An adaptive algorithm is an algorithm that changes its behavior at the time it is run, based on information available and on a priori defined reward mechanism (or criterion). Such information could be the story of recently received data, information on the available computational resources, or other run-time acquired (or a priori known) information related to the environment in which it operates. Among the most used adaptive algorithms is the Widrow-Hoff’s least mean squares (LMS), which represents a class of stochastic gradient-descent algorithms used in adaptive filtering and machine learning. In adaptive filtering the LMS is used to mimic a desired filter by finding the filter coefficients that relate to producing the least mean square of the error signal (difference between the desired and the actual signal). For example, stable partition, using no additional memory is O(n lg n) but given O(n) memory, it can be O(n) in time. As implemented by the C++ Standard Library, stable_partition is adaptive and so it acquires as much memory as it can get (up to what it would need at most) and applies the algorithm using that available memory. Another example is adaptive sort, whose behavior changes upon the presortedness of its input. An example of an adaptive algorithm in radar systems is the constant false alarm rate (CFAR) detector. In machine learning and optimization, many algorithms are adaptive or have adaptive variants, which usually means that the algorithm parameters such as learning rate are automatically adjusted according to statistics about the optimisation thus far (e.g. the rate of convergence). Examples include adaptive simulated annealing, adaptive coordinate descent, adaptive quadrature, AdaBoost, Adagrad, Adadelta, RMSprop, and Adam. In data compression, adaptive coding algorithms such as Adaptive Huffman coding or Prediction by partial matching can take a stream of data as input, and adapt their compression technique based on the symbols that they have already encountered. In signal processing, the Adaptive Transform Acoustic Coding (ATRAC) codec used in MiniDisc recorders is called "adaptive" because the window length (the size of an audio "chunk") can change according to the nature of the sound being compressed, to try to achieve the best-sounding compression strategy.
Biopython
Biopython is an open-source collection of non-commercial Python modules for computational biology and bioinformatics. It makes robust and well-tested code easily accessible to researchers. Python is an object-oriented programming language and is a suitable choice for automation of common tasks. The availability of reusable libraries saves development time and lets researchers focus on addressing scientific questions. Biopython is constantly updated and maintained by a large team of volunteers across the globe. Biopython contains parsers for diverse bioinformatic sequence, alignment, and structure formats. Sequence formats include FASTA, FASTQ, GenBank, and EMBL. Alignment formats include Clustal, BLAST, PHYLIP, and NEXUS. Structural formats include the PDB, which contains the 3D atomic coordinates of the macromolecules. It has provisions to access information from biological databases like NCBI, Expasy, PBD, and BioSQL. This can be used in scripts or incorporated into their software. Biopython contains a standard sequence class, sequence alignment, and motif analysis tools. It also has clustering algorithms, a module for structural biology, and a module for phylogenetics analysis. == History == The development of Biopython began in 1999, and it was first released in July 2000. First "semi-complete" and "semi-stable" release was done in March 2001 and December 2002 respectively. It was developed during a similar time frame and with analogous goals to other projects that added bioinformatics capabilities to their respective programming languages, including BioPerl, BioRuby and BioJava. Early developers on the project included Jeff Chang, Andrew Dalke and Brad Chapman, though over 100 people have made contributions to date. In 2007, a similar Python project, namely PyCogent, was established. The initial scope of Biopython involved accessing, indexing and processing biological sequence files. The retrieved data from common biological databases will then be parsed into a python data structure. While this is still a major focus, over the following years added modules have extended its functionality to cover additional areas of biology. The key challenge in the design of parsers for bioinformatics file formats is the frequency at which the data formats change. This is due to inadequate curation of the structure of the data, and changes in the database contents. This problem is overcome by the application of a standard event-oriented parser design (see Key features and examples). As of version 1.77, Biopython no longer supports Python 2. The current stable release of Biopython version 1.85 was released on 15 January 2025. It only supports Python 3 and the recent releases