Compositional Data in Biomedical Research

Modern methods of compositional data analysis are not well known in biomedical research. Moreover, there appear to be few mathematical and statistical researchers working on compositional biomedical problems. Like the earth and environmental sciences, biomedicine has many problems in which the relevant scienti c information is encoded in the relative abundance of key species or categories. I introduce three problems in cancer research in which analysis of compositions plays an important role. The problems involve 1) the classi cation of serum proteomic pro les for early detection of lung cancer, 2) inference of the relative amounts of di erent tissue types in a diagnostic tumor biopsy, and 3) the subcellular localization of the BRCA1 protein, and it's role in breast cancer patient prognosis. For each of these problems I outline a partial solution. However, none of these problems is \solved". I attempt to identify areas in which additional statistical development is needed with the hope of encouraging more compositional data analysts to become involved in biomedical research

Markov chain montecarlo method applied to rounding zeros of compositional data: first approach

As stated in Aitchison (1986), a proper study of relative variation in a compositional data set should be based on logratios, and dealing with logratios excludes dealing with zeros. Nevertheless, it is clear that zero observations might be present in real data sets, either because the corresponding part is completely absent –essential zeros– or because it is below detection limit –rounded zeros. Because the second kind of zeros is usually understood as “a trace too small to measure”, it seems reasonable to replace them by a suitable small value, and this has been the traditional approach. As stated, e.g. by Tauber (1999) and by Martín-Fernández, Barceló-Vidal, and Pawlowsky-Glahn (2000), the principal problem in compositional data analysis is related to rounded zeros. One should be careful to use a replacement strategy that does not seriously distort the general structure of the data. In particular, the covariance structure of the involved parts –and thus the metric properties– should be preserved, as otherwise further analysis on subpopulations could be misleading. Following this point of view, a non-parametric imputation method is introduced in Martín-Fernández, Barceló-Vidal, and Pawlowsky-Glahn (2000). This method is analyzed in depth by Martín-Fernández, Barceló-Vidal, and Pawlowsky-Glahn (2003) where it is shown that the theoretical drawbacks of the additive zero replacement method proposed in Aitchison (1986) can be overcome using a new multiplicative approach on the non-zero parts of a composition. The new approach has reasonable properties from a compositional point of view. In particular, it is “natural” in the sense that it recovers the “true” composition if replacement values are identical to the missing values, and it is coherent with the basic operations on the simplex. This coherence implies that the covariance structure of subcompositions with no zeros is preserved. As a generalization of the multiplicative replacement, in the same paper a substitution method for missing values on compositional data sets is introduced

alr approach for replacing values below the detection limit

All of the imputation techniques usually applied for replacing values below the detection limit in compositional data sets have adverse effects on the variability. In this work we propose a modification of the EM algorithm that is applied using the additive log-ratio transformation. This new strategy is applied to a compositional data set and the results are compared with the usual imputation techniques

GRASS GIS for the distinction of vegetation from buildings using LiDAR altimetric data

La tecnología LiDAR (Light Detection and Ranging), basada en el escaneado del territorio por un telémetro láser aerotransportado, permite la construcción de Modelos Digitales de Superficie (DSM) mediante una simple interpolación, así como de Modelos Digitales del Terreno (DTM) mediante la identificación y eliminación de los objetos existentes en el terreno (edificios, puentes o árboles). El Laboratorio de Geomática del Politécnico de Milán – Campus de Como- desarrolló un algoritmo de filtrado de datos LiDAR basado en la interpolación con splines bilineares y bicúbicas con una regularización de Tychonov en una aproximación de mínimos cuadrados. Sin embargo, en muchos casos son todavía necesarios modelos más refinados y complejos en los cuales se hace obligatorio la diferenciación entre edificios y vegetación. Este puede ser el caso de algunos modelos de prevención de riesgos hidrológicos, donde la vegetación no es necesaria; o la modelización tridimensional de centros urbanos, donde la vegetación es factor problemático. (...)

