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.
Gradient descentIn mathematics, gradient descent (also often called steepest descent) is a iterative optimization algorithm for finding a local minimum of a differentiable function. The idea is to take repeated steps in the opposite direction of the gradient (or approximate gradient) of the function at the current point, because this is the direction of steepest descent. Conversely, stepping in the direction of the gradient will lead to a local maximum of that function; the procedure is then known as gradient ascent.
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.
Gradient boostingGradient boosting is a machine learning technique used in regression and classification tasks, among others. It gives a prediction model in the form of an ensemble of weak prediction models, i.e., models that make very few assumptions about the data, which are typically simple decision trees. When a decision tree is the weak learner, the resulting algorithm is called gradient-boosted trees; it usually outperforms random forest.
Chicken (Scheme implementation)Chicken (stylized as CHICKEN) is a programming language, specifically a compiler and interpreter which implement a dialect of the programming language Scheme, and which compiles Scheme source code to standard C. It is mostly R5RS compliant and offers many extensions to the standard. The newer R7RS standard is supported through an extension library. Chicken is free and open-source software available under a BSD license. It is implemented mostly in Scheme, with some parts in C for performance or to make embedding into C programs easier.
Stochastic gradient descentStochastic gradient descent (often abbreviated SGD) is an iterative method for optimizing an objective function with suitable smoothness properties (e.g. differentiable or subdifferentiable). It can be regarded as a stochastic approximation of gradient descent optimization, since it replaces the actual gradient (calculated from the entire data set) by an estimate thereof (calculated from a randomly selected subset of the data).
Free electron modelIn solid-state physics, the free electron model is a quantum mechanical model for the behaviour of charge carriers in a metallic solid. It was developed in 1927, principally by Arnold Sommerfeld, who combined the classical Drude model with quantum mechanical Fermi–Dirac statistics and hence it is also known as the Drude–Sommerfeld model.
Program optimizationIn computer science, program optimization, code optimization, or software optimization, is the process of modifying a software system to make some aspect of it work more efficiently or use fewer resources. In general, a computer program may be optimized so that it executes more rapidly, or to make it capable of operating with less memory storage or other resources, or draw less power. Although the word "optimization" shares the same root as "optimal", it is rare for the process of optimization to produce a truly optimal system.
Optimal controlOptimal control theory is a branch of mathematical optimization that deals with finding a control for a dynamical system over a period of time such that an objective function is optimized. It has numerous applications in science, engineering and operations research. For example, the dynamical system might be a spacecraft with controls corresponding to rocket thrusters, and the objective might be to reach the moon with minimum fuel expenditure.
Scheme (programming language)Scheme is a dialect of the Lisp family of programming languages. Scheme was created during the 1970s at the MIT Computer Science and Artificial Intelligence Laboratory (MIT AI Lab) and released by its developers, Guy L. Steele and Gerald Jay Sussman, via a series of memos now known as the Lambda Papers. It was the first dialect of Lisp to choose lexical scope and the first to require implementations to perform tail-call optimization, giving stronger support for functional programming and associated techniques such as recursive algorithms.
