Search results for "hierarchical data."
showing 10 items of 17 documents
Using latent variable models to identify large networks of species‐to‐species associations at different spatial scales
2015
Summary We present a hierarchical latent variable model that partitions variation in species occurrences and co-occurrences simultaneously at multiple spatial scales. We illustrate how the parameterized model can be used to predict the occurrences of a species by using as predictors not only the environmental covariates, but also the occurrences of all other species, at all spatial scales. We leverage recent progress in Bayesian latent variable models to implement a computationally effective algorithm that enables one to consider large communities and extensive sampling schemes. We exemplify the framework with a community of 98 fungal species sampled in c. 22 500 dead wood units in 230 plot…
Evo-devo mechanisms underlying the continuum between homology and homoplasy
2015
The different manifestations of equivalence and similarity in structure throughout evolution suggest a continuous and hierarchical process that starts out with the origin of a morphological novelty, unit, or homologue. Once a morphological unit has originated, its properties change subsequently into variants that differ, in magnitude, from the original properties found in the common ancestor. We will look into the nature of morphological units and their degrees of modification, which will provide the starting point for restructuring the concept of “homology,” keeping the use of homology as the identity of an anatomical part, and homogeny, as the specific variation of that anatomical part du…
Applications and Limitations of Robust Bayesian Bounds and Type II MLE
1994
Three applications of robust Bayesian analysis and three examples of its limitations are given. The applications that are reviewed are the development of an automatic Ockham’s Razor, outlier detection, and analysis of weighted distributions. Limitations of robust Bayesian bounds are highlighted through examples that include analysis of a paranormal experiment and a hierarchical model. This last example shows a disturbing difference between actual hierarchical Bayesian analysis and robust Bayesian bounds, a difference which also arises if, instead, a Type II MLE or empirical Bayes analysis is performed.
The problem of interoperability: A common data format for quantum chemistry codes
2007
A common format for quantum chemistry (QC), enhancing code interoperability and communication between different programs, has been designed and implemented. An XML-based format, QC-ML, is presented for representing quantities such as geometry, basis set, and so on, while an HDF5-based format is presented for the storage of large binary data files. Some preliminary applications that use the format have been implemented and are also described. This activity was carried out within the COST in Chemistry D23 project “MetaChem,” in the Working Group “A meta-laboratory for code integration in ab initio methods.” © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
A Hierarchical Model for Analysing Consumption Patterns in Italy Before and During the Great Recession
2016
The paper aims to explore how the Great Recession of the twenty-first century has impacted on the consumption behaviour of Italian households. Following a hierarchical approach, the study investigates differences in consumption behaviour at both household and regional levels. Using micro data on Italian Household Expenditure for the years 2002, 2006, 2010 and 2012, multilevel and two-step regression models have been estimated. The analysis has been performed for four different consumption categories: food, housing, work-related and leisure. The analysis reveals that the economic crisis led to increasing income elasticity for each category of consumption, especially for food, the most essent…
On utilizing an enhanced object partitioning scheme to optimize self-organizing lists-on-lists
2020
With the advent of “Big Data” as a field, in and of itself, there are at least three fundamentally new questions that have emerged, namely the Artificially Intelligence (AI)-based algorithms required, the hardware to process the data, and the methods to store and access the data efficiently. This paper (The work of the second author was partially supported by NSERC, the Natural Sciences and Engineering Council of Canada. We are very grateful for the feedback from the anonymous Referees of the original submission. Their input significantly improved the quality of this final version.) presents some novel schemes for the last of the three areas. There have been thousands of papers written rega…
Self-service Ad-hoc Querying Using Controlled Natural Language
2016
The ad-hoc querying process is slow and error prone due to inability of business experts of accessing data directly without involving IT experts. The problem lies in complexity of means used to query data. We propose a new natural language- and semistar ontology-based ad-hoc querying approach which lowers the steep learning curve required to be able to query data. The proposed approach would significantly shorten the time needed to master the ad-hoc querying and to gain the direct access to data by business experts, thus facilitating the decision making process in enterprises, government institutions and other organizations.
Mass appraisal of residential real estate using multilevel modelling
2016
Mass appraisal, or the automatic valuation of a large number of real estate assets, has attracted the attention of many researchers, who have mainly approached this issue employing traditional econometric models such as Ordinary Least Squares (OLS). However, this method does not consider the hierarchical structure of the data and therefore assumes the unrealistic hypothesis of the independence of the individuals in the sample. This paper proposes the use of the Hierarchical Linear Model (HLM) to overcome this limitation. The HLM also gives valuable information on the percentage of the variance error caused by each level in the hierarchical model. In this study HLM was applied to a large dat…
A Decentralized Ontology Versioning Model Designed for Inter-operability and Multi-organizational Data Exchange
2021
Current information systems operated in a multi-organization context use centralized or hierarchical data models proven inefficient as the network’s scale rapidly increases. The introduction of blockchain and decentralized specific mechanisms stimulate the use of ontology-based data models. While the adoption of blockchain as a communication medium facilitates the communication and data exchange in a more reliably and securely fashion, this opens new challenges regarding the evolution and versioning of the ontology. This paper proposes a versioning mechanism tailored to the decentralized environment. It provides the conceptual building blocks allowing an ontology to evolve under the supervi…
OpenTIMS, TimsPy, and TimsR: Open and Easy Access to timsTOF Raw Data
2021
The Bruker timsTOF Pro is an instrument that couples trapped ion mobility spectrometry (TIMS) to high-resolution time-of-flight (TOF) mass spectrometry (MS). For proteomics, lipidomics, and metabolomics applications, the instrument is typically interfaced with a liquid chromatography (LC) system. The resulting LC-TIMS-MS data sets are, in general, several gigabytes in size and are stored in the proprietary Bruker Tims data format (TDF). The raw data can be accessed using proprietary binaries in C, C++, and Python on Windows and Linux operating systems. Here we introduce a suite of computer programs for data accession, including OpenTIMS, TimsR, and TimsPy. OpenTIMS is a C++ library capable …