Search results for "Markov Chains"
showing 10 items of 73 documents
Quadratic speedup for finding marked vertices by quantum walks
2020
A quantum walk algorithm can detect the presence of a marked vertex on a graph quadratically faster than the corresponding random walk algorithm (Szegedy, FOCS 2004). However, quantum algorithms that actually find a marked element quadratically faster than a classical random walk were only known for the special case when the marked set consists of just a single vertex, or in the case of some specific graphs. We present a new quantum algorithm for finding a marked vertex in any graph, with any set of marked vertices, that is (up to a log factor) quadratically faster than the corresponding classical random walk.
A multi-layer method to study genome-scale positions of nucleosomes
2009
AbstractThe basic unit of eukaryotic chromatin is the nucleosome, consisting of about 150 bp of DNA wrapped around a protein core made of histone proteins. Nucleosomes position is modulated in vivo to regulate fundamental nuclear processes. To measure nucleosome positions on a genomic scale both theoretical and experimental approaches have been recently reported. We have developed a new method, Multi-Layer Model (MLM), for the analysis of nucleosome position data obtained with microarray-based approach. The MLM is a feature extraction method in which the input data is processed by a classifier to distinguish between several kinds of patterns. We applied our method to simulated-synthetic and…
Forecasting Hepatitis C liver disease burden on real-life data. Does the hidden iceberg matter to reach the elimination goals?
2018
Abstract Background & Aims Advances in direct‐acting antiviral treatment of HCV have reinvigorated public health initiatives aimed at identifying affected individuals. We evaluated the possible impact of only diagnosed and linked‐to‐care individuals on overall HCV burden estimates and identified a possible strategy to achieve the WHO targets by 2030. Methods Using a modelling approach grounded in Italian real‐life data of diagnosed and treated patients, different linkage‐to‐care scenarios were built to evaluate potential strategies in achieving the HCV elimination goals. Results Under the 40% linked‐to‐care scenario, viraemic burden would decline (60%); however, eligible patients to treat w…
A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from Isotope Tracer Addition Experiments
2020
Understanding how nutrients flow through food webs is central in ecosystem ecology. Tracer addition experiments are powerful tools to reconstruct nutrient flows by adding an isotopically enriched element into an ecosystem and tracking its fate through time. Historically, the design and analysis of tracer studies have varied widely, ranging from descriptive studies to modeling approaches of varying complexity. Increasingly, isotope tracer data are being used to compare ecosystems and analyze experimental manipulations. Currently, a formal statistical framework for analyzing such experiments is lacking, making it impossible to calculate the estimation errors associated with the model fit, the…
Altered metabolism of gut microbiota contributes to chronic immune activation in HIV-infected individuals.
2015
Altered interplay between gut mucosa and microbiota during treated HIV infection may possibly contribute to increased bacterial translocation and chronic immune activation, both of which are predictors of morbidity and mortality. Although a dysbiotic gut microbiota has recently been reported in HIV + individuals, the metagenome gene pool associated with HIV infection remains unknown. The aim of this study is to characterize the functional gene content of gut microbiota in HIV + patients and to define the metabolic pathways of this bacterial community, which is potentially associated with immune dysfunction. We determined systemic markers of innate and adaptive immunity in a cohort of HIV-in…
Inverted and mirror repeats in model nucleotide sequences.
2007
We analytically and numerically study the probabilistic properties of inverted and mirror repeats in model sequences of nucleic acids. We consider both perfect and non-perfect repeats, i.e. repeats with mismatches and gaps. The considered sequence models are independent identically distributed (i.i.d.) sequences, Markov processes and long range sequences. We show that the number of repeats in correlated sequences is significantly larger than in i.i.d. sequences and that this discrepancy increases exponentially with the repeat length for long range sequences.
Economic Consequences of Investing in Anti-HCV Antiviral Treatment from the Italian NHS Perspective: A Real-World-Based Analysis of PITER Data
2019
OBJECTIVE:\ud We estimated the cost consequence of Italian National Health System (NHS) investment in direct-acting antiviral (DAA) therapy according to hepatitis C virus (HCV) treatment access policies in Italy.\ud \ud METHODS:\ud A multistate, 20-year time horizon Markov model of HCV liver disease progression was developed. Fibrosis stage, age and genotype distributions were derived from the Italian Platform for the Study of Viral Hepatitis Therapies (PITER) cohort. The treatment efficacy, disease progression probabilities and direct costs in each health state were obtained from the literature. The break-even point in time (BPT) was defined as the period of time required for the cumulativ…
Early Treatment in HCV: Is it a Cost-Utility Option from the Italian Perspective?
2016
In Italy, the Italian Pharmaceutical Agency (AIFA) criteria used F3–F4 fibrosis stages as the threshold to prioritise the treatment with interferon (IFN)-free regimens, while in genotype 1 chronic hepatitis C (G1 CHC) patients with fibrosis of liver stage 2, an approach with pegylated interferon (PEG-IFN)-based triple therapy with simeprevir was suggested. The key clinical question is whether, in an era of financial constraints, the application of a universal IFN-free strategy in naive G1 CHC patients is feasible within a short time horizon. The aim of this study is to perform an economic analysis to estimate the cost-utility of the early innovative therapy in Italy for managing hepatitis C…
Variable length Markov chains and dynamical sources
2010
Infinite random sequences of letters can be viewed as stochastic chains or as strings produced by a source, in the sense of information theory. The relationship between Variable Length Markov Chains (VLMC) and probabilistic dynamical sources is studied. We establish a probabilistic frame for context trees and VLMC and we prove that any VLMC is a dynamical source for which we explicitly build the mapping. On two examples, the ``comb'' and the ``bamboo blossom'', we find a necessary and sufficient condition for the existence and the unicity of a stationary probability measure for the VLMC. These two examples are detailed in order to provide the associated Dirichlet series as well as the gener…
Comparison of Different Hypotheses Regarding the Spread of Alzheimer’s Disease Using Markov Random Fields and Multimodal Imaging
2018
Alzheimer’s disease (AD) is characterized by a cascade of pathological processes that can be assessed in vivo using different neuroimaging methods. Recent research suggests a systematic sequence of pathogenic events on a global biomarker level, but little is known about the associations and dependencies of distinct lesion patterns on a regional level. Markov random fields are a probabilistic graphical modeling approach that represent the interaction between individual random variables by an undirected graph. We propose the novel application of this approach to study the interregional associations and dependencies between multimodal imaging markers of AD pathology and to compare different hy…