Causal modelIn the philosophy of science, a causal model (or structural causal model) is a conceptual model that describes the causal mechanisms of a system. Several types of causal notation may be used in the development of a causal model. Causal models can improve study designs by providing clear rules for deciding which independent variables need to be included/controlled for. They can allow some questions to be answered from existing observational data without the need for an interventional study such as a randomized controlled trial.
Directed acyclic graphIn mathematics, particularly graph theory, and computer science, a directed acyclic graph (DAG) is a directed graph with no directed cycles. That is, it consists of vertices and edges (also called arcs), with each edge directed from one vertex to another, such that following those directions will never form a closed loop. A directed graph is a DAG if and only if it can be topologically ordered, by arranging the vertices as a linear ordering that is consistent with all edge directions.
Directed graphIn mathematics, and more specifically in graph theory, a directed graph (or digraph) is a graph that is made up of a set of vertices connected by directed edges, often called arcs. In formal terms, a directed graph is an ordered pair where V is a set whose elements are called vertices, nodes, or points; A is a set of ordered pairs of vertices, called arcs, directed edges (sometimes simply edges with the corresponding set named E instead of A), arrows, or directed lines.
Cycle (graph theory)In graph theory, a cycle in a graph is a non-empty trail in which only the first and last vertices are equal. A directed cycle in a directed graph is a non-empty directed trail in which only the first and last vertices are equal. A graph without cycles is called an acyclic graph. A directed graph without directed cycles is called a directed acyclic graph. A connected graph without cycles is called a tree. A circuit is a non-empty trail in which the first and last vertices are equal (closed trail).
HypergraphIn mathematics, a hypergraph is a generalization of a graph in which an edge can join any number of vertices. In contrast, in an ordinary graph, an edge connects exactly two vertices. Formally, a directed hypergraph is a pair , where is a set of elements called nodes, vertices, points, or elements and is a set of pairs of subsets of . Each of these pairs is called an edge or hyperedge; the vertex subset is known as its tail or domain, and as its head or codomain. The order of a hypergraph is the number of vertices in .
Cycle graphIn graph theory, a cycle graph or circular graph is a graph that consists of a single cycle, or in other words, some number of vertices (at least 3, if the graph is simple) connected in a closed chain. The cycle graph with n vertices is called C_n. The number of vertices in C_n equals the number of edges, and every vertex has degree 2; that is, every vertex has exactly two edges incident with it. There are many synonyms for "cycle graph".
Orientation (graph theory)In graph theory, an orientation of an undirected graph is an assignment of a direction to each edge, turning the initial graph into a directed graph. A directed graph is called an oriented graph if none of its pairs of vertices is linked by two symmetric edges. Among directed graphs, the oriented graphs are the ones that have no 2-cycles (that is at most one of (x, y) and (y, x) may be arrows of the graph). A tournament is an orientation of a complete graph. A polytree is an orientation of an undirected tree.
Acyclic orientationIn graph theory, an acyclic orientation of an undirected graph is an assignment of a direction to each edge (an orientation) that does not form any directed cycle and therefore makes it into a directed acyclic graph. Every graph has an acyclic orientation. The chromatic number of any graph equals one more than the length of the longest path in an acyclic orientation chosen to minimize this path length. Acyclic orientations are also related to colorings through the chromatic polynomial, which counts both acyclic orientations and colorings.
Tree (graph theory)In graph theory, a tree is an undirected graph in which any two vertices are connected by path, or equivalently a connected acyclic undirected graph. A forest is an undirected graph in which any two vertices are connected by path, or equivalently an acyclic undirected graph, or equivalently a disjoint union of trees. A polytree (or directed tree or oriented tree or singly connected network) is a directed acyclic graph (DAG) whose underlying undirected graph is a tree.
Causal inferenceCausal inference is the process of determining the independent, actual effect of a particular phenomenon that is a component of a larger system. The main difference between causal inference and inference of association is that causal inference analyzes the response of an effect variable when a cause of the effect variable is changed. The science of why things occur is called etiology, and can be described using the language of scientific causal notation. Causal inference is said to provide the evidence of causality theorized by causal reasoning.
CausalityCausality (also called causation, or cause and effect) is influence by which one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly responsible for the effect, and the effect is partly dependent on the cause. In general, a process has many causes, which are also said to be causal factors for it, and all lie in its past. An effect can in turn be a cause of, or causal factor for, many other effects, which all lie in its future.
Rubin causal modelThe Rubin causal model (RCM), also known as the Neyman–Rubin causal model, is an approach to the statistical analysis of cause and effect based on the framework of potential outcomes, named after Donald Rubin. The name "Rubin causal model" was first coined by Paul W. Holland. The potential outcomes framework was first proposed by Jerzy Neyman in his 1923 Master's thesis, though he discussed it only in the context of completely randomized experiments.
Causal loop diagramA causal loop diagram (CLD) is a causal diagram that aids in visualizing how different variables in a system are causally interrelated. The diagram consists of a set of words and arrows. Causal loop diagrams are accompanied by a narrative which describes the causally closed situation the CLD describes. Closed loops, or causal feedback loops, in the diagram are very important features of CLDs. The words with arrows coming in and out represent variables, or quantities whose value changes over time and the links represent a causal relationship between the two variables (i.
Hamming distanceIn information theory, the Hamming distance between two strings of equal length is the number of positions at which the corresponding symbols are different. In other words, it measures the minimum number of substitutions required to change one string into the other, or the minimum number of errors that could have transformed one string into the other. In a more general context, the Hamming distance is one of several string metrics for measuring the edit distance between two sequences.
Max-flow min-cut theoremIn computer science and optimization theory, the max-flow min-cut theorem states that in a flow network, the maximum amount of flow passing from the source to the sink is equal to the total weight of the edges in a minimum cut, i.e., the smallest total weight of the edges which if removed would disconnect the source from the sink. This is a special case of the duality theorem for linear programs and can be used to derive Menger's theorem and the Kőnig–Egerváry theorem.
Machine learningMachine learning (ML) is an umbrella term for solving problems for which development of algorithms by human programmers would be cost-prohibitive, and instead the problems are solved by helping machines 'discover' their 'own' algorithms, without needing to be explicitly told what to do by any human-developed algorithms. Recently, generative artificial neural networks have been able to surpass results of many previous approaches.
Structural alignmentStructural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions.
Root cause analysisIn science and engineering, root cause analysis (RCA) is a method of problem solving used for identifying the root causes of faults or problems. It is widely used in IT operations, manufacturing, telecommunications, industrial process control, accident analysis (e.g., in aviation, rail transport, or nuclear plants), medicine (for medical diagnosis), healthcare industry (e.g., for epidemiology), etc. Root cause analysis is a form of inductive (first create a theory [root] based on empirical evidence [causes]) and deductive (test the theory [underlying causal mechanisms] with empirical data) inference.
Feature learningIn machine learning, feature learning or representation learning is a set of techniques that allows a system to automatically discover the representations needed for feature detection or classification from raw data. This replaces manual feature engineering and allows a machine to both learn the features and use them to perform a specific task. Feature learning is motivated by the fact that machine learning tasks such as classification often require input that is mathematically and computationally convenient to process.
Structural bioinformaticsStructural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models.
