AI For Business Specialization

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  Visualization (graphics)

  Visualization (or visualisation in Commonwealth English; see spelling differences), also known as graphics visualization, is any technique for creating images, diagrams, or animations to communicate a message. Visualization through visual imagery has been an effective way to communicate both abstract and concrete ideas since the dawn of humanity. Examples from history include cave paintings, Egyptian hieroglyphs, Greek geometry, and Leonardo da Vinci's revolutionary methods of technical drawing for engineering purposes that actively involve scientific requirements. Visualization today has ever-expanding applications in science, education, engineering (e.g., product visualization), interactive multimedia, medicine, etc. Typical of a visualization application is the field of computer graphics. The invention of computer graphics (and 3D computer graphics) may be the most important development in visualization since the invention of central perspective in the Renaissance period. The development of animation also helped advance visualization. == Overview == The use of visualization to present information is not a new phenomenon. It has been used in maps, scientific drawings, and data plots for over a thousand years. Examples from cartography include Ptolemy's Geographia (2nd century AD), a map of China (1137 AD), and Minard's map (1861) of Napoleon's invasion of Russia a century and a half ago. Most of the concepts learned in devising these images carry over in a straightforward manner to computer visualization. Edward Tufte has written three critically acclaimed books that explain many of these principles. Computer graphics has from its beginning been used to study scientific problems. However, in its early days the lack of graphics power often limited its usefulness. The recent emphasis on visualization started in 1987 with the publication of Visualization in Scientific Computing, a special issue of Computer Graphics. Since then, there have been several conferences and workshops, co-sponsored by the IEEE Computer Society and ACM SIGGRAPH, devoted to the general topic, and special areas in the field, for example volume visualization. Most people are familiar with the digital animations produced to present meteorological data during weather reports on television, though few can distinguish between those models of reality and the satellite photos that are also shown on such programs. TV also offers scientific visualizations when it shows computer drawn and animated reconstructions of road or airplane accidents. Some of the most popular examples of scientific visualizations are computer-generated images that show real spacecraft in action, out in the void far beyond Earth, or on other planets. Dynamic forms of visualization, such as educational animation or timelines, have the potential to enhance learning about systems that change over time. Apart from the distinction between interactive visualizations and animation, the most useful categorization is probably between abstract and model-based scientific visualizations. The abstract visualizations show completely conceptual constructs in 2D or 3D. These generated shapes are completely arbitrary. The model-based visualizations either place overlays of data on real or digitally constructed images of reality or make a digital construction of a real object directly from the scientific data. Scientific visualization is usually done with specialized software, though there are a few exceptions, noted below. Some of these specialized programs have been released as open source software, having very often its origins in universities, within an academic environment where sharing software tools and giving access to the source code is common. There are also many proprietary software packages of scientific visualization tools. Models and frameworks for building visualizations include the data flow models popularized by systems such as AVS, IRIS Explorer, and VTK toolkit, and data state models in spreadsheet systems such as the Spreadsheet for Visualization and Spreadsheet for Images. == Applications == === Scientific visualization === As a subject in computer science, scientific visualization is the use of interactive, sensory representations, typically visual, of abstract data to reinforce cognition, hypothesis building, and reasoning. Scientific visualization is the transformation, selection, or representation of data from simulations or experiments, with an implicit or explicit geometric structure, to allow the exploration, analysis, and understanding of the data. Scientific visualization focuses and emphasizes the representation of higher order data using primarily graphics and animation techniques. It is a very important part of visualization and maybe the first one, as the visualization of experiments and phenomena is as old as science itself. Traditional areas of scientific visualization are flow visualization, medical visualization, astrophysical visualization, and chemical visualization. There are several different techniques to visualize scientific data, with isosurface reconstruction and direct volume rendering being the more common. === Data and information visualization === Data visualization is a related subcategory of visualization dealing with statistical graphics and geospatial data (as in thematic cartography) that is abstracted in schematic form. Information visualization concentrates on the use of computer-supported tools to explore large amount of abstract data. The term "information visualization" was originally coined by the User Interface Research Group at Xerox PARC and included Jock Mackinlay. Practical application of information visualization in computer programs involves selecting, transforming, and representing abstract data in a form that facilitates human interaction for exploration and understanding. Important aspects of information visualization are dynamics of visual representation and the interactivity. Strong techniques enable the user to modify the visualization in real-time, thus affording unparalleled perception of patterns and structural relations in the abstract data in question. === Educational visualization === Educational visualization is using a simulation to create an image of something so it can be taught about. This is very useful when teaching about a topic that is difficult to otherwise see, for example, atomic structure, because atoms are far too small to be studied easily without expensive and difficult to use scientific equipment. === Knowledge visualization === The use of visual representations to transfer knowledge between at least two persons aims to improve the transfer of knowledge by using computer and non-computer-based visualization methods complementarily. Thus properly designed visualization is an important part of not only data analysis but knowledge transfer process, too. Knowledge transfer may be significantly improved using hybrid designs as it enhances information density but may decrease clarity as well. For example, visualization of a 3D scalar field may be implemented using iso-surfaces for field distribution and textures for the gradient of the field. Examples of such visual formats are sketches, diagrams, images, objects, interactive visualizations, information visualization applications, and imaginary visualizations as in stories. While information visualization concentrates on the use of computer-supported tools to derive new insights, knowledge visualization focuses on transferring insights and creating new knowledge in groups. Beyond the mere transfer of facts, knowledge visualization aims to further transfer insights, experiences, attitudes, values, expectations, perspectives, opinions, and estimates in different fields by using various complementary visualizations. See also: picture dictionary, visual dictionary === Product visualization === Product visualization involves visualization software technology for the viewing and manipulation of 3D models, technical drawing and other related documentation of manufactured components and large assemblies of products. It is a key part of product lifecycle management. Product visualization software typically provides high levels of photorealism so that a product can be viewed before it is actually manufactured. This supports functions ranging from design and styling to sales and marketing. Technical visualization is an important aspect of product development. Originally technical drawings were made by hand, but with the rise of advanced computer graphics the drawing board has been replaced by computer-aided design (CAD). CAD-drawings and models have several advantages over hand-made drawings such as the possibility of 3-D modeling, rapid prototyping, and simulation. 3D product visualization promises more interactive experiences for online shoppers, but also challenges retailers to overcome hurdles in the production of 3D content, as large-scale 3D content production can be extremel

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  Deterministic blockmodeling

  Deterministic blockmodeling is an approach in blockmodeling that does not assume a probabilistic model, and instead relies on the exact or approximate algorithms, which are used to find blockmodel(s). This approach typically minimizes some inconsistency that can occur with the ideal block structure. Such analysis is focused on clustering (grouping) of the network (or adjacency matrix) that is obtained with minimizing an objective function, which measures discrepancy from the ideal block structure. However, some indirect approaches (or methods between direct and indirect approaches, such as CONCOR) do not explicitly minimize inconsistencies or optimize some criterion function. This approach was popularized in the 1970s, due to the presence of two computer packages (CONCOR and STRUCTURE) that were used to "find a permutation of the rows and columns in the adjacency matrix leading to an approximate block structure". The opposite approach to deterministic blockmodeling is a stochastic blockmodeling approach.

