Categorical Nature of Major Factor Selection via Information Theoretic Measurements

Without assuming any functional or distributional structure, we select collections of major factors embedded within response-versus-covariate (Re-Co) dynamics via selection criteria [C1: confirmable] and [C2: irrepaceable], which are based on information theoretic measurements. The two criteria are constructed based on the computing paradigm called Categorical Exploratory Data Analysis (CEDA) and linked to Wiener–Granger causality. All the information theoretical measurements, including conditional mutual information and entropy, are evaluated through the contingency table platform, which primarily rests on the categorical nature within all involved features of any data types: quantitative or qualitative. Our selection task identifies one chief collection, together with several secondary collections of major factors of various orders underlying the targeted Re-Co dynamics. Each selected collection is checked with algorithmically computed reliability against the finite sample phenomenon, and so is each member’s major factor individually. The developments of our selection protocol are illustrated in detail through two experimental examples: a simple one and a complex one. We then apply this protocol on two data sets pertaining to two somewhat related but distinct pitching dynamics of two pitch types: slider and fastball. In particular, we refer to a specific Major League Baseball (MLB) pitcher and we consider data of multiple seasons.

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Goodness-of-Fit Tests for Bivariate Time Series of Counts

Econometrics ◽

10.3390/econometrics9010010 ◽

2021 ◽

Vol 9 (1) ◽

pp. 10

Author(s):

Šárka Hudecová ◽

Marie Hušková ◽

Simos G. Meintanis

Keyword(s):

Goodness Of Fit ◽

Probability Generating Function ◽

Parametric Bootstrap ◽

Real Data ◽

Data Sets ◽

Test Statistics ◽

Finite Sample ◽

Generalized Poisson ◽

Goodness Of Fit Tests ◽

Monte Carlo Experiments

This article considers goodness-of-fit tests for bivariate INAR and bivariate Poisson autoregression models. The test statistics are based on an L2-type distance between two estimators of the probability generating function of the observations: one being entirely nonparametric and the second one being semiparametric computed under the corresponding null hypothesis. The asymptotic distribution of the proposed tests statistics both under the null hypotheses as well as under alternatives is derived and consistency is proved. The case of testing bivariate generalized Poisson autoregression and extension of the methods to dimension higher than two are also discussed. The finite-sample performance of a parametric bootstrap version of the tests is illustrated via a series of Monte Carlo experiments. The article concludes with applications on real data sets and discussion.

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Do galactic bars depend on environment?: an information theoretic analysis of Galaxy Zoo 2

Monthly Notices of the Royal Astronomical Society ◽

10.1093/mnras/staa3665 ◽

2020 ◽

Vol 501 (1) ◽

pp. 994-1001

Author(s):

Suman Sarkar ◽

Biswajit Pandey ◽

Snehasish Bhattacharjee

Keyword(s):

Spatial Distribution ◽

Mutual Information ◽

Local Density ◽

Statistical Significance ◽

Distribution Functions ◽

Cumulative Distribution ◽

Host Galaxy ◽

Data Sets ◽

Data Set ◽

Information Theoretic

ABSTRACT We use an information theoretic framework to analyse data from the Galaxy Zoo 2 project and study if there are any statistically significant correlations between the presence of bars in spiral galaxies and their environment. We measure the mutual information between the barredness of galaxies and their environments in a volume limited sample (Mr ≤ −21) and compare it with the same in data sets where (i) the bar/unbar classifications are randomized and (ii) the spatial distribution of galaxies are shuffled on different length scales. We assess the statistical significance of the differences in the mutual information using a t-test and find that both randomization of morphological classifications and shuffling of spatial distribution do not alter the mutual information in a statistically significant way. The non-zero mutual information between the barredness and environment arises due to the finite and discrete nature of the data set that can be entirely explained by mock Poisson distributions. We also separately compare the cumulative distribution functions of the barred and unbarred galaxies as a function of their local density. Using a Kolmogorov–Smirnov test, we find that the null hypothesis cannot be rejected even at $75{{\ \rm per\ cent}}$ confidence level. Our analysis indicates that environments do not play a significant role in the formation of a bar, which is largely determined by the internal processes of the host galaxy.