LiDAR data filtering with GRASS GIS for the determination of digital terrain models

In the last years, the use of every type of Digital Elevation Models has iimproved. The LiDAR (Light Detection and Ranging) technology, based on the scansion of the territory b airborne laser telemeters, allows the construction of digital Surface Models (DSM), in an easy way by a simple data interpolation

Large-Area Photo-Mosaics Using Global Alignment and Navigation Data

Seafloor imagery is a rich source of data for the study of biological and geological processes. Among several applications, still images of the ocean floor can be used to build image composites referred to as photo-mosaics. Photo-mosaics provide a wide-area visual representation of the benthos, and enable applications as diverse as geological surveys, mapping and detection of temporal changes in the morphology of biodiversity. We present an approach for creating globally aligned photo-mosaics using 3D position estimates provided by navigation sensors available in deep water surveys. Without image registration, such navigation data does not provide enough accuracy to produce useful composite images. Results from a challenging data set of the Lucky Strike vent field at the Mid Atlantic Ridge are reported

Proposal of a parallel architecture for a motion detection algorithm

This paper proposes a parallel architecture for estimation of the motion of an underwater robot. It is well known that image processing requires a huge amount of computation, mainly at low-level processing where the algorithms are dealing with a great number of data. In a motion estimation algorithm, correspondences between two images have to be solved at the low level. In the underwater imaging, normalised correlation can be a solution in the presence of non-uniform illumination. Due to its regular processing scheme, parallel implementation of the correspondence problem can be an adequate approach to reduce the computation time. Taking into consideration the complexity of the normalised correlation criteria, a new approach using parallel organisation of every processor from the architecture is proposed

SQualTrack: A Tool for Robust Fault Detection

One of the techniques used to detect faults in dynamic systems is analytical redundancy. An important difficulty in applying this technique to real systems is dealing with the uncertainties associated with the system itself and with the measurements. In this paper, this uncertainty is taken into account by the use of intervals for the parameters of the model and for the measurements. The method that is proposed in this paper checks the consistency between the system's behavior, obtained from the measurements, and the model's behavior; if they are inconsistent, then there is a fault. The problem of detecting faults is stated as a quantified real constraint satisfaction problem, which can be solved using the modal interval analysis (MIA). MIA is used because it provides powerful tools to extend the calculations over real functions to intervals. To improve the results of the detection of the faults, the simultaneous use of several sliding time windows is proposed. The result of implementing this method is semiqualitative tracking (SQualTrack), a fault-detection tool that is robust in the sense that it does not generate false alarms, i.e., if there are false alarms, they indicate either that the interval model does not represent the system adequately or that the interval measurements do not represent the true values of the variables adequately. SQualTrack is currently being used to detect faults in real processes. Some of these applications using real data have been developed within the European project advanced decision support system for chemical/petrochemical manufacturing processes and are also described in this paper

Time misalignments in fault detection and diagnosis

El desalineamiento temporal es la incorrespondencia de dos señales debido a una distorsión en el eje temporal. La Detección y Diagnóstico de Fallas (Fault Detection and Diagnosis-FDD) permite la detección, el diagnóstico y la corrección de fallos en un proceso. La metodología usada en FDD está dividida en dos categorías: técnicas basadas en modelos y no basadas en modelos. Esta tesis doctoral trata sobre el estudio del efecto del desalineamiento temporal en FDD. Nuestra atención se enfoca en el análisis y el diseño de sistemas FDD en caso de problemas de comunicación de datos, como retardos y pérdidas. Se proponen dos técnicas para reducir estos problemas: una basada en programación dinámica y la otra en optimización. Los métodos propuestos han sido validados sobre diferentes sistemas dinámicos: control de posición de un motor de corriente continua, una planta de laboratorio y un problema de sistemas eléctricos conocido como hueco de tensión.