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  UIMA

  UIMA ( yoo-EE-mə), short for Unstructured Information Management Architecture, is an OASIS standard for content analytics, originally developed at IBM. It provides a component software architecture for the development, discovery, composition, and deployment of multi-modal analytics for the analysis of unstructured information and integration with search technologies. == Structure == The UIMA architecture can be thought of in four dimensions: It specifies component interfaces in an analytics pipeline. It describes a set of design patterns. It suggests two data representations: an in-memory representation of annotations for high-performance analytics and an XML representation of annotations for integration with remote web services. It suggests development roles allowing tools to be used by users with diverse skills. == Implementations and uses == Apache UIMA, a reference implementation of UIMA, is maintained by the Apache Software Foundation. UIMA is used in a number of software projects: IBM Research's Watson uses UIMA for analyzing unstructured data. The Clinical Text Analysis and Knowledge Extraction System (Apache cTAKES) is a UIMA-based system for information extraction from medical records. DKPro Core is a collection of reusable UIMA components for general-purpose natural language processing.

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  BookCorpus

  BookCorpus (also sometimes referred to as the Toronto Book Corpus) is a dataset consisting of the text of around 7,000 self-published books scraped from the indie ebook distribution website Smashwords. It was the main corpus used to train the initial GPT model by OpenAI, and has been used as training data for other early large language models including Google's BERT. The dataset consists of around 985 million words, and the books that comprise it span a range of genres, including romance, science fiction, and fantasy. The corpus was introduced in a 2015 paper by researchers from the University of Toronto and MIT titled "Aligning Books and Movies: Towards Story-like Visual Explanations by Watching Movies and Reading Books". The authors described it as consisting of "free books written by yet unpublished authors," yet this is factually incorrect. These books were published by self-published ("indie") authors who priced them at free; the books were downloaded without the consent or permission of Smashwords or Smashwords authors and in violation of the Smashwords Terms of Service. The dataset was initially hosted on a University of Toronto webpage. An official version of the original dataset is no longer publicly available, though at least one substitute, BookCorpusOpen, has been created. Though not documented in the original 2015 paper, the site from which the corpus's books were scraped is now known to be Smashwords.

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  Coupled pattern learner

  Coupled Pattern Learner (CPL) is a machine learning algorithm which couples the semi-supervised learning of categories and relations to forestall the problem of semantic drift associated with boot-strap learning methods. == Coupled Pattern Learner == Semi-supervised learning approaches using a small number of labeled examples with many unlabeled examples are usually unreliable as they produce an internally consistent, but incorrect set of extractions. CPL solves this problem by simultaneously learning classifiers for many different categories and relations in the presence of an ontology defining constraints that couple the training of these classifiers. It was introduced by Andrew Carlson, Justin Betteridge, Estevam R. Hruschka Jr. and Tom M. Mitchell in 2009. == CPL overview == CPL is an approach to semi-supervised learning that yields more accurate results by coupling the training of many information extractors. Basic idea behind CPL is that semi-supervised training of a single type of extractor such as ‘coach’ is much more difficult than simultaneously training many extractors that cover a variety of inter-related entity and relation types. Using prior knowledge about the relationships between these different entities and relations CPL makes unlabeled data as a useful constraint during training. For e.g., ‘coach(x)’ implies ‘person(x)’ and ‘not sport(x)’. == CPL description == === Coupling of predicates === CPL primarily relies on the notion of coupling the learning of multiple functions so as to constrain the semi-supervised learning problem. CPL constrains the learned function in two ways. Sharing among same-arity predicates according to logical relations Relation argument type-checking === Sharing among same-arity predicates === Each predicate P in the ontology has a list of other same-arity predicates with which P is mutually exclusive. If A is mutually exclusive with predicate B, A’s positive instances and patterns become negative instances and negative patterns for B. For example, if ‘city’, having an instance ‘Boston’ and a pattern ‘mayor of arg1’, is mutually exclusive with ‘scientist’, then ‘Boston’ and ‘mayor of arg1’ will become a negative instance and a negative pattern respectively for ‘scientist.’ Further, Some categories are declared to be a subset of another category. For e.g., ‘athlete’ is a subset of ‘person’. === Relation argument type-checking === This is a type checking information used to couple the learning of relations and categories. For example, the arguments of the ‘ceoOf’ relation are declared to be of the categories ‘person’ and ‘company’. CPL does not promote a pair of noun phrases as an instance of a relation unless the two noun phrases are classified as belonging to the correct argument types. === Algorithm description === Following is a quick summary of the CPL algorithm. Input: An ontology O, and a text corpus C Output: Trusted instances/patterns for each predicate for i=1,2,...,∞ do foreach predicate p in O do EXTRACT candidate instances/contextual patterns using recently promoted patterns/instances; FILTER candidates that violate coupling; RANK candidate instances/patterns; PROMOTE top candidates; end end ==== Inputs ==== A large corpus of Part-Of-Speech tagged sentences and an initial ontology with predefined categories, relations, mutually exclusive relationships between same-arity predicates, subset relationships between some categories, seed instances for all predicates, and seed patterns for the categories. ==== Candidate extraction ==== CPL finds new candidate instances by using newly promoted patterns to extract the noun phrases that co-occur with those patterns in the text corpus. CPL extracts, Category Instances Category Patterns Relation Instances Relation Patterns ==== Candidate filtering ==== Candidate instances and patterns are filtered to maintain high precision, and to avoid extremely specific patterns. An instance is only considered for assessment if it co-occurs with at least two promoted patterns in the text corpus, and if its co-occurrence count with all promoted patterns is at least three times greater than its co-occurrence count with negative patterns. ==== Candidate ranking ==== CPL ranks candidate instances using the number of promoted patterns that they co-occur with so that candidates that occur with more patterns are ranked higher. Patterns are ranked using an estimate of the precision of each pattern. ==== Candidate promotion ==== CPL ranks the candidates according to their assessment scores and promotes at most 100 instances and 5 patterns for each predicate. Instances and patterns are only promoted if they co-occur with at least two promoted patterns or instances, respectively. == Meta-Bootstrap Learner == Meta-Bootstrap Learner (MBL) was also proposed by the authors of CPL. Meta-Bootstrap learner couples the training of multiple extraction techniques with a multi-view constraint, which requires the extractors to agree. It makes addition of coupling constraints on top of existing extraction algorithms, while treating them as black boxes, feasible. MBL assumes that the errors made by different extraction techniques are independent. Following is a quick summary of MBL. Input: An ontology O, a set of extractors ε Output: Trusted instances for each predicate for i=1,2,...,∞ do foreach predicate p in O do foreach extractor e in ε do Extract new candidates for p using e with recently promoted instances; end FILTER candidates that violate mutual-exclusion or type-checking constraints; PROMOTE candidates that were extracted by all extractors; end end Subordinate algorithms used with MBL do not promote any instance on their own, they report the evidence about each candidate to MBL and MBL is responsible for promoting instances. == Applications == In their paper authors have presented results showing the potential of CPL to contribute new facts to existing repository of semantic knowledge, Freebase

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  GeWorkbench

  geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a component architecture. As of 2016, there are more than 70 plug-ins available, providing for the visualization and analysis of gene expression, sequence, and structure data. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing funded through the NIH Roadmap (NIH Common Fund). Many systems and structure biology tools developed by MAGNet investigators are available as geWorkbench plugins. == Features == Computational analysis tools such as t-test, hierarchical clustering, self-organizing maps, regulatory network reconstruction, BLAST searches, pattern-motif discovery, protein structure prediction, structure-based protein annotation, etc. Visualization of gene expression (heatmaps, volcano plot), molecular interaction networks (through Cytoscape), protein sequence and protein structure data (e.g., MarkUs). Integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. Component integration through platform management of inputs and outputs. Among data that can be shared between components are expression datasets, interaction networks, sample and marker (gene) sets and sequences. Dataset history tracking - complete record of data sets used and input settings. Integration with 3rd party tools such as GenePattern, Cytoscape, and Genomespace. Demonstrations of each feature described can be found at GeWorkbench-web Tutorials. == Versions == geWorkbench is open-source software that can be downloaded and installed locally. A zip file of the released version Java source is also available. Prepackaged installer versions also exist for Windows, Macintosh, and Linux.

