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.
Unsupervised learningUnsupervised learning, is paradigm in machine learning where, in contrast to supervised learning and semi-supervised learning, algorithms learn patterns exclusively from unlabeled data. Neural network tasks are often categorized as discriminative (recognition) or generative (imagination). Often but not always, discriminative tasks use supervised methods and generative tasks use unsupervised (see Venn diagram); however, the separation is very hazy. For example, object recognition favors supervised learning but unsupervised learning can also cluster objects into groups.
Coarse-grained modelingCoarse-grained modeling, coarse-grained models, aim at simulating the behaviour of complex systems using their coarse-grained (simplified) representation. Coarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins, nucleic acids, lipid membranes, carbohydrates or water.
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
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.
Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Online machine learningIn computer science, online machine learning is a method of machine learning in which data becomes available in a sequential order and is used to update the best predictor for future data at each step, as opposed to batch learning techniques which generate the best predictor by learning on the entire training data set at once. Online learning is a common technique used in areas of machine learning where it is computationally infeasible to train over the entire dataset, requiring the need of out-of-core algorithms.
Supervised learningSupervised learning (SL) is a paradigm in machine learning where input objects (for example, a vector of predictor variables) and a desired output value (also known as human-labeled supervisory signal) train a model. The training data is processed, building a function that maps new data on expected output values. An optimal scenario will allow for the algorithm to correctly determine output values for unseen instances. This requires the learning algorithm to generalize from the training data to unseen situations in a "reasonable" way (see inductive bias).
Molecular modelA molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an important role in understanding chemistry and generating and testing hypotheses. The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their graphical depiction is referred to as molecular graphics. The term, "molecular model" refer to systems that contain one or more explicit atoms (although solvent atoms may be represented implicitly) and where nuclear structure is neglected.
Self-supervised learningSelf-supervised learning (SSL) is a paradigm in machine learning for processing data of lower quality, rather than improving ultimate outcomes. Self-supervised learning more closely imitates the way humans learn to classify objects. The typical SSL method is based on an artificial neural network or other model such as a decision list. The model learns in two steps. First, the task is solved based on an auxiliary or pretext classification task using pseudo-labels which help to initialize the model parameters.
