potential towards unravelling the mechanisms of various diseases at the molecular level. The biggest challenge in both human- and computer-based visual analysis of micrographs is the variety of nanostructures and mitochondrial morphologies. The state-of-the-art is, however, dominated by supervised manual data annotation and early attempts to automate the segmentation process were based on supervised machine learning techniques which require large datasets for training. Given a minimal number of training sequences or none at all, unsupervised machine learning formulations, such as spectral dimensionality reduction, are known to be superior in detecting salient image structures. This thesis presents three major contributions developed around the spectral clustering framework which is proven to capture perceptual organization features. Firstly, we approach the problem of mitochondria localization. We propose a novel grouping method for the extracted line segments which describes the normal mitochondrial morphology. Experimental findings show that the clusters obtained successfully model the inner mitochondrial membrane folding and therefore can be used as markers for the subsequent segmentation approaches. Secondly, we developed an unsupervised mitochondria segmentation framework. This method follows the evolutional ability of human vision to extrapolate salient membrane structures in a micrograph. Furthermore, we designed robust non-parametric similarity models according to Gestaltic laws of visual segregation. Experiments demonstrate that such models automatically adapt to the statistical structure of the biological domain and return optimal performance in pixel classification tasks under the wide variety of distributional assumptions. The last major contribution addresses the computational complexity of spectral clustering. Here, we introduced a new anticorrelation-based spectral clustering formulation with the objective to improve both: speed and quality of segmentation. The experimental findings showed the applicability of our dimensionality reduction algorithm to very large scale problems as well as asymmetric, dense and non-Euclidean datasets

Temporal Mapper: Transition networks in simulated and real neural dynamics

AbstractCharacterizing large-scale dynamic organization of the brain relies on both data-driven and mechanistic modeling, which demands a low versus high level of prior knowledge and assumptions about how constituents of the brain interact. However, the conceptual translation between the two is not straightforward. The present work aims to provide a bridge between data-driven and mechanistic modeling. We conceptualize brain dynamics as a complex landscape that is continuously modulated by internal and external changes. The modulation can induce transitions between one stable brain state (attractor) to another. Here, we provide a novel method—Temporal Mapper—built upon established tools from the field of topological data analysis to retrieve the network of attractor transitions from time series data alone. For theoretical validation, we use a biophysical network model to induce transitions in a controlled manner, which provides simulated time series equipped with a ground-truth attractor transition network. Our approach reconstructs the ground-truth transition network from simulated time series data better than existing time-varying approaches. For empirical relevance, we apply our approach to fMRI data gathered during a continuous multitask experiment. We found that occupancy of the high-degree nodes and cycles of the transition network was significantly associated with subjects’ behavioral performance. Taken together, we provide an important first step toward integrating data-driven and mechanistic modeling of brain dynamics