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  Analogical modeling

  Analogical modeling (AM) is a formal theory of exemplar based analogical reasoning, proposed by Royal Skousen, professor of Linguistics and English language at Brigham Young University in Provo, Utah. It is applicable to language modeling and other categorization tasks. Analogical modeling is related to connectionism and nearest neighbor approaches, in that it is data-based rather than abstraction-based; but it is distinguished by its ability to cope with imperfect datasets (such as caused by simulated short term memory limits) and to base predictions on all relevant segments of the dataset, whether near or far. In language modeling, AM has successfully predicted empirically valid forms for which no theoretical explanation was known (see the discussion of Finnish morphology in Skousen et al. 2002). == Implementation == === Overview === An exemplar-based model consists of a general-purpose modeling engine and a problem-specific dataset. Within the dataset, each exemplar (a case to be reasoned from, or an informative past experience) appears as a feature vector: a row of values for the set of parameters that define the problem. For example, in a spelling-to-sound task, the feature vector might consist of the letters of a word. Each exemplar in the dataset is stored with an outcome, such as a phoneme or phone to be generated. When the model is presented with a novel situation (in the form of an outcome-less feature vector), the engine algorithmically sorts the dataset to find exemplars that helpfully resemble it, and selects one, whose outcome is the model's prediction. The particulars of the algorithm distinguish one exemplar-based modeling system from another. In AM, we think of the feature values as characterizing a context, and the outcome as a behavior that occurs within that context. Accordingly, the novel situation is known as the given context. Given the known features of the context, the AM engine systematically generates all contexts that include it (all of its supracontexts), and extracts from the dataset the exemplars that belong to each. The engine then discards those supracontexts whose outcomes are inconsistent (this measure of consistency will be discussed further below), leaving an analogical set of supracontexts, and probabilistically selects an exemplar from the analogical set with a bias toward those in large supracontexts. This multilevel search exponentially magnifies the likelihood of a behavior's being predicted as it occurs reliably in settings that specifically resemble the given context. === Analogical modeling in detail === AM performs the same process for each case it is asked to evaluate. The given context, consisting of n variables, is used as a template to generate 2 n {\displaystyle 2^{n}} supracontexts. Each supracontext is a set of exemplars in which one or more variables have the same values that they do in the given context, and the other variables are ignored. In effect, each is a view of the data, created by filtering for some criteria of similarity to the given context, and the total set of supracontexts exhausts all such views. Alternatively, each supracontext is a theory of the task or a proposed rule whose predictive power needs to be evaluated. It is important to note that the supracontexts are not equal peers one with another; they are arranged by their distance from the given context, forming a hierarchy. If a supracontext specifies all of the variables that another one does and more, it is a subcontext of that other one, and it lies closer to the given context. (The hierarchy is not strictly branching; each supracontext can itself be a subcontext of several others, and can have several subcontexts.) This hierarchy becomes significant in the next step of the algorithm. The engine now chooses the analogical set from among the supracontexts. A supracontext may contain exemplars that only exhibit one behavior; it is deterministically homogeneous and is included. It is a view of the data that displays regularity, or a relevant theory that has never yet been disproven. A supracontext may exhibit several behaviors, but contain no exemplars that occur in any more specific supracontext (that is, in any of its subcontexts); in this case it is non-deterministically homogeneous and is included. Here there is no great evidence that a systematic behavior occurs, but also no counterargument. Finally, a supracontext may be heterogeneous, meaning that it exhibits behaviors that are found in a subcontext (closer to the given context), and also behaviors that are not. Where the ambiguous behavior of the nondeterministically homogeneous supracontext was accepted, this is rejected because the intervening subcontext demonstrates that there is a better theory to be found. The heterogeneous supracontext is therefore excluded. This guarantees that we see an increase in meaningfully consistent behavior in the analogical set as we approach the given context. With the analogical set chosen, each appearance of an exemplar (for a given exemplar may appear in several of the analogical supracontexts) is given a pointer to every other appearance of an exemplar within its supracontexts. One of these pointers is then selected at random and followed, and the exemplar to which it points provides the outcome. This gives each supracontext an importance proportional to the square of its size, and makes each exemplar likely to be selected in direct proportion to the sum of the sizes of all analogically consistent supracontexts in which it appears. Then, of course, the probability of predicting a particular outcome is proportional to the summed probabilities of all the exemplars that support it. (Skousen 2002, in Skousen et al. 2002, pp. 11–25, and Skousen 2003, both passim) === Formulas === Given a context with n {\displaystyle n} elements: total number of pairings: n 2 {\displaystyle n^{2}} number of agreements for outcome i: n i 2 {\displaystyle n_{i}^{2}} number of disagreements for outcome i: n i ( n − n i ) {\displaystyle n_{i}(n-n_{i})} total number of agreements: ∑ n i 2 {\displaystyle \sum {n_{i}^{2}}} total number of disagreements: ∑ n i ( n − n i ) = n 2 − ∑ n i 2 {\displaystyle \sum {n_{i}(n-n_{i})}=n^{2}-\sum {n_{i}^{2}}} === Example === This terminology is best understood through an example. In the example used in the second chapter of Skousen (1989), each context consists of three variables with potential values 0-3 Variable 1: 0,1,2,3 Variable 2: 0,1,2,3 Variable 3: 0,1,2,3 The two outcomes for the dataset are e and r, and the exemplars are: 3 1 0 e 0 3 2 r 2 1 0 r 2 1 2 r 3 1 1 r We define a network of pointers like so: The solid lines represent pointers between exemplars with matching outcomes; the dotted lines represent pointers between exemplars with non-matching outcomes. The statistics for this example are as follows: n = 5 {\displaystyle n=5} n r = 4 {\displaystyle n_{r}=4} n e = 1 {\displaystyle n_{e}=1} total number of pairings: n 2 = 25 {\displaystyle n^{2}=25} number of agreements for outcome r: n r 2 = 16 {\displaystyle n_{r}^{2}=16} number of agreements for outcome e: n e 2 = 1 {\displaystyle n_{e}^{2}=1} number of disagreements for outcome r: n r ( n − n r ) = 4 {\displaystyle n_{r}(n-n_{r})=4} number of disagreements for outcome e: n e ( n − n e ) = 4 {\displaystyle n_{e}(n-n_{e})=4} total number of agreements: n r 2 + n e 2 = 17 {\displaystyle n_{r}^{2}+n_{e}^{2}=17} total number of disagreements: n r ( n − n r ) + n e ( n − n e ) = n 2 − ( n r 2 + n e 2 ) = 8 {\displaystyle n_{r}(n-n_{r})+n_{e}(n-n_{e})=n^{2}-(n_{r}^{2}+n_{e}^{2})=8} uncertainty or fraction of disagreement: 8 / 25 = .32 {\displaystyle 8/25=.32} Behavior can only be predicted for a given context; in this example, let us predict the outcome for the context "3 1 2". To do this, we first find all of the contexts containing the given context; these contexts are called supracontexts. We find the supracontexts by systematically eliminating the variables in the given context; with m variables, there will generally be 2 m {\displaystyle 2^{m}} supracontexts. The following table lists each of the sub- and supracontexts; x means "not x", and - means "anything". These contexts are shown in the venn diagram below: The next step is to determine which exemplars belong to which contexts in order to determine which of the contexts are homogeneous. The table below shows each of the subcontexts, their behavior in terms of the given exemplars, and the number of disagreements within the behavior: Analyzing the subcontexts in the table above, we see that there is only 1 subcontext with any disagreements: "3 1 2", which in the dataset consists of "3 1 0 e" and "3 1 1 r". There are 2 disagreements in this subcontext; 1 pointing from each of the exemplars to the other (see the pointer network pictured above). Therefore, only supracontexts containing this subcontext will contain any disagreements. We use a simple rule to identify the homogeneous supraco