of Biopython require NumPy (and not Numeric). == Design == Wherever possible, Biopython follows the conventions used by the Python programming language to make it easier for users familiar with Python. For example, Seq and SeqRecord objects can be manipulated via slicing, in a manner similar to Python's strings and lists. It is also designed to be functionally similar to other Bio projects, such as BioPerl. It is organized into modular sub-packages, e.g., Bio.Seq, Bio.Align, Bio.PDB, Bio.Entrez each of them useful in a different bioinformatics domain. It used principles, like encapsulation and polymorphism, notably in classes Seq, SeqRecord, and Bio.PDB.Structure. It can also interoperate with other Python tools (Pandas, Matplotlib and SciPy). Biopython can read and write most common file formats for each of its functional areas, and its license is permissive and compatible with most other software licenses, which allows Biopython to be used in a variety of software projects. == Requirements == Biopython is currently supported and tested with the following Python implementations: Python 3 or PyPy3 NumPy == Key features and examples == === Input and output === Biopython can read and write to a number of common formats. When reading files, descriptive information in the file is used to populate the members of Biopython classes, such as SeqRecord. This allows records of one file format to be converted into others. Very large sequence files can exceed a computer's memory resources, so Biopython provides various options for accessing records in large files. They can be loaded entirely into memory in Python data structures, such as lists or dictionaries, providing fast access at the cost of memory usage. Alternatively, the files can be read from disk as needed, with slower performance but lower memory requirements. === Sequences === A core concept in Biopython is the biological sequence, and this is represented by the Seq class. A Biopython Seq object is similar to a Python string in many respects: it supports the Python slice notation, can be concatenated with other sequences and is immutable. This object includes both general string-like and biological sequence-specific methods. It is best to store information about the biological type (DNA, RNA, protein) separately from the sequence, rather than using an explicit alphabet argument. === Sequence annotation === The SeqRecord class describes sequences, along with information such as name, description and features in the form of SeqFeature objects. Each SeqFeature object specifies the type of the feature and its location. Feature types can be ‘gene’, ‘CDS’ (coding sequence), ‘repeat_region’, ‘mobile_element’ or others, and the position of features in the sequence can be exact or approximate. === Accessing online databases === Through the Bio.Entrez module, users of Biopython can download biological data from NCBI databases. Each of the functions provided by the Entrez search engine is available through functions in this module, including searching for and downloading records. === Phylogeny === The Bio.Phylo module provides tools for working with and visualising phylogenetic trees. A variety of file formats are supported for reading and writing, including Newick, NEXUS and phyloXML. Common tree manipulations and traversals are supported via the Tree and Clade objects. Examples include converting and collating tree files, extracting subsets from a tree, changing a tree's root, and analysing branch features such as length or score. Rooted trees can be drawn in ASCII or using matplotlib (see Figure 1), and the Graphviz library can be used to create unrooted layouts (see Figure 2). === Genome diagrams === The GenomeDiagram module provides methods of visualising sequences within Biopython. Sequences can be drawn in a linear or circular form (see Figure 3), and many output formats are supported, including PDF and PNG. Diagrams are created by making tracks and then adding sequence features to those tracks. By looping over a sequence's features and using their attributes to decide if and how they are added to the diagram's tracks, one can exercise much control over the appearance of the final diagram. Cross-links can be drawn between different tracks, allowing one to compare multiple sequences in a single diagram. === Macromolecular structure === The Bio.PDB module can load molecular structures from PDB and mmCIF files, and was added to Biopython in 2003. The Structure object is central to this module, and it organises macromolecular structure in a hierarchical fashion: Structure objects contain Model objects which contain Chain objects which contain Residue objects which contain Atom objects. Disordered residues and atoms get their own classes, DisorderedResidue and DisorderedAtom, that describe their uncertain positions. Using Bio.PDB, one can navigate through individual components of a macromolecular structure file, such as examining each atom in a protein. Common analyses can be carried out, such as measuring