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A hidden Markov model (HMM) is a Markov model in which the observations are dependent on a latent Markov process. An HMM requires that there be an observable process whose outcomes depend on the outcomes of in a known way. Since cannot be observed directly, the goal is to learn about state of by observing By definition of being a Markov model, an HMM has an additional requirement that the outcome of at time must be "influenced" exclusively by the outcome of at and that the outcomes of and at must be conditionally independent of at given at time Estimation of the parameters in an HMM can be performed using maximum likelihood. For linear chain HMMs, the Baum–Welch algorithm can be used to estimate the parameters.
A Bayesian network is a probabilistic graphical model that represents a set of variables and their conditional dependencies via a directed acyclic graph (DAG). While it is one of several forms of causal notation, causal networks are special cases of Bayesian networks. Bayesian networks are ideal for taking an event that occurred and predicting the likelihood that any one of several possible known causes was the contributing factor. For example, a Bayesian network could represent the probabilistic relationships between diseases and symptoms. Given symptoms, the network can be used to compute the probabilities of the presence of various diseases.
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an N-glycosylation site motif can be defined as Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro residue.
A graphical model or probabilistic graphical model (PGM) or structured probabilistic model is a probabilistic model for which a graph expresses the conditional dependence structure between random variables. They are commonly used in probability theory, statistics—particularly Bayesian statistics—and machine learning.
In statistics, Gibbs sampling or a Gibbs sampler is a Markov chain Monte Carlo (MCMC) algorithm for sampling from a specified multivariate probability distribution when direct sampling from the joint distribution is difficult, but sampling from the conditional distribution is more practical. This sequence can be used to approximate the joint distribution ; to approximate the marginal distribution of one of the variables, or some subset of the variables ; or to compute an integral. Typically, some of the variables correspond to observations whose values are known, and hence do not need to be sampled.
The Bioinformatics Centre is an interdisciplinary research in bioinformatics at the University of Copenhagen (UCPH). The centre is housed in the Section for Computational and RNA Biology at the Department of Biology within the Faculty of Science.
In statistics and machine learning, when one wants to infer a random variable with a set of variables, usually a subset is enough, and other variables are useless. Such a subset that contains all the useful information is called a Markov blanket. If a Markov blanket is minimal, meaning that it cannot drop any variable without losing information, it is called a Markov boundary. Identifying a Markov blanket or a Markov boundary helps to extract useful features. The terms of Markov blanket and Markov boundary were coined by Judea Pearl in 1988. A Markov blanket can be constituted by a set of Markov chains.
A dynamic Bayesian network (DBN) is a Bayesian network (BN) which relates variables to each other over adjacent time steps.
In the domain of physics and probability, a Markov random field (MRF), Markov network or undirected graphical model is a set of random variables having a Markov property described by an undirected graph. In other words, a random field is said to be a Markov random field if it satisfies Markov properties. The concept originates from the Sherrington–Kirkpatrick model.
Cis-regulatory elements (CREs) or Cis-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morphogenesis, the development of anatomy, and other aspects of embryonic development, studied in evolutionary developmental biology.
Conditional random fields (CRFs) are a class of statistical modeling methods often applied in pattern recognition and machine learning and used for structured prediction. Whereas a classifier predicts a label for a single sample without considering "neighbouring" samples, a CRF can take context into account. To do so, the predictions are modelled as a graphical model, which represents the presence of dependencies between the predictions. What kind of graph is used depends on the application. For example, in natural language processing, "linear chain" CRFs are popular, for which each prediction is dependent only on its immediate neighbours. In image processing, the graph typically connects locations to nearby and/or similar locations to enforce that they receive similar predictions.
Bayesian inference of phylogeny combines the information in the prior and in the data likelihood to create the so-called posterior probability of trees, which is the probability that the tree is correct given the data, the prior and the likelihood model. Bayesian inference was introduced into molecular phylogenetics in the 1990s by three independent groups: Bruce Rannala and Ziheng Yang in Berkeley, Bob Mau in Madison, and Shuying Li in University of Iowa, the last two being PhD students at the time. The approach has become very popular since the release of the MrBayes software in 2001, and is now one of the most popular methods in molecular phylogenetics.
In the mathematical theory of stochastic processes, variable-order Markov (VOM) models are an important class of models that extend the well known Markov chain models. In contrast to the Markov chain models, where each random variable in a sequence with a Markov property depends on a fixed number of random variables, in VOM models this number of conditioning random variables may vary based on the specific observed realization.
Statistical relational learning (SRL) is a subdiscipline of artificial intelligence and machine learning that is concerned with domain models that exhibit both uncertainty and complex, relational structure. Typically, the knowledge representation formalisms developed in SRL use first-order logic to describe relational properties of a domain in a general manner and draw upon probabilistic graphical models to model the uncertainty; some also build upon the methods of inductive logic programming. Significant contributions to the field have been made since the late 1990s.
In probability theory, a Markov model is a stochastic model used to model pseudo-randomly changing systems. It is assumed that future states depend only on the current state, not on the events that occurred before it. Generally, this assumption enables reasoning and computation with the model that would otherwise be intractable. For this reason, in the fields of predictive modelling and probabilistic forecasting, it is desirable for a given model to exhibit the Markov property.
In statistics, a hidden Markov random field is a generalization of a hidden Markov model. Instead of having an underlying Markov chain, hidden Markov random fields have an underlying Markov random field.
The following outline is provided as an overview of and topical guide to machine learning:
Machine learning in bioinformatics is the application of machine learning algorithms to bioinformatics, including genomics, proteomics, microarrays, systems biology, evolution, and text mining.
In network theory, collective classification is the simultaneous prediction of the labels for multiple objects, where each label is predicted using information about the object's observed features, the observed features and labels of its neighbors, and the unobserved labels of its neighbors. Collective classification problems are defined in terms of networks of random variables, where the network structure determines the relationship between the random variables. Inference is performed on multiple random variables simultaneously, typically by propagating information between nodes in the network to perform approximate inference. Approaches that use collective classification can make use of relational information when performing inference. Examples of collective classification include predicting attributes of individuals in a social network, classifying webpages in the World Wide Web, and inferring the research area of a paper in a scientific publication dataset.
References
- ↑ Ben-Gal, I.; Shani A.; Gohr A.; Grau J.; Arviv S.; Shmilovici A.; Posch S.; Grosse I. (2005). "Identification of Transcription Factor Binding Sites with Variable-order Bayesian Networks". Bioinformatics. 21 (11): 2657–2666. doi:10.1093/bioinformatics/bti410. PMID 15797905.
- ↑ Grau, J.; Ben-Gal I.; Posch S.; Grosse I. (2006). "VOMBAT: Prediction of Transcription Factor Binding Sites using Variable Order Bayesian Trees" (PDF). Nucleic Acids Research. 34 (Web Server issue): 529–533. doi:10.1093/nar/gkl212. PMC 1538886 . PMID 16845064.
- ↑ Boutilier, C.; Friedman, N.; Goldszmidt, M.; Koller, D. (1996). Context-specific independence in Bayesian networks. 12th Conference on Uncertainty in Artificial Intelligence (August 1–4, 1996). Reed College, Portland, Oregon, USA. pp. 115–123. arXiv: 1302.3562 .