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  Operational taxonomic unit

  An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, where an "operational taxonomic unit" is simply the group of organisms currently being studied. In this sense, an OTU is a pragmatic definition to group individuals by similarity, equivalent to but not necessarily in line with classical Linnaean taxonomy or modern evolutionary taxonomy. Nowadays, however, the term is commonly used in a different context and refers to clusters of (uncultivated or unknown) organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene (originally coined as mOTU; molecular OTU). In other words, OTUs are pragmatic proxies for "species" at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopic organisms. For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes) marker gene sequence datasets. == Molecular OTU by clustering of marker gene sequences == In the approach represented by DNA barcoding, a particular locus is chosen to be used as the marker gene for classification. This locus should be universally present in the scope selected, variable enough to be different among close-related species, and be flanked by conservative sequences that allow for easy amplification and detection. There are databases containing sequences for such marker genes from many different species, allowing for comparison. (Sometimes only using one locus does not provide sufficient resolution, so multiple marker genes are used. This is the case for plants, where rbcL+matK is common.) Sequences obtained this way can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold set by the researcher. The exact threshold depends on the taxa in question and the mutational rates of the selected locus in the taxon. 97–99% are commonly used, but "it is now recognized to be somewhat arbitrary as sequence variation within and among species varies across taxa". 100% similarity (fully identical) is also common, also known as single variants. It remains debatable how well this commonly used method recapitulates true microbial species phylogeny or ecology. Although OTUs can be calculated differently when using different algorithms or thresholds, research by Schmidt et al. (2014) demonstrated that 16S-derived microbial OTUs were generally ecologically consistent across habitats and several clustering approaches. The number of OTUs defined may be inflated due to errors in DNA sequencing. === OTU clustering approaches === There are three main approaches to clustering OTUs: De novo, for which the clustering is based on similarities between sequencing reads. Closed-reference, for which the clustering is performed against a reference database of sequences. Open-reference, where clustering is first performed against a reference database of sequences, then any remaining sequences that could not be mapped to the reference are clustered de novo. Using a reference provides taxonomic context for the OTUs found. Alternatively, taxonomic context can be found after the construction of clusters by comparing representative sequences from clusters against a reference database. There are also specialized classifiers for this purpose which are much faster than naive comparison using BLAST. === OTU clustering algorithms === Hierarchical clustering algorithms (HCA): uclust & cd-hit & ESPRIT Bayesian clustering: CROP == Molecular OTU by other methods == In addition to similarity-based grouping, marker gene sequences can be sorted into OTUs using molecular phylogeny, k-mer composition, or hybrid methods combining these methods with similarity. There are also Bayesian tree-less methods and machine learning approaches. Using phylogeny often involves manually assigning terminal clades or single nodes to an OTU, so this is usually only done for refinement. Genome skimming can be used to obtain high-copy DNA without the need to choose marker genes or to design PCR primers for the chosen genes. It can provide fairly good coverage of organelle DNA and repetitive elements such as ribosomal DNA, both of which can be used like marker genes in OTU analysis. Whole-genome sequencing is more expensive and involves the production and processing of more data. By considering the entire genome, many (sometimes over 100) marker genes can be used at the same time, producing highly resolved phylogenies that correctly identify problematic taxa. It is also possible to use entire genomes for OTU assignment. For example, genomes from different bacterial species almost always have an average nucleotide identity lower than 95%, a fact that can be used to define new OTUs (and likely new species).

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  Meta-learning (computer science)