distances or angles, comparing residues and calculating residue depth. === Population genetics === The Bio.PopGen module adds support to Biopython for Genepop, a software package for statistical analysis of population genetics. This allows for analyses of Hardy–Weinberg equilibrium, linkage disequilibrium and other features of a population's allele frequencies. This module can also carry out population genetic simulations using coalescent theory with the fastsimcoal2 program. === Wrappers for command line tools === Biopython previously included command-line wrappers for tools such as BLAST, Clustal, EMBOSS, and SAMtools. This option allowed users to run external tool commands from within the code using specialized Biopython classes. However, Bio.Application modules and their wrappers have deprecated and will be removed in future Biopython releases. The main reason for this is the high maintenance burden of updating them with the evolving external tools. The recommended approach is to directly construct and execute command-line tool commands using Python’s built-in subprocess module. This method provides flexibility and removes the dependency on the Biopython wrappers. subprocess is a native Python module useful for running ext
Empowerment (artificial intelligence)
Empowerment in the field of artificial intelligence formalises and quantifies (via information theory) the potential an agent perceives that it has to influence its environment. An agent which follows an empowerment maximising policy, acts to maximise future options (typically up to some limited horizon). Empowerment can be used as a (pseudo) utility function that depends only on information gathered from the local environment to guide action, rather than seeking an externally imposed goal, thus is a form of intrinsic motivation. The empowerment formalism depends on a probabilistic model commonly used in artificial intelligence. An autonomous agent operates in the world by taking in sensory information and acting to change its state, or that of the environment, in a cycle of perceiving and acting known as the perception-action loop. Agent state and actions are modelled by random variables ( S : s ∈ S , A : a ∈ A {\displaystyle S:s\in {\mathcal {S}},A:a\in {\mathcal {A}}} ) and time ( t {\displaystyle t} ). The choice of action depends on the current state, and the future state depends on the choice of action, thus the perception-action loop unrolled in time forms a causal bayesian network. == Definition == Empowerment ( E {\displaystyle {\mathfrak {E}}} ) is defined as the channel capacity ( C {\displaystyle C} ) of the actuation channel of the agent, and is formalised as the maximal possible information flow between the actions of the agent and the effect of those actions some time later. Empowerment can be thought of as the future potential of the agent to affect its environment, as measured by its sensors. E := C ( A t ⟶ S t + 1 ) ≡ max p ( a t ) I ( A t ; S t + 1 ) {\displaystyle {\mathfrak {E}}:=C(A_{t}\longrightarrow S_{t+1})\equiv \max _{p(a_{t})}I(A_{t};S_{t+1})} In a discrete time model, Empowerment can be computed for a given number of cycles into the future, which is referred to in the literature as 'n-step' empowerment. E ( A t n ⟶ S t + n ) = max p ( a t , . . . , a t + n − 1 ) I ( A t , . . . , A t + n − 1 ; S t + n ) {\displaystyle {\mathfrak {E}}(A_{t}^{n}\longrightarrow S_{t+n})=\max _{p(a_{t},...,a_{t+n-1})}I(A_{t},...,A_{t+n-1};S_{t+n})} The unit of empowerment depends on the logarithm base. Base 2 is commonly used in which case the unit is bits. === Contextual Empowerment === In general the choice of action (action distribution) that maximises empowerment varies from state to state. Knowing the empowerment of an agent in a specific state is useful, for example to construct an empowerment maximising policy. State-specific empowerment can be found using the more general formalism for 'contextual empowerment'. C {\displaystyle C} is a random variable describing the context (e.g. state). E ( A t n ⟶ S t + n ∣ C ) = ∑ c ∈ C p ( c ) E ( A t n ⟶ S t + n ∣ C = c ) {\displaystyle {\mathfrak {E}}(A_{t}^{n}\longrightarrow S_{t+n}{\mid }C)=\sum _{c{\in }C}p(c){\mathfrak {E}}(A_{t}^{n}\longrightarrow S_{t+n}{\mid }C=c)} == Application == Empowerment maximisation can be used as a pseudo-utility function to enable agents to exhibit intelligent behaviour without requiring the definition of external goals, for example balancing a pole in a cart-pole balancing scenario where no indication of the task is provided to the agent. Empowerment has been applied in studies of collective behaviour and in continuous domains. As is the case with Bayesian methods in general, computation of empowerment becomes computationally expensive as the number of actions and time horizon extends, but approaches to improve efficiency have led to usage in real-time control. Empowerment has been used for intrinsically motivated reinforcement learning agents playing video games, and in the control of underwater vehicles.