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Accelerating Causal Inference and Feature Selection Methods through G-Test Computation Reuse

Entropy ◽

10.3390/e23111501 ◽

2021 ◽

Vol 23 (11) ◽

pp. 1501

Author(s):

Camil Băncioiu ◽

Remus Brad

Keyword(s):

Feature Selection ◽

Causal Inference ◽

Selection Methods ◽

Conditional Mutual Information ◽

Selection Algorithm ◽

Feature Selection Algorithm ◽

Inference Method ◽

Information Theoretic ◽

Theoretic Concept ◽

Test Computation

This article presents a novel and remarkably efficient method of computing the statistical G-test made possible by exploiting a connection with the fundamental elements of information theory: by writing the G statistic as a sum of joint entropy terms, its computation is decomposed into easily reusable partial results with no change in the resulting value. This method greatly improves the efficiency of applications that perform a series of G-tests on permutations of the same features, such as feature selection and causal inference applications because this decomposition allows for an intensive reuse of these partial results. The efficiency of this method is demonstrated by implementing it as part of an experiment involving IPC–MB, an efficient Markov blanket discovery algorithm, applicable both as a feature selection algorithm and as a causal inference method. The results show outstanding efficiency gains for IPC–MB when the G-test is computed with the proposed method, compared to the unoptimized G-test, but also when compared to IPC–MB++, a variant of IPC–MB which is enhanced with an AD–tree, both static and dynamic. Even if this proposed method of computing the G-test is presented here in the context of IPC–MB, it is in fact bound neither to IPC–MB in particular, nor to feature selection or causal inference applications in general, because this method targets the information-theoretic concept that underlies the G-test, namely conditional mutual information. This aspect grants it wide applicability in data sciences.

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ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis

F1000Research ◽

10.12688/f1000research.4431.1 ◽

2014 ◽

Vol 3 ◽

pp. 146 ◽

Cited By ~ 2

Author(s):

Guanming Wu ◽

Eric Dawson ◽

Adrian Duong ◽

Robin Haw ◽

Lincoln Stein

Keyword(s):

Experimental Data ◽

Data Analysis ◽

Graphical Models ◽

High Throughput ◽

Interaction Network ◽

Large Data ◽

Relevant Information ◽

Data Sets ◽

Data Types ◽

Biological Studies

High-throughput experiments are routinely performed in modern biological studies. However, extracting meaningful results from massive experimental data sets is a challenging task for biologists. Projecting data onto pathway and network contexts is a powerful way to unravel patterns embedded in seemingly scattered large data sets and assist knowledge discovery related to cancer and other complex diseases. We have developed a Cytoscape app called “ReactomeFIViz”, which utilizes a highly reliable gene functional interaction network and human curated pathways from Reactome and other pathway databases. This app provides a suite of features to assist biologists in performing pathway- and network-based data analysis in a biologically intuitive and user-friendly way. Biologists can use this app to uncover network and pathway patterns related to their studies, search for gene signatures from gene expression data sets, reveal pathways significantly enriched by genes in a list, and integrate multiple genomic data types into a pathway context using probabilistic graphical models. We believe our app will give researchers substantial power to analyze intrinsically noisy high-throughput experimental data to find biologically relevant information.

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Extending the usage of graphics processing units on the cloud for cost savings on seismic data regularization

Brazilian Journal of Geophysics ◽

10.22564/rbgf.v38i2.2048 ◽

2021 ◽

Vol 38 (2) ◽

Author(s):

Nicholas Torres Okita ◽

Tiago A. Coimbra ◽

José Ribeiro ◽

Martin Tygel

Keyword(s):

Cloud Computing ◽

Graphics Processing Units ◽

Cost Savings ◽

Data Sets ◽

Computing Paradigm ◽

Common Reflection Surface ◽

User Demand ◽

Computationally Intensive ◽

Zero Offset ◽

Graphics Processing

ABSTRACT. The usage of graphics processing units is already known as an alternative to traditional multi-core CPU processing, offering faster performance in the order of dozens of times in parallel tasks. Another new computing paradigm is cloud computing usage as a replacement to traditional in-house clusters, enabling seemingly unlimited computation power, no maintenance costs, and cutting-edge technology, dynamically on user demand. Previously those two tools were used to accelerate the estimation of Common Reflection Surface (CRS) traveltime parameters, both in zero-offset and finite-offset domain, delivering very satisfactory results with large time savings from GPU devices alongside cost savings on the cloud. This work extends those results by using GPUs on the cloud to accelerate the Offset Continuation Trajectory (OCT) traveltime parameter estimation. The results have shown that the time and cost savings from GPU devices’ usage are even larger than those seen in the CRS results, being up to fifty times faster and sixty times cheaper. This analysis reaffirms that it is possible to save both time and money when using GPU devices on the cloud and concludes that the larger the data sets are and the more computationally intensive the traveltime operators are, we can see larger improvements.Keywords: cloud computing, GPU, seismic processing. Estendendo o uso de placas gráficas na nuvem para economias em regularização de dados sísmicosRESUMO. O uso de aceleradores gráficos para processamento já é uma alternativa conhecida ao uso de CPUs multi-cores, oferecendo um desempenho na ordem de dezenas de vezes mais rápido em tarefas paralelas. Outro novo paradigma de computação é o uso da nuvem computacional como substituta para os tradicionais clusters internos, possibilitando o uso de um poder computacional aparentemente infinito sem custo de manutenção e com tecnologia de ponta, dinamicamente sob demanda de usuário. Anteriormente essas duas ferramentas foram utilizadas para acelerar a estimação de parâmetros do tempo de trânsito de Common Reflection Surface (CRS), tanto em zero-offset quanto em offsets finitos, obtendo resultados satisfatórios com amplas economias tanto de tempo quanto de dinheiro na nuvem. Este trabalho estende os resultados obtidos anteriormente, desta vez utilizando GPUs na nuvem para acelerar a estimação de parâmetros do tempo de trânsito em Offset Continuation Trajectory (OCT). Os resultados obtidos mostraram que as economias de tempo e dinheiro foram ainda maiores do que aquelas obtidas no CRS, sendo até cinquenta vezes mais rápido e sessenta vezes mais barato. Esta análise reafirma que é possível economizar tanto tempo quanto dinheiro usando GPUs na nuvem, e conclui que quanto maior for o dado e quanto mais computacionalmente intenso for o operador, maiores serão os ganhos de desempenho observados e economias.Palavras-chave: computação em nuvem, GPU, processamento sísmico.