  Meta-learning is a subfield of machine learning where automatic learning algorithms are applied to metadata about machine learning experiments. As of 2017, the term had not found a standard interpretation, however the main goal is to use such metadata to understand how automatic learning can become flexible in solving learning problems, hence to improve the performance of existing learning algorithms or to learn (induce) the learning algorithm itself, hence the alternative term learning to learn. Flexibility is important because each learning algorithm is based on a set of assumptions about the data, its inductive bias. This means that it will only learn well if the bias matches the learning problem. A learning algorithm may perform very well in one domain, but not on the next. This poses strong restrictions on the use of machine learning or data mining techniques, since the relationship between the learning problem (often some kind of database) and the effectiveness of different learning algorithms is not yet understood. By using different kinds of metadata, like properties of the learning problem, algorithm properties (like performance measures), or patterns previously derived from the data, it is possible to learn, select, alter or combine different learning algorithms to effectively solve a given learning problem. Critiques of meta-learning approaches bear a strong resemblance to the critique of metaheuristic, a possibly related problem. A good analogy to meta-learning, and the inspiration for Jürgen Schmidhuber's early work (1987) and Yoshua Bengio et al.'s work (1991), considers that genetic evolution learns the learning procedure encoded in genes and executed in each individual's brain. In an open-ended hierarchical meta-learning system using genetic programming, better evolutionary methods can be learned by meta evolution, which itself can be improved by meta meta evolution, etc. == Definition == A proposed definition for a meta-learning system combines three requirements: The system must include a learning subsystem. Experience is gained by exploiting meta knowledge extracted in a previous learning episode on a single dataset, or from different domains. Learning bias must be chosen dynamically. Bias refers to the assumptions that influence the choice of explanatory hypotheses and not the notion of bias represented in the bias-variance dilemma. Meta-learning is concerned with two aspects of learning bias. Declarative bias specifies the representation of the space of hypotheses, and affects the size of the search space (e.g., represent hypotheses using linear functions only). Procedural bias imposes constraints on the ordering of the inductive hypotheses (e.g., preferring smaller hypotheses). == Common approaches == There are three common approaches: using (cyclic) networks with external or internal memory (model-based) learning effective distance metrics (metrics-based) explicitly optimizing model parameters for fast learning (optimization-based). === Model-Based === Model-based meta-learning models updates its parameters rapidly with a few training steps, which can be achieved by its internal architecture or controlled by another meta-learner model. ==== Memory-Augmented Neural Networks ==== A Memory-Augmented Neural Network, or MANN for short, is claimed to be able to encode new information quickly and thus to adapt to new tasks after only a few examples. ==== Meta Networks ==== Meta Networks (MetaNet) learns a meta-level knowledge across tasks and shifts its inductive biases via fast parameterization for rapid generalization. === Metric-Based === The core idea in metric-based meta-learning is similar to nearest neighbors algorithms, which weight is generated by a kernel function. It aims to learn a metric or distance function over objects. The notion of a good metric is problem-dependent. It should represent the relationship between inputs in the task space and facilitate problem solving. ==== Convolutional Siamese Neural Network ==== Siamese neural network is composed of two twin networks whose output is jointly trained. There is a function above to learn the relationship between input data sample pairs. The two networks are the same, sharing the same weight and network parameters. ==== Matching Networks ==== Matching Networks learn a network that maps a small labelled support set and an unlabelled example to its label, obviating the need for fine-tuning to adapt to new class types. ==== Relation Network ==== The Relation Network (RN), is trained end-to-end from scratch. During meta-learning, it learns to learn a deep distance metric to compare a small number of images within episodes, each of which is designed to simulate the few-shot setting. ==== Prototypical Networks ==== Prototypical Networks learn a metric space in which classification can be performed by computing distances to prototype representations of each class. Compared to recent approaches for few-shot learning, they reflect a simpler inductive bias that is beneficial in this limited-data regime, and achieve satisfied results. === Optimization-Based === What optimization-based meta-learning algorithms intend for is to adjust the optimization algorithm so that the model can be good at learning with a few examples. ==== LSTM Meta-Learner ==== LSTM-based meta-learner is to learn the exact optimization algorithm used to train another learner neural network classifier in the few-shot regime. The parametrization allows it to learn appropriate parameter updates specifically for the scenario where a set amount of updates will be made, while also learning a general initialization of the learner (classifier) network that allows for quick convergence of training. ==== Temporal Discreteness ==== Model-Agnostic Meta-Learning (MAML) is a fairly general optimization algorithm, compatible with any model that learns through gradient descent. ==== Reptile ==== Reptile is a remarkably simple meta-learning optimization algorithm, given that both of its components rely on meta-optimization through gradient descent and both are model-agnostic. == Examples == Some approaches which have been viewed as instances of meta-learning: Recurrent neural networks (RNNs) are universal computers. In 1993, Jürgen Schmidhuber showed how "self-referential" RNNs can in principle learn by backpropagation to run their own weight change algorithm, which may be quite different from backpropagation. In 2001, Sepp Hochreiter & A.S. Younger & P.R. Conwell built a successful supervised meta-learner based on Long short-term memory RNNs. It learned through backpropagation a learning algorithm for quadratic functions that is much faster than backpropagation. Researchers at Deepmind (Marcin Andrychowicz et al.) extended this approach to optimization in 2017. In the 1990s, Meta Reinforcement Learning or Meta RL was achieved in Schmidhuber's research group through self-modifying policies written in a universal programming language that contains special instructions for changing the policy itself. There is a single lifelong trial. The goal of the RL agent is to maximize reward. It learns to accelerate reward intake by continually improving its own learning algorithm which is part of the "self-referential" policy. An extreme type of Meta Reinforcement Learning is embodied by the Gödel machine, a theoretical construct which can inspect and modify any part of its own software which also contains a general theorem prover. It can achieve recursive self-improvement in a provably optimal way. Model-Agnostic Meta-Learning (MAML) was introduced in 2017 by Chelsea Finn et al. Given a sequence of tasks, the parameters of a given model are trained such that few iterations of gradient descent with few training data from a new task will lead to good generalization performance on that task. MAML "trains the model to be easy to fine-tune." MAML was successfully applied to few-shot image classification benchmarks and to policy-gradient-based reinforcement learning. Variational Bayes-Adaptive Deep RL (VariBAD) was introduced in 2019. While MAML is optimization-based, VariBAD is a model-based method for meta reinforcement learning, and leverages a variational autoencoder to capture the task information in an internal memory, thus conditioning its decision making on the task. When addressing a set of tasks, most meta learning approaches optimize the average score across all tasks. Hence, certain tasks may be sacrificed in favor of the average score, which is often unacceptable in real-world applications. By contrast, Robust Meta Reinforcement Learning (RoML) focuses on improving low-score tasks, increasing robustness to the selection of task. RoML works as a meta-algorithm, as it can be applied on top of other meta learning algorithms (such as MAML and VariBAD) to increase their robustness. It is applicable to both supervised meta learning and meta reinforcement learning. Discovering meta-knowledge works by inducing knowledge

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  Implicit blockmodeling

  Implicit blockmodeling is an approach in blockmodeling, similar to a valued and homogeneity blockmodeling, where initially an additional normalization is used and then while specifying the parameter of the relevant link is replaced by the block maximum. This approach was first proposed by Batagelj and Ferligoj in 2000, and developed by Aleš Žiberna in 2007/08. Comparing with homogeneity, the implicit blockmodeling will perform similarly with max-regular equivalence, but slightly worse in other settings. It will perform worse than valued and homogeneity blockmodeling with a pre-specified blockmodel.

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  Semantic mapping (statistics)

  Semantic mapping (SM) is a statistical method for dimensionality reduction (the transformation of data from a high-dimensional space into a low-dimensional space). SM can be used in a set of multidimensional vectors of features to extract a few new features that preserves the main data characteristics. SM performs dimensionality reduction by clustering the original features in semantic clusters and combining features mapped in the same cluster to generate an extracted feature. Given a data set, this method constructs a projection matrix that can be used to map a data element from a high-dimensional space into a reduced dimensional space. SM can be applied in construction of text mining and information retrieval systems, as well as systems managing vectors of high dimensionality. SM is an alternative to random mapping, principal components analysis and latent semantic indexing methods.

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  ImageNets

  ImageNets is an open source framework for rapid prototyping of machine vision algorithms, developed by the Institute of Automation. == Description == ImageNets is an open source and platform independent (Windows & Linux) framework for rapid prototyping of machine vision algorithms. With the GUI ImageNet Designer, no programming knowledge is required to perform operations on images. A configured ImageNet can be loaded and executed from C++ code without the need for loading the ImageNet Designer GUI to achieve higher execution performance. == History == ImageNets was developed by the Institute of Automation, University of Bremen, Germany. The software was first publicly released in 2010. Originally, ImageNets was developed for the Care-Providing Robot FRIEND but it can be used for a wide range of computer vision applications.