Computational intelligence
In computer science, computational intelligence (CI) refers to concepts, paradigms, algorithms and implementations of systems that are designed to show "intelligent" behavior in complex and changing environments. These systems are aimed at mastering complex tasks in a wide variety of technical or commercial areas and offer solutions that recognize and interpret patterns, control processes, support decision-making or autonomously manoeuvre vehicles or robots in unknown environments, among other things. These concepts and paradigms are characterized by the ability to learn or adapt to new situations, to generalize, to abstract, to discover and associate. Nature-analog or nature-inspired methods play a key role in this. CI approaches primarily address those complex real-world problems for which traditional or mathematical modeling is not appropriate for various reasons: the processes cannot be described exactly with complete knowledge, the processes are too complex for mathematical reasoning, they contain some uncertainties during the process, such as unforeseen changes in the environment or in the process itself, or the processes are simply stochastic in nature. Thus, CI techniques are properly aimed at processes that are ill-defined, complex, nonlinear, time-varying and/or stochastic. A recent definition of the IEEE Computational Intelligence Societey describes CI as the theory, design, application and development of biologically and linguistically motivated computational paradigms. Traditionally the three main pillars of CI have been Neural Networks, Fuzzy Systems and Evolutionary Computation. ... CI is an evolving field and at present in addition to the three main constituents, it encompasses computing paradigms like ambient intelligence, artificial life, cultural learning, artificial endocrine networks, social reasoning, and artificial hormone networks. ... Over the last few years there has been an explosion of research on Deep Learning, in particular deep convolutional neural networks. Nowadays, deep learning has become the core method for artificial intelligence. In fact, some of the most successful AI systems are based on CI. However, as CI is an emerging and developing field there is no final definition of CI, especially in terms of the list of concepts and paradigms that belong to it. The general requirements for the development of an “intelligent system” are ultimately always the same, namely the simulation of intelligent thinking and action in a specific area of application. To do this, the knowledge about this area must be represented in a model so that it can be processed. The quality of the resulting system depends largely on how well the model was chosen in the development process. Sometimes data-driven methods are suitable for finding a good model and sometimes logic-based knowledge representations deliver better results. Hybrid models are usually used in real applications. According to actual textbooks, the following methods and paradigms, which largely complement each other, can be regarded as parts of CI: Fuzzy systems Neural networks and, in particular, convolutional neural networks Evolutionary computation and, in particular, multi-objective evolutionary optimization Swarm intelligence Bayesian networks Artificial immune systems Learning theory Probabilistic methods == Relationship between hard and soft computing and artificial and computational intelligence == Artificial intelligence (AI) is used in the media, but also by some of the scientists involved, as a kind of umbrella term for the various techniques associated with it or with CI. Craenen and Eiben state that attempts to define or at least describe CI can usually be assigned to one or more of the following groups: "Relative definition” comparing CI to AI Conceptual treatment of key notions and their roles in CI Listing of the (established) areas that belong to it The relationship between CI and AI has been a frequently discussed topic during the development of CI. While the above list implies that they are synonyms, the vast majority of AI/CI researchers working on the subject consider them to be distinct fields, where either CI is an alternative to AI AI includes CI CI includes AI The view of the first of the above three points goes back to Zadeh, the founder of the fuzzy set theory, who differentiated machine intelligence into hard and soft computing techniques, which are used in artificial intelligence on the one hand and computational intelligence on the other. In hard computing (HC) and traditional AI (e.g. expert systems), inaccuracy and uncertainty are undesirable characteristics of a system, while soft computing (SC) and thus CI focus on dealing with these characteristics. The adjacent figure illustrates this view and lists the most important CI techniques. Another frequently mentioned distinguishing feature is the representation of information in symbolic form in AI and in sub-symbolic form in CI techniques. Hard computing is a conventional computing method based on the principles of certainty and accuracy and it is deterministic. It requires a precisely stated analytical model of the task to be processed and a prewritten program, i.e. a fixed set of instructions. The models used are based on Boolean logic (also called crisp logic), where e.g. an element can be either a member of a set or not and there is nothing in between. When applied to real-world tasks, systems based on HC result in specific control actions defined by a mathematical model or algorithm. If an unforeseen situation occurs that is not included in the model or algorithm used, the action will most likely fail. Soft computing, on the other hand, is based on the fact that the human mind is capable of storing information and processing it in a goal-oriented way, even if it is imprecise and lacks certainty. SC is based on the model of the human brain with probabilistic thinking, fuzzy logic and multi-valued logic. Soft computing can process a wealth of data and perform a large number of computations, which may not be exact, in parallel. For hard problems for which no satisfying exact solutions based on HC are available, SC methods can be applied successfully. SC methods are usually stochastic in nature i.e., they are a randomly defined processes that can be analyzed statistically but not with precision. Up to now, the results of some CI methods, such as deep learning, cannot be verified and it is also not clear what they are based on. This problem represents an important scientific issue for the future. AI and CI are catchy terms, but they are also so similar that they can be confused. The meaning of