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Bulk private curves require large conditional mutual information

Journal of High Energy Physics ◽

10.1007/jhep09(2021)042 ◽

2021 ◽

Vol 2021 (9) ◽

Author(s):

Alex May

Keyword(s):

Mutual Information ◽

Boundary Region ◽

Theoretic Approach ◽

Strong Correlations ◽

Conditional Mutual Information ◽

Information Theoretic ◽

Causal Curve ◽

Resource Requirements ◽

Theoretic Argument ◽

Information Theoretic Approach

Abstract We prove a theorem showing that the existence of “private” curves in the bulk of AdS implies two regions of the dual CFT share strong correlations. A private curve is a causal curve which avoids the entanglement wedge of a specified boundary region $$ \mathcal{U} $$ U . The implied correlation is measured by the conditional mutual information $$ I\left({\mathcal{V}}_1:\left.{\mathcal{V}}_2\right|\mathcal{U}\right) $$ I V 1 : V 2 U , which is O(1/GN) when a private causal curve exists. The regions $$ {\mathcal{V}}_1 $$ V 1 and $$ {\mathcal{V}}_2 $$ V 2 are specified by the endpoints of the causal curve and the placement of the region $$ \mathcal{U} $$ U . This gives a causal perspective on the conditional mutual information in AdS/CFT, analogous to the causal perspective on the mutual information given by earlier work on the connected wedge theorem. We give an information theoretic argument for our theorem, along with a bulk geometric proof. In the geometric perspective, the theorem follows from the maximin formula and entanglement wedge nesting. In the information theoretic approach, the theorem follows from resource requirements for sending private messages over a public quantum channel.

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Uncovering the mesendoderm gene regulatory network through multi-omic data integration

10.1101/2020.11.01.362053 ◽

2020 ◽

Author(s):

Camden Jansen ◽

Kitt D. Paraiso ◽

Jeff J. Zhou ◽

Ira L. Blitz ◽

Margaret B. Fish ◽

...

Keyword(s):

Cell Differentiation ◽

Cell Fate ◽

Data Sets ◽

List Type ◽

Rna Seq ◽

Data Types ◽

Cell Fate Decisions ◽

Gene Regulatory ◽

Genome Scale ◽

Omic Data

SummaryMesendodermal specification is one of the earliest events in embryogenesis, where cells first acquire distinct identities. Cell differentiation is a highly regulated process that involves the function of numerous transcription factors (TFs) and signaling molecules, which can be described with gene regulatory networks (GRNs). Cell differentiation GRNs are difficult to build because existing mechanistic methods are low-throughput, and high-throughput methods tend to be non-mechanistic. Additionally, integrating highly dimensional data comprised of more than two data types is challenging. Here, we use linked self-organizing maps to combine ChIP-seq/ATAC-seq with temporal, spatial and perturbation RNA-seq data from Xenopus tropicalis mesendoderm development to build a high resolution genome scale mechanistic GRN. We recovered both known and previously unsuspected TF-DNA/TF-TF interactions and validated through reporter assays. Our analysis provides new insights into transcriptional regulation of early cell fate decisions and provides a general approach to building GRNs using highly-dimensional multi-omic data sets.HighlightsBuilt a generally applicable pipeline to creating GRNs using highly-dimensional multi-omic data setsPredicted new TF-DNA/TF-TF interactions during mesendoderm developmentGenerate the first genome scale GRN for vertebrate mesendoderm and expanded the core mesendodermal developmental network with high fidelityDeveloped a resource to visualize hundreds of RNA-seq and ChIP-seq data using 2D SOM metaclusters.