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  Inbox by Gmail

  Inbox by Gmail was an email service developed by Google. Announced on a limited invitation-only basis on October 22, 2014, it was officially released to the public on May 28, 2015. Inbox was shut down by Google on April 2, 2019. Available on the web, and through mobile apps for Android and iOS, Inbox by Gmail aimed to improve email productivity and organization through several key features. Bundles gathered emails on the same topic together; highlighted surface key details from messages, reminders and assists; and a "snooze" functionality enabled users to control when specific information would appear. Updates to the service enabled an "undo send" feature; a "Smart Reply" feature that automatically generated short reply examples for certain emails; integration with Google Calendar for event organization, previews of newsletters; and a "Save to Inbox" feature that let users save links for later use. Inbox by Gmail received generally positive reviews. At its launch, it was called "minimalist and lovely, full of layers and easy to navigate", with features deemed helpful in finding the right messages—one reviewer noted that the service felt "a lot like the future of email". However, it also received criticism, particularly for a low density of information, algorithms that needed tweaking, and because the service required users to "give up the control" of organizing their own email, meaning that "Anyone who already has a system for organizing their emails will likely find themselves fighting Google's system". Google noted in March 2016 that 10% of all replies on mobile originated from Inbox's Smart Reply feature. Google announced it would discontinue Inbox by Gmail in March 2019, with many of its features integrated into Gmail proper. == Features == Inbox by Gmail scanned the user's incoming Gmail messages for information. It gathered email messages related to the same overall topic into an organized bundle, with a title describing the bundle's content. For example, flight tickets, car rentals, and hotel reservations were grouped under "Travel", giving the user an easier overview of emails. Users could also group emails together manually, to "teach" the Inbox how the user worked. The service highlighted key details and important information in messages, such as flight itineraries, event information, photos and documents. Inbox could retrieve updated information from the Internet, including the real-time status of flights and package deliveries. Users could set reminders to bring up important messages later. When a user needed particular information, Inbox could assist the user by displaying the necessary details. Where Inbox highlights information was not needed immediately, users could "snooze" a message or reminder, with options to make the information reappear at a later time or specific location. In June 2015, Google added an "Undo Send" feature to Inbox, giving the user 10 seconds to undo sending a message. In November 2015, Google added "Smart Reply" functionality to the mobile apps. With Smart Reply, Inbox determined which emails could be answered with a short reply, generating three example responses from which the user could select one with a single tap. Smart Reply (initially available only on the Android and iOS mobile apps) was added to the Inbox website in March 2016, Google announcing that "10% of all your replies on mobile already use Smart Reply". By May 2017, Google said Smart Reply was driving about 12% of replies in inbox on mobile. In April 2016, Google updated Inbox with three new features; Google Calendar event organization, newsletter previews, and a "Save to Inbox" functionality that let the user save links for later use, rather than having to email links to themselves. In December 2017, Google introduced an "Unsubscribe" card that let users easily unsubscribe from mailing lists. The card appeared for email messages (from specific senders) that the user had not opened for a month. A few popular Inbox by Gmail features were subsequently added to Gmail: "Snoozing" of emails Nudges: Gmail could move old messages back to the top of the inbox when it thought a follow up or reply might be required. Hover actions: Placing the mouse cursor over a certain part of the message could quickly effect an action, such as archiving, without its being opened. Smart reply: This feature employed boilerplate text to suggest appropriate replies. Google reportedly wished, at a time then to be decided, to add the "bundles" feature to Gmail, which at the time was available only in Inbox for Gmail. By March 2020, many Inbox features were still missing from Gmail. == Platforms == Inbox by Gmail was announced on a limited invitation-only basis on October 22, 2014, available on the web, and through the Android and iOS mobile operating systems. It was officially released to the public on May 28, 2015. == Reception == David Pierce of The Verge praised the service, writing that it was "minimalist and lovely, full of layers and easy to navigate. It's remarkably fast and smooth on all platforms, and far better on iOS than the Gmail app". However, he criticized the app's low density of information, with only a few emails visible on the screen at a time, making it "a bit of a challenge" for users who need to go through "hundreds of emails" every day. Although positive that "Inbox feels a lot like the future of email", Pierce wrote that there was "plenty of algorithm tweaking and design condensing to do", with particular attention needed on a "compact view" for denser view of information on the screen. Sarah Mitroff of CNET also praised Inbox, writing, "Not only is it visually appealing, it's also full of features that help you find every message you need, when you need it". She added that users must "give up the control" to organize their email, and that it "won't vibe with everyone", but admitted that "if you're willing ... the app will reward you with a smarter and cleaner inbox." Mitroff noted that, initially, users had to coach the app about which bundle was appropriate for certain emails, writing, "It's a tedious process at first, by [sic] in just a few days Inbox starts to get it right." Regarding any downsides of the service, Mitroff wrote that "Inbox has a built-in strategy for managing your emails that works best on its own. Anyone who already has a system for organizing their emails will likely find themselves fighting Google's system". == Discontinuation and legacy == Google ended the service in March 2019. Google called Inbox "a great place to experiment with new ideas" and noted that many of those ideas had been migrated to Gmail. The company wanted, going forward, to focus its resources on a single email system. Several services, like Shortwave, attempted to resurrect some of the features of Inbox by Gmail to attract its old users. Similarly, Inbox Reborn, an actively maintained browser extension developed by a team of volunteer developers from around the world since 2018, aims to recreate the core features and visual style of Inbox by Gmail within the standard Gmail interface. The project continues to focus on preserving functionalities such as email bundling and streamlined workflows to provide users with a familiar productivity experience. Afterwards, most people moved to Spark, Spike, or Newton. According to a product manager at Google, a "more focused approach" regarding email was the companies goal. This is likely the reason they moved away from Inbox.

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  Latent Dirichlet allocation

