DiffusionDiffusion is the net movement of anything (for example, atoms, ions, molecules, energy) generally from a region of higher concentration to a region of lower concentration. Diffusion is driven by a gradient in Gibbs free energy or chemical potential. It is possible to diffuse "uphill" from a region of lower concentration to a region of higher concentration, like in spinodal decomposition. Diffusion is a stochastic process due to the inherent randomness of the diffusing entity and can be used to model many real-life stochastic scenarios.
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.
Protein structure predictionProtein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).
PredictionA prediction (Latin præ-, "before," and dicere, "to say"), or forecast, is a statement about a future event or data. They are often, but not always, based upon experience or knowledge. There is no universal agreement about the exact difference from "estimation"; different authors and disciplines ascribe different connotations. Future events are necessarily uncertain, so guaranteed accurate information about the future is impossible. Prediction can be useful to assist in making plans about possible developments.
Total variation denoisingIn signal processing, particularly , total variation denoising, also known as total variation regularization or total variation filtering, is a noise removal process (filter). It is based on the principle that signals with excessive and possibly spurious detail have high total variation, that is, the integral of the absolute is high. According to this principle, reducing the total variation of the signal—subject to it being a close match to the original signal—removes unwanted detail whilst preserving important details such as .
SequenceIn mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called elements, or terms). The number of elements (possibly infinite) is called the length of the sequence. Unlike a set, the same elements can appear multiple times at different positions in a sequence, and unlike a set, the order does matter. Formally, a sequence can be defined as a function from natural numbers (the positions of elements in the sequence) to the elements at each position.
Gene predictionIn computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced. In its earliest days, "gene finding" was based on painstaking experimentation on living cells and organisms.
Foundation modelsA foundation model (also called base model) is a large machine learning (ML) model trained on a vast quantity of data at scale (often by self-supervised learning or semi-supervised learning) such that it can be adapted to a wide range of downstream tasks. Foundation models have helped bring about a major transformation in how artificial intelligence (AI) systems are built, such as by powering prominent chatbots and other user-facing AI.
Anisotropic diffusionIn and computer vision, anisotropic diffusion, also called Perona–Malik diffusion, is a technique aiming at reducing without removing significant parts of the image content, typically edges, lines or other details that are important for the interpretation of the image. Anisotropic diffusion resembles the process that creates a scale space, where an image generates a parameterized family of successively more and more blurred images based on a diffusion process.
Scale spaceScale-space theory is a framework for multi-scale signal representation developed by the computer vision, and signal processing communities with complementary motivations from physics and biological vision. It is a formal theory for handling image structures at different scales, by representing an image as a one-parameter family of smoothed images, the scale-space representation, parametrized by the size of the smoothing kernel used for suppressing fine-scale structures.
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.
Scale-invariant feature transformThe scale-invariant feature transform (SIFT) is a computer vision algorithm to detect, describe, and match local features in images, invented by David Lowe in 1999. Applications include object recognition, robotic mapping and navigation, , 3D modeling, gesture recognition, video tracking, individual identification of wildlife and match moving. SIFT keypoints of objects are first extracted from a set of reference images and stored in a database.
Limit of a sequenceAs the positive integer becomes larger and larger, the value becomes arbitrarily close to . We say that "the limit of the sequence equals ." In mathematics, the limit of a sequence is the value that the terms of a sequence "tend to", and is often denoted using the symbol (e.g., ). If such a limit exists, the sequence is called convergent. A sequence that does not converge is said to be divergent. The limit of a sequence is said to be the fundamental notion on which the whole of mathematical analysis ultimately rests.
Scenario planningScenario planning, scenario thinking, scenario analysis, scenario prediction and the scenario method all describe a strategic planning method that some organizations use to make flexible long-term plans. It is in large part an adaptation and generalization of classic methods used by military intelligence. In the most common application of the method, analysts generate simulation games for policy makers.
Human population planningHuman population planning is the practice of managing the growth rate of a human population. The practice, traditionally referred to as population control, had historically been implemented mainly with the goal of increasing population growth, though from the 1950s to the 1980s, concerns about overpopulation and its effects on poverty, the environment and political stability led to efforts to reduce population growth rates in many countries.
Large language modelA large language model (LLM) is a language model characterized by its large size. Their size is enabled by AI accelerators, which are able to process vast amounts of text data, mostly scraped from the Internet. The artificial neural networks which are built can contain from tens of millions and up to billions of weights and are (pre-)trained using self-supervised learning and semi-supervised learning. Transformer architecture contributed to faster training.
Fick's laws of diffusionFick's laws of diffusion describe diffusion and were first posited by Adolf Fick in 1855 on the basis of largely experimental results. They can be used to solve for the diffusion coefficient, D. Fick's first law can be used to derive his second law which in turn is identical to the diffusion equation. A diffusion process that obeys Fick's laws is called normal or Fickian diffusion; otherwise, it is called anomalous diffusion or non-Fickian diffusion.
Sequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
Digital image processingDigital image processing is the use of a digital computer to process s through an algorithm. As a subcategory or field of digital signal processing, digital image processing has many advantages over . It allows a much wider range of algorithms to be applied to the input data and can avoid problems such as the build-up of noise and distortion during processing. Since images are defined over two dimensions (perhaps more) digital image processing may be modeled in the form of multidimensional systems.
Noise reductionNoise reduction is the process of removing noise from a signal. Noise reduction techniques exist for audio and images. Noise reduction algorithms may distort the signal to some degree. Noise rejection is the ability of a circuit to isolate an undesired signal component from the desired signal component, as with common-mode rejection ratio. All signal processing devices, both analog and digital, have traits that make them susceptible to noise.