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Linking Norms, Ratings, and Relations of Words and Concepts Across Multiple Language Varieties

10.31234/osf.io/tgw3z ◽

2020 ◽

Author(s):

Annika Tjuka ◽

Robert Forkel ◽

Johann-Mattis List

Keyword(s):

Web Application ◽

Age Of Acquisition ◽

Data Curation ◽

Data Sets ◽

Data Types ◽

Word Meanings ◽

Language Varieties ◽

Diverse Data ◽

Multiple Languages ◽

Word Frequencies

Psychologists and linguists have collected a great diversity of data for word and concept properties. In psychology, many studies accumulate norms and ratings such as word frequencies or age-of-acquisition often for a large number of words. Linguistics, on the other hand, provides valuable insights into relations of word meanings. We present a collection of those data sets for norms, ratings, and relations that cover different languages: ‘NoRaRe.’ To enable a comparison between the diverse data types, we established workflows that facilitate the expansion of the database. A web application allows convenient access to the data (https://digling.org/norare/). Furthermore, a software API ensures consistent data curation by providing tests to validate the data sets. The NoRaRe collection is linked to the database curated by the Concepticon project (https://concepticon.clld.org) which offers a reference catalog of unified concept sets. The link between words in the data sets and the Concepticon concept sets makes a cross-linguistic comparison possible. In three case studies, we test the validity of our approach, the accuracy of our workflow, and the applicability of our database. The results indicate that the NoRaRe database can be applied for the study of word properties across multiple languages. The data can be used by psychologists and linguists to benefit from the knowledge rooted in both research disciplines.

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Full-waveform inversion for full-wavefield imaging: Decades in the making

The Leading Edge ◽

10.1190/tle40050324.1 ◽

2021 ◽

Vol 40 (5) ◽

pp. 324-334

Author(s):

Rongxin Huang ◽

Zhigang Zhang ◽

Zedong Wu ◽

Zhiyuan Wei ◽

Jiawei Mei ◽

...

Keyword(s):

Model Building ◽

Seismic Imaging ◽

Structural Information ◽

Waveform Inversion ◽

Velocity Model ◽

Data Sets ◽

Full Waveform Inversion ◽

Data Types ◽

Velocity Models ◽

Full Waveform

Seismic imaging using full-wavefield data that includes primary reflections, transmitted waves, and their multiples has been the holy grail for generations of geophysicists. To be able to use the full-wavefield data effectively requires a forward-modeling process to generate full-wavefield data, an inversion scheme to minimize the difference between modeled and recorded data, and, more importantly, an accurate velocity model to correctly propagate and collapse energy of different wave modes. All of these elements have been embedded in the framework of full-waveform inversion (FWI) since it was proposed three decades ago. However, for a long time, the application of FWI did not find its way into the domain of full-wavefield imaging, mostly owing to the lack of data sets with good constraints to ensure the convergence of inversion, the required compute power to handle large data sets and extend the inversion frequency to the bandwidth needed for imaging, and, most significantly, stable FWI algorithms that could work with different data types in different geologic settings. Recently, with the advancement of high-performance computing and progress in FWI algorithms at tackling issues such as cycle skipping and amplitude mismatch, FWI has found success using different data types in a variety of geologic settings, providing some of the most accurate velocity models for generating significantly improved migration images. Here, we take a step further to modify the FWI workflow to output the subsurface image or reflectivity directly, potentially eliminating the need to go through the time-consuming conventional seismic imaging process that involves preprocessing, velocity model building, and migration. Compared with a conventional migration image, the reflectivity image directly output from FWI often provides additional structural information with better illumination and higher signal-to-noise ratio naturally as a result of many iterations of least-squares fitting of the full-wavefield data.

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Generalizing Benfordʼs Law

Benford's Law ◽

10.23943/princeton/9780691147611.003.0017 ◽

2015 ◽

Author(s):

Joanne Lee ◽

Wendy K. Tam Cho ◽

George Judge

Keyword(s):

Scientific Misconduct ◽

Adaptive Methods ◽

Data Sets ◽

Federal Grants ◽

Information Theoretic ◽

Data Adaptive ◽

The University ◽

University Of Vermont ◽

Case Data ◽

Information Theoretic Methods

This chapter examines and searches for evidence of fraud in two clinical data sets from a highly publicized case of scientific misconduct. In this case, data were falsified by Eric Poehlman, a faculty member at the University of Vermont, who pleaded guilty to fabricating more than a decade of data, some connected to federal grants from the National Institutes of Health. Poehlman had authored influential studies on many topics; including obesity, menopause, lipids, and aging. The chapter's classical Benford analysis along with a presentation of a more general class of Benford-like distributions highlights interesting insights into this and similar cases. In addition, this chapter demonstrates how information-theoretic methods and other data-adaptive methods are promising tools for generating benchmark distributions of first significant digits (FSDs) and examining data sets for departures from expectations.

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