  In natural language processing, latent Dirichlet allocation (LDA) is a generative statistical model that explains how a collection of text documents can be described by a set of unobserved "topics." For example, given a set of news articles, LDA might discover that one topic is characterized by words like "president", "government", and "election", while another is characterized by "team", "game", and "score". It is one of the most common topic models. The LDA model was first presented as a graphical model for population genetics by J. K. Pritchard, M. Stephens and P. Donnelly in 2000. The model was subsequently applied to machine learning by David Blei, Andrew Ng, and Michael I. Jordan in 2003. Although its most frequent application is in modeling text corpora, it has also been used for other problems, such as in clinical psychology, social science, and computational musicology. The core assumption of LDA is that documents are represented as a random mixture of latent topics, and each topic is characterized by a probability distribution over words. The model is a generalization of probabilistic latent semantic analysis (pLSA), differing primarily in that LDA treats the topic mixture as a Dirichlet prior, leading to more reasonable mixtures and less susceptibility to overfitting. Learning the latent topics and their associated probabilities from a corpus is typically done using Bayesian inference, often with methods like Gibbs sampling or variational Bayes. == History == In the context of population genetics, LDA was proposed by J. K. Pritchard, M. Stephens and P. Donnelly in 2000. LDA was applied in machine learning by David Blei, Andrew Ng and Michael I. Jordan in 2003. == Overview == === Population genetics === In population genetics, the model is used to detect the presence of structured genetic variation in a group of individuals. The model assumes that alleles carried by individuals under study have origin in various extant or past populations. The model and various inference algorithms allow scientists to estimate the allele frequencies in those source populations and the origin of alleles carried by individuals under study. The source populations can be interpreted ex-post in terms of various evolutionary scenarios. In association studies, detecting the presence of genetic structure is considered a necessary preliminary step to avoid confounding. === Clinical psychology, mental health, and social science === In clinical psychology research, LDA has been used to identify common themes of self-images experienced by young people in social situations. Other social scientists have used LDA to examine large sets of topical data from discussions on social media (e.g., tweets about prescription drugs). Additionally, supervised Latent Dirichlet Allocation with covariates (SLDAX) has been specifically developed to combine latent topics identified in texts with other manifest variables. This approach allows for the integration of text data as predictors in statistical regression analyses, improving the accuracy of mental health predictions. One of the main advantages of SLDAX over traditional two-stage approaches is its ability to avoid biased estimates and incorrect standard errors, allowing for a more accurate analysis of psychological texts. In the field of social sciences, LDA has proven to be useful for analyzing large datasets, such as social media discussions. For instance, researchers have used LDA to investigate tweets discussing socially relevant topics, like the use of prescription drugs and cultural differences in China. By analyzing these large text corpora, it is possible to uncover patterns and themes that might otherwise go unnoticed, offering valuable insights into public discourse and perception in real time. === Musicology === In the context of computational musicology, LDA has been used to discover tonal structures in different corpora. === Machine learning === One application of LDA in machine learning – specifically, topic discovery, a subproblem in natural language processing – is to discover topics in a collection of documents, and then automatically classify any individual document within the collection in terms of how "relevant" it is to each of the discovered topics. A topic is considered to be a set of terms (i.e., individual words or phrases) that, taken together, suggest a shared theme. For example, in a document collection related to pet animals, the terms dog, spaniel, beagle, golden retriever, puppy, bark, and woof would suggest a DOG_related theme, while the terms cat, siamese, Maine coon, tabby, manx, meow, purr, and kitten would suggest a CAT_related theme. There may be many more topics in the collection – e.g., related to diet, grooming, healthcare, behavior, etc. that we do not discuss for simplicity's sake. (Very common, so called stop words in a language – e.g., "the", "an", "that", "are", "is", etc., – would not discriminate between topics and are usually filtered out by pre-processing before LDA is performed. Pre-processing also converts terms to their "root" lexical forms – e.g., "barks", "barking", and "barked" would be converted to "bark".) If the document collection is sufficiently large, LDA will discover such sets of terms (i.e., topics) based upon the co-occurrence of individual terms, though the task of assigning a meaningful label to an individual topic (i.e., that all the terms are DOG_related) is up to the user, and often requires specialized knowledge (e.g., for collection of technical documents). The LDA approach assumes that: The semantic content of a document is composed by combining one or more terms from one or more topics. Certain terms are ambiguous, belonging to more than one topic, with different probability. (For example, the term training can apply to both dogs and cats, but are more likely to refer to dogs, which are used as work animals or participate in obedience or skill competitions.) However, in a document, the accompanying presence of specific neighboring terms (which belong to only one topic) will disambiguate their usage. Most documents will contain only a relatively small number of topics. In the collection, e.g., individual topics will occur with differing frequencies. That is, they have a probability distribution, so that a given document is more likely to contain some topics than others. Within a topic, certain terms will be used much more frequently than others. In other words, the terms within a topic will also have their own probability distribution. When LDA machine learning is employed, both sets of probabilities are computed during the training phase, using Bayesian methods and an expectation–maximization algorithm. LDA is a generalization of older approach of probabilistic latent semantic analysis (pLSA), The pLSA model is equivalent to LDA under a uniform Dirichlet prior distribution. pLSA relies on only the first two assumptions above and does not care about the remainder. While both methods are similar in principle and require the user to specify the number of topics to be discovered before the start of training (as with k-means clustering) LDA has the following advantages over pLSA: LDA yields better disambiguation of words and a more precise assignment of documents to topics. Computing probabilities allows a "generative" process by which a collection of new "synthetic documents" can be generated that would closely reflect the statistical characteristics of the original collection. Unlike LDA, pLSA is vulnerable to overfitting especially when the size of corpus increases. The LDA algorithm is more readily amenable to scaling up for large data sets using the MapReduce approach on a computing cluster. == Model == With plate notation, which is often used to represent probabilistic graphical models (PGMs), the dependencies among the many variables can be captured concisely. The boxes are "plates" representing replicates, which are repeated entities. The outer plate represents documents, while the inner plate represents the repeated word positions in a given document; each position is associated with a choice of topic and word. The variable names are defined as follows: M denotes the number of documents N is number of words in a given document (document i has N i {\displaystyle N_{i}} words) α is the parameter of the Dirichlet prior on the per-document topic distributions β is the parameter of the Dirichlet prior on the per-topic word distribution θ i {\displaystyle \theta _{i}} is the topic distribution for document i φ k {\displaystyle \varphi _{k}} is the word distribution for topic k z i j {\displaystyle z_{ij}} is the topic for the j-th word in document i w i j {\displaystyle w_{ij}} is the specific word. The fact that W is grayed out means that words w i j {\displaystyle w_{ij}} are the only observable variables, and the other variables are latent variables. As proposed in the original paper, a sparse Dirichlet prior can be used to model the to

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  Proximal policy optimization

