Markov chainA Markov chain or Markov process is a stochastic model describing a sequence of possible events in which the probability of each event depends only on the state attained in the previous event. Informally, this may be thought of as, "What happens next depends only on the state of affairs now." A countably infinite sequence, in which the chain moves state at discrete time steps, gives a discrete-time Markov chain (DTMC). A continuous-time process is called a continuous-time Markov chain (CTMC).
Markov propertyIn probability theory and statistics, the term Markov property refers to the memoryless property of a stochastic process, which means that its future evolution is independent of its history. It is named after the Russian mathematician Andrey Markov. The term strong Markov property is similar to the Markov property, except that the meaning of "present" is defined in terms of a random variable known as a stopping time. The term Markov assumption is used to describe a model where the Markov property is assumed to hold, such as a hidden Markov model.
Sequence analysisIn bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. Methodologies used include sequence alignment, searches against biological databases, and others. Since the development of methods of high-throughput production of gene and protein sequences, the rate of addition of new sequences to the databases increased very rapidly.
Discriminative modelDiscriminative models, also referred to as conditional models, are a class of logistical models used for classification or regression. They distinguish decision boundaries through observed data, such as pass/fail, win/lose, alive/dead or healthy/sick. Typical discriminative models include logistic regression (LR), conditional random fields (CRFs) (specified over an undirected graph), decision trees, and many others. Typical generative model approaches include naive Bayes classifiers, Gaussian mixture models, variational autoencoders, generative adversarial networks and others.
Multiple sequence alignmentMultiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins.
Variational Bayesian methodsVariational Bayesian methods are a family of techniques for approximating intractable integrals arising in Bayesian inference and machine learning. They are typically used in complex statistical models consisting of observed variables (usually termed "data") as well as unknown parameters and latent variables, with various sorts of relationships among the three types of random variables, as might be described by a graphical model. As typical in Bayesian inference, the parameters and latent variables are grouped together as "unobserved variables".
Markov information sourceIn mathematics, a Markov information source, or simply, a Markov source, is an information source whose underlying dynamics are given by a stationary finite Markov chain. An information source is a sequence of random variables ranging over a finite alphabet , having a stationary distribution. A Markov information source is then a (stationary) Markov chain , together with a function that maps states in the Markov chain to letters in the alphabet .
Homology modelingHomology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence.
Counterfactual conditionalCounterfactual conditionals (also subjunctive or X-marked) are conditional sentences which discuss what would have been true under different circumstances, e.g. "If Peter believed in ghosts, he would be afraid to be here." Counterfactuals are contrasted with indicatives, which are generally restricted to discussing open possibilities. Counterfactuals are characterized grammatically by their use of fake tense morphology, which some languages use in combination with other kinds of morphology including aspect and mood.
Sequence motifIn 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. When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical element of the overall structure of the protein.
