Learning Markov networks with context-specific independences

Learning the Markov network structure from data is a problem that has received considerable attention in machine learning, and in many other application fields. This work focuses on a particular approach for this purpose called independence-based learning. Such approach guarantees the learning of the correct structure efficiently, whenever data is sufficient for representing the underlying distribution. However, an important issue of such approach is that the learned structures are encoded in an undirected graph. The problem with graphs is that they cannot encode some types of independence relations, such as the context-specific independences. They are a particular case of conditional independences that is true only for a certain assignment of its conditioning set, in contrast to conditional independences that must hold for all its assignments. In this work we present CSPC, an independence-based algorithm for learning structures that encode context-specific independences, and encoding them in a log-linear model, instead of a graph. The central idea of CSPC is combining the theoretical guarantees provided by the independence-based approach with the benefits of representing complex structures by using features in a log-linear model. We present experiments in a synthetic case, showing that CSPC is more accurate than the state-of-the-art IB algorithms when the underlying distribution contains CSIs.Comment: 8 pages, 6 figure

The IBMAP approach for Markov networks structure learning

In this work we consider the problem of learning the structure of Markov networks from data. We present an approach for tackling this problem called IBMAP, together with an efficient instantiation of the approach: the IBMAP-HC algorithm, designed for avoiding important limitations of existing independence-based algorithms. These algorithms proceed by performing statistical independence tests on data, trusting completely the outcome of each test. In practice tests may be incorrect, resulting in potential cascading errors and the consequent reduction in the quality of the structures learned. IBMAP contemplates this uncertainty in the outcome of the tests through a probabilistic maximum-a-posteriori approach. The approach is instantiated in the IBMAP-HC algorithm, a structure selection strategy that performs a polynomial heuristic local search in the space of possible structures. We present an extensive empirical evaluation on synthetic and real data, showing that our algorithm outperforms significantly the current independence-based algorithms, in terms of data efficiency and quality of learned structures, with equivalent computational complexities. We also show the performance of IBMAP-HC in a real-world application of knowledge discovery: EDAs, which are evolutionary algorithms that use structure learning on each generation for modeling the distribution of populations. The experiments show that when IBMAP-HC is used to learn the structure, EDAs improve the convergence to the optimum

Aprendizaje de independencias específicas del contexto en Markov random fields

Los modelos no dirigidos o Markov random fields son ampliamente utilizados para problemas que aprenden una distribución desconocida desde un conjunto de datos. Esto es porque permiten representar una distribución eficientemente al hacer explícitas las independencias condicionales que pueden existir entre sus variables. Además de estas independencias es posible representar otras, las Independencias Específicas del Contexto (CSIs) que a diferencia de las anteriores sólo son válidas bajo ciertos valores que pueden tomar subconjuntos de sus variables. Debido a esto son complicadas de representar y aprenderlas desde datos. En este trabajo presentamos un enfoque para representar CSIs en modelos no dirigidos y un algoritmo que las aprende desde datos utilizando tests estadísticos. Mostramos resultados donde los modelos aprendidos por nuestro algoritmo resultan ser mejores o comparables a modelos aprendidos por otros sin utilizar CSIs.Presentado en el XII Workshop Agentes y Sistemas Inteligentes (WASI)Red de Universidades con Carreras en Informática (RedUNCI