  Proximal policy optimization (PPO) is a reinforcement learning (RL) algorithm for training an intelligent agent. Specifically, it is a policy gradient method, often used for deep RL when the policy network is very large. == History == The predecessor to PPO, Trust Region Policy Optimization (TRPO), was published in 2015. It addressed the instability issue of another algorithm, the Deep Q-Network (DQN), by using the trust region method to limit the KL divergence between the old and new policies. However, TRPO uses the Hessian matrix (a matrix of second derivatives) to enforce the trust region, but the Hessian is inefficient for large-scale problems. PPO was published in 2017. It was essentially an approximation of TRPO that does not require computing the Hessian. The KL divergence constraint was approximated by simply clipping the policy gradient. Since 2018, PPO was the default RL algorithm at OpenAI. PPO has been applied to many areas, such as controlling a robotic arm, beating professional players at Dota 2 (OpenAI Five), and playing Atari games. == TRPO == TRPO, the predecessor of PPO, is an on-policy algorithm. It can be used for environments with either discrete or continuous action spaces. The pseudocode is as follows: Input: initial policy parameters θ 0 {\textstyle \theta _{0}} , initial value function parameters ϕ 0 {\textstyle \phi _{0}} Hyperparameters: KL-divergence limit δ {\textstyle \delta } , backtracking coefficient α {\textstyle \alpha } , maximum number of backtracking steps K {\textstyle K} for k = 0 , 1 , 2 , … {\textstyle k=0,1,2,\ldots } do Collect set of trajectories D k = { τ i } {\textstyle {\mathcal {D}}_{k}=\left\{\tau _{i}\right\}} by running policy π k = π ( θ k ) {\textstyle \pi _{k}=\pi \left(\theta _{k}\right)} in the environment. Compute rewards-to-go R ^ t {\textstyle {\hat {R}}_{t}} . Compute advantage estimates, A ^ t {\textstyle {\hat {A}}_{t}} (using any method of advantage estimation) based on the current value function V ϕ k {\textstyle V_{\phi _{k}}} . Estimate policy gradient as g ^ k = 1 | D k | ∑ τ ∈ D k ∑ t = 0 T ∇ θ log ⁡ π θ ( a t ∣ s t ) | θ k A ^ t {\displaystyle {\hat {g}}_{k}=\left.{\frac {1}{\left|{\mathcal {D}}_{k}\right|}}\sum _{\tau \in {\mathcal {D}}_{k}}\sum _{t=0}^{T}\nabla _{\theta }\log \pi _{\theta }\left(a_{t}\mid s_{t}\right)\right|_{\theta _{k}}{\hat {A}}_{t}} Use the conjugate gradient algorithm to compute x ^ k ≈ H ^ k − 1 g ^ k {\displaystyle {\hat {x}}_{k}\approx {\hat {H}}_{k}^{-1}{\hat {g}}_{k}} where H ^ k {\textstyle {\hat {H}}_{k}} is the Hessian of the sample average KL-divergence. Update the policy by backtracking line search with θ k + 1 = θ k + α j 2 δ x ^ k T H ^ k x ^ k x ^ k {\displaystyle \theta _{k+1}=\theta _{k}+\alpha ^{j}{\sqrt {\frac {2\delta }{{\hat {x}}_{k}^{T}{\hat {H}}_{k}{\hat {x}}_{k}}}}{\hat {x}}_{k}} where j ∈ { 0 , 1 , 2 , … K } {\textstyle j\in \{0,1,2,\ldots K\}} is the smallest value which improves the sample loss and satisfies the sample KL-divergence constraint. Fit value function by regression on mean-squared error: ϕ k + 1 = arg ⁡ min ϕ 1 | D k | T ∑ τ ∈ D k ∑ t = 0 T ( V ϕ ( s t ) − R ^ t ) 2 {\displaystyle \phi _{k+1}=\arg \min _{\phi }{\frac {1}{\left|{\mathcal {D}}_{k}\right|T}}\sum _{\tau \in {\mathcal {D}}_{k}}\sum _{t=0}^{T}\left(V_{\phi }\left(s_{t}\right)-{\hat {R}}_{t}\right)^{2}} typically via some gradient descent algorithm. == PPO == The pseudocode is as follows: Input: initial policy parameters θ 0 {\textstyle \theta _{0}} , initial value function parameters ϕ 0 {\textstyle \phi _{0}} for k = 0 , 1 , 2 , … {\textstyle k=0,1,2,\ldots } do Collect set of trajectories D k = { τ i } {\textstyle {\mathcal {D}}_{k}=\left\{\tau _{i}\right\}} by running policy π k = π ( θ k ) {\textstyle \pi _{k}=\pi \left(\theta _{k}\right)} in the environment. Compute rewards-to-go R ^ t {\textstyle {\hat {R}}_{t}} . Compute advantage estimates, A ^ t {\textstyle {\hat {A}}_{t}} (using any method of advantage estimation) based on the current value function V ϕ k {\textstyle V_{\phi _{k}}} . Update the policy by maximizing the PPO-Clip objective: θ k + 1 = arg ⁡ max θ 1 | D k | T ∑ τ ∈ D k ∑ t = 0 T min ( π θ ( a t ∣ s t ) π θ k ( a t ∣ s t ) A π θ k ( s t , a t ) , g ( ϵ , A π θ k ( s t , a t ) ) ) {\displaystyle \theta _{k+1}=\arg \max _{\theta }{\frac {1}{\left|{\mathcal {D}}_{k}\right|T}}\sum _{\tau \in {\mathcal {D}}_{k}}\sum _{t=0}^{T}\min \left({\frac {\pi _{\theta }\left(a_{t}\mid s_{t}\right)}{\pi _{\theta _{k}}\left(a_{t}\mid s_{t}\right)}}A^{\pi _{\theta _{k}}}\left(s_{t},a_{t}\right),\quad g\left(\epsilon ,A^{\pi _{\theta _{k}}}\left(s_{t},a_{t}\right)\right)\right)} typically via stochastic gradient ascent with Adam. Fit value function by regression on mean-squared error: ϕ k + 1 = arg ⁡ min ϕ 1 | D k | T ∑ τ ∈ D k ∑ t = 0 T ( V ϕ ( s t ) − R ^ t ) 2 {\displaystyle \phi _{k+1}=\arg \min _{\phi }{\frac {1}{\left|{\mathcal {D}}_{k}\right|T}}\sum _{\tau \in {\mathcal {D}}_{k}}\sum _{t=0}^{T}\left(V_{\phi }\left(s_{t}\right)-{\hat {R}}_{t}\right)^{2}} typically via some gradient descent algorithm. Like all policy gradient methods, PPO is used for training an RL agent whose actions are determined by a differentiable policy function by gradient ascent. Intuitively, a policy gradient method takes small policy update steps, so the agent can reach higher and higher rewards in expectation. Policy gradient methods may be unstable: A step size that is too big may direct the policy in a suboptimal direction, thus having little possibility of recovery; a step size that is too small lowers the overall efficiency. To solve the instability, PPO implements a clip function that constrains the policy update of an agent from being too large, so that larger step sizes may be used without negatively affecting the gradient ascent process. === Basic concepts === To begin the PPO training process, the agent is set in an environment to perform actions based on its current input. In the early phase of training, the agent can freely explore solutions and keep track of the result. Later, with a certain amount of transition samples and policy updates, the agent will select an action to take by randomly sampling from the probability distribution P ( A | S ) {\displaystyle P(A|S)} generated by the policy network. The actions that are most likely to be beneficial will have the highest probability of being selected from the random sample. After an agent arrives at a different scenario (a new state) by acting, it is rewarded with a positive reward or a negative reward. The objective of an agent is to maximize the cumulative reward signal across sequences of states, known as episodes. === Policy gradient laws: the advantage function === The advantage function (denoted as A {\displaystyle A} ) is central to PPO, as it tries to answer the question of whether a specific action of the agent is better or worse than some other possible action in a given state. By definition, the advantage function is an estimate of the relative value for a selected action. If the output of this function is positive, it means that the action in question is better than the average return, so the possibilities of selecting that specific action will increase. The opposite is true for a negative advantage output. The advantage function can be defined as A = Q − V {\displaystyle A=Q-V} , where Q {\displaystyle Q} is the discounted sum of rewards (the total weighted reward for the completion of an episode) and V {\displaystyle V} is the baseline estimate. Since the advantage function is calculated after the completion of an episode, the program records the outcome of the episode. Therefore, calculating advantage is essentially an unsupervised learning problem. The baseline estimate comes from the value function that outputs the expected discounted sum of an episode starting from the current state. In the PPO algorithm, the baseline estimate will be noisy (with some variance), as it also uses a neural network, like the policy function itself. With Q {\displaystyle Q} and V {\displaystyle V} computed, the advantage function is calculated by subtracting the baseline estimate from the actual discounted return. If A > 0 {\displaystyle A>0} , the actual return of the action is better than the expected return from experience; if A < 0 {\displaystyle A<0} , the actual return is worse. === Ratio function === In PPO, the ratio function ( r t {\displaystyle r_{t}} ) calculates the probability of selecting action a {\displaystyle a} in state s {\displaystyle s} given the current policy network, divided by the previous probability under the old policy. In other words: If r t ( θ ) > 1 {\displaystyle r_{t}(\theta )>1} , where θ {\displaystyle \theta } are the policy network parameters, then selecting action a {\displaystyle a} in state s {\displaystyle s} is more likely based on the current policy than the previous policy. If 0 ≤ r t ( θ ) < 1 {\displaystyle 0\leq r_{t}(\theta )<1} , then selecting actio

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