Search results for "Quantitative"
showing 10 items of 2409 documents
Finding optimal finite biological sequences over finite alphabets: the OptiFin toolbox
2017
International audience; In this paper, we present a toolbox for a specific optimization problem that frequently arises in bioinformatics or genomics. In this specific optimisation problem, the state space is a set of words of specified length over a finite alphabet. To each word is associated a score. The overall objective is to find the words which have the lowest possible score. This type of general optimization problem is encountered in e.g 3D conformation optimisation for protein structure prediction, or largest core genes subset discovery based on best supported phylogenetic tree for a set of species. In order to solve this problem, we propose a toolbox that can be easily launched usin…
Selectivity in Probabilistic Causality: Drawing Arrows from Inputs to Stochastic Outputs
2011
Given a set of several inputs into a system (e.g., independent variables characterizing stimuli) and a set of several stochastically non-independent outputs (e.g., random variables describing different aspects of responses), how can one determine, for each of the outputs, which of the inputs it is influenced by? The problem has applications ranging from modeling pairwise comparisons to reconstructing mental processing architectures to conjoint testing. A necessary and sufficient condition for a given pattern of selective influences is provided by the Joint Distribution Criterion, according to which the problem of "what influences what" is equivalent to that of the existence of a joint distr…
Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases
2019
AbstractThe widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with ‘ready-to-use’ deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotatio…
Nonlinearities and Adaptation of Color Vision from Sequential Principal Curves Analysis
2016
Mechanisms of human color vision are characterized by two phenomenological aspects: the system is nonlinear and adaptive to changing environments. Conventional attempts to derive these features from statistics use separate arguments for each aspect. The few statistical explanations that do consider both phenomena simultaneously follow parametric formulations based on empirical models. Therefore, it may be argued that the behavior does not come directly from the color statistics but from the convenient functional form adopted. In addition, many times the whole statistical analysis is based on simplified databases that disregard relevant physical effects in the input signal, as, for instance…
Gap Filling of Biophysical Parameter Time Series with Multi-Output Gaussian Processes
2018
In this work we evaluate multi-output (MO) Gaussian Process (GP) models based on the linear model of coregionalization (LMC) for estimation of biophysical parameter variables under a gap filling setup. In particular, we focus on LAI and fAPAR over rice areas. We show how this problem cannot be solved with standard single-output (SO) GP models, and how the proposed MO-GP models are able to successfully predict these variables even in high missing data regimes, by implicitly performing an across-domain information transfer.
Disentangling the Link Between Image Statistics and Human Perception
2023
In the 1950s Horace Barlow and Fred Attneave suggested a connection between sensory systems and how they are adapted to the environment: early vision evolved to maximise the information it conveys about incoming signals. Following Shannon's definition, this information was described using the probability of the images taken from natural scenes. Previously, direct accurate predictions of image probabilities were not possible due to computational limitations. Despite the exploration of this idea being indirect, mainly based on oversimplified models of the image density or on system design methods, these methods had success in reproducing a wide range of physiological and psychophysical phenom…
Retrieval of aboveground crop nitrogen content with a hybrid machine learning method
2020
Abstract Hyperspectral acquisitions have proven to be the most informative Earth observation data source for the estimation of nitrogen (N) content, which is the main limiting nutrient for plant growth and thus agricultural production. In the past, empirical algorithms have been widely employed to retrieve information on this biochemical plant component from canopy reflectance. However, these approaches do not seek for a cause-effect relationship based on physical laws. Moreover, most studies solely relied on the correlation of chlorophyll content with nitrogen, and thus neglected the fact that most N is bound in proteins. Our study presents a hybrid retrieval method using a physically-base…
Human experts vs. machines in taxa recognition
2020
The step of expert taxa recognition currently slows down the response time of many bioassessments. Shifting to quicker and cheaper state-of-the-art machine learning approaches is still met with expert scepticism towards the ability and logic of machines. In our study, we investigate both the differences in accuracy and in the identification logic of taxonomic experts and machines. We propose a systematic approach utilizing deep Convolutional Neural Nets with the transfer learning paradigm and extensively evaluate it over a multi-pose taxonomic dataset with hierarchical labels specifically created for this comparison. We also study the prediction accuracy on different ranks of taxonomic hier…
Critical comments on EEG sensor space dynamical connectivity analysis
2019
Many different analysis techniques have been developed and applied to EEG recordings that allow one to investigate how different brain areas interact. One particular class of methods, based on the linear parametric representation of multiple interacting time series, is widely used to study causal connectivity in the brain. However, the results obtained by these methods should be interpreted with great care. The goal of this paper is to show, both theoretically and using simulations, that results obtained by applying causal connectivity measures on the sensor (scalp) time series do not allow interpretation in terms of interacting brain sources. This is because (1) the channel locations canno…
Futures pricing in electricity markets based on stable CARMA spot models
2012
We present a new model for the electricity spot price dynamics, which is able to capture seasonality, low-frequency dynamics and the extreme spikes in the market. Instead of the usual purely deterministic trend we introduce a non-stationary independent increments process for the low-frequency dynamics, and model the large uctuations by a non-Gaussian stable CARMA process. The model allows for analytic futures prices, and we apply these to model and estimate the whole market consistently. Besides standard parameter estimation, an estimation procedure is suggested, where we t the non-stationary trend using futures data with long time until delivery, and a robust L 1 -lter to nd the states of …