both terms has developed and changed over a long period of time, with AI being used first. Bezdek describes this impressively and concludes that such buzzwords are frequently used and hyped by the scientific community, science management and (science) journalism. Not least because AI and biological intelligence are emotionally charged terms and it is still difficult to find a generally accepted definition for the basic term intelligence. == History == In 1950, Alan Turing, one of the founding fathers of computer science, developed a test for computer intelligence known as the Turing test. In this test, a person can ask questions via a keyboard and a monitor without knowing whether his counterpart is a human or a computer. A computer is considered intelligent if the interrogator cannot distinguish the computer from a human. This illustrates the discussion about intelligent computers at the beginning of the computer age. The term Computational Intelligence was first used as the title of the journal of the same name in 1985 and later by the IEEE Neural Networks Council (NNC), which was founded 1989 by a group of researchers interested in the development of biological and artificial neural networks. On November 21, 2001, the NNC became the IEEE Neural Networks Society, to become the IEEE Computational Intelligence Society two years later by including new areas of interest such as fuzzy systems and evolutionary computation. The NNC helped organize the first IEEE World Congress on Computational Intelligence in Orlando, Florida in 1994. On this conference the first clear definition of Computational Intelligence was introduced by Bezdek: A system is computationally intelligent when it: deals with only numerical (low-level) data, has pattern-recognition components, does not use knowledge in the AI sense; and additionally when it (begins to) exhibit (1) computational adaptivity; (2) computational fault tolerance; (3) speed approaching human-like turnaround and (4) error rates that approximate human performance. Today, with machine learning and deep learning in particular utilizing a breadth of supervised, unsupervised, and reinforcement learning approaches, the CI landscape has been greatly enhanced, with novell intelligent approaches. == The main algorithmic approaches of CI and their applicati
Hybrid intelligent system
Hybrid intelligent system denotes a software system which employs, in parallel, a combination of methods and techniques from artificial intelligence subfields, such as: Neuro-symbolic systems Neuro-fuzzy systems Hybrid connectionist-symbolic models Fuzzy expert systems Connectionist expert systems Evolutionary neural networks Genetic fuzzy systems Rough fuzzy hybridization Reinforcement learning with fuzzy, neural, or evolutionary methods as well as symbolic reasoning methods. From the cognitive science perspective, every natural intelligent system is hybrid because it performs mental operations on both the symbolic and subsymbolic levels. For the past few years, there has been an increasing discussion of the importance of A.I. Systems Integration. Based on notions that there have already been created simple and specific AI systems (such as systems for computer vision, speech synthesis, etc., or software that employs some of the models mentioned above) and now is the time for integration to create broad AI systems. Proponents of this approach are researchers such as Marvin Minsky, Ron Sun, Aaron Sloman, Angelo Dalli and Michael A. Arbib. An example hybrid is a hierarchical control system in which the lowest, reactive layers are sub-symbolic. The higher layers, having relaxed time constraints, are capable of reasoning from an abstract world model and performing planning (even by hybrid wisdom). Intelligent systems usually rely on hybrid reasoning processes, which include induction, deduction, abduction and reasoning by analogy.
Fragment (computer graphics)
In computer graphics, a fragment is the data necessary to generate a single pixel's worth of a drawing primitive in the frame buffer. These data may include, but are not limited to: raster position depth interpolated attributes (color, texture coordinates, etc.) stencil alpha window ID As a scene is drawn, drawing primitives (the basic elements of graphics output, such as points, lines, circles, text etc.) are rasterized into fragments which are textured and combined with the existing frame buffer. How a fragment is combined with the data already in the frame buffer depends on various settings. In a typical case, a fragment may be discarded if it is further away than the pixel which is already at that location (according to the depth buffer). If it is nearer than the existing pixel, it may replace what is already there, or, if alpha blending is in use, the pixel's color may be replaced with a mixture of the fragment's color and the pixel's existing color, as in the case of drawing a translucent object. In general, a fragment can be thought of as the data needed to shade the pixel, plus the data needed to test whether the fragment survives to become a pixel (depth, alpha, stencil, scissor, window ID, etc.). Shading a fragment is done through a fragment shader (or pixel shaders in Direct3D). In computer graphics, a fragment is not necessarily opaque, and could contain an alpha value specifying its degree of transparency. The alpha is typically normalized to the range of [0, 1], with 0 denotes totally transparent and 1 denotes totally opaque. If the fragment is not totally opaque, then part of its background object could show through, which is known as alpha blending.
Google Clips
Google Clips is a discontinued miniature clip-on camera device developed by Google. == History == It was announced on October 4, 2017 and went on sale on January 27, 2018. Google Clips automatically captured video clips (without audio) at moments its machine learning algorithms determined to be interesting or relevant. An indicator flashed when the camera was looking for scenes to capture. Google Clips' artificial intelligence (AI) could learn the faces of people to take photographs with certain people, and could automatically set lighting and framing. It had 16 GB of storage built-in storage and could record clips for up to 3 hours. This camera was originally priced at US$249 in the United States. It was withdrawn from sale on October 15, 2019, but supported until the end of December 2021. == Reception == The Independent wrote that Google Clips is "an impressive little device, but one that also has the potential to feel very creepy." According to The Verge's generally negative review, "it didn't capture anything special" over two weeks of testing.