Male sterility and somatic hybridization in plant breeding

Plant male sterility refers to the failure in the production of fertile pollen. It occurs spontaneously in natural populations and may be caused by genes encoded in the nuclear (genic male sterility; GMS) or mitochondrial (cytoplasmic male sterility; CMS) genomes. This feature has great agronomic value for the production of hybrid seeds, since it prevents selfpollination without the need of emasculation which is time-consuming and cost-intensive. CMS has been widely used in crops, such as corn, rice, wheat, citrus, and several species of the family Solanaceae. Mitochondrial genes determining CMS have been uncovered in a wide range of plant species. The modes of action of CMS have been classified in terms of the effect they produce in the cell, which ultimately leads to a failure in the production of fertile pollen. Male fertility can be restored by nuclear-encoded genes, termed restorer-offertility (Rf) factors. CMS from wild plants has been transferred to species of agronomic interest through somatic hybridization. Somatic hybrids have also been produced to generate CMS de novo upon recombination of the mitochondrial genomes of two parental plants or by separating the CMS cytoplasm from the nuclear Rf alleles. As a result, somatic hybridization can be used as a highly efficient and useful strategy to incorporate CMS in breeding programs. Highlights Plant cytoplasmic male sterility (CMS) has great agronomic value for the production of hybrid seeds. Male fertility can be restored by nuclear-encoded genes, termed restorer-of-fertility (Rf) factors. Somatic hybridization is a useful scheme to uncover novel CMS/Rf systems to integrate in plant breeding programs. CMS from wild plants can be transferred to species of agronomic interest through somatic hybridization. The molecular mechanisms responsible for CMS are highly variable and involve RNA editing, homologous and non-homologous recombination, as well as a variety of gene regulators like non coding RNA.Plant male sterility refers to the failure in the production of fertile pollen. It occurs spontaneously in natural populations and may be caused by genes encoded in the nuclear (genic male sterility; GMS) or mitochondrial (cytoplasmic male sterility; CMS) genomes. This feature has great agronomic value for the production of hybrid seeds, since it prevents selfpollination without the need of emasculation which is time-consuming and cost-intensive. CMS has been widely used in crops, such as corn, rice, wheat, citrus, and several species of the family Solanaceae. Mitochondrial genes determining CMS have been uncovered in a wide range of plant species. The modes of action of CMS have been classified in terms of the effect they produce in the cell, which ultimately leads to a failure in the production of fertile pollen. Male fertility can be restored by nuclear-encoded genes, termed restorer-offertility (Rf) factors. CMS from wild plants has been transferred to species of agronomic interest through somatic hybridization. Somatic hybrids have also been produced to generate CMS de novo upon recombination of the mitochondrial genomes of two parental plants or by separating the CMS cytoplasm from the nuclear Rf alleles. As a result, somatic hybridization can be used as a highly efficient and useful strategy to incorporate CMS in breeding programs. Highlights Plant cytoplasmic male sterility (CMS) has great agronomic value for the production of hybrid seeds. Male fertility can be restored by nuclear-encoded genes, termed restorer-of-fertility (Rf) factors. Somatic hybridization is a useful scheme to uncover novel CMS/Rf systems to integrate in plant breeding programs. CMS from wild plants can be transferred to species of agronomic interest through somatic hybridization. The molecular mechanisms responsible for CMS are highly variable and involve RNA editing, homologous and non-homologous recombination, as well as a variety of gene regulators like non coding RNA

Male sterility and somatic hybridization in plant breeding

Plant male sterility refers to the failure in the production of fertile pollen. It occurs spon-taneously in natural populations and may be caused by genes encoded in the nuclear (genicmale sterility; GMS) or mitochondrial (cytoplasmic male sterility; CMS) genomes. Thisfeature has great agronomic value for the production of hybrid seeds, since it prevents self-pollination without the need of emasculation which is time-consuming and cost-intensive.CMS has been widely used in crops, such as corn, rice, wheat, citrus, and several speciesof the family Solanaceae. Mitochondrial genes determining CMS have been uncovered ina wide range of plant species. The modes of action of CMS have been classified in terms ofthe effect they produce in the cell, which ultimately leads to a failure in the production offertile pollen. Male fertility can be restored by nuclear-encoded genes, termed restorer-of-fertility (Rf) factors. CMS from wild plants has been transferred to species of agronomicinterest through somatic hybridization. Somatic hybrids have also been produced togenerate CMS de novo upon recombination of the mitochondrial genomes of two parentalplants or by separating the CMS cytoplasm from the nuclear Rf alleles. As a result, somatichybridization can be used as a highly efficient and useful strategy to incorporate CMS inbreeding programs.Fil: Garcia, Laura Evangelina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina. Universidad Nacional de Cuyo; ArgentinaFil: Edera, Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Marfil, Carlos Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Sánchez Puerta, María Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentin

Male sterility and somatic hybridization in plant breeding

Plant male sterility refers to the failure in the production of fertile pollen. It occurs spontaneously in natural populations and may be caused by genes encoded in the nuclear (genic male sterility; GMS) or mitochondrial (cytoplasmic male sterility; CMS) genomes. This feature has great agronomic value for the production of hybrid seeds, since it prevents selfpollination without the need of emasculation which is time-consuming and cost-intensive. CMS has been widely used in crops, such as corn, rice, wheat, citrus, and several species of the family Solanaceae. Mitochondrial genes determining CMS have been uncovered in a wide range of plant species. The modes of action of CMS have been classified in terms of the effect they produce in the cell, which ultimately leads to a failure in the production of fertile pollen. Male fertility can be restored by nuclear-encoded genes, termed restorer-offertility (Rf) factors. CMS from wild plants has been transferred to species of agronomic interest through somatic hybridization. Somatic hybrids have also been produced to generate CMS de novo upon recombination of the mitochondrial genomes of two parental plants or by separating the CMS cytoplasm from the nuclear Rf alleles. As a result, somatic hybridization can be used as a highly efficient and useful strategy to incorporate CMS in breeding programs. Highlights Plant cytoplasmic male sterility (CMS) has great agronomic value for the production of hybrid seeds. Male fertility can be restored by nuclear-encoded genes, termed restorer-of-fertility (Rf) factors. Somatic hybridization is a useful scheme to uncover novel CMS/Rf systems to integrate in plant breeding programs. CMS from wild plants can be transferred to species of agronomic interest through somatic hybridization. The molecular mechanisms responsible for CMS are highly variable and involve RNA editing, homologous and non-homologous recombination, as well as a variety of gene regulators like non coding RNA.Plant male sterility refers to the failure in the production of fertile pollen. It occurs spontaneously in natural populations and may be caused by genes encoded in the nuclear (genic male sterility; GMS) or mitochondrial (cytoplasmic male sterility; CMS) genomes. This feature has great agronomic value for the production of hybrid seeds, since it prevents selfpollination without the need of emasculation which is time-consuming and cost-intensive. CMS has been widely used in crops, such as corn, rice, wheat, citrus, and several species of the family Solanaceae. Mitochondrial genes determining CMS have been uncovered in a wide range of plant species. The modes of action of CMS have been classified in terms of the effect they produce in the cell, which ultimately leads to a failure in the production of fertile pollen. Male fertility can be restored by nuclear-encoded genes, termed restorer-offertility (Rf) factors. CMS from wild plants has been transferred to species of agronomic interest through somatic hybridization. Somatic hybrids have also been produced to generate CMS de novo upon recombination of the mitochondrial genomes of two parental plants or by separating the CMS cytoplasm from the nuclear Rf alleles. As a result, somatic hybridization can be used as a highly efficient and useful strategy to incorporate CMS in breeding programs. Highlights Plant cytoplasmic male sterility (CMS) has great agronomic value for the production of hybrid seeds. Male fertility can be restored by nuclear-encoded genes, termed restorer-of-fertility (Rf) factors. Somatic hybridization is a useful scheme to uncover novel CMS/Rf systems to integrate in plant breeding programs. CMS from wild plants can be transferred to species of agronomic interest through somatic hybridization. The molecular mechanisms responsible for CMS are highly variable and involve RNA editing, homologous and non-homologous recombination, as well as a variety of gene regulators like non coding RNA

aedera/m6anormalization: release

Calculate k-mer constants to normalize m6a levels inferred from DNA Nanopore read

A complex interplay between histone variants and DNA methylation

International audienceNucleosomes, the chromatin building blocks, play an important role in controlling DNA and chromatin accessibility. Nucleosome remodeling and the incorporation of distinct histone variants confer unique structural and biochemical properties, influencing the targeting of multiple epigenetic pathways, particularly DNA methylation. This stable epigenetic mark suppresses transposable element expression in plants and mammals, serving as an additional layer of chromatin regulation. In this review we explore recent advances in our understanding of the complex interplays between histone variants and DNA methylation in plants, and discuss the role that chromatin remodeling plays in coordinating histone exchange and